bluuebunny/crossref_metadata_2025_split huggingface dataset:
Compositing effects for high thermoelectric performance of Cu2Se-based materials
Authors: Zhou Zhifang , Huang Yi , Wei Bin , Yang Yueyang , Yu Dehong , Zheng Yunpeng , He Dongsheng , Zhang Wenyu , Zou Mingchu , Lan Jin-Le , He Jiaqing , Nan Ce-Wen , Lin Yuan-Hua 
Published: April 2023

AbstractThermoelectric materials can realize direct conversion between heat and electricity, showing excellent potential for waste heat recovery. Cu2Se is a typical superionic conductor thermoelectric material having extraordinary ZT values, but its superionic feature causes poor service stability and low mobility. Here, we reported a fast preparation method of self-propagating high-temperature synthesis to realize in situ compositing of BiCuSeO and Cu2Se to optimize the service stability. Additionally, using the interface design by introducing graphene in these composites, the carrier mobility could be obviously enhanced, and the strong phonon scatterings could lead to lower lattice thermal conductivity. Ultimately, the Cu2Se-BiCuSeO-graphene composites presented excellent thermoelectric properties with a ZTmax value of ~2.82 at 1000 K and a ZTave value of ~1.73 from 473 K to 1000 K. This work provides a facile and effective strategy to largely improve the performance of Cu2Se-based thermoelectric materials, which could be further adopted in other thermoelectric systems.
BICD2 phosphorylation regulates dynein function and centrosome separation in G2 and M
Authors: Gallisà-Suñé Núria , Sànchez-Fernàndez-de-Landa Paula , Zimmermann Fabian , Serna Marina , Regué Laura , Paz Joel , Llorca Oscar , Lüders Jens , Roig Joan 
Published: April 2023

AbstractThe activity of dynein is regulated by a number of adaptors that mediate its interaction with dynactin, effectively activating the motor complex while also connecting it to different cargos. The regulation of adaptors is consequently central to dynein physiology but remains largely unexplored. We now describe that one of the best-known dynein adaptors, BICD2, is effectively activated through phosphorylation. In G2, phosphorylation of BICD2 by CDK1 promotes its interaction with PLK1. In turn, PLK1 phosphorylation of a single residue in the N-terminus of BICD2 results in a structural change that facilitates the interaction with dynein and dynactin, allowing the formation of active motor complexes. Moreover, modified BICD2 preferentially interacts with the nucleoporin RanBP2 once RanBP2 has been phosphorylated by CDK1. BICD2 phosphorylation is central for dynein recruitment to the nuclear envelope, centrosome tethering to the nucleus and centrosome separation in the G2 and M phases of the cell cycle. This work reveals adaptor activation through phosphorylation as crucial for the spatiotemporal regulation of dynein activity.
Mesolimbic dopamine release precedes actively sought aversive stimuli in mice
Authors: Yawata Yosuke , Shikano Yu , Ogasawara Jun , Makino Kenichi , Kashima Tetsuhiko , Ihara Keiko , Yoshimoto Airi , Morikawa Shota , Yagishita Sho , Tanaka Kenji F. , Ikegaya Yuji 
Published: April 2023

AbstractIn some models, animals approach aversive stimuli more than those housed in an enriched environment. Here, we found that male mice in an impoverished and unstimulating (i.e., boring) chamber without toys sought aversive air puffs more often than those in an enriched chamber. Using this animal model, we identified the insular cortex as a regulator of aversion-seeking behavior. Activation and inhibition of the insular cortex increased and decreased the frequencies of air-puff self-stimulation, respectively, and the firing patterns of insular neuron ensembles predicted the self-stimulation timing. Dopamine levels in the ventrolateral striatum decreased with passive air puffs but increased with actively sought puffs. Around 20% of mice developed intense self-stimulation despite being offered toys, which was prevented by administering opioid receptor antagonists. This study establishes a basis for comprehending the neural underpinnings of usually avoided stimulus-seeking behaviors.
DNA polymerase POLD1 promotes proliferation and metastasis of bladder cancer by stabilizing MYC
Authors: Wang Yejinpeng , Ju Lingao , Wang Gang , Qian Kaiyu , Jin Wan , Li Mingxing , Yu Jingtian , Shi Yiliang , Wang Yongzhi , Zhang Yi , Xiao Yu , Wang Xinghuan 
Published: April 2023

AbstractTo date, most studies on the DNA polymerase, POLD1, have focused on the effect of POLD1 inactivation mutations in tumors. However, the implications of high POLD1 expression in tumorigenesis remains elusive. Here, we determine that POLD1 has a pro-carcinogenic role in bladder cancer (BLCA) and is associated to the malignancy and prognosis of BLCA. Our studies demonstrate that POLD1 promotes the proliferation and metastasis of BLCA via MYC. Mechanistically, POLD1 stabilizes MYC in a manner independent of its’ DNA polymerase activity. Instead, POLD1 attenuates FBXW7-mediated ubiquitination degradation of MYC by directly binding to the MYC homology box 1 domain competitively with FBXW7. Moreover, we find that POLD1 forms a complex with MYC to promote the transcriptional activity of MYC. In turn, MYC increases expression of POLD1, forming a POLD1-MYC positive feedback loop to enhance the pro-carcinogenic effect of POLD1-MYC on BLCA. Overall, our study identifies POLD1 as a promotor of BCLA via a MYC driven mechanism and suggest its potential as biomarker for BLCA.
HMGN1 enhances CRISPR-directed dual-function A-to-G and C-to-G base editing
Authors: Yang Chao , Ma Zhenzhen , Wang Keshan , Dong Xingxiao , Huang Meiyu , Li Yaqiu , Zhu Xiagu , Li Ju , Cheng Zhihui , Bi Changhao , Zhang Xueli 
Published: April 2023

AbstractC-to-G base editors have been successfully constructed recently, but limited work has been done on concurrent C-to-G and A-to-G base editing. In addition, there is also limited data on how chromatin-associated factors affect the base editing. Here, we test a series of chromatin-associated factors, and chromosomal protein HMGN1 was found to enhance the efficiency of both C-to-G and A-to-G base editing. By fusing HMGN1, GBE and ABE to Cas9, we develop a CRISPR-based dual-function A-to-G and C-to-G base editor (GGBE) which is capable of converting simultaneous A and C to G conversion with substantial editing efficiency. Accordingly, the HMGN1 role shown in this work and the resulting GGBE tool further broaden the genome manipulation capacity of CRISPR-directed base editors.
Resurgence of Omicron BA.2 in SARS-CoV-2 infection-naive Hong Kong
Authors: Xie Ruopeng , Edwards Kimberly M. , Adam Dillon C. , Leung Kathy S. M. , Tsang Tim K. , Gurung Shreya , Xiong Weijia , Wei Xiaoman , Ng Daisy Y. M. , Liu Gigi Y. Z. , Krishnan Pavithra , Chang Lydia D. J. , Cheng Samuel M. S. , Gu Haogao , Siu Gilman K. H. , Wu Joseph T. , Leung Gabriel M. , Peiris Malik , Cowling Benjamin J. , Poon Leo L. M. , Dhanasekaran Vijaykrishna 
Published: April 2023

AbstractHong Kong experienced a surge of Omicron BA.2 infections in early 2022, resulting in one of the highest per-capita death rates of COVID-19. The outbreak occurred in a dense population with low immunity towards natural SARS-CoV-2 infection, high vaccine hesitancy in vulnerable populations, comprehensive disease surveillance and the capacity for stringent public health and social measures (PHSMs). By analyzing genome sequences and epidemiological data, we reconstructed the epidemic trajectory of BA.2 wave and found that the initial BA.2 community transmission emerged from cross-infection within hotel quarantine. The rapid implementation of PHSMs suppressed early epidemic growth but the effective reproduction number (Re) increased again during the Spring festival in early February and remained around 1 until early April. Independent estimates of point prevalence and incidence using phylodynamics also showed extensive superspreading at this time, which likely contributed to the rapid expansion of the epidemic. Discordant inferences based on genomic and epidemiological data underscore the need for research to improve near real-time epidemic growth estimates by combining multiple disparate data sources to better inform outbreak response policy.
Sensory perception relies on fitness-maximizing codes
Authors: Schaffner Jonathan , Bao Sherry Dongqi , Tobler Philippe N. , Hare Todd A. , Polania Rafael 
Published: April 2023

AbstractSensory information encoded by humans and other organisms is generally presumed to be as accurate as their biological limitations allow. However, perhaps counterintuitively, accurate sensory representations may not necessarily maximize the organism’s chances of survival. To test this hypothesis, we developed a unified normative framework for fitness-maximizing encoding by combining theoretical insights from neuroscience, computer science, and economics. Behavioural experiments in humans revealed that sensory encoding strategies are flexibly adapted to promote fitness maximization, a result confirmed by deep neural networks with information capacity constraints trained to solve the same task as humans. Moreover, human functional MRI data revealed that novel behavioural goals that rely on object perception induce efficient stimulus representations in early sensory structures. These results suggest that fitness-maximizing rules imposed by the environment are applied at early stages of sensory processing in humans and machines.
Nano-DMS-MaP allows isoform-specific RNA structure determination
Authors: Bohn Patrick , Gribling-Burrer Anne-Sophie , Ambi Uddhav B. , Smyth Redmond P. 
Published: April 2023

AbstractGenome-wide measurements of RNA structure can be obtained using reagents that react with unpaired bases, leading to adducts that can be identified by mutational profiling on next-generation sequencing machines. One drawback of these experiments is that short sequencing reads can rarely be mapped to specific transcript isoforms. Consequently, information is acquired as a population average in regions that are shared between transcripts, thus blurring the underlying structural landscape. Here, we present nanopore dimethylsulfate mutational profiling (Nano-DMS-MaP)—a method that exploits long-read sequencing to provide isoform-resolved structural information of highly similar RNA molecules. We demonstrate the value of Nano-DMS-MaP by resolving the complex structural landscape of human immunodeficiency virus-1 transcripts in infected cells. We show that unspliced and spliced transcripts have distinct structures at the packaging site within the common 5′ untranslated region, likely explaining why spliced viral RNAs are excluded from viral particles. Thus, Nano-DMS-MaP is a straightforward method to resolve biologically important transcript-specific RNA structures that were previously hidden in short-read ensemble analyses.
PediCXR: An open, large-scale chest radiograph dataset for interpretation of common thoracic diseases in children
Authors: Pham Hieu H. , Nguyen Ngoc H. , Tran Thanh T. , Nguyen Tuan N. M. , Nguyen Ha Q. 
Published: April 2023

AbstractComputer-aided diagnosis systems in adult chest radiography (CXR) have recently achieved great success thanks to the availability of large-scale, annotated datasets and the advent of high-performance supervised learning algorithms. However, the development of diagnostic models for detecting and diagnosing pediatric diseases in CXR scans is undertaken due to the lack of high-quality physician-annotated datasets. To overcome this challenge, we introduce and release PediCXR, a new pediatric CXR dataset of 9,125 studies retrospectively collected from a major pediatric hospital in Vietnam between 2020 and 2021. Each scan was manually annotated by a pediatric radiologist with more than ten years of experience. The dataset was labeled for the presence of 36 critical findings and 15 diseases. In particular, each abnormal finding was identified via a rectangle bounding box on the image. To the best of our knowledge, this is the first and largest pediatric CXR dataset containing lesion-level annotations and image-level labels for the detection of multiple findings and diseases. For algorithm development, the dataset was divided into a training set of 7,728 and a test set of 1,397. To encourage new advances in pediatric CXR interpretation using data-driven approaches, we provide a detailed description of the PediCXR data sample and make the dataset publicly available on https://physionet.org/content/vindr-pcxr/1.0.0/.
Multi-modal brain magnetic resonance imaging database covering marmosets with a wide age range
Authors: Hata Junichi , Nakae Ken , Tsukada Hiromichi , Woodward Alexander , Haga Yawara , Iida Mayu , Uematsu Akiko , Seki Fumiko , Ichinohe Noritaka , Gong Rui , Kaneko Takaaki , Yoshimaru Daisuke , Watakabe Akiya , Abe Hiroshi , Tani Toshiki , Hamda Hiro Taiyo , Gutierrez Carlos Enrique , Skibbe Henrik , Maeda Masahide , Papazian Frederic , Hagiya Kei , Kishi Noriyuki , Ishii Shin , Doya Kenji , Shimogori Tomomi , Yamamori Tetsuo , Tanaka Keiji , Okano Hirotaka James , Okano Hideyuki 
Published: April 2023

AbstractMagnetic resonance imaging (MRI) is a non-invasive neuroimaging
technique that is useful for identifying normal developmental and aging processes
and for data sharing. Marmosets have a relatively shorter life expectancy than other
primates, including humans, because they grow and age faster. Therefore, the common
marmoset model is effective in aging research. The current study investigated the
aging process of the marmoset brain and provided an open MRI database of marmosets
across a wide age range. The Brain/MINDS Marmoset Brain MRI Dataset contains brain
MRI information from 216 marmosets ranging in age from 1 and 10 years. At the time
of its release, it is the largest public dataset in the world. It also includes
multi-contrast MRI images. In addition, 91 of 216 animals have corresponding
high-resolution ex vivo MRI datasets. Our MRI
database, available at the Brain/MINDS Data Portal, might help to understand the
effects of various factors, such as age, sex, body size, and fixation, on the brain.
It can also contribute to and accelerate brain science studies worldwide.
De novo transcriptomes of six calanoid copepods (Crustacea): a resource for the discovery of novel genes
Authors: Hartline Daniel K. , Cieslak Matthew C. , Castelfranco Ann M. , Lieberman Brandon , Roncalli Vittoria , Lenz Petra H. 
Published: April 2023

AbstractThis study presents eight new high-quality de novo transcriptomes from six co-occurring species of calanoid copepods, the first published for Neocalanus plumchrus, N. cristatus, Eucalanus bungii and Metridia pacifica and additional ones for N. flemingeri and Calanus marshallae. They are ecologically-important members of sub-arctic North Pacific marine zooplankton communities. ‘Omics data for this diverse and numerous taxonomic group are sparse and difficult to obtain. Total RNA from single individuals was used to construct gene libraries that were sequenced on an Illumina Next-Seq platform. Quality filtered reads were assembled with Trinity software and validated using multiple criteria. The study’s primary purpose is to provide a resource for gene expression studies. The integrated database can be used for quantitative inter- and intra-species comparisons of gene expression patterns across biological processes. An example of an additional use is provided for discovering novel and evolutionarily-significant proteins within the Calanoida. A workflow was designed to find and characterize unannotated transcripts with homologies across de novo assemblies that have also been shown to be eco-responsive.
Generating Detailed Spectral Libraries for Canine Proteomes Obtained from Serum and Urine
Authors: Ahn Hee-Sung , Yeom Jeonghun , Yu Jiyoung , Oh Yumi , Hong JeongYeon , Kim Minjung , Kim Kyunggon 
Published: April 2023

AbstractDomestic dogs (Canis lupus familiaris) are popular companion animals. Increase in medical expenses associated with them and demand for extending their lifespan in a healthy manner has created the need to develop new diagnostic technology. Companion dogs also serve as important animal models for non-clinical research as they can provide various biological phenotypes. Proteomics have been increasingly used on dogs and humans to identify novel biomarkers of various diseases. Despite the growing applications of proteomics in liquid biopsy in veterinary medicine, no publicly available spectral assay libraries have been created for the proteome of canine serum and urine. In this study, we generated spectral assay libraries for the two-representative liquid-biopsy samples using mid-pH fractionation that allows in-depth understanding of proteome coverage. The resultant canine serum and urine spectral assay libraries include 1,132 and 4,749 protein groups and 5,483 and 25,228 peptides, respectively. We built these complimentary accessible resources for proteomic biomarker discovery studies through ProteomeXchange with the identifier PXD034770.
Land-use change is associated with multi-century loss of elephant ecosystems in Asia
Authors: de Silva Shermin , Wu Tiffany , Nyhus Philip , Weaver Ashley , Thieme Alison , Johnson Josiah , Wadey Jamie , Mossbrucker Alexander , Vu Thinh , Neang Thy , Chen Becky Shu , Songer Melissa , Leimgruber Peter 
Published: April 2023

AbstractUnderstanding historic patterns of land use and land cover change across large temporal and spatial scales is critical for developing effective biodiversity conservation management and policy. We quantify the extent and fragmentation of suitable habitat across the continental range of Asian elephants (Elephas maximus) based on present-day occurrence data and land-use variables between 850 and 2015 A.D. We found that following centuries of relative stability, over 64% (3.36 million km2) of suitable elephant habitat across Asia was lost since the year 1700, coincident with colonial-era land-use practices in South Asia and subsequent agricultural intensification in Southeast Asia. Average patch size dropped 83% from approximately 99,000–16,000 km2and the area occupied by the largest patch decreased 83% from ~ 4 million km2(45% of area) to 54,000 km2(~ 7.5% of area). Whereas 100% of the area within 100 km of the current elephant range could have been considered suitable habitat in the year 1700, over half was unsuitable by 2015, driving potential conflict with people. These losses reflect long-term decline of non-forested ecosystems, exceeding estimates of deforestation within this century. Societies must consider ecological histories in addition to proximate threats to develop more just and sustainable land-use and conservation strategies.
Aphanothece sp. as promising biostimulant to alleviate heavy metals stress in Solanum lycopersicum L. by enhancing physiological, biochemical, and metabolic responses
Authors: Fal Soufiane , Aasfar Abderrahim , Ouhssain Ali , Choukri Hasnae , Smouni Abelaziz , El Arroussi Hicham 
Published: April 2023

AbstractHeavy metals (H.M) are a major environmental concern around the world. They have harmful impact on plant productivity and pose a serious risk to humans and animals health. In the present study, we investigated the effect of Aphanothece crude extract (ACE) on physiological, biochemical, and metabolic responses of tomato plant exposed to 2 mM Pb and Cd. The results showed a significant reduction of tomato plant weights and perturbation in nutrients absorption under 2 mM Pb and Cd conditions. Moreover, ACE treatment showed a significant enhancement of plant biomass compared to plants under Pb and Cd. On the other hand, ACE application favoured H.M accumulation in root and inhibited their translocation to shoot. In addition, ACE treatment significantly enhanced several stress responses in plant under Pb and Cd stress such as scavenging enzymes and molecules: POD, CAT, SOD, proline, and polyphenols etc. Furthermore, ACE treatment showed remodulation of metabolic pathways related to plant tolerance such as wax construction mechanism, particularly SFA, UFA, VLFA, alkanes, alkenes, and sterols biosynthesis to enhance tolerance and resistance to H.M stress. In the present study, we emphasized that ACE alleviates H.M stress by minimizing metal translocation to above-part of plant and enhancing plant growth, nutrients absorption, and biochemical responses.
Excess mortality in Ukraine during the course of COVID-19 pandemic in 2020–2021
Authors: Shishkin Aleksandr , Lhewa Pema , Yang Chen , Gankin Yuriy , Chowell Gerardo , Norris Michael , Skums Pavel , Kirpich Alexander 
Published: April 2023

AbstractIn this work, the COVID-19 pandemic burden in Ukraine is investigated retrospectively using the excess mortality measures during 2020–2021. In particular, the epidemic impact on the Ukrainian population is studied via the standardized both all-cause and cause-specific mortality scores before and during the epidemic. The excess mortality counts during the pandemic were predicted based on historic data using parametric and nonparametric modeling and then compared with the actual reported counts to quantify the excess. The corresponding standardized mortality P-score metrics were also compared with the neighboring countries. In summary, there were three “waves” of excess all-cause mortality in Ukraine in December 2020, April 2021 and November 2021 with excess of 32%, 43% and 83% above the expected mortality. Each new “wave” of the all-cause mortality was higher than the previous one and the mortality “peaks” corresponded in time to three “waves” of lab-confirmed COVID-19 mortality. The lab-confirmed COVID-19 mortality constituted 9% to 24% of the all-cause mortality during those three peak months. Overall, the mortality trends in Ukraine over time were similar to neighboring countries where vaccination coverage was similar to that in Ukraine. For cause-specific mortality, the excess observed was due to pneumonia as well as circulatory system disease categories that peaked at the same times as the all-cause and lab-confirmed COVID-19 mortality, which was expected. The pneumonias as well as circulatory system disease categories constituted the majority of all cases during those peak times. The seasonality in mortality due to the infectious and parasitic disease category became less pronounced during the pandemic. While the reported numbers were always relatively low, alcohol-related mortality also declined during the pandemic.
Population-specific facial traits and diagnosis accuracy of genetic and rare diseases in an admixed Colombian population
Authors: Echeverry-Quiceno Luis M. , Candelo Estephania , Gómez Eidith , Solís Paula , Ramírez Diana , Ortiz Diana , González Alejandro , Sevillano Xavier , Cuéllar Juan Carlos , Pachajoa Harry , Martínez-Abadías Neus 
Published: April 2023

AbstractUp to 40% of rare disorders (RD) present facial dysmorphologies, and visual assessment is commonly used for clinical diagnosis. Quantitative approaches are more objective, but mostly rely on European descent populations, disregarding diverse population ancestry. Here, we assessed the facial phenotypes of Down (DS), Morquio (MS), Noonan (NS) and Neurofibromatosis type 1 (NF1) syndromes in a Latino-American population, recording the coordinates of 18 landmarks in 2D images from 79 controls and 51 patients. We quantified facial differences using Euclidean Distance Matrix Analysis, and assessed the diagnostic accuracy of Face2Gene, an automatic deep-learning algorithm. Individuals diagnosed with DS and MS presented severe phenotypes, with 58.2% and 65.4% of significantly different facial traits. The phenotype was milder in NS (47.7%) and non-significant in NF1 (11.4%). Each syndrome presented a characteristic dysmorphology pattern, supporting the diagnostic potential of facial biomarkers. However, population-specific traits were detected in the Colombian population. Diagnostic accuracy was 100% in DS, moderate in NS (66.7%) but lower in comparison to a European population (100%), and below 10% in MS and NF1. Moreover, admixed individuals showed lower facial gestalt similarities. Our results underscore that incorporating populations with Amerindian, African and European ancestry is crucial to improve diagnostic methods of rare disorders.