bluuebunny/crossref_metadata_2025_split huggingface dataset:
Rehybridization dynamics into the pericyclic minimum of an electrocyclic reaction imaged in real-time
Authors: Liu Y. , Sanchez D. M. , Ware M. R. , Champenois E. G. , Yang J. , Nunes J. P. F. , Attar A. , Centurion M. , Cryan J. P. , Forbes R. , Hegazy K. , Hoffmann M. C. , Ji F. , Lin M.-F. , Luo D. , Saha S. K. , Shen X. , Wang X. J. , Martínez T. J. , Wolf T. J. A. 
Published: May 2023

AbstractElectrocyclic reactions are characterized by the concerted formation and cleavage of both σ and π bonds through a cyclic structure. This structure is known as a pericyclic transition state for thermal reactions and a pericyclic minimum in the excited state for photochemical reactions. However, the structure of the pericyclic geometry has yet to be observed experimentally. We use a combination of ultrafast electron diffraction and excited state wavepacket simulations to image structural dynamics through the pericyclic minimum of a photochemical electrocyclic ring-opening reaction in the molecule α-terpinene. The structural motion into the pericyclic minimum is dominated by rehybridization of two carbon atoms, which is required for the transformation from two to three conjugated π bonds. The σ bond dissociation largely happens after internal conversion from the pericyclic minimum to the electronic ground state. These findings may be transferrable to electrocyclic reactions in general.
Convergence of dominance and neglect in flying insect diversity
Authors: Srivathsan Amrita , Ang Yuchen , Heraty John M. , Hwang Wei Song , Jusoh Wan F. A. , Kutty Sujatha Narayanan , Puniamoorthy Jayanthi , Yeo Darren , Roslin Tomas , Meier Rudolf 
Published: May 2023

AbstractMost of arthropod biodiversity is unknown to science. Consequently, it has been unclear whether insect communities around the world are dominated by the same or different taxa. This question can be answered through standardized sampling of biodiversity followed by estimation of species diversity and community composition with DNA barcodes. Here this approach is applied to flying insects sampled by 39 Malaise traps placed in five biogeographic regions, eight countries and numerous habitats (>225,000 specimens belonging to >25,000 species in 458 families). We find that 20 insect families (10 belonging to Diptera) account for >50% of local species diversity regardless of clade age, continent, climatic region and habitat type. Consistent differences in family-level dominance explain two-thirds of variation in community composition despite massive levels of species turnover, with most species (>97%) in the top 20 families encountered at a single site only. Alarmingly, the same families that dominate insect diversity are ‘dark taxa’ in that they suffer from extreme taxonomic neglect, with little signs of increasing activities in recent years. Taxonomic neglect tends to increase with diversity and decrease with body size. Identifying and tackling the diversity of ‘dark taxa’ with scalable techniques emerge as urgent priorities in biodiversity science.
A continent-wide detailed geological map dataset of Antarctica
Authors: Cox Simon C. , Smith Lyttle Belinda , Elkind Samuel , Smith Siddoway Christine , Morin Paul , Capponi Giovanni , Abu-Alam Tamer , Ballinger Matilda , Bamber Lauren , Kitchener Brett , Lelli Luigi , Mawson Jasmine , Millikin Alexie , Dal Seno Nicola , Whitburn Louis , White Tristan , Burton-Johnson Alex , Crispini Laura , Elliot David , Elvevold Synnøve , Goodge John , Halpin Jacqueline , Jacobs Joachim , Martin Adam P. , Mikhalsky Eugene , Morgan Fraser , Scadden Phil , Smellie John , Wilson Gary 
Published: May 2023

AbstractA dataset to describe exposed bedrock and surficial geology of Antarctica has been constructed by the GeoMAP Action Group of the Scientific Committee on Antarctic Research (SCAR) and GNS Science. Our group captured existing geological map data into a geographic information system (GIS), refined its spatial reliability, harmonised classification, and improved representation of glacial sequences and geomorphology, thereby creating a comprehensive and coherent representation of Antarctic geology. A total of 99,080 polygons were unified for depicting geology at 1:250,000 scale, but locally there are some areas with higher spatial resolution. Geological unit definition is based on a mixed chronostratigraphic- and lithostratigraphic-based classification. Description of rock and moraine polygons employs the international Geoscience Markup Language (GeoSciML) data protocols to provide attribute-rich and queryable information, including bibliographic links to 589 source maps and scientific literature. GeoMAP is the first detailed geological map dataset covering all of Antarctica. It depicts ‘known geology’ of rock exposures rather than ‘interpreted’ sub-ice features and is suitable for continent-wide perspectives and cross-discipline interrogation.
Fast response and recovery polyaniline montmorillonite reduce graphene oxide polymer nanocomposite material for detection of hydrogen cyanide gas
Authors: Singh Aparna , Dipak Pukhrambam , Iqbal Asif , Samadhiya Anuradha , Dwivedi Shailendra Kumar , Tiwari Dinesh Chandra , Tiwari Rajendra Kumar , Pandey Kailash Nath 
Published: May 2023

AbstractIn the present work, we have developed a polymer based gas sensor. The polymer nanocomposites are synthesized by the chemical oxidative polymerization of aniline with ammonium persulfate and sulfuric acid. The fabricated sensor is able to achieve a sensing response of 4.56% for PANI/MMT-rGO at 2 ppm of hydrogen cyanide (HCN) gas. The sensitivity of the sensors PANI/MMT and PANI/MMT-rGO are 0.89 ppm−1 and 1.1174 ppm−1 respectively. The increase in the sensitivity of the sensor may be due to an increase in the surface area provided by MMT and rGO which provided more binding sites for the HCN gas. The sensing response of the sensor increases as the concentration of the gas exposed increases but saturates after 10 ppm. The sensor recovers automatically. The sensor is stable and can work for 8 months.
Revealing the immune cell subtype reconstitution profile in patients from the CLARITY study using deconvolution algorithms after cladribine tablets treatment
Authors: Kalatskaya Irina , Giovannoni Gavin , Leist Thomas , Cerra Joseph , Boschert Ursula , Rolfe P. Alexander 
Published: May 2023

AbstractImmune Cell Deconvolution methods utilizing gene expression profiling to quantify immune cells in tissues and blood are an appealing alternative to flow cytometry. Our objective was to investigate the applicability of deconvolution approaches in clinical trial settings to better investigate the mode of action of drugs for autoimmune diseases. Popular deconvolution methods CIBERSORT and xCell were validated using gene expression from the publicly available GSE93777 dataset that has comprehensive matching flow cytometry. As shown in theonline tool, ~ 50% of signatures show strong correlation (r > 0.5) with the remainder showing moderate correlation, or in a few cases, no correlation. Deconvolution methods were then applied to gene expression data from the phase III CLARITY study (NCT00213135) to evaluate the immune cell profile of relapsing multiple sclerosis patients treated with cladribine tablets. At 96 weeks after treatment, deconvolution scores showed the following changes vs placebo: naïve, mature, memory CD4+and CD8+T cells, non-class switched, and class switched memory B cells and plasmablasts were significantly reduced, naïve B cells and M2 macrophages were more abundant. Results confirm previously described changes in immune cell composition following cladribine tablets treatment and reveal immune homeostasis of pro- vs anti-inflammatory immune cell subtypes, potentially supporting long-term efficacy.
Spatiotemporal bias of the human gaze toward hierarchical visual features during natural scene viewing
Authors: Akamatsu Kazuaki , Nishino Tomohiro , Miyawaki Yoichi 
Published: May 2023

AbstractThe human gaze is directed at various locations from moment to moment in acquiring information necessary to recognize the external environment at the fine resolution of foveal vision. Previous studies showed that the human gaze is attracted to particular locations in the visual field at a particular time, but it remains unclear what visual features produce such spatiotemporal bias. In this study, we used a deep convolutional neural network model to extract hierarchical visual features from natural scene images and evaluated how much the human gaze is attracted to the visual features in space and time. Eye movement measurement and visual feature analysis using the deep convolutional neural network model showed that the gaze was more strongly attracted to spatial locations containing higher-order visual features than to locations containing lower-order visual features or to locations predicted by conventional saliency. Analysis of the time course of gaze attraction revealed that the bias to higher-order visual features was prominent within a short period after the beginning of observation of the natural scene images. These results demonstrate that higher-order visual features are a strong gaze attractor in both space and time, suggesting that the human visual system uses foveal vision resources to extract information from higher-order visual features with higher spatiotemporal priority.
Improved water purification by PVDF ultrafiltration membrane modified with GO-PVA-NaAlg hydrogel
Authors: Ghobadi Moghadam Armin , Hemmati Alireza 
Published: May 2023

AbstractThis work presents a modified polyvinylidene fluoride (PVDF) ultrafiltration membrane blended with graphene oxide-polyvinyl alcohol-sodium alginate (GO-PVA-NaAlg) hydrogel (HG) and polyvinylpyrrolidone (PVP) prepared by the immersion precipitation induced phase inversion approach. Characteristics of the membranes with different HG and PVP concentrations were analyzed by field emission scanning electron microscopy (FESEM), Atomic force microscopy (AFM), contact angle measurement (CA), and Attenuated total reflectance Fourier transform infrared spectroscopy (ATR-FTIR). The FESEM images showed an asymmetric structure of the fabricated membranes, and possessing a thin dense layer over the top and a layer finger-like. With increasing HG content, membrane surface roughness increases so that highest surface roughness for the membrane containing 1wt% HG is with a Ra value of 281.4 nm. Also, the contact angle of the membrane reaches from 82.5° in bare PVDF membrane to 65.1° in the membrane containing 1wt% HG. The influences of adding HG and PVP to the casting solution on pure water flux (PWF), hydrophilicity, anti-fouling ability, and dye rejection efficiency were evaluated. The highest water flux reached 103.2 L/m2 h at 3 bar for the modified PVDF membranes containing 0.3 wt% HG and 1.0wt% PVP. This membrane exhibited a rejection efficiency of higher than 92%, 95%, and 98% for Methyl Orange (MO), Conge Red (CR), and Bovine Serum Albumin (BSA), respectively. All nanocomposite membranes possessed a flux recovery ratio (FRR) higher than bare PVDF membranes, and the best anti-fouling performance of 90.1% was relevant to the membrane containing 0.3 wt% HG. The improved filtration performance of the HG-modified membranes was due to the enhanced hydrophilicity, porosity, mean pore size, and surface roughness after introducing HG.
PastoCovac and PastoCovac Plus as protein subunit COVID-19 vaccines led to great humoral immune responses in BBIP-CorV immunized individuals
Authors: Ramezani Amitis , Sorouri Rahim , Haji Maghsoudi Saiedeh , Dahmardeh Sarah , Doroud Delaram , Sadat Larijani Mona , Eybpoosh Sana , Mostafavi Ehsan , Olyaeemanesh Alireza , Salehi-Vaziri Mostafa , Bavand Anahita , Zarghani Ghazaleh , Moradi Ladan , Ashrafian Fatemeh , Bagheri Amiri Fahimeh , Mashayekhi Parisa , Tahmasebi Zahra , Biglari Alireza 
Published: May 2023

AbstractThe optimal booster vaccine schedule against COVID-19 is still being explored. The present study aimed at assessment of the immunogenicity and antibody persistency of inactivated-virus based vaccine, BBIP-CorV and protein-subunit based vaccines, PastoCovac/Plus through heterologous and homologous prime-boost vaccination. Totally, 214 individuals who were previously primed with BBIBP-CorV vaccines were divided into three arms on their choice as heterologous regimens BBIBP-CorV/PastoCovac (n = 68), BBIBP-CorV/PastoCovac Plus (n = 72) and homologous BBIBP-CorV (n = 74). PastoCovac booster recipients achieved the highest rate of anti-Spike IgG titer rise with a fourfold rise in 50% of the group. Anti-RBD IgG and neutralizing antibody mean rise and fold rise were almost similar between the PastoCovac and PastoCovac Plus booster receivers. The antibody durability results indicated that the generated antibodies were persistent until day 180 in all three groups. Nevertheless, a higher rate of antibody titer was seen in the heterologous regimen compared to BBIP-CorV group. Furthermore, no serious adverse event was recorded. The protein subunit-based booster led to a stronger humoral immune response in comparison with the BBIP-CorV booster receivers. Both the protein subunit boosters neutralized SARS-CoV-2 significantly more than BBIP-CorV. Notably, PastoCovac protein subunit-based vaccine could be successfully applied as a booster with convenient immunogenicity and safety profile.
Cognitive test performance in chronic cannabis flower users, concentrate users, and non-users
Authors: Cuttler Carrie , Petrucci Aria S. , LaFrance Emily M. 
Published: May 2023

AbstractExtremely high-potency cannabis concentrates are becoming increasingly available and popular among consumers. While prior research indicates these products are perceived to have greater detrimental effects relative to cannabis flower, few studies have examined their relative objective effects, and no existing studies have compared the cognitive test performance of sober flower users, concentrate users, and non-users. A total of 198 healthy adults (98 non-users, 46 exclusive flower users, and 54 concentrate users) were administered a battery of tests of memory, psychomotor speed, attention, and executive functioning under sober laboratory-controlled conditions. Significant group differences were detected on tests of verbal free recall and episodic prospective memory, with both the flower users and concentrate users demonstrating significantly worse performance than non-users. Concentrate (but not flower) users performed worse than non-users on a measure of source memory, but contrary to our hypothesis, there were no significant differences between flower and concentrate users on any of the cognitive tests. Results indicate that, under sober conditions, individuals who regularly use concentrates are no more cognitively impacted than those who exclusively use flower. These null findings may reflect the tendency for concentrate users to self-titrate and use significantly lower quantities of concentrates than flower.
Genetic mutations linked to field‐evolved Cry1Fa-resistance in the European corn borer, Ostrinia nubilalis
Authors: Farhan Yasmine , Smith Jocelyn L. , Sovic Michael G. , Michel Andrew P. 
Published: May 2023

AbstractTransgenic corn, Zea mays (L.), expressing insecticidal toxins such as Cry1Fa, from Bacillus thuringiensis (Bt corn) targeting Ostrinia nubilalis (Hübner) (Lepidoptera: Crambidae) resulted in over 20 years of management success. The first case of practical field-evolved resistance by O. nubilalis to a Bt corn toxin, Cry1Fa, was discovered in Nova Scotia, Canada, in 2018. Laboratory-derived Cry1Fa-resistance by O. nubilalis was linked to a genome region encoding the ATP Binding Cassette subfamily C2 (ABCC2) gene; however, the involvement of ABCC2 and specific mutations in the gene leading to resistance remain unknown. Using a classical candidate gene approach, we report on O. nubilalis ABCC2 gene mutations linked to laboratory-derived and field-evolved Cry1Fa-resistance. Using these mutations, a DNA-based genotyping assay was developed to test for the presence of the Cry1Fa-resistance alleles in O. nubilalis strains collected in Canada. Screening data provide strong evidence that field-evolved Cry1Fa-resistance in O. nubilalis maps to the ABCC2 gene and demonstrates the utility of this assay for detecting the Cry1Fa resistance allele in O. nubilalis. This study is the first to describe mutations linked to Bt resistance in O. nubilalis and provides a DNA-based detection method that can be used for monitoring.
Calculation of IFT in porous media in the presence of different gas and normal alkanes using the modified EoS
Authors: Hamidpour Sareh , Safaei Ali , Kazemzadeh Yousef , Hasan-Zadeh Atefeh , Khormali Azizollah 
Published: May 2023

AbstractGas injection can increase oil recovery because the gas–oil interfacial tension is less than the water–oil interfacial tension (IFT) and tends to zero in the miscibility state. However, little information has been provided on the gas–oil movement and penetration mechanisms in the fracture system at the porosity scale. The IFT of oil and gas in the porous medium changes and can control oil recovery. In this study, the IFT and the minimum miscibility pressure (MMP) are calculated using the cubic Peng-Robinson equation of state that has been modified using the mean pore radius and capillary pressure. The calculated IFT and MMP change with the pore radius and capillary pressure. To investigate the effect of a porous medium on the IFT during the injection of CH4, CO2, and N2 in the presence of n-alkanes and for validation, measured experimental values in references have been used. According to the results of this paper, changes in IFT vary in terms of pressure in the presence of different gases and, the proposed model has good accuracy for measuring the IFT and the MMP during the injection of hydrocarbon gases and CO2. In addition, as the average radius of the pores gets smaller, the interfacial tension tends to lower values. This effect is different with increasing the mean size of interstice in two different intervals. In the first interval, i.e. the Rp from 10 to 5000 nm, the IFT changes from 3 to 10.78 mN/m and in the second interval, i.e. the Rp from 5000 nm to infinity, the IFT changes from 10.78 to 10.85 mN/m. In other words, increasing the diameter of the porous medium to a certain threshold (i.e. 5000 nm) increases the IFT. As a rule, changes in IFT affected by exposure to a porous medium affect the values of the MMP. In general, IFT decreases in very fine porous media, causing miscibility at lower pressures.
Debiased ambient vibrations optical coherence elastography to profile cell, organoid and tissue mechanical properties
Authors: Mason Jonathan H. , Luo Lu , Reinwald Yvonne , Taffetani Matteo , Hallas-Potts Amelia , Herrington C. Simon , Srsen Vlastimil , Lin Chih-Jen , Barroso Inês A. , Zhang Zhihua , Zhang Zhibing , Ghag Anita K. , Yang Ying , Waters Sarah , El Haj Alicia J. , Bagnaninchi Pierre O. 
Published: May 2023

AbstractThe role of the mechanical environment in defining tissue function, development and growth has been shown to be fundamental. Assessment of the changes in stiffness of tissue matrices at multiple scales has relied mostly on invasive and often specialist equipment such as AFM or mechanical testing devices poorly suited to the cell culture workflow.In this paper, we have developed a unbiased passive optical coherence elastography method, exploiting ambient vibrations in the sample that enables real-time noninvasive quantitative profiling of cells and tissues. We demonstrate a robust method that decouples optical scattering and mechanical properties by actively compensating for scattering associated noise bias and reducing variance. The efficiency for the method to retrieve ground truth is validated in silico and in vitro, and exemplified for key applications such as time course mechanical profiling of bone and cartilage spheroids, tissue engineering cancer models, tissue repair models and single cell. Our method is readily implementable with any commercial optical coherence tomography system without any hardware modifications, and thus offers a breakthrough in on-line tissue mechanical assessment of spatial mechanical properties for organoids, soft tissues and tissue engineering.
Asymmetric conformations of cleaved HIV-1 envelope glycoprotein trimers in styrene-maleic acid lipid nanoparticles
Authors: Wang Kunyu , Zhang Shijian , Go Eden P. , Ding Haitao , Wang Wei Li , Nguyen Hanh T. , Kappes John C. , Desaire Heather , Sodroski Joseph , Mao Youdong 
Published: May 2023

AbstractDuring virus entry, the pretriggered human immunodeficiency virus (HIV-1) envelope glycoprotein (Env) trimer initially transits into a default intermediate state (DIS) that remains structurally uncharacterized. Here, we present cryo-EM structures at near-atomic resolution of two cleaved full-length HIV-1 Env trimers purified from cell membranes in styrene-maleic acid lipid nanoparticles without antibodies or receptors. The cleaved Env trimers exhibited tighter subunit packing than uncleaved trimers. Cleaved and uncleaved Env trimers assumed remarkably consistent yet distinct asymmetric conformations, with one smaller and two larger opening angles. Breaking conformational symmetry is allosterically coupled with dynamic helical transformations of the gp41 N-terminal heptad repeat (HR1N) regions in two protomers and with trimer tilting in the membrane. The broken symmetry of the DIS potentially assists Env binding to two CD4 receptors—while resisting antibody binding—and promotes extension of the gp41 HR1 helical coiled-coil, which relocates the fusion peptide closer to the target cell membrane.
Stereochemical engineering yields a multifunctional peptide macrocycle inhibitor of Akt2 by fine-tuning macrocycle-cell membrane interactions
Authors: Nag Arundhati , Mafi Amirhossein , Das Samir , Yu Mary Beth , Alvarez-Villalonga Belen , Kim Soo-Kyung , Su Yapeng , Goddard William A. , Heath James R. 
Published: May 2023

AbstractMacrocycle peptides are promising constructs for imaging and inhibiting extracellular, and cell membrane proteins, but their use for targeting intracellular proteins is typically limited by poor cell penetration. We report the development of a cell-penetrant high-affinity peptide ligand targeted to the phosphorylated Ser474 epitope of the (active) Akt2 kinase. This peptide can function as an allosteric inhibitor, an immunoprecipitation reagent, and a live cell immunohistochemical staining reagent. Two cell penetrant stereoisomers were prepared and shown to exhibit similar target binding affinities and hydrophobic character but 2-3-fold different rates of cell penetration. Experimental and computational studies resolved that the ligands’ difference in cell penetration could be assigned to their differential interactions with cholesterol in the membrane. These results expand the tool kit for designing new chiral-based cell-penetrant ligands.