bluuebunny/crossref_metadata_2025_split huggingface dataset:
Enriched Regions of 228Ra Along the U.S. GEOTRACES Pacific Meridional Transect (GP15)
Authors: Moore Willard S. , Charette Matthew A. , Henderson Paul B. , Hammond Douglas E. , Kemnitz Nathaniel , Le Roy Emilie , Kwon Eun Young , Hult Mikael 
Published: March 2024

AbstractThe half‐life of 228Ra (5.7 years) aligns well with near‐surface and near‐bottom ocean mixing timescales. Because 228Ra is sourced from sediments, regions of enhanced activity represent water that has recently interacted with sediments on the continental margin or seabed. The GP15 meridional transect from Alaska to Tahiti along152°W encountered several regions in the upper ocean where 228Ra was enriched. These enrichments follow surface and subsurface ocean current patterns and pair with earlier measurements of 228Ra and transient radionuclides to reveal the origins of these enriched regions. An enriched region at Alaska margin stations 1–3 was sourced locally but did not extend to the Alaskan trench at station 4. A large shallow region between 47° and 32°N. was sourced from the west by the North Pacific Current; another shallow enriched region between 11° and 5° N was also sourced from the west by the North Equatorial Countercurrent. Subsurface enrichments (100–400 m) between 18 and 47°N were associated with Central Mode Water and North Pacific Intermediate Water. The 228Ra activities in the upper Pacific were six times lower than activities in the Atlantic. In deep waters the primary enrichment was 27°–47°N. Two stations (32° and 37°N) were especially enriched, having near‐bottom inventories several times greater than other stations. With these two exceptions the remaining Pacific stations exhibited averaged inventories lower than those in the Atlantic. There was one region of enriched 223Ra (half‐life = 11 days) above the Puna Ridge near Hawaii.
Design, simulation, and testing of a tunable MEMS multi-threshold inertial switch
Authors: Xu Qiu , Rocha Rodrigo T. , Algoos Yousef , Feron Eric , Younis Mohammad I. 
Published: March 2024

AbstractThis paper presents a tunable multi-threshold micro-electromechanical inertial switch with adjustable threshold capability. The demonstrated device combines the advantages of accelerometers in providing quantitative acceleration measurements and g-threshold switches in saving power when in the inactive state upon experiencing acceleration below the thresholds. The designed proof-of-concept device with two thresholds consists of a cantilever microbeam and two stationary electrodes placed at different positions in the sensing direction. The adjustable threshold capability and the effect of the shock duration on the threshold acceleration are analytically investigated using a nonlinear beam model. Results are shown for the relationships among the applied bias voltage, the duration of shock impact, and the tunable threshold. The fabricated prototypes are tested using a shock-table system. The analytical results agree with the experimental results. The designed device concept is very promising for the classification of the shock and impact loads in transportation and healthcare applications.
Phenotypes for general behavior, activity, and body temperature in 3q29 deletion model mice
Authors: Mori Daisuke , Ikeda Ryosuke , Sawahata Masahito , Yamaguchi Sho , Kodama Akiko , Hirao Takashi , Arioka Yuko , Okumura Hiroki , Inami Chihiro , Suzuki Toshiaki , Hayashi Yu , Kato Hidekazu , Nawa Yoshihiro , Miyata Seiko , Kimura Hiroki , Kushima Itaru , Aleksic Branko , Mizoguchi Hiroyuki , Nagai Taku , Nakazawa Takanobu , Hashimoto Ryota , Kaibuchi Kozo , Kume Kazuhiko , Yamada Kiyofumi , Ozaki Norio 
Published: March 2024

AbstractWhole genome analysis has identified rare copy number variations (CNV) that are strongly involved in the pathogenesis of psychiatric disorders, and 3q29 deletion has been found to have the largest effect size. The 3q29 deletion mice model (3q29-del mice) has been established as a good pathological model for schizophrenia based on phenotypic analysis; however, circadian rhythm and sleep, which are also closely related to neuropsychiatric disorders, have not been investigated. In this study, our aims were to reevaluate the pathogenesis of 3q29-del by recreating model mice and analyzing their behavior and to identify novel new insights into the temporal activity and temperature fluctuations of the mouse model using a recently developed small implantable accelerometer chip, Nano-tag. We generated 3q29-del mice using genome editing technology and reevaluated common behavioral phenotypes. We next implanted Nano-tag in the abdominal cavity of mice for continuous measurements of long-time activity and body temperature. Our model mice exhibited weight loss similar to that of other mice reported previously. A general behavioral battery test in the model mice revealed phenotypes similar to those observed in mouse models of schizophrenia, including increased rearing frequency. Intraperitoneal implantation of Nano-tag, a miniature acceleration sensor, resulted in hypersensitive and rapid increases in the activity and body temperature of 3q29-del mice upon switching to lights-off condition. Similar to the 3q29-del mice reported previously, these mice are a promising model animals for schizophrenia. Successive quantitative analysis may provide results that could help in treating sleep disorders closely associated with neuropsychiatric disorders.
Enhancing prime editor activity by directed protein evolution in yeast
Authors: Weber Yanik , Böck Desirée , Ivașcu Anastasia , Mathis Nicolas , Rothgangl Tanja , Ioannidi Eleonora I. , Blaudt Alex C. , Tidecks Lisa , Vadovics Máté , Muramatsu Hiromi , Reichmuth Andreas , Marquart Kim F. , Kissling Lucas , Pardi Norbert , Jinek Martin , Schwank Gerald 
Published: March 2024

AbstractPrime editing is a highly versatile genome editing technology that enables the introduction of base substitutions, insertions, and deletions. However, compared to traditional Cas9 nucleases prime editors (PEs) are less active. In this study we use OrthoRep, a yeast-based platform for directed protein evolution, to enhance the editing efficiency of PEs. After several rounds of evolution with increased selection pressure, we identify multiple mutations that have a positive effect on PE activity in yeast cells and in biochemical assays. Combining the two most effective mutations – the A259D amino acid substitution in nCas9 and the K445T substitution in M-MLV RT – results in the variant PE_Y18. Delivery of PE_Y18, encoded on DNA, mRNA or as a ribonucleoprotein complex into mammalian cell lines increases editing rates up to 3.5-fold compared to PEmax. In addition, PE_Y18 supports higher prime editing rates when delivered in vivo into the liver or brain. Our study demonstrates proof-of-concept for the application of OrthoRep to optimize genome editing tools in eukaryotic cells.
ProTInSeq: transposon insertion tracking by ultra-deep DNA sequencing to identify translated large and small ORFs
Authors: Miravet-Verde Samuel , Mazzolini Rocco , Segura-Morales Carolina , Broto Alicia , Lluch-Senar Maria , Serrano Luis 
Published: March 2024

AbstractIdentifying open reading frames (ORFs) being translated is not a trivial task. ProTInSeq is a technique designed to characterize proteomes by sequencing transposon insertions engineered to express a selection marker when they occur in-frame within a protein-coding gene. In the bacterium Mycoplasma pneumoniae, ProTInSeq identifies 83% of its annotated proteins, along with 5 proteins and 153 small ORF-encoded proteins (SEPs; ≤100 aa) that were not previously annotated. Moreover, ProTInSeq can be utilized for detecting translational noise, as well as for relative quantification and transmembrane topology estimation of fitness and non-essential proteins. By integrating various identification approaches, the number of initially annotated SEPs in this bacterium increases from 27 to 329, with a quarter of them predicted to possess antimicrobial potential. Herein, we describe a methodology complementary to Ribo-Seq and mass spectroscopy that can identify SEPs while providing other insights in a proteome with a flexible and cost-effective DNA ultra-deep sequencing approach.
Disentangling top-down drivers of mortality underlying diel population dynamics of Prochlorococcus in the North Pacific Subtropical Gyre
Authors: Beckett Stephen J. , Demory David , Coenen Ashley R. , Casey John R. , Dugenne Mathilde , Follett Christopher L. , Connell Paige , Carlson Michael C. G. , Hu Sarah K. , Wilson Samuel T. , Muratore Daniel , Rodriguez-Gonzalez Rogelio A. , Peng Shengyun , Becker Kevin W. , Mende Daniel R. , Armbrust E. Virginia , Caron David A. , Lindell Debbie , White Angelicque E. , Ribalet François , Weitz Joshua S. 
Published: March 2024

AbstractPhotosynthesis fuels primary production at the base of marine food webs. Yet, in many surface ocean ecosystems, diel-driven primary production is tightly coupled to daily loss. This tight coupling raises the question: which top-down drivers predominate in maintaining persistently stable picocyanobacterial populations over longer time scales? Motivated by high-frequency surface water measurements taken in the North Pacific Subtropical Gyre (NPSG), we developed multitrophic models to investigate bottom-up and top-down mechanisms underlying the balanced control of Prochlorococcus populations. We find that incorporating photosynthetic growth with viral- and predator-induced mortality is sufficient to recapitulate daily oscillations of Prochlorococcus abundances with baseline community abundances. In doing so, we infer that grazers in this environment function as the predominant top-down factor despite high standing viral particle densities. The model-data fits also reveal the ecological relevance of light-dependent viral traits and non-canonical factors to cellular loss. Finally, we leverage sensitivity analyses to demonstrate how variation in life history traits across distinct oceanic contexts, including variation in viral adsorption and grazer clearance rates, can transform the quantitative and even qualitative importance of top-down controls in shaping Prochlorococcus population dynamics.
Natural variation in BnaA9.NF-YA7 contributes to drought tolerance in Brassica napus L
Authors: Wang Jia , Mao Lin , Li Yangyang , Lu Kun , Qu Cunmin , Tang Zhanglin , Li Jiana , Liu Liezhao 
Published: March 2024

AbstractRapeseed (Brassica napus) is one of the important oil crops worldwide. Its production is often threatened by drought stress. Here, we identify a transcription factor (BnaA9.NF-YA7) that negatively regulates drought tolerance through genome-wide association study in B. napus. The presence of two SNPs within a CCAAT cis element leads to downregulation of BnaA9.NF-YA7 expression. In addition, the M63I (G-to-C) substitution in the transactivation domain can activate low level expression of BnaA4.DOR, which is an inhibitory factor of ABA-induced stomatal closure. Furthermore, we determine that Bna.ABF3/4s directly regulate the expression of BnaA9.NF-YA7, and BnaA9.NF-YA7 indirectly suppresses the expression of Bna.ABF3/4s by regulation of Bna.ASHH4s. Our findings uncover that BnaA9.NF-YA7 serves as a supplementary role for ABA signal balance under drought stress conditions, and provide a potential molecular target to breed drought-tolerant B. napus cultivars.
Chloride intracellular channel (CLIC) proteins function as fusogens
Authors: Manori Bar , Vaknin Alisa , Vaňková Pavla , Nitzan Anat , Zaidel-Bar Ronen , Man Petr , Giladi Moshe , Haitin Yoni 
Published: March 2024

AbstractChloride Intracellular Channel (CLIC) family members uniquely transition between soluble and membrane-associated conformations. Despite decades of extensive functional and structural studies, CLICs’ function as ion channels remains debated, rendering our understanding of their physiological role incomplete. Here, we expose the function of CLIC5 as a fusogen. We demonstrate that purified CLIC5 directly interacts with the membrane and induces fusion, as reflected by increased liposomal diameter and lipid and content mixing between liposomes. Moreover, we show that this activity is facilitated by acidic pH, a known trigger for CLICs’ transition to a membrane-associated conformation, and that increased exposure of the hydrophobic inter-domain interface is crucial for this process. Finally, mutation of a conserved hydrophobic interfacial residue diminishes the fusogenic activity of CLIC5 in vitro and impairs excretory canal extension inC. elegansin vivo. Together, our results unravel the long-sought physiological role of these enigmatic proteins.
Human IgG Fc-engineering for enhanced plasma half-life, mucosal distribution and killing of cancer cells and bacteria
Authors: Foss Stian , Sakya Siri A. , Aguinagalde Leire , Lustig Marta , Shaughnessy Jutamas , Cruz Ana Rita , Scheepmaker Lisette , Mathiesen Line , Ruso-Julve Fulgencio , Anthi Aina Karen , Gjølberg Torleif Tollefsrud , Mester Simone , Bern Malin , Evers Mitchell , Bratlie Diane B. , Michaelsen Terje E. , Schlothauer Tilman , Sok Devin , Bhattacharya Jayanta , Leusen Jeanette , Valerius Thomas , Ram Sanjay , Rooijakkers Suzan H. M. , Sandlie Inger , Andersen Jan Terje 
Published: March 2024

AbstractMonoclonal IgG antibodies constitute the fastest growing class of therapeutics. Thus, there is an intense interest to design more potent antibody formats, where long plasma half-life is a commercially competitive differentiator affecting dosing, frequency of administration and thereby potentially patient compliance. Here, we report on an Fc-engineered variant with three amino acid substitutions Q311R/M428E/N434W (REW), that enhances plasma half-life and mucosal distribution, as well as allows for needle-free delivery across respiratory epithelial barriers in human FcRn transgenic mice. In addition, the Fc-engineered variant improves on-target complement-mediated killing of cancer cells as well as both gram-positive and gram-negative bacteria. Hence, this versatile Fc technology should be broadly applicable in antibody design aiming for long-acting prophylactic or therapeutic interventions.
Inter-site structural heterogeneity induction of single atom Fe catalysts for robust oxygen reduction
Authors: Zhang Peng , Chen Hsiao-Chien , Zhu Houyu , Chen Kuo , Li Tuya , Zhao Yilin , Li Jiaye , Hu Ruanbo , Huang Siying , Zhu Wei , Liu Yunqi , Pan Yuan 
Published: March 2024

AbstractMetal-nitrogen-carbon catalysts with hierarchically dispersed porosity are deemed as efficient geometry for oxygen reduction reaction (ORR). However, catalytic performance determined by individual and interacting sites originating from structural heterogeneity is particularly elusive and yet remains to be understood. Here, an efficient hierarchically porous Fe single atom catalyst (Fe SAs-HP) is prepared with Fe atoms densely resided at micropores and mesopores. Fe SAs-HP exhibits robust ORR performance with half-wave potential of 0.94 V and turnover frequency of 5.99 e−1s−1site−1 at 0.80 V. Theoretical simulations unravel a structural heterogeneity induced optimization, where mesoporous Fe-N4 acts as real active centers as a result of long-range electron regulation by adjacent microporous sites, facilitating O2 activation and desorption of key intermediate *OH. Multilevel operando characterization results identify active Fe sites undergo a dynamic evolution from basic Fe-N4 to active Fe-N3 under working conditions. Our findings reveal the structural origin of enhanced intrinsic activity for hierarchically porous Fe-N4 sites.
Control of feeding by a bottom-up midbrain-subthalamic pathway
Authors: Reis Fernando M. C. V. , Maesta-Pereira Sandra , Ollivier Matthias , Schuette Peter J. , Sethi Ekayana , Miranda Blake A. , Iniguez Emily , Chakerian Meghmik , Vaughn Eric , Sehgal Megha , Nguyen Darren C. T. , Yuan Faith T. H. , Torossian Anita , Ikebara Juliane M. , Kihara Alexandre H. , Silva Alcino J. , Kao Jonathan C. , Khakh Baljit S. , Adhikari Avishek 
Published: March 2024

AbstractInvestigative exploration and foraging leading to food consumption have vital importance, but are not well-understood. Since GABAergic inputs to the lateral and ventrolateral periaqueductal gray (l/vlPAG) control such behaviors, we dissected the role of vgat-expressing GABAergic l/vlPAG cells in exploration, foraging and hunting. Here, we show that in mice vgat l/vlPAG cells encode approach to food and consumption of both live prey and non-prey foods. The activity of these cells is necessary and sufficient for inducing food-seeking leading to subsequent consumption. Activation of vgat l/vlPAG cells produces exploratory foraging and compulsive eating without altering defensive behaviors. Moreover, l/vlPAG vgat cells are bidirectionally interconnected to several feeding, exploration and investigation nodes, including the zona incerta. Remarkably, the vgat l/vlPAG projection to the zona incerta bidirectionally controls approach towards food leading to consumption. These data indicate the PAG is not only a final downstream target of top-down exploration and foraging-related inputs, but that it also influences these behaviors through a bottom-up pathway.
Safety assessment and gastrointestinal retention of orally administered cerium oxide nanoparticles in rats
Authors: Han Hyoung-Yun , Kim Bo-Kyung , Rho Jinhyung , Park Se-Myo , Choi Mi-Sun , Kim Soojin , Heo Min Beom , Yang Young-Su , Oh Jung-Hwa , Lee Tae Geol , Yoon Seokjoo 
Published: March 2024

AbstractCerium oxide nanoparticles (CeO2 NPs, NM-212) are well-known for their catalytic properties and antioxidant potential, and have many applications in various industries, drug delivery, and cosmetic formulations. CeO2 NPs exhibit strong antimicrobial activity and can be used to efficiently remove pathogens from different environments. However, knowledge of the toxicological evaluation of CeO2 NPs is too limited to support their safe use. In this study, CeO2 NPs were orally administered to Sprague Dawley rats for 13 weeks at the doses of 0, 10, 100, and 1000 mg/kg bw/day, followed by a four week recovery period. The hematology values for the absolute and relative reticulocyte counts in male rats treated with 1000 mg/kg bw/day CeO2 NPs were lower than those in control rats. The clinical chemistry values for sodium and chloride in the treated male rat groups (100 and 1000 mg/kg/day) and total protein and calcium in the treated female rat groups (100 mg/kg/day) were higher than those in the control groups. However, these changes were not consistent in both sexes, and no abnormalities were found in the corresponding pathological findings. The results showed no adverse effects on any of the parameters assessed. CeO2 NPs accumulated in the jejunum, colon, and stomach wall of rats administered 1000 mg/kg CeO2 NPs for 90 days. However, these changes were not abnormal in the corresponding histopathological and immunohistochemical examinations. Therefore, 1000 mg/kg bw/day may be considered the “no observed adverse effect level” of CeO2 NPs (NM-212) in male and female SD rats under the present experimental conditions.
Direct TAMRA-dUTP labeling of M. tuberculosis genes using loop-mediated isothermal amplification (LAMP)
Authors: Altattan Basma , Ullrich Jasmin , Mattig Emily , Poppe Aline , Martins Renata , Bier Frank F. 
Published: March 2024

AbstractFluorescent molecule-based direct labeling of amplified DNA is a sensitive method employed across diverse DNA detection and diagnostics systems. However, using pre-labeled primers only allows for the attachment of a single fluorophore to each DNA strand and any modifications of the system are less flexible, requiring new sets of primers. As an alternative, direct labeling of amplified products with modified nucleotides is available, but still poorly characterized. To address these limitations, we sought a direct and adaptable approach to label amplicons produced through Loop-mediated isothermal amplification (LAMP), using labeled nucleotides (dUTPs) rather than primers. The focus of this study was the development and examination of a direct labeling technique of specific genes, including those associated with drug resistance in Mycobacterium tuberculosis. We used 5-(3-Aminoallyl)-2′-deoxyuridine-5′triphosphate, tagged with 5/6-TAMRA (TAMRA-dUTP) for labeling LAMP amplicons during the amplification process and characterized amplification and incorporation efficiency. The optimal TAMRA-dUTP concentration was first determined based on amplification efficiency (0.5% to total dNTPs). Higher concentrations of modified nucleotides reduced or completely inhibited the amplification yield. Target size also showed to be determinant to the success of amplification, as longer sequences showed lower amplification rates, thus less TAMRA incorporated amplicons. Finally, we were able to successfully amplify all four M. tuberculosis target genes using LAMP and TAMRA-modified dUTPs.
Exploring solar dynamo behavior using an annually resolved carbon-14 compilation during multiple grand solar minima
Authors: Inceoglu Fadil 
Published: March 2024

AbstractIn this study, we, for the first time, compiled all publicly available annually or biannually resolved $$^{14}$$

14

C records, which fully covers 7 grand solar minima at an annual and bi-annual resolution. Our results from 7 grand solar minima showed a clear relationship between the rate of decrease (increase) in solar activity levels and how long the onset (termination) of the grand solar minima will last. Additionally, we show a weaker relationship between the durations of onsets and terminations and between the rate of increase and decrease of solar activity levels. Our results also suggest there might be two or more types of grand solar minima.
A multimodal submillimeter MRI atlas of the human cerebellum
Authors: Lyu Wenjiao , Wu Ye , Huynh Khoi Minh , Ahmad Sahar , Yap Pew-Thian 
Published: March 2024

AbstractThe human cerebellum is engaged in a broad array of tasks related to motor coordination, cognition, language, attention, memory, and emotional regulation. A detailed cerebellar atlas can facilitate the investigation of the structural and functional organization of the cerebellum. However, existing cerebellar atlases are typically limited to a single imaging modality with insufficient characterization of tissue properties. Here, we introduce a multifaceted cerebellar atlas based on high-resolution multimodal MRI, facilitating the understanding of the neurodevelopment and neurodegeneration of the cerebellum based on cortical morphology, tissue microstructure, and intra-cerebellar and cerebello-cerebral connectivity.
Identification of microbial pathogens in Neolithic Scandinavian humans
Authors: Bergfeldt Nora , Kırdök Emrah , Oskolkov Nikolay , Mirabello Claudio , Unneberg Per , Malmström Helena , Fraser Magdalena , Sanchez-Quinto Federico , Jorgensen Roger , Skar Birgitte , Lidén Kerstin , Jakobsson Mattias , Storå Jan , Götherström Anders 
Published: March 2024

AbstractWith the Neolithic transition, human lifestyle shifted from hunting and gathering to farming. This change altered subsistence patterns, cultural expression, and population structures as shown by the archaeological/zooarchaeological record, as well as by stable isotope and ancient DNA data. Here, we used metagenomic data to analyse if the transitions also impacted the microbiome composition in 25 Mesolithic and Neolithic hunter-gatherers and 13 Neolithic farmers from several Scandinavian Stone Age cultural contexts. Salmonella enterica, a bacterium that may have been the cause of death for the infected individuals, was found in two Neolithic samples from Battle Axe culture contexts. Several species of the bacterial genus Yersinia were found in Neolithic individuals from Funnel Beaker culture contexts as well as from later Neolithic context. Transmission of e.g. Y. enterocolitica may have been facilitated by the denser populations in agricultural contexts.