bluuebunny/crossref_metadata_2025_split huggingface dataset:
Structural rearrangements allow nucleic acid discrimination by type I-D Cascade
Authors: Schwartz Evan A. , McBride Tess M. , Bravo Jack P. K. , Wrapp Daniel , Fineran Peter C. , Fagerlund Robert D. , Taylor David W. 
Published: May 2022

AbstractCRISPR-Cas systems are adaptive immune systems that protect prokaryotes from foreign nucleic acids, such as bacteriophages. Two of the most prevalent CRISPR-Cas systems include type I and type III. Interestingly, the type I-D interference proteins contain characteristic features of both type I and type III systems. Here, we present the structures of type I-D Cascade bound to both a double-stranded (ds)DNA and a single-stranded (ss)RNA target at 2.9 and 3.1 Å, respectively. We show that type I-D Cascade is capable of specifically binding ssRNA and reveal how PAM recognition of dsDNA targets initiates long-range structural rearrangements that likely primes Cas10d for Cas3′ binding and subsequent non-target strand DNA cleavage. These structures allow us to model how binding of the anti-CRISPR protein AcrID1 likely blocks target dsDNA binding via competitive inhibition of the DNA substrate engagement with the Cas10d active site. This work elucidates the unique mechanisms used by type I-D Cascade for discrimination of single-stranded and double stranded targets. Thus, our data supports a model for the hybrid nature of this complex with features of type III and type I systems.
Molecular basis for gating of cardiac ryanodine receptor explains the mechanisms for gain- and loss-of function mutations
Authors: Kobayashi Takuya , Tsutsumi Akihisa , Kurebayashi Nagomi , Saito Kei , Kodama Masami , Sakurai Takashi , Kikkawa Masahide , Murayama Takashi , Ogawa Haruo 
Published: May 2022

AbstractCardiac ryanodine receptor (RyR2) is a large Ca2+ release channel in the sarcoplasmic reticulum and indispensable for excitation-contraction coupling in the heart. RyR2 is activated by Ca2+ and RyR2 mutations are implicated in severe arrhythmogenic diseases. Yet, the structural basis underlying channel opening and how mutations affect the channel remains unknown. Here, we address the gating mechanism of RyR2 by combining high-resolution structures determined by cryo-electron microscopy with quantitative functional analysis of channels carrying various mutations in specific residues. We demonstrated two fundamental mechanisms for channel gating: interactions close to the channel pore stabilize the channel to prevent hyperactivity and a series of interactions in the surrounding regions is necessary for channel opening upon Ca2+ binding. Mutations at the residues involved in the former and the latter mechanisms cause gain-of-function and loss-of-function, respectively. Our results reveal gating mechanisms of the RyR2 channel and alterations by pathogenic mutations at the atomic level.
Proteome allocations change linearly with the specific growth rate of Saccharomyces cerevisiae under glucose limitation
Authors: Xia Jianye , Sánchez Benjamin J. , Chen Yu , Campbell Kate , Kasvandik Sergo , Nielsen Jens 
Published: May 2022

AbstractSaccharomyces cerevisiaeis a widely used cell factory; therefore, it is important to understand how it organizes key functional parts when cultured under different conditions. Here, we perform a multiomics analysis ofS. cerevisiaeby culturing the strain with a wide range of specific growth rates using glucose as the sole limiting nutrient. Under these different conditions, we measure the absolute transcriptome, the absolute proteome, the phosphoproteome, and the metabolome. Most functional protein groups show a linear dependence on the specific growth rate. Proteins engaged in translation show a perfect linear increase with the specific growth rate, while glycolysis and chaperone proteins show a linear decrease under respiratory conditions. Glycolytic enzymes and chaperones, however, show decreased phosphorylation with increasing specific growth rates; at the same time, an overall increased flux through these pathways is observed. Further analysis show that even though mRNA levels do not correlate with protein levels for all individual genes, the transcriptome level of functional groups correlates very well with its corresponding proteome. Finally, using enzyme-constrained genome-scale modeling, we find that enzyme usage plays an important role in controlling flux in amino acid biosynthesis.
HER2-low-positive breast cancer: evolution from primary tumor to residual disease after neoadjuvant treatment
Authors: Miglietta Federica , Griguolo Gaia , Bottosso Michele , Giarratano Tommaso , Lo Mele Marcello , Fassan Matteo , Cacciatore Matilde , Genovesi Elisa , De Bartolo Debora , Vernaci Grazia , Amato Ottavia , Porra Francesca , Conte PierFranco , Guarneri Valentina , Dieci Maria Vittoria 
Published: May 2022

AbstractApproximately a half of breast tumors classified as HER2-negative exhibit HER2-low-positive expression. We recently described a high instability of HER2-low-positive expression from primary breast cancer (BC) to relapse. Previous studies reporting discordance in HER2 status between baseline biopsy and residual disease (RD) in patients undergoing neoadjuvant treatment did not include the HER2-low-positive category. The aim of this study is to track the evolution of HER2-low-positive expression from primary BC to RD after neoadjuvant treatment. Patients undergoing neoadjuvant treatment with available baseline tumor tissue and matched samples of RD (in case of no pCR) were included. HER2-negative cases were sub-classified as HER2-0 or HER2-low-positive (IHC 1+ or 2+ and ISH negative). Four-hundred forty-six patients were included. Primary BC phenotype was: HR-positive/HER2-negative 23.5%, triple-negative (TN) 35%, HER2-positive 41.5%. HER2-low-positive cases were 55.6% of the HER2-negative cohort and were significantly enriched in the HR-positive/HER2-negative vs. TN subgroup (68.6% vs. 46.8%, p = 0.001 χ2 test). In all, 35.3% of non-pCR patients (n = 291) had a HER2-low-positive expression on RD. The overall rate of HER2 expression discordance was 26.4%, mostly driven by HER2-negative cases converting either from (14.8%) or to (8.9%) HER2-low-positive phenotype. Among HR-positive/HER2-negative patients with HER2-low-positive expression on RD, 32.0% and 57.1% had an estimated high risk of relapse according to the residual proliferative cancer burden and CPS-EG score, respectively. In conclusion, HER2-low-positive expression showed high instability from primary BC to RD after neoadjuvant treatment. HER2-low-positive expression on RD may guide personalized adjuvant treatment for high-risk patients in the context of clinical trials with novel anti-HER2 antibody-drug conjugates.
How advances in low-g plumbing enable space exploration
Authors: Weislogel M. M. , Graf J. C. , Wollman A. P. , Turner C. C. , Cardin K. J. T. , Torres L. J. , Goodman J. E. , Buchli J. C. 
Published: May 2022

AbstractIn many ways, plumbing is essential to life support. In fact, the advance of humankind on Earth is directly linked to the advance of clean, healthy, reliable plumbing solutions. Shouldn’t this also be true for the advancement of humankind in space? Unfortunately, the reliability of even the simplest plumbing element aboard spacecraft is rarely that of its terrestrial counterpart. This state of affairs is due entirely to the near-weightless “low-g” state of orbiting and coast spacecraft. But the combined passive capillary effects of surface tension, wetting, and system geometry in space can be exploited to replace the passive role of gravity on earth, and thus achieve similar outcomes there. In this paper, we review a selection of experiments conducted in low-g environments (i.e., ISS and drop towers) that focus on capillary fluidic phenomena. The results of each experiment are highly applicable to subsequent advances in spacecraft plumbing. With examples ranging from spurious droplet ejections to passive bubble coalescence, to droplet bouncing, to complex container wicking, we show how simple low-g demonstrations can lead to significant reliability improvements in practical passive plumbing processes from pipetting to liquid-gas separations, to wastewater transport, to drinking in space.
Convolutional neural network-based reconstruction for positronium annihilation localization
Authors: Jegal Jin , Jeong Dongwoo , Seo Eun-Suk , Park HyeoungWoo , Kim Hongjoo 
Published: May 2022

AbstractA novel hermetic detector composed of 200 bismuth germanium oxide crystal scintillators and 393 channel silicon photomultipliers has been developed for positronium (Ps) annihilation studies. This compact 4π detector is capable of simultaneously detecting γ-ray decay in all directions, enabling not only the study of visible and invisible exotic decay processes but also tumor localization in positron emission tomography for small animals. In this study, we investigate the use of a convolutional neural network (CNN) for the localization of Ps annihilation synonymous with tumor localization. Two-γ decay systems of the Ps annihilation from 22Na and 18F radioactive sources are simulated using a GEANT4 simulation. The simulated datasets are preprocessed by applying energy cutoffs. The spatial error in the XY plane from the CNN is compared to that from the classical weighted k-means algorithm centroiding, and the feasibility of CNN-based Ps annihilation reconstruction with tumor localization is discussed.
Type 1 diabetes and the challenges of emotional support in crisis situations: results from a feasibility study of a multidisciplinary teleintervention
Authors: Alessi Janine , Becker Alice Scalzilli , Amaral Bibiana , de Oliveira Giovana Berger , Franco Débora Wilke , Knijnik Carolina Padilla , Kobe Gabriel Luiz , de Brito Ariane , de Carvalho Taíse Rosa , Telo Guilherme Heiden , Schaan Beatriz D. , Telo Gabriela Heiden 
Published: May 2022

AbstractThe association between type 1 diabetes and mental health disorders could be exacerbated in a stressful environment. This study aimed to evaluate the feasibility of a teleguided intervention on emotional disorders in patients with type 1 diabetes during the COVID-19 outbreak. This study was performed during the social distancing period in the COVID-19 outbreak in Brazil. Individuals with type 1 diabetes aged ≥ 18 years were selected to receive a teleguided multidisciplinary intervention or the usual care plus an educational website access. The proposed intervention aimed addressing aspects of mental health, diabetes care and lifestyle habits during the pandemic. The feasibility outcome included the assessment of recruitment capability and adherence to the proposed intervention. Moreover, we evaluated the presence of positive screening for emotional disorders (Self Report Questionnaire 20) after a 16-week intervention, patients’ perceptions of pandemic-related changes, diabetes-related emotional distress, eating disorders, and sleep disorders. Data were analyzed with the intent‐to‐treat principle. Fifty-eight individuals (mean age, 43.8 ± 13.6 years) were included (intervention group, n = 29; control group, n = 29). At the end of the study, a total of 5 participants withdrew from the study in the intervention group compared to only 1 in the control group. Participants who dropout from the study had similar mean age, sex and income to those who remained in the study. The analysis of mental health disorders was not different between the groups at the follow up: a positive screening result was found in 48.3% and 34.5% of participants in the intervention and control groups, respectively (P = 0.29). The intervention group felt more supported in their diabetes care during the social distancing period (82.8% vs. 48.3% in the control group, P < 0.01). Our study identified a disproportionate higher number of withdrawals in the intervention group when compared to the control group. This difference may have compromised the power of the study for the proposed assessments and should be reevaluated in future studies.Trial registration: ClinicalTrials.gov (NCT04344210). Date of registration: 14/04/2020.
Impact of different pretreatments and attachment materials on shear bond strength between monolithic zirconia restorations and metal brackets
Authors: Jungbauer Rebecca , Proff Peter , Edelhoff Daniel , Stawarczyk Bogna 
Published: May 2022

AbstractTo investigate the influence of different pretreatment methods, attachment materials and artificial aging on shear bond strength (SBS) between monolithic zirconia and metal brackets. Zirconia substrates were pretreated with silica coated alumina (CoJet) and (1) clearfill ceramic primer plus (CF), (2) RelyX ceramic primer (RXP), (3) Futurabond U (FU). The brackets were bonded with (1) Transbond XT Adhesive (TB), (2) BrackFix Adhesive (BF), (3) bracepaste adhesive (BP). SBS was tested after 24 h, 500 thermal cycles, 90 d at 37 °C with a universal testing machine. SBS values reached from 8.3 to 16.9 MPa. The Weibull moduli ranged between 0.37 (RXP combined with BP after 90 d) and 7.42 (CF combined with TB after 24 h). The pretreatment with FU after 90 d, independent of the attachment material, and RXP with BF resulted in the lowest SBS values 8.3–9.9 MPa, the combination of RXP or CF with TB showed the highest (13.2–16.9 MPa) independent of aging. After FU pretreatment the proportion of ARI 1 and 0 was higher, of ARI 3 lower as after CF and RXP pretreatment. All tested combinations showed sufficiently high SBS values for clinical use. Pretreatment with FU presented the lowest values after 90 days.
Murine cardiac fibrosis localization using adaptive Bayesian cardiac strain imaging in vivo
Authors: Al Mukaddim Rashid , Weichmann Ashley M. , Taylor Rachel , Hacker Timothy A. , Pier Thomas , Hardin Joseph , Graham Melissa , Mitchell Carol C. , Varghese Tomy 
Published: May 2022

AbstractAn adaptive Bayesian regularized cardiac strain imaging (ABR-CSI) algorithm for in vivo murine myocardial function assessment is presented. We report on 31 BALB/CJ mice (n = 17 females, n = 14 males), randomly stratified into three surgical groups: myocardial infarction (MI, n = 10), ischemia–reperfusion (IR, n = 13) and control (sham, n = 8) imaged pre-surgery (baseline- BL), and 1, 2, 7 and 14 days post-surgery using a high frequency ultrasound imaging system (Vevo 2100). End-systole (ES) radial and longitudinal strain images were used to generate cardiac fibrosis maps using binary thresholding. Percentage fibrotic myocardium (PFM) computed from regional fibrosis maps demonstrated statistically significant differences post-surgery in scar regions. For example, the MI group had significantly higher PFMRadial (%) values in the anterior mid region (p = 0.006) at Day 14 (n = 8, 42.30 ± 14.57) compared to BL (n = 12, 1.32 ± 0.85). A random forest classifier automatically detected fibrotic regions from ground truth Masson’s trichrome stained histopathology whole slide images. Both PFMRadial (r = 0.70) and PFMLongitudinal (r = 0.60) results demonstrated strong, positive correlation with PFMHistopathology (p < 0.001).
Deep learning network for integrated coil inhomogeneity correction and brain extraction of mixed MRI data
Authors: Chuang Kai-Hsiang , Wu Pei-Huan , Li Zengmin , Fan Kang-Hsing , Weng Jun-Cheng 
Published: May 2022

AbstractMagnetic Resonance Imaging (MRI) has been widely used to acquire structural and functional information about the brain. In a group- or voxel-wise analysis, it is essential to correct the bias field of the radiofrequency coil and to extract the brain for accurate registration to the brain template. Although automatic methods have been developed, manual editing is still required, particularly for echo-planar imaging (EPI) due to its lower spatial resolution and larger geometric distortion. The needs of user interventions slow down data processing and lead to variable results between operators. Deep learning networks have been successfully used for automatic postprocessing. However, most networks are only designed for a specific processing and/or single image contrast (e.g., spin-echo or gradient-echo). This limitation markedly restricts the application and generalization of deep learning tools. To address these limitations, we developed a deep learning network based on the generative adversarial net (GAN) to automatically correct coil inhomogeneity and extract the brain from both spin- and gradient-echo EPI without user intervention. Using various quantitative indices, we show that this method achieved high similarity to the reference target and performed consistently across datasets acquired from rodents. These results highlight the potential of deep networks to integrate different postprocessing methods and adapt to different image contrasts. The use of the same network to process multimodality data would be a critical step toward a fully automatic postprocessing pipeline that could facilitate the analysis of large datasets with high consistency.
A facile hydrothermal synthesis of high-efficient NiO nanocatalyst for preparation of 3,4-dihydropyrimidin-2(1H)-ones
Authors: Khashaei Maryam , Kafi-Ahmadi Leila , Khademinia Shahin , Poursattar Marjani Ahmad , Nozad Ehsan 
Published: May 2022

AbstractThe present work introduces a one-step and facile hydrothermal procedure as a green process for the first time to synthesize nickel(II) oxide (NiO) nanoparticles. The as-prepared nanomaterials were used as high efficient, low toxic and cost catalyst for the synthesis of some organic compounds. Ni(NO3)2 and some natural extract were used as a surfactant for the first time to synthesis NiO nanomaterials. A high synthesis yield (91%) was obtained for S2. Rietveld analysis affirmed the cubic crystal system of the obtained NiO nanocatalyst. The morphology studies were carried out with the FESEM method and the images revealed a change from non-homogenous to homogenous spherical particles when the Barberryas was used instead of orange blossom surfactant. Besides, the images revealed that the particle size distribution was in the range of 20 to 60 nm. The synthesized catalysts were used for the first time in Biginelli multicomponent reactions (MCRs) for the preparation of 3,4-dihydropyrimidin-2(1H)-ones (DHPMs) under the present facile reaction conditions. High yield (97%) of the final product was achieved at the optimum condensation reaction conditions (Catalyst: 60 mg; temperature: 90 °C and time: 90 min) when ethyl acetoacetate/methyl acetoacetate (1 mmol), benzaldehyde (1 mmol) and urea (1.2 mmol) were used. A kinetic study affirmed pseudo-first-order model for Biginelli reactions followed the pseudo-first-order model.
Determination of sub-ps lattice dynamics in FeRh thin films
Authors: Grimes Michael , Ueda Hiroki , Ozerov Dmitry , Pressacco Federico , Parchenko Sergii , Apseros Andreas , Scholz Markus , Kubota Yuya , Togashi Tadashi , Tanaka Yoshikazu , Heyderman Laura , Thomson Thomas , Scagnoli Valerio 
Published: May 2022

AbstractUnderstanding the ultrashort time scale structural dynamics of the FeRh metamagnetic phase transition is a key element in developing a complete explanation of the mechanism driving the evolution from an antiferromagnetic to ferromagnetic state. Using an X-ray free electron laser we determine, with sub-ps time resolution, the time evolution of the (–101) lattice diffraction peak following excitation using a 35 fs laser pulse. The dynamics at higher laser fluence indicates the existence of a transient lattice state distinct from the high temperature ferromagnetic phase. By extracting the lattice temperature and comparing it with values obtained in a quasi-static diffraction measurement, we estimate the electron–phonon coupling in FeRh thin films as a function of laser excitation fluence. A model is presented which demonstrates that the transient state is paramagnetic and can be reached by a subset of the phonon bands. A complete description of the FeRh structural dynamics requires consideration of coupling strength variation across the phonon frequencies.
Seroprevalence and risk factors for COVID-19 in the metropolis of the Brazilian Amazon
Authors: da Silva Torres Maria Karoliny , Lopes Felipe Teixeira , de Lima Aline Cecy Rocha , Lima Carlos Neandro Cordeiro , dos Santos Brito Wandrey Roberto , dos Santos Bernardo Cintra , de Sousa Renata Santos , Gomes Jayanne Lilian Carvalho , Botelho Bruno José Sarmento , Correa Ana Carolina Alves , Machado Luiz Fernando A. , Feitosa Rosimar Neris Martins , Lima Sandra Souza , Vallinoto Izaura Maria Vieira Cayres , Vallinoto Antonio Carlos R. 
Published: May 2022

AbstractThe devastating effect of health system overload was observed after cases of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) peaked in April 2020 in Belém, a capital metropolis in the Brazilian Amazon. Our results showed a high seroprevalence (39.24%) of anti-SARS-CoV-2 IgG antibodies among the population of the capital of the state of Pará after the first wave of the pandemic. Old age, mixed race, a high school education level, low income and contact with infected individuals are risk factors and may be driving seropositivity and exposure to SARS-CoV-2 in this population. This study is one of the first to provide important information to understand the socioeconomic inequalities, behavioral characteristics and viral transmission dynamics associated with the risk of SARS-CoV-2 infection in the capital of the state of Pará, northern Brazil.
Partial oxidation of methane to methanol on boron nitride at near critical acetonitrile
Authors: Kapuge Tharindu Kankanam , Moharreri Ehsan , Perera Inosh , Eddy Nicholas , Kriz David , Nisly Nathaniel , Shuster Seth , Nandi Partha , Suib Steven L. 
Published: May 2022

AbstractDirect catalytic conversion of methane to methanol with O2 has been a fundamental challenge in unlocking abundant natural gas supplies. Metal-free methane conversion with 17% methanol yield based on the limiting reagent O2 at 275 °C was achieved with near supercritical acetonitrile in the presence of boron nitride. Reaction temperature, catalyst loading, dwell time, methane–oxygen molar ratio, and solvent-oxygen molar ratios were identified as critical factors controlling methane activation and the methanol yield. Extension of the study to ethane (C2) showed moderate yields of methanol (3.6%) and ethanol (4.5%).
Indirect organogenesis for high frequency shoot regeneration of two cultivars of Sansevieria trifasciata Prain differing in fiber production
Authors: García-Hernández Eleazar , Loera-Quezada Maribel M. , Morán-Velázquez Dalia C. , López Mercedes G. , Chable-Vega Manuel A. , Santillán-Fernández Alberto , Zavaleta-Mancera Hilda A. , Tang John Z. , Azadi Parastoo , Ibarra-Laclette Enrique , Alatorre-Cobos Fulgencio 
Published: May 2022

AbstractSansevieria trifasciata is used as an indoor plant, in traditional medicine and as a fiber source. Here we characterized fibers of two of varieties of S. trifasciata, Lorentii and Hahnii, and report a protocol for their propagation based on indirect shoot organogenesis. Structural and ribbon fibers were scattered within leaf parenchyma when viewed with confocal laser scanning microscopy. Chemical analysis of the fibers by mass spectrometry and high-performance chromatography revealed higher contents of cellulose and xylose in Lorentii than in Hahnii and significant differences for total lignin between both. A protocol for de novo shoot production was then developed using leaf explants. Time-course histological analyses showed that the first events of transdifferentiation were triggered preferentially in cells surrounding fibers and vascular bundles. Callogenesis and shoot performances were quantified for both varieties, and 2,4-D at 2 and 3 mg·L-1 yielded the best results for primary calli induction and fresh calli mass. The length, number, and mass of shoots produced did not differ significantly between the two cultivars. The fast morphogenic response of S. trifasciata to in vitro culture may be useful for mass propagation or other biotechnological purposes such as metabolite production.