bluuebunny/crossref_metadata_2025_split huggingface dataset:
De novo design and directed folding of disulfide-bridged peptide heterodimers
Authors: Yao Sicong , Moyer Adam , Zheng Yiwu , Shen Yang , Meng Xiaoting , Yuan Chong , Zhao Yibing , Yao Hongwei , Baker David , Wu Chuanliu 
Published: March 2022

AbstractPeptide heterodimers are prevalent in nature, which are not only functional macromolecules but molecular tools for chemical and synthetic biology. Computational methods have also been developed to design heterodimers of advanced functions. However, these peptide heterodimers are usually formed through noncovalent interactions, which are prone to dissociate and subject to concentration-dependent nonspecific aggregation. Heterodimers crosslinked with interchain disulfide bonds are more stable, but it represents a formidable challenge for both the computational design of heterodimers and the manipulation of disulfide pairing for heterodimer synthesis and applications. Here, we report the design, synthesis and application of interchain disulfide-bridged peptide heterodimers with mutual orthogonality by combining computational de novo designs with a directed disulfide pairing strategy. These heterodimers can be used as not only scaffolds for generating functional molecules but chemical tools or building blocks for protein labeling and construction of crosslinking hybrids. This study thus opens the door for using this unexplored dimeric structure space for many biological applications.
Impact of green clay authigenesis on element sequestration in marine settings
Authors: Baldermann Andre , Banerjee Santanu , Czuppon György , Dietzel Martin , Farkaš Juraj , Lӧhr Stefan , Moser Ulrike , Scheiblhofer Esther , Wright Nicky M. , Zack Thomas 
Published: March 2022

AbstractRetrograde clay mineral reactions (reverse weathering), including glauconite formation, are first-order controls on element sequestration in marine sediments. Here, we report substantial element sequestration by glauconite formation in shallow marine settings from the Triassic to the Holocene, averaging 3 ± 2 mmol·cm−²·kyr−1 for K, Mg and Al, 16 ± 9 mmol·cm−²·kyr−1 for Si and 6 ± 3 mmol·cm−²·kyr−1 for Fe, which is ~2 orders of magnitude higher than estimates for deep-sea settings. Upscaling of glauconite abundances in shallow-water (0–200 m) environments predicts a present-day global uptake of ~≤ 0.1 Tmol·yr−1 of K, Mg and Al, and ~0.1–0.4 Tmol·yr−1 of Fe and Si, which is ~half of the estimated Mesozoic elemental flux. Clay mineral authigenesis had a large impact on the global marine element cycles throughout Earth’s history, in particular during ‘greenhouse’ periods with sea level highstand, and is key for better understanding past and present geochemical cycling in marine sediments.
Brain-wide projection reconstruction of single functionally defined neurons
Authors: Wang Meng , Liu Ke , Pan Junxia , Li Jialin , Sun Pei , Zhang Yongsheng , Li Longhui , Guo Wenyan , Xin Qianqian , Zhao Zhikai , Liu Yurong , Zhou Zhenqiao , Lyu Jing , Zheng Ting , Han Yunyun , Zhang Chunqing , Liao Xiang , Zeng Shaoqun , Jia Hongbo , Chen Xiaowei 
Published: March 2022

AbstractReconstructing axonal projections of single neurons at the whole-brain level is currently a converging goal of the neuroscience community that is fundamental for understanding the logic of information flow in the brain. Thousands of single neurons from different brain regions have recently been morphologically reconstructed, but the corresponding physiological functional features of these reconstructed neurons are unclear. By combining two-photon Ca2+ imaging with targeted single-cell plasmid electroporation, we reconstruct the brain-wide morphologies of single neurons that are defined by a sound-evoked response map in the auditory cortices (AUDs) of awake mice. Long-range interhemispheric projections can be reliably labelled via co-injection with an adeno-associated virus, which enables enhanced expression of indicator protein in the targeted neurons. Here we show that this method avoids the randomness and ambiguity of conventional methods of neuronal morphological reconstruction, offering an avenue for developing a precise one-to-one map of neuronal projection patterns and physiological functional features.
Identification of a protein responsible for the synthesis of archaeal membrane-spanning GDGT lipids
Authors: Zeng Zhirui , Chen Huahui , Yang Huan , Chen Yufei , Yang Wei , Feng Xi , Pei Hongye , Welander Paula V. 
Published: March 2022

AbstractGlycerol dibiphytanyl glycerol tetraethers (GDGTs) are archaeal monolayer membrane lipids that can provide a competitive advantage in extreme environments. Here, we identify a radical SAM protein, tetraether synthase (Tes), that participates in the synthesis of GDGTs. Attempts to generate a tes-deleted mutant in Sulfolobus acidocaldarius were unsuccessful, suggesting that the gene is essential in this organism. Heterologous expression of tes homologues leads to production of GDGT and structurally related lipids in the methanogen Methanococcus maripaludis (which otherwise does not synthesize GDGTs and lacks a tes homolog, but produces a putative GDGT precursor, archaeol). Tes homologues are encoded in the genomes of many archaea, as well as in some bacteria, in which they might be involved in the synthesis of bacterial branched glycerol dialkyl glycerol tetraethers.
Phylotranscriptomic insights into a Mesoproterozoic–Neoproterozoic origin and early radiation of green seaweeds (Ulvophyceae)
Authors: Hou Zheng , Ma Xiaoya , Shi Xuan , Li Xi , Yang Lingxiao , Xiao Shuhai , De Clerck Olivier , Leliaert Frederik , Zhong Bojian 
Published: March 2022

AbstractThe Ulvophyceae, a major group of green algae, is of particular evolutionary interest because of its remarkable morphological and ecological diversity. Its phylogenetic relationships and diversification timeline, however, are still not fully resolved. In this study, using an extensive nuclear gene dataset, we apply coalescent- and concatenation-based approaches to reconstruct the phylogeny of the Ulvophyceae and to explore the sources of conflict in previous phylogenomic studies. The Ulvophyceae is recovered as a paraphyletic group, with the Bryopsidales being a sister group to the Chlorophyceae, and the remaining taxa forming a clade (Ulvophyceaesensu stricto). Molecular clock analyses with different calibration strategies emphasize the large impact of fossil calibrations, and indicate a Meso-Neoproterozoic origin of the Ulvophyceae (sensu stricto), earlier than previous estimates. The results imply that ulvophyceans may have had a profound influence on oceanic redox structures and global biogeochemical cycles at the Mesoproterozoic-Neoproterozoic transition.
Do current family history-based genetic testing guidelines contribute to breast cancer health inequities?
Authors: Jakuboski Samantha H. , McDonald Jasmine A. , Terry Mary Beth 
Published: March 2022

AbstractPrior to the recommended age for population-based breast cancer screening by mammography, which ranges from 40−50 years depending on guidelines, the main way to identify higher risk women for earlier breast cancer (BC) screening to improve outcomes and discuss targeted chemoprevention is through specific clinical guidelines which are largely based on family history of breast cancer and known mutations in breast cancer susceptibility genes. The annual percent change (APC) in early-onset BC continues to rise, with the higher early-onset cancer burden and mortality continuing to be seen in non-Hispanic black (NHB) women compared to non-Hispanic white (NHW) women. Coupled with the increasing incidence overall as well as the lower percent of BC family history reported in NHB women compared with that of NHW women means that continued reliance on guidelines to identify women for genetic screening and initiation of early BC screening based largely on family history could lead to even greater BC health inequities. The similarity in the prevalence of mutations in key BC susceptibility genes between NHB and NHW women contrasts sharply to the differences in age-specific incidence rates between NHB and NHW women, supporting that there must be environmental modifiers that are contributing to the increased incidence in NHB women. This reality further argues for identifying NHB women early in adulthood through genetic testing who may benefit from tailored BC risk-reduction programs and early BC screening.
Van der Waals force-induced intralayer ferroelectric-to-antiferroelectric transition via interlayer sliding in bilayer group-IV monochalcogenides
Authors: Xu Bo , Deng Junkai , Ding Xiangdong , Sun Jun , Liu Jefferson Zhe 
Published: March 2022

AbstractTwo-dimensional materials with ferroelectric properties break the size effect of conventional ferroelectric materials and unlock unprecedented potentials of ferroelectric-related application at small length scales. Using first-principles calculations, a sliding-induced ferroelectric-to-antiferroelectric behavior in bilayer group-IV monochalcogenides (MX, with M = Ge, Sn and X = S, Se) is discovered. Upon this mechanism, the top layer exhibits a reversible intralayer ferroelectric switching, leading to a reversible transition between the ferroelectric and antiferroelectric states in the bilayer MXs. Further results show that the interlayer van der Waals interaction, which is usually considered to be weak, can actually generate an in-plane lattice distortion and thus cause the breaking/forming of intralayer covalent bonds in the top layer, leading to the observed anomalous phenomenon. This unique property has advantages for energy harvesting over existing piezoelectric and triboelectric nanogenerators. The interlayer sliding-induced big polarization change (40 μC cm−2) and ultrahigh polarization changing rate generate an open-circuit voltage two orders of magnitude higher than that of MoS2-based nanogenerators. The theoretical prediction of power output for this bilayer MXs at a moderate sliding speed 1 m s−1 is four orders of magnitude higher than the MoS2 nanogenerator, indicating great potentials in energy harvesting applications.
Estimated date of delivery with electronic medical records by a hybrid GBDT-GRU model
Authors: Wu Yina , Zhang Yichao , Zou Xu , Yuan Zhenming , Hu Wensheng , Lu Sha , Sun Xiaoyan , Wu Yingfei 
Published: March 2022

AbstractAn accurate estimated date of delivery (EDD) helps pregnant women make adequate preparations before delivery and avoid the panic of parturition. EDD is normally derived from some formulates or estimated by doctors based on last menstruation period and ultrasound examinations. This study attempted to combine antenatal examinations and electronic medical records to develop a hybrid model based on Gradient Boosting Decision Tree and Gated Recurrent Unit (GBDT-GRU). Besides exploring the features that affect the EDD, GBDT-GRU model obtained the results by dynamic prediction of different stages. The mean square error (MSE) and coefficient of determination (R2) were used to compare the performance among the different prediction methods. In addition, we evaluated predictive performances of different prediction models by comparing the proportion of pregnant women under the error of different days. Experimental results showed that the performance indexes of hybrid GBDT-GRU model outperformed other prediction methods because it focuses on analyzing the time-series predictors of pregnancy. The results of this study are helpful for the development of guidelines for clinical delivery treatments, as it can assist clinicians in making correct decisions during obstetric examinations.
Comparison of GentleWave system and passive ultrasonic irrigation with minimally invasive and conventional instrumentation against LPS in infected root canals
Authors: Velardi Johnathan P. , Alquria Theeb A. , Alfirdous Rayyan A. , Corazza Bruna J. M. , Gomes Ana P. M. , Silva Eduardo G. , Griffin Ina L. , Tordik Patricia A. , Martinho Frederico C. 
Published: March 2022

AbstractThis study compared the effectiveness of GentleWave system (GWS) and passive ultrasonic irrigation (PUI) in removing lipopolysaccharides (LPS) from infected root canals after minimally invasive (MIT) and conventional instrumentation (CIT) techniques. Sixty first premolars with two roots were inoculated with fluorescent LPS conjugate (Alexa Fluor 594). Of those, twelve were dentin pretreated, inoculated with fluorescent LPS conjugate, and submitted to confocal laser scanning microscopy (CLSM) to validate the LPS-infection model. Forty-eight teeth were randomly divided into treatment groups: GWS + MIT, GWS + CIT, PUI + MIT, and PUI + CIT (all, n = 12). Teeth were instrumented with Vortex Blue rotary file size 15/0.04 for MIT and 35/0.04 for CIT. Samples were collected before (s1) and after a root canal procedure (s2) and after cryogenically ground the teeth (s3) for intraradicular LPS analysis. LPS were quantified with LAL assay (KQCL test). GWS + MIT and GWS + CIT were the most effective protocols against LPS, with no difference between them (p > 0.05). PUI + CIT was more effective than PUI + MIT (p < 0.05) but less effective than GWS + MIT and GWS + CIT. GWS was the most effective protocol against LPS in infected root canals using MIT and CIT techniques.
Determinants of misuse of antibiotics among parents of children attending clinics in regional referral hospitals in Tanzania
Authors: Mutagonda Ritah F. , Marealle Alphonce I. , Nkinda Lilian , Kibwana Upendo , Maganda Betty A. , Njiro Belinda J. , Ndumwa Harrieth P. , Kilonzi Manase , Mikomangwa Wigilya P. , Mlyuka Hamu J. , Felix Fatuma F. , Myemba David T. , Mwakawanga Dorkasi L. , Sambayi Godfrey , Kunambi Peter P. , Ndayishimiye Pacifique , Sirili Nathanael , Mfaume Rashid , Nshau Arapha , Nyankesha Elevanie , Scherpbier Robert , Bwire George M. 
Published: March 2022

AbstractParents are the important implementers on appropriate/inappropriate use of antibiotics, especially in the pediatric population. Limited studies have associated poor knowledge, attitude, and practice (KAP) among parents with antibiotics misuse. Therefore, this study was conducted to determine the parents’ KAP and factors associated with inappropriate use of antibiotics among Tanzanian children. A hospital-based cross-sectional study was conducted in 14 regional referral hospitals (RRHs) in Tanzania between June and September 2020. KAP was estimated using a Likert scale, whereas KAP factors were determined using logistic regression models. A total of 2802 parents were enrolled in the study. The median age (interquartile range) of parents was 30.0 (25–36) years where 82.4% (n = 2305) were female parents. The majority of the parents had primary education, 56.1% (n = 1567). Of 2802 parents, only 10.9% (n = 298) had good knowledge about antibiotics, 16.4% (n = 455) had positive attitude whereas 82.0% (n = 2275) had poor practice on the appropriate use of antibiotics. Parents' education level, i.e., having a university degree (aOR: 3.27 95% CI 1.62–6.63, p = 0.001), good knowledge (aOR: 1.70, 95% CI 1.19–2.23, p = 0.003) and positive attitudes (aOR: 5.56, 95% CI 4.09–7.56, p < 0.001) were significantly associated with the appropriate use of antibiotics in children. Most parents had poor knowledge, negative attitude, and poor practice towards antibiotics use in children. Parents’ education level, employment status, knowledge on antibiotic use, and good attitude contributed to the appropriate use of antibiotics in children attending clinics at RRHs.
LMS parameters, percentile, and Z-score growth curves for axial length in Chinese schoolchildren in Wuhan
Authors: Sanz Diez Pablo , Yang Li-Hua , Lu Mei-Xia , Kiess Wieland , Wahl Siegfried 
Published: March 2022

AbstractUnderstanding the ocular structural changes are fundamental to defining strategies for myopia prevention and management. This study aimed to establish age-gender specific normative LMS parameters for axial length to generate percentile and Z-score growth curves in a population of Chinese schoolchildren. A total of 14,760 individuals aged 6 to 15 years from Wuhan, central China, contributed to this study. The LMS method was used for the calculation of LMS parameters and the generation of percentile and Z-score growth curves for axial length. Growth curves derived from the LMS parameters were compared with those originally calculated. Axial elongation was age- and percentile-dependent. The highest elongation rate occurred at the 98th percentile in the range 6 to 9 years, being up to 1.46 mm in boys and 1.42 mm in girls. The largest differences between original and newly generated growth curves were detected at the 98th percentile at age 15; 0.78 mm (females) and 0.63 mm (males). Multinomial logistic regression and receiver operating characteristic analyses revealed Z-scores as a good predictor for estimating high myopia development. The axial length growth curves presented in this study provide a technically solid instrument that depicts the best description of physiological eye growth for Chinese schoolchildren aged 6 to 15 years.
The ideal habitat for leaf-cutting ant queens to build their nests
Authors: Sousa Kátia K. A. , Camargo Roberto S. , Caldato Nadia , Farias Adriano P. , Calca Marcus V. C. , Dal Pai Alexandre , Matos Carlos A. O. , Zanuncio José C. , Santos Isabel C. L. , Forti Luiz C. 
Published: March 2022

AbstractQueens of Atta sexdens Forel (Hymenoptera: Formicidae) face biotic and abiotic environmental factors in the environment while establishing their nests. Biotic factors such as predation, microbial pathogens, successful symbiotic fungus regurgitation, excavation effort and abiotic factors such as radiant sunlight, temperature, density, and soil moisture exert selection pressures on ant queens. Biotic factors such as temperature and solar irradiation affect the survival of the initial colony differently, in different environments in the field. Queens of the leaf-cutting ant A. sexdens, were installed in sunny and shaded conditions to test this hypothesis. Two hundred A. sexdens queens were collected and individualized in two experimental areas (sunny and shaded), each in an experimental area (25 m2) in the center of a square (50 × 50 cm). Temperature, irradiance, nest depth, rainfall and queen mortality were evaluated. Atta sexdens colony development was better in the shaded environment, and the depth and volume of the initial chamber, fungus garden biomass and number of eggs, larvae, pupae and workers were greater. The queen masses were similar in both environments but mortality was higher in the sunny environment. The worse parameter values for A. sexdens nests in the sunny environment are due to the greater solar irradiance, increasing the variation range of the internal temperature of the initial chamber of the nest. On the other hand, the more stable internal temperature of this chamber in the shaded environment, is due to the lower incidence of solar irradiance, which is also more advantageous for queen survival and the formation and development of A. sexdens colonies. Shaded environments are a better micro habitat for nesting A. sexdens than sunny ones.
A hierarchical Bayesian entry time realignment method to study the long-term natural history of diseases
Authors: Shen Liangbo L. , Del Priore Lucian V. , Warren Joshua L. 
Published: March 2022

AbstractA major question in clinical science is how to study the natural course of a chronic disease from inception to end, which is challenging because it is impractical to follow patients over decades. Here, we developed BETR (Bayesian entry time realignment), a hierarchical Bayesian method for investigating the long-term natural history of diseases using data from patients followed over short durations. A simulation study shows that BETR outperforms an existing method that ignores patient-level variation in progression rates. BETR, when combined with a common Bayesian model comparison tool, can identify the correct disease progression function nearly 100% of the time, with high accuracy in estimating the individual disease durations and progression rates. Application of BETR in patients with geographic atrophy, a disease with a known natural history model, shows that it can identify the correct disease progression model. Applying BETR in patients with Huntington’s disease demonstrates that the progression of motor symptoms follows a second order function over approximately 20 years.
In vivo imaging with two-photon microscopy to assess the tumor-selective binding of an anti-CD137 switch antibody
Authors: Kaneko Chisato , Tsutsui Haruka , Ozeki Kazuhisa , Honda Masaki , Haraya Kenta , Narita Yoshinori , Kamata-Sakurai Mika , Kikuta Junichi , Tabo Mitsuyasu , Ishii Masaru 
Published: March 2022

AbstractSTA551, a novel anti-CD137 switch antibody, binds to CD137 in an extracellular ATP concentration-dependent manner. Although STA551 is assumed to show higher target binding in tumor tissues than in normal tissues, quantitative detection of the target binding of the switch antibody in vivo is technically challenging. In this study, we investigated the target binding of STA551 in vivo using intravital imaging with two-photon microscopy. Tumor-bearing human CD137 knock-in mice were intravenously administered fluorescently labeled antibodies. Flow cytometry analysis of antibody-binding cells and intravital imaging using two-photon microscopy were conducted. Higher CD137 expression in tumor than in spleen tissues was detected by flow cytometry analysis, and T cells and NK cells were the major CD137-expressing cells. In the intravital imaging experiment, conventional and switch anti-CD137 antibodies showed binding in tumors. However, in the spleen, the fluorescence of the switch antibody was much weaker than that of the conventional anti-CD137 antibody and comparable with that of the isotype control. In conclusion, we were able to assess switch antibody biodistribution in vivo through intravital imaging with two-photon microscopy. These results suggest that the tumor-selective binding of STA551 leads to a wide therapeutic window and potent antitumor efficacy without systemic immune activation.