bluuebunny/crossref_metadata_2025_split huggingface dataset:
Quantitative single-protein imaging reveals molecular complex formation of integrin, talin, and kindlin during cell adhesion
Authors: Fischer Lisa S. , Klingner Christoph , Schlichthaerle Thomas , Strauss Maximilian T. , Böttcher Ralph , Fässler Reinhard , Jungmann Ralf , Grashoff Carsten 
Published: February 2021

AbstractSingle-molecule localization microscopy (SMLM) enabling the investigation of individual proteins on molecular scales has revolutionized how biological processes are analysed in cells. However, a major limitation of imaging techniques reaching single-protein resolution is the incomplete and often unknown labeling and detection efficiency of the utilized molecular probes. As a result, fundamental processes such as complex formation of distinct molecular species cannot be reliably quantified. Here, we establish a super-resolution microscopy framework, called quantitative single-molecule colocalization analysis (qSMCL), which permits the identification of absolute molecular quantities and thus the investigation of molecular-scale processes inside cells. The method combines multiplexed single-protein resolution imaging, automated cluster detection, in silico data simulation procedures, and widely applicable experimental controls to determine absolute fractions and spatial coordinates of interacting species on a true molecular level, even in highly crowded subcellular structures. The first application of this framework allowed the identification of a long-sought ternary adhesion complex—consisting of talin, kindlin and active β1-integrin—that specifically forms in cell-matrix adhesion sites. Together, the experiments demonstrate that qSMCL allows an absolute quantification of multiplexed SMLM data and thus should be useful for investigating molecular mechanisms underlying numerous processes in cells.
In3SbTe2 as a programmable nanophotonics material platform for the infrared
Authors: Heßler Andreas , Wahl Sophia , Leuteritz Till , Antonopoulos Antonios , Stergianou Christina , Schön Carl-Friedrich , Naumann Lukas , Eicker Niklas , Lewin Martin , Maß Tobias W. W. , Wuttig Matthias , Linden Stefan , Taubner Thomas 
Published: February 2021

AbstractThe high dielectric optical contrast between the amorphous and crystalline structural phases of non-volatile phase-change materials (PCMs) provides a promising route towards tuneable nanophotonic devices. Here, we employ the next-generation PCM In3SbTe2 (IST) whose optical properties change from dielectric to metallic upon crystallization in the whole infrared spectral range. This distinguishes IST as a switchable infrared plasmonic PCM and enables a programmable nanophotonics material platform. We show how resonant metallic nanostructures can be directly written, modified and erased on and below the meta-atom level in an IST thin film by a pulsed switching laser, facilitating direct laser writing lithography without need for cumbersome multi-step nanofabrication. With this technology, we demonstrate large resonance shifts of nanoantennas of more than 4 µm, a tuneable mid-infrared absorber with nearly 90% absorptance as well as screening and nanoscale “soldering” of metallic nanoantennas. Our concepts can empower improved designs of programmable nanophotonic devices for telecommunications, (bio)sensing and infrared optics, e.g. programmable infrared detectors, emitters and reconfigurable holograms.
Divergent rhodium-catalyzed electrochemical vinylic C–H annulation of acrylamides with alkynes
Authors: Xing Yi-Kang , Chen Xin-Ran , Yang Qi-Liang , Zhang Shuo-Qing , Guo Hai-Ming , Hong Xin , Mei Tian-Sheng 
Published: February 2021

Abstractα-Pyridones and α-pyrones are ubiquitous structural motifs found in natural products and biologically active small molecules. Here, we report an Rh-catalyzed electrochemical vinylic C–H annulation of acrylamides with alkynes, affording cyclic products in good to excellent yield. Divergent syntheses of α-pyridones and cyclic imidates are accomplished by employing N-phenyl acrylamides and N-tosyl acrylamides as substrates, respectively. Additionally, excellent regioselectivities are achieved when using unsymmetrical alkynes. This electrochemical process is environmentally benign compared to traditional transition metal-catalyzed C–H annulations because it avoids the use of stoichiometric metal oxidants. DFT calculations elucidated the reaction mechanism and origins of substituent-controlled chemoselectivity. The sequential C–H activation and alkyne insertion under rhodium catalysis leads to the seven-membered ring vinyl-rhodium intermediate. This intermediate undergoes either the classic neutral concerted reductive elimination to produce α-pyridones, or the ionic stepwise pathway to produce cyclic imidates.
Replication dynamics of recombination-dependent replication forks
Authors: Naiman Karel , Campillo-Funollet Eduard , Watson Adam T. , Budden Alice , Miyabe Izumi , Carr Antony M. 
Published: February 2021

AbstractReplication forks restarted by homologous recombination are error prone and replicate both strands semi-conservatively using Pol δ. Here, we use polymerase usage sequencing to visualize in vivo replication dynamics of HR-restarted forks at an S. pombe replication barrier, RTS1, and model replication by Monte Carlo simulation. We show that HR-restarted forks synthesise both strands with Pol δ for up to 30 kb without maturing to a δ/ε configuration and that Pol α is not used significantly on either strand, suggesting the lagging strand template remains as a gap that is filled in by Pol δ later. We further demonstrate that HR-restarted forks progress uninterrupted through a fork barrier that arrests canonical forks. Finally, by manipulating lagging strand resection during HR-restart by deleting pku70, we show that the leading strand initiates replication at the same position, signifying the stability of the 3′ single strand in the context of increased resection.
The metabolic impact of small intestinal nutrient sensing
Authors: Duca Frank A. , Waise T. M. Zaved , Peppler Willem T. , Lam Tony K. T. 
Published: February 2021

AbstractThe gastrointestinal tract maintains energy and glucose homeostasis, in part through nutrient-sensing and subsequent signaling to the brain and other tissues. In this review, we highlight the role of small intestinal nutrient-sensing in metabolic homeostasis, and link high-fat feeding, obesity, and diabetes with perturbations in these gut-brain signaling pathways. We identify how lipids, carbohydrates, and proteins, initiate gut peptide release from the enteroendocrine cells through small intestinal sensing pathways, and how these peptides regulate food intake, glucose tolerance, and hepatic glucose production. Lastly, we highlight how the gut microbiota impact small intestinal nutrient-sensing in normal physiology, and in disease, pharmacological and surgical settings. Emerging evidence indicates that the molecular mechanisms of small intestinal nutrient sensing in metabolic homeostasis have physiological and pathological impact as well as therapeutic potential in obesity and diabetes.
SARS-CoV-2 antibody prevalence in England following the first peak of the pandemic
Authors: Ward Helen , Atchison Christina , Whitaker Matthew , Ainslie Kylie E. C. , Elliott Joshua , Okell Lucy , Redd Rozlyn , Ashby Deborah , Donnelly Christl A. , Barclay Wendy , Darzi Ara , Cooke Graham , Riley Steven , Elliott Paul 
Published: February 2021

AbstractEngland has experienced a large outbreak of SARS-CoV-2, disproportionately affecting people from disadvantaged and ethnic minority communities. It is unclear how much of this excess is due to differences in exposure associated with structural inequalities. Here, we report from the REal-time Assessment of Community Transmission-2 (REACT-2) national study of over 100,000 people. After adjusting for test characteristics and re-weighting to the population, overall antibody prevalence is 6.0% (95% CI: 5.8-6.1). An estimated 3.4 million people had developed antibodies to SARS-CoV-2 by mid-July 2020. Prevalence is two- to three-fold higher among health and care workers compared with non-essential workers, and in people of Black or South Asian than white ethnicity, while age- and sex-specific infection fatality ratios are similar across ethnicities. Our results indicate that higher hospitalisation and mortality from COVID-19 in minority ethnic groups may reflect higher rates of infection rather than differential experience of disease or care.
Lighting up solid states using a rubber
Authors: Li Zhongyu , Wang Yanjie , Baryshnikov Gleb , Shen Shen , Zhang Man , Zou Qi , Ågren Hans , Zhu Liangliang 
Published: February 2021

AbstractIt is crucial and desirable to develop green and high-efficient strategies to regulate solid-state structures and their related material properties. However, relative to solution, it is more difficult to break and generate chemical bonds in solid states. In this work, a rubbing-induced photoluminescence on the solid states of ortho-pyridinil phenol family was achieved. This rubbing response relied on an accurately designed topochemical tautomerism, where a negative charge, exactly provided by the triboelectric effect of a rubber, can induce a proton transfer in a double H-bonded dimeric structure. This process instantaneously led to a bright-form tautomer that can be stabilized in the solid-state settings, leading to an up to over 450-fold increase of the fluorescent quantum yield of the materials. The property can be repeatedly used due to the reversibility of the tautomerism, enabling encrypted applications. Moreover, a further modification to the structure can be accomplished to achieve different properties, opening up more possibilities for the design of new-generation smart materials.
Automatic deep learning-driven label-free image-guided patch clamp system
Authors: Koos Krisztian , Oláh Gáspár , Balassa Tamas , Mihut Norbert , Rózsa Márton , Ozsvár Attila , Tasnadi Ervin , Barzó Pál , Faragó Nóra , Puskás László , Molnár Gábor , Molnár József , Tamás Gábor , Horvath Peter 
Published: February 2021

AbstractPatch clamp recording of neurons is a labor-intensive and time-consuming procedure. Here, we demonstrate a tool that fully automatically performs electrophysiological recordings in label-free tissue slices. The automation covers the detection of cells in label-free images, calibration of the micropipette movement, approach to the cell with the pipette, formation of the whole-cell configuration, and recording. The cell detection is based on deep learning. The model is trained on a new image database of neurons in unlabeled brain tissue slices. The pipette tip detection and approaching phase use image analysis techniques for precise movements. High-quality measurements are performed on hundreds of human and rodent neurons. We also demonstrate that further molecular and anatomical analysis can be performed on the recorded cells. The software has a diary module that automatically logs patch clamp events. Our tool can multiply the number of daily measurements to help brain research.
Long-ranged Cu-based order with $$d_{z^2}$$ orbital character at a YBa2Cu3O7/ manganite interface
Authors: Gaina Roxana , Nicholson Christopher W. , Rumo Maxime , Sarkar Subhrangsu , Khmaladze Jarji , Paris Eugenio , Tseng Yi , Zhang Wenliang , Asmara Teguh C. , McNally Daniel , Piamonteze Cinthia , Weschke Eugen , Schmitt Thorsten , Monney Claude , Bernhard Christian 
Published: February 2021

AbstractThe interplay of nearly degenerate orders in quantum materials can lead to a myriad of emergent phases. A prominent case is that of the high-Tc cuprates for which the relationship between superconductivity and a short-ranged, incommensurate charge density wave in the CuO2 planes involving the $$d_{x^2 - y^2}$$

d

x

2

−

y

2

orbitals (Cu-CDW) is a subject of great current interest. Strong modifications of the strength and coherence of this Cu-CDW have been achieved by applying large magnetic fields, uniaxial pressure, or via the interfacial coupling in cuprate/manganite multilayers. However, such modifications do not alter the dominant orbital character. Here we investigate cuprate/manganite multilayers with resonant inelastic X-ray scattering (RIXS) and show that a new kind of Cu-based density wave order can be induced that has not been previously observed in the cuprates. This order has an unusually small in-plane wave vector in the range of Q|| < 0.1 reciprocal lattice units (r.l.u.), a large correlation length of about 40 nm, and a predominant $$d_{z^2}$$

d

z

2

orbital character, instead of the typical $$d_{x^2 - y^2}$$

d

x

2

−

y

2

one. Its appearance is determined by the hole doping of the manganite which is a key parameter controlling the interfacial charge transfer and orbital reconstruction. We anticipate that the observation of a previously unknown type of density wave order at the YBCO interface will allow for fresh perspectives on the enigmatic relation between superconductivity and charge order (CO) in the cuprates.
Expansion and characterization of epithelial stem cells with potential for cyclical hair regeneration
Authors: Takeo Makoto , Asakawa Kyosuke , Toyoshima Koh-ei , Ogawa Miho , Tong JingJing , Irié Tarou , Yanagisawa Masayuki , Sato Akio , Tsuji Takashi 
Published: February 2021

AbstractIn mammals, organ induction occurs only during embryonic development except for hair follicles (HFs). However, HF-resident epithelial stem cells (HFSCs), which are responsible for repetitive HF regeneration, are not fully characterized. Here, we establish in vitro culture systems that are capable of controlling the ability of HFSCs to regenerate HFs. Based on a method that precisely controlled the number of HFs for regeneration, functional analysis revealed that CD34/CD49f/integrin β5 (Itgβ5)-triple-positive (CD34+/CD49f+/Itgβ5+) cells have multipotency and functional significance for continual hair regeneration. In native HFs, these cells reside in the uppermost area of the bulge region, which is surrounded by tenascin in mice and humans. This study unveils the subpopulation of HFSCs responsible for long-term hair cycling of HFs regenerated from bioengineered HF germ, suggesting the presence of functional heterogeneity among bulge HFSCs and the utility of our culture system to achieve HF regenerative therapy.
Landscape-induced spatial oscillations in population dynamics
Authors: Dornelas Vivian , Colombo Eduardo H. , López Cristóbal , Hernández-García Emilio , Anteneodo Celia 
Published: February 2021

AbstractWe study the effect that disturbances in the ecological landscape exert on the spatial distribution of a population that evolves according to the nonlocal FKPP equation. Using both numerical and analytical techniques, we characterize, as a function of the interaction kernel, the three types of stationary profiles that can develop near abrupt spatial variations in the environmental conditions vital for population growth: sustained oscillations, decaying oscillations and exponential relaxation towards a flat profile. Through the mapping between the features of the induced wrinkles and the shape of the interaction kernel, we discuss how heterogeneities can reveal information that would be hidden in a flat landscape.
Ensemble machine learning prediction and variable importance analysis of 5-year mortality after cardiac valve and CABG operations
Authors: Castela Forte José , Mungroop Hubert E. , de Geus Fred , van der Grinten Maureen L. , Bouma Hjalmar R. , Pettilä Ville , Scheeren Thomas W. L. , Nijsten Maarten W. N. , Mariani Massimo A. , van der Horst Iwan C. C. , Henning Robert H. , Wiering Marco A. , Epema Anne H. 
Published: February 2021

AbstractDespite having a similar post-operative complication profile, cardiac valve operations are associated with a higher mortality rate compared to coronary artery bypass grafting (CABG) operations. For long-term mortality, few predictors are known. In this study, we applied an ensemble machine learning (ML) algorithm to 88 routinely collected peri-operative variables to predict 5-year mortality after different types of cardiac operations. The Super Learner algorithm was trained using prospectively collected peri-operative data from 8241 patients who underwent cardiac valve, CABG and combined operations. Model performance and calibration were determined for all models, and variable importance analysis was conducted for all peri-operative parameters. Results showed that the predictive accuracy was the highest for solitary mitral (0.846 [95% CI 0.812–0.880]) and solitary aortic (0.838 [0.813–0.864]) valve operations, confirming that ensemble ML using routine data collected perioperatively can predict 5-year mortality after cardiac operations with high accuracy. Additionally, post-operative urea was identified as a novel and strong predictor of mortality for several types of operation, having a seemingly additive effect to better known risk factors such as age and postoperative creatinine.
TERRA G-quadruplex RNA interaction with TRF2 GAR domain is required for telomere integrity
Authors: Mei Yang , Deng Zhong , Vladimirova Olga , Gulve Nitish , Johnson F. Brad , Drosopoulos William C. , Schildkraut Carl L. , Lieberman Paul M. 
Published: February 2021

AbstractTelomere dysfunction causes chromosomal instability which is associated with many cancers and age-related diseases. The non-coding telomeric repeat-containing RNA (TERRA) forms a structural and regulatory component of the telomere that is implicated in telomere maintenance and chromosomal end protection. The basic N-terminal Gly/Arg-rich (GAR) domain of telomeric repeat-binding factor 2 (TRF2) can bind TERRA but the structural basis and significance of this interaction remains poorly understood. Here, we show that TRF2 GAR recognizes G-quadruplex features of TERRA. We show that small molecules that disrupt the TERRA-TRF2 GAR complex, such as N-methyl mesoporphyrin IX (NMM) or genetic deletion of TRF2 GAR domain, result in the loss of TERRA, and the induction of γH2AX-associated telomeric DNA damage associated with decreased telomere length, and increased telomere aberrations, including telomere fragility. Taken together, our data indicates that the G-quadruplex structure of TERRA is an important recognition element for TRF2 GAR domain and this interaction between TRF2 GAR and TERRA is essential to maintain telomere stability.
Separation of phenyl acetic acid and 6-aminopenicillanic acid applying aqueous two-phase systems based on copolymers and salts
Authors: Ahsaie Farzaneh Ghazizadeh , Pazuki Gholamreza 
Published: February 2021

Abstract6-Aminopenicillanic acid (6-APA) is used for synthesis of semisynthetic antibiotics. Polymer-salt aqueous two-phase systems (ATPSs) were applied for separation of 6-APA and phenyl acetic acid (PAA), as the products of hydrolyzation reaction of Penicillin G/Penicillin V. The binodal curves of ATPS composed of a copolymer (reverse Pluronic 10R5, Pluronic L35 and PEG-ran-PPG) and a salt (Tri-sodium citrate, tri-potassium citrate, di-potassium phosphate, sodium sulphate and magnesium sulphate) were obtained. The results show that, at a fixed PPG/PEG ratio, block copolymers have larger two-phase region compared with random copolymer. After screening on the partition coefficient of PAA and 6-APA separately, Na2SO4 was selected for studying the effect of the copolymer structure and the composition of salt and copolymer on partitioning, considering higher selectivity of PAA and 6-APA. 10R5-Na2SO4 ATPS was selected as the most appropriate system for separation of 6-APA and PAA. This system was used for separation of mixture of 6-APA and PAA. The results show that selectivity was $$\approx$$
≈
53 and smaller in a system, containing a mixture of 6-APA and PAA. This observation can be justified by the interaction between 6-APA and PAA. Molecular interaction between these two molecules were investigated by the Flory–Huggins interaction parameter.
Eyewitness identification performance is not affected by time-of-day optimality
Authors: Yaremenko Sergii , Sauerland Melanie , Hope Lorraine 
Published: February 2021

AbstractThe circadian rhythm regulates arousal levels throughout the day and determines optimal periods for engaging in mental activities. Individuals differ in the time of day at which they reach their peak: Morning-type individuals are at their best in the morning and evening types perform better in the evening. Performance in recall and recognition of non-facial stimuli is generally superior at an individual’s circadian peak. In two studies (Ns = 103 and 324), we tested the effect of time-of-testing optimality on eyewitness identification performance. Morning- and evening-type participants viewed stimulus films depicting staged crimes and made identification decisions from target-present and target-absent lineups either at their optimal or non-optimal time-of-day. We expected that participants would make more accurate identification decisions and that the confidence-accuracy and decision time-accuracy relationships would be stronger at optimal compared to non-optimal time of day. In Experiment 1, identification accuracy was unexpectedly superior at non-optimal compared to optimal time of day in target-present lineups. In Experiment 2, identification accuracy did not differ between the optimal and non-optimal time of day. Contrary to our expectations, confidence-accuracy relationship was generally stronger at non-optimal compared to optimal time of day. In line with our predictions, non-optimal testing eliminated decision-time-accuracy relationship in Experiment 1.
Untargeted analysis of first trimester serum to reveal biomarkers of pregnancy complications: a case–control discovery phase study
Authors: Harville E. W. , Li Y.-Y. , Pan K. , McRitchie S. , Pathmasiri W. , Sumner S. 
Published: February 2021

AbstractUnderstanding of causal biology and predictive biomarkers are lacking for hypertensive disorders of pregnancy (HDP) and preterm birth (PTB). First-trimester serum specimens from 51 cases of HDP, including 18 cases of pre-eclampsia (PE) and 33 cases of gestational hypertension (GH); 53 cases of PTB; and 109 controls were obtained from the Global Alliance to Prevent Prematurity and Stillbirth repository. Metabotyping was conducted using liquid chromatography high resolution mass spectroscopy and nuclear magnetic resonance spectroscopy. Multivariable logistic regression was used to identify signals that differed between groups after controlling for confounders. Signals important to predicting HDP and PTB were matched to an in-house physical standards library and public databases. Pathway analysis was conducted using GeneGo MetaCore. Over 400 signals for endogenous and exogenous metabolites that differentiated cases and controls were identified or annotated, and models that included these signals produced substantial improvements in predictive power beyond models that only included known risk factors. Perturbations of the aminoacyl-tRNA biosynthesis, l-threonine, and renal secretion of organic electrolytes pathways were associated with both HDP and PTB, while pathways related to cholesterol transport and metabolism were associated with HDP. This untargeted metabolomics analysis identified signals and common pathways associated with pregnancy complications.