bluuebunny/crossref_metadata_2025_split huggingface dataset:
Crystal structure of steroid reductase SRD5A reveals conserved steroid reduction mechanism
Authors: Han Yufei , Zhuang Qian , Sun Bo , Lv Wenping , Wang Sheng , Xiao Qingjie , Pang Bin , Zhou Youli , Wang Fuxing , Chi Pengliang , Wang Qisheng , Li Zhen , Zhu Lizhe , Li Fuping , Deng Dong , Chiang Ying-Chih , Li Zhenfei , Ren Ruobing 
Published: January 2021

AbstractSteroid hormones are essential in stress response, immune system regulation, and reproduction in mammals. Steroids with 3-oxo-Δ4structure, such as testosterone or progesterone, are catalyzed by steroid 5α-reductases (SRD5As) to generate their corresponding 3-oxo-5α steroids, which are essential for multiple physiological and pathological processes. SRD5A2 is already a target of clinically relevant drugs. However, the detailed mechanism of SRD5A-mediated reduction remains elusive. Here we report the crystal structure of PbSRD5A fromProteobacteria bacterium, a homolog of both SRD5A1 and SRD5A2, in complex with the cofactor NADPH at 2.0 Å resolution. PbSRD5A exists as a monomer comprised of seven transmembrane segments (TMs). The TM1-4 enclose a hydrophobic substrate binding cavity, whereas TM5-7 coordinate cofactor NADPH through extensive hydrogen bonds network. Homology-based structural models of HsSRD5A1 and -2, together with biochemical characterization, define the substrate binding pocket of SRD5As, explain the properties of disease-related mutants and provide an important framework for further understanding of the mechanism of NADPH mediated steroids 3-oxo-Δ4reduction. Based on these analyses, the design of therapeutic molecules targeting SRD5As with improved specificity and therapeutic efficacy would be possible.
Over half of western United States' most abundant tree species in decline
Authors: Stanke Hunter , Finley Andrew O. , Domke Grant M. , Weed Aaron S. , MacFarlane David W. 
Published: January 2021

AbstractChanging forest disturbance regimes and climate are driving accelerated tree mortality across temperate forests. However, it remains unknown if elevated mortality has induced decline of tree populations and the ecological, economic, and social benefits they provide. Here, we develop a standardized forest demographic index and use it to quantify trends in tree population dynamics over the last two decades in the western United States. The rate and pattern of change we observe across species and tree size-distributions is alarming and often undesirable. We observe significant population decline in a majority of species examined, show decline was particularly severe, albeit size-dependent, among subalpine tree species, and provide evidence of widespread shifts in the size-structure of montane forests. Our findings offer a stark warning of changing forest composition and structure across the western US, and suggest that sustained anthropogenic and natural stress will likely result in broad-scale transformation of temperate forests globally.
Jarosite formation in deep Antarctic ice provides a window into acidic, water-limited weathering on Mars
Authors: Baccolo Giovanni , Delmonte Barbara , Niles P. B. , Cibin Giannantonio , Di Stefano Elena , Hampai Dariush , Keller Lindsay , Maggi Valter , Marcelli Augusto , Michalski Joseph , Snead Christopher , Frezzotti Massimo 
Published: January 2021

AbstractMany interpretations have been proposed to explain the presence of jarosite within Martian surficial sediments, including the possibility that it precipitated within paleo-ice deposits owing to englacial weathering of dust. However, until now a similar geochemical process was not observed on Earth nor in other planetary settings. We report a multi-analytical indication of jarosite formation within deep ice. Below 1000 m depth, jarosite crystals adhering on residual silica-rich particles have been identified in the Talos Dome ice core (East Antarctica) and interpreted as products of weathering involving aeolian dust and acidic atmospheric aerosols. The progressive increase of ice metamorphism and re-crystallization with depth, favours the relocation and concentration of dust and the formation of acidic brines in isolated environments, allowing chemical reactions and mineral neo-formation to occur. This is the first described englacial diagenetic mechanism occurring in deep Antarctic ice and supports the ice-weathering model for jarosite formation on Mars, highlighting the geologic importance of paleo ice-related processes on this planet. Additional implications concern the preservation of dust-related signals in deep ice cores with respect to paleoclimatic reconstructions and the englacial history of meteorites from Antarctic blue ice fields.
A self-matched leaky-wave antenna for ultrahigh-field magnetic resonance imaging with low specific absorption rate
Authors: Solomakha G. , Svejda J. T. , van Leeuwen C. , Rennings A. , Raaijmakers A. J. , Glybovski S. , Erni D. 
Published: January 2021

AbstractThe technology of magnetic resonance imaging is developing towards higher magnetic fields to improve resolution and contrast. However, whole-body imaging at 7 T or even higher flux densities remains challenging due to wave interference, tissue inhomogeneities, and high RF power deposition. Nowadays, proper RF excitation of a human body in prostate and cardiac MRI is only possible to achieve by using phased arrays of antennas attached to the body (so-called surface coils). Due to safety concerns, the design of such coils aims at minimization of the local specific absorption rate (SAR), keeping the highest possible RF signal in the region of interest. Most previously demonstrated approaches were based on resonant structures such as e.g. dipoles, capacitively-loaded loops, TEM-line sections. In this study, we show that there is a better compromise between the transmit signal $${{\bf{B}}}_{{\bf{1}}}^{{\boldsymbol{+}}}$$

B

1

+

and the local SAR using non-resonant surface coils generating a low electric field in the proximity of their conductors. With this aim, we propose and experimentally demonstrate a leaky-wave antenna implemented as a periodically-slotted microstrip transmission line. Due to its non-resonant radiation, it induces only slightly over half the peak local SAR compared to a state-of-the-art dipole antenna but has the same transmit efficiency in prostate imaging at 7 T. Unlike other antennas for MRI, the leaky-wave antenna does not require to be tuned and matched when placed on a body, which makes it easy-to-use in prostate imaging at 7 T MRI.
Boosting anti-PD-1 therapy with metformin-loaded macrophage-derived microparticles
Authors: Wei Zhaohan , Zhang Xiaoqiong , Yong Tuying , Bie Nana , Zhan Guiting , Li Xin , Liang Qingle , Li Jianye , Yu Jingjing , Huang Gang , Yan Yuchen , Zhang Zelong , Zhang Bixiang , Gan Lu , Huang Bo , Yang Xiangliang 
Published: January 2021

AbstractThe main challenges for programmed cell death 1(PD-1)/PD-1 ligand (PD-L1) checkpoint blockade lie in a lack of sufficient T cell infiltration, tumor immunosuppressive microenvironment, and the inadequate tumor accumulation and penetration of anti-PD-1/PD-L1 antibody. Resetting tumor-associated macrophages (TAMs) is a promising strategy to enhance T-cell antitumor immunity and ameliorate tumor immunosuppression. Here, mannose-modified macrophage-derived microparticles (Man-MPs) loading metformin (Met@Man-MPs) are developed to efficiently target to M2-like TAMs to repolarize into M1-like phenotype. Met@Man-MPs-reset TAMs remodel the tumor immune microenvironment by increasing the recruitment of CD8+ T cells into tumor tissues and decreasing immunosuppressive infiltration of myeloid-derived suppressor cells and regulatory T cells. More importantly, the collagen-degrading capacity of Man-MPs contributes to the infiltration of CD8+ T cells into tumor interiors and enhances tumor accumulation and penetration of anti-PD-1 antibody. These unique features of Met@Man-MPs contribute to boost anti-PD-1 antibody therapy, improving anticancer efficacy and long-term memory immunity after combination treatment. Our results support Met@Man-MPs as a potential drug to improve tumor resistance to anti-PD-1 therapy.
A network-based framework for shape analysis enables accurate characterization of leaf epidermal cells
Authors: Nowak Jacqueline , Eng Ryan Christopher , Matz Timon , Waack Matti , Persson Staffan , Sampathkumar Arun , Nikoloski Zoran 
Published: January 2021

AbstractCell shape is crucial for the function and development of organisms. Yet, versatile frameworks for cell shape quantification, comparison, and classification remain underdeveloped. Here, we introduce a visibility graph representation of shapes that facilitates network-driven characterization and analyses across shapes encountered in different domains. Using the example of complex shape of leaf pavement cells, we show that our framework accurately quantifies cell protrusions and invaginations and provides additional functionality in comparison to the contending approaches. We further show that structural properties of the visibility graphs can be used to quantify pavement cell shape complexity and allow for classification of plants into their respective phylogenetic clades. Therefore, the visibility graphs provide a robust and unique framework to accurately quantify and classify the shape of different objects.
Low-carbon pathways for the booming express delivery sector in China
Authors: Kang Peng , Song Guanghan , Xu Ming , Miller Travis R. , Wang Haikun , Zhang Hui , Liu Gang , Zhou Ya , Ren Junshu , Zhong Ruoyu , Duan Huabo 
Published: January 2021

AbstractExpress delivery services are booming in both developed and emerging economies due to their low cost, convenience, and the fast growth in online shopping. The increasing environmental impacts of express delivery services and mitigation potentials, however, remain largely unexplored. Here we addressed such a gap for China, a country which is expanding online retail sales and express delivery rapidly. We found a total of 8.8 Mt of scrap packaging materials were generated by the express delivery sector in China in 2018. Its transportation-related GHG emissions surged from 0.3 Mt in 2007 to 13.7 Mt of CO2-equivalent (CO2e) in 2018, with an average of 0.27 kgCO2e per piece. Over 80% from online shopping deliveries. We predict these emissions will reach 75 MtCO2e by 2035. Nevertheless, it is possible to mitigate such GHG emissions by 102~134 MtCO2e between 2020 and 2035 if a suite of policies is adopted, including a slowdown of delivery speed, fuel system upgrades, packaging materials reduction, logistics optimization, and carbon pricing.
Preserving a robust CsPbI3 perovskite phase via pressure-directed octahedral tilt
Authors: Ke Feng , Wang Chenxu , Jia Chunjing , Wolf Nathan R. , Yan Jiejuan , Niu Shanyuan , Devereaux Thomas P. , Karunadasa Hemamala I. , Mao Wendy L. , Lin Yu 
Published: January 2021

AbstractFunctional CsPbI3 perovskite phases are not stable at ambient conditions and spontaneously convert to a non-perovskite δ phase, limiting their applications as solar cell materials. We demonstrate the preservation of a black CsPbI3 perovskite structure to room temperature by subjecting the δ phase to pressures of 0.1 – 0.6 GPa followed by heating and rapid cooling. Synchrotron X-ray diffraction and Raman spectroscopy indicate that this perovskite phase is consistent with orthorhombic γ-CsPbI3. Once formed, γ-CsPbI3 could be then retained after releasing pressure to ambient conditions and shows substantial stability at 35% relative humidity. First-principles density functional theory calculations indicate that compression directs the out-of-phase and in-phase tilt between the [PbI6]4− octahedra which in turn tune the energy difference between δ- and γ-CsPbI3, leading to the preservation of γ-CsPbI3. Here, we present a high-pressure strategy for manipulating the (meta)stability of halide perovskites for the synthesis of desirable phases with enhanced materials functionality.
Cataract type and pupillary response to blue and white light stimuli
Authors: Kuze Manami , Negishi Kazuno , Koyasu Toshiyuki , Kondo Mineo , Tsubota Kazuo , Ayaki Masahiko 
Published: January 2021

AbstractWe evaluated the pupil reaction to blue and white light stimulation in 70 eyes with cataract and in 38 eyes with a selective blue-light filtering intra-ocular lens. The diameter of the pupil before stimulation was set as baseline (BPD) and, after a stimulus duration of 1 s, the post-illumination pupillary response (PIPR) was measured using an electronic pupillometer. The BPD showed no significant difference among three grades of nuclear sclerosis (NS). In contrast, the PIPRs differed significantly among the NS grades eyes including with and without subcapsular cataract (SC) and IOL eyes for white light (p < 0.05, Kruskal–Wallis test), but not for blue light. Subcapsular opacity did not affect the BPD or PIPR in all cataract grades for either light stimulus. The tendency of larger PIPR in the pseudophakic eyes than the cataract eyes for both lights, however significant difference was found only for white light (p < 0.05 for white light, p > 0.05 for blue light). Our study demonstrates retention of the PIPR for blue light, but not for white light in cataract eyes. We also confirmed that the pupillary response in pseudohakic eyes with a selective blue light-filtering intra ocular lens was greater than that in cataractous eyes for white light.
Role of dislocation elastic field on impurity segregation in Fe-based alloys
Authors: Medouni I. , Portavoce A. , Maugis P. , Eyméoud P. , Yescas M. , Hoummada K. 
Published: January 2021

AbstractDislocation engineering in crystalline materials is essential when designing materials for a large range of applications. Segregation of additional elements at dislocations is frequently used to modify the influence of dislocations on material properties. Thus, the influence of the dislocation elastic field on impurity segregation is of major interest, as its understanding should lead to engineering solutions that improve the material properties. We report the experimental study of the elastic field influence on atomic segregation in the core and in the area surrounding edge dislocations in Fe-based alloys. Each element is found either to segregate in the edge dislocation core or to form atmospheres. The elastic field has a strong effect on the segregation atmosphere, but no effect on the dislocation core segregation. The theory is in good agreement with experiments, and should support dislocation engineering.
Potential biomarkers of childhood brain tumor identified by proteomics of cerebrospinal fluid from extraventricular drainage (EVD)
Authors: Bruschi Maurizio , Petretto Andrea , Cama Armando , Pavanello Marco , Bartolucci Martina , Morana Giovanni , Ramenghi Luca Antonio , Garré Maria Luisa , Ghiggeri Gian Marco , Panfoli Isabella , Candiano Giovanni 
Published: January 2021

AbstractBrain tumors are the most common solid tumors in childhood. There is the need for biomarkers of residual disease, therapy response and recurrence. Cerebrospinal fluid (CSF) is a source of brain tumor biomarkers. We analyzed the proteome of waste CSF from extraventricular drainage (EVD) from 29 children bearing different brain tumors and 17 controls needing EVD insertion for unrelated causes. 1598 and 1526 proteins were identified by liquid chromatography-coupled tandem mass spectrometry proteomics in CSF control and brain tumor patients, respectively, 263 and 191 proteins being exclusive of either condition. Bioinformatic analysis revealed promising protein biomarkers for the discrimination between control and tumor (TATA-binding protein-associated factor 15 and S100 protein B). Moreover, Thymosin beta-4 (TMSB4X) and CD109, and 14.3.3 and HSP90 alpha could discriminate among other brain tumors and low-grade gliomas plus glyoneuronal tumors/pilocytic astrocytoma, or embryonal tumors/medulloblastoma. Biomarkers were validated by ELISA assay. Our method was able to distinguish among brain tumor vs non-tumor/hemorrhagic conditions (controls) and to differentiate two large classes of brain tumors. Further prospective studies may assess whether the biomarkers proposed by our discovery approach can be identified in other bodily fluids, therefore less invasively, and are useful to guide therapy and predict recurrences.
Differential relationships of PTSD symptom clusters with cortical thickness and grey matter volumes among women with PTSD
Authors: Crombie Kevin M. , Ross Marisa C. , Letkiewicz Allison M. , Sartin-Tarm Anneliis , Cisler Josh M. 
Published: January 2021

AbstractStructural neuroimaging studies of posttraumatic stress disorder (PTSD) have typically reported reduced cortical thickness (CT) and gray matter volume (GMV) in subcortical structures and networks involved in memory retrieval, emotional processing and regulation, and fear acquisition and extinction. Although PTSD is more common in women, and interpersonal violence (IPV) exposure is a more potent risk factor for developing PTSD relative to other forms of trauma, most of the existing literature examined combat-exposed men with PTSD. Vertex-wise CT and subcortical GMV analyses were conducted to examine potential differences in a large, well-characterized sample of women with PTSD stemming from IPV-exposure (n = 99) compared to healthy trauma-free women without a diagnosis of PTSD (n = 22). Subgroup analyses were also conducted to determine whether symptom severity within specific PTSD symptom clusters (e.g., re-experiencing, active avoidance, hyperarousal) predict CT and GMV after controlling for comorbid depression and anxiety. Results indicated that a diagnosis of PTSD in women with IPV-exposure did not significantly predict differences in CT across the cortex or GMV in the amygdala or hippocampus compared to healthy controls. However, within the PTSD group, greater re-experiencing symptom severity was associated with decreased CT in the left inferior and middle temporal gyrus, and decreased CT in the right parahippocampal and medial temporal gyrus. In contrast, greater active avoidance symptom severity was associated with greater CT in the left lateral fissure, postcentral gyrus, and middle/lateral occipital cortex, and greater CT in the right paracentral, posterior cingulate, and superior occipital gyrus. In terms of GMV, greater hyperarousal symptom severity was associated with reduced left amygdala GMV, while greater active avoidance symptom severity was associated with greater right amygdala GMV. These findings suggest that structural brain alterations among women with IPV-related PTSD may be driven by symptom severity within specific symptom clusters and that PTSD symptom clusters may have a differential (increased or decreased) association with brain structures.
Blood-based protein profiling identifies serum protein c-KIT as a novel biomarker for hypertrophic cardiomyopathy
Authors: Sonnenschein Kristina , Fiedler Jan , de Gonzalo-Calvo David , Xiao Ke , Pfanne Angelika , Just Annette , Zwadlo Carolin , Soltani Samira , Bavendiek Udo , Kraft Theresia , Dos Remedios Cristobal , Cebotari Serghei , Bauersachs Johann , Thum Thomas 
Published: January 2021

AbstractHypertrophic cardiomyopathy (HCM) is one of the most common hereditary heart diseases and can be classified into an obstructive (HOCM) and non-obstructive (HNCM) form. Major characteristics for HCM are the hypertrophy of cardiomyocytes and development of cardiac fibrosis. Patients with HCM have a higher risk for sudden cardiac death compared to a healthy population. In the present study, we investigated the abundancy of selected proteins as potential biomarkers in patients with HCM. We included 60 patients with HCM and 28 healthy controls and quantitatively measured the rate of a set of 92 proteins already known to be associated with cardiometabolic processes via protein screening using the proximity extension assay technology in a subgroup of these patients (20 HCM and 10 healthy controls). After validation of four hits in the whole cohort of patients consisting of 88 individuals (60 HCM patients, 28 healthy controls) we found only one candidate, c-KIT, which was regulated significantly different between HCM patients and healthy controls and thus was chosen for further analyses. c-KIT is a tyrosine-protein kinase acting as receptor for the stem cell factor and activating several pathways essential for cell proliferation and survival, hematopoiesis, gametogenesis and melanogenesis. Serum protein levels of c-KIT were significantly lower in patients with HCM than in healthy controls, even after adjusting for confounding factors age and sex. In addition, c-KIT levels in human cardiac tissue of patients with HOCM were significant higher compared to controls indicating high levels of c-KIT in fibrotic myocardium. Furthermore, c-KIT concentration in serum significantly correlated with left ventricular end-diastolic diameter in HOCM, but not HCM patients. The present data suggest c-KIT as a novel biomarker differentiating between patients with HCM and healthy population and might provide further functional insights into fibrosis-related processes of HOCM.
Classification and prediction of protein–protein interaction interface using machine learning algorithm
Authors: Das Subhrangshu , Chakrabarti Saikat 
Published: January 2021

AbstractStructural insight of the protein–protein interaction (PPI) interface can provide knowledge about the kinetics, thermodynamics and molecular functions of the complex while elucidating its role in diseases and further enabling it as a potential therapeutic target. However, owing to experimental lag in solving protein–protein complex structures, three-dimensional (3D) knowledge of the PPI interfaces can be gained via computational approaches like molecular docking and post-docking analyses. Despite development of numerous docking tools and techniques, success in identification of native like interfaces based on docking score functions is limited. Hence, we employed an in-depth investigation of the structural features of the interface that might successfully delineate native complexes from non-native ones. We identify interface properties, which show statistically significant difference between native and non-native interfaces belonging to homo and hetero, protein–protein complexes. Utilizing these properties, a support vector machine (SVM) based classification scheme has been implemented to differentiate native and non-native like complexes generated using docking decoys. Benchmarking and comparative analyses suggest very good performance of our SVM classifiers. Further, protein interactions, which are proven via experimental findings but not resolved structurally, were subjected to this approach where 3D-models of the complexes were generated and most likely interfaces were predicted. A web server calledProteinComplexPrediction byInterfaceProperties (PCPIP) is developed to predict whether interface of a given protein–protein dimer complex resembles known protein interfaces. The server is freely available athttp://www.hpppi.iicb.res.in/pcpip/.