bluuebunny/crossref_metadata_2025_split huggingface dataset:
De novo design of a reversible phosphorylation-dependent switch for membrane targeting
Authors: Harrington Leon , Fletcher Jordan M. , Heermann Tamara , Woolfson Derek N. , Schwille Petra 
Published: March 2021

AbstractModules that switch protein-protein interactions on and off are essential to develop synthetic biology; for example, to construct orthogonal signaling pathways, to control artificial protein structures dynamically, and for protein localization in cells or protocells. In nature, the E. coli MinCDE system couples nucleotide-dependent switching of MinD dimerization to membrane targeting to trigger spatiotemporal pattern formation. Here we present a de novo peptide-based molecular switch that toggles reversibly between monomer and dimer in response to phosphorylation and dephosphorylation. In combination with other modules, we construct fusion proteins that couple switching to lipid-membrane targeting by: (i) tethering a ‘cargo’ molecule reversibly to a permanent membrane ‘anchor’; and (ii) creating a ‘membrane-avidity switch’ that mimics the MinD system but operates by reversible phosphorylation. These minimal, de novo molecular switches have potential applications for introducing dynamic processes into designed and engineered proteins to augment functions in living cells and add functionality to protocells.
MINFLUX nanometer-scale 3D imaging and microsecond-range tracking on a common fluorescence microscope
Authors: Schmidt Roman , Weihs Tobias , Wurm Christian A. , Jansen Isabelle , Rehman Jasmin , Sahl Steffen J. , Hell Stefan W. 
Published: March 2021

AbstractThe recently introduced minimal photon fluxes (MINFLUX) concept pushed the resolution of fluorescence microscopy to molecular dimensions. Initial demonstrations relied on custom made, specialized microscopes, raising the question of the method’s general availability. Here, we show that MINFLUX implemented with a standard microscope stand can attain 1–3 nm resolution in three dimensions, rendering fluorescence microscopy with molecule-scale resolution widely applicable. Advances, such as synchronized electro-optical and galvanometric beam steering and a stabilization that locks the sample position to sub-nanometer precision with respect to the stand, ensure nanometer-precise and accurate real-time localization of individually activated fluorophores. In our MINFLUX imaging of cell- and neurobiological samples, ~800 detected photons suffice to attain a localization precision of 2.2 nm, whereas ~2500 photons yield precisions <1 nm (standard deviation). We further demonstrate 3D imaging with localization precision of ~2.4 nm in the focal plane and ~1.9 nm along the optic axis. Localizing with a precision of <20 nm within ~100 µs, we establish this spatio-temporal resolution in single fluorophore tracking and apply it to the diffusion of single labeled lipids in lipid-bilayer model membranes.
Selective E to Z isomerization of 1,3-Dienes Enabled by A Dinuclear Mechanism
Authors: Kudo Eiji , Sasaki Kota , Kawamata Shiori , Yamamoto Koji , Murahashi Tetsuro 
Published: March 2021

AbstractThe E/Z stereocontrol in a C=C bond is a fundamental issue in olefin synthesis. Although the thermodynamically more stable E geometry is readily addressable by thermal Z to E geometric isomerization through equilibrium, it has remained difficult to undergo thermal geometric isomerization to the reverse E to Z direction in a selective manner, because it requires kinetic trapping of Z-isomer with injection of chemical energy. Here we report that a dinuclear PdI−PdI complex mediates selective isomerization of E-1,3-diene to its Z-isomer without photoirradiation, where kinetic trapping is achieved through rational sequences of dinuclear elementary steps. The chemical energy required for the E to Z isomerization can be injected from an organic conjugate reaction through sharing of common Pd species.
Tumor methionine metabolism drives T-cell exhaustion in hepatocellular carcinoma
Authors: Hung Man Hsin , Lee Joo Sang , Ma Chi , Diggs Laurence P. , Heinrich Sophia , Chang Ching Wen , Ma Lichun , Forgues Marshonna , Budhu Anuradha , Chaisaingmongkol Jittiporn , Ruchirawat Mathuros , Ruppin Eytan , Greten Tim F. , Wang Xin Wei 
Published: March 2021

AbstractT-cell exhaustion denotes a hypofunctional state of T lymphocytes commonly found in cancer, but how tumor cells drive T-cell exhaustion remains elusive. Here, we find T-cell exhaustion linked to overall survival in 675 hepatocellular carcinoma (HCC) patients with diverse ethnicities and etiologies. Integrative omics analyses uncover oncogenic reprograming of HCC methionine recycling with elevated 5-methylthioadenosine (MTA) and S-adenosylmethionine (SAM) to be tightly linked to T-cell exhaustion. SAM and MTA induce T-cell dysfunction in vitro. Moreover, CRISPR-Cas9-mediated deletion of MAT2A, a key SAM producing enzyme, results in an inhibition of T-cell dysfunction and HCC growth in mice. Thus, reprogramming of tumor methionine metabolism may be a viable therapeutic strategy to improve HCC immunity.
Ice cream properties affected by carrageenan form seaweed deference type drying methods
Authors: Irawan I , Fitriyana  
Published: March 2021

Abstract
This study was aimed to investigate on physical properties of ice cream samples prepared with combined κ-carrageenan from seaweed by using two methods of drying seaweed which is direct sun-drying and drying using sauna techniques, the results the highest overrun was in ice cream with κ-carrageenan with sauna system (59.54±0.55 %). The highest melting rate was ice cream with Sodium carboxymethyl cellulose (1.72±0.05 g/min). The highest of viscosity was κ-carrageenan with the sauna system (143.67±1.52 cP). The highest of hardness was κ-carrageenan with the Sodium carboxymethyl cellulose (405.20±0.26 g/cm2). The sauna technique good for overrun, viscosity and direct sun-drying good for hardness.
Effect of the addition of crude fish oil (CFO) in feed to the content of EPA and DHA in mud crab (Scylla serrata)
Authors: Wijaya T , Agustono  , Arif M A A 
Published: March 2021

Abstract
Mud crabs (Scylla serrata) cannot synthesize essential fatty acids, so it needs a supply of Omega-3 fatty acids. One source of unsaturated fatty acids are Omega-3 in Crude Fish Oil (CFO). CFO is a source of essential fatty acids which contains EPA and DHA. The aim is to determine the provision of CFO on trash fish feed to the content of Omega-3 in mud crab. The method is experimentally using completely randomized design with five treatments and four replications. The number of CFO doses that added in a trash fish feed are P0 (0%), P1 (2%), P2 (4%), P3 (6%) and P4 (8%). Analysis of the content of EPA and DHA in mud crab performed using gas chromatography-mass spectrometry equipped with a column of silica and helium as a gas booster. The results showed that the addition of CFO on the feed provides a significantly different effect (P <0.05) of Omega-3 (EPA and DHA). Content of EPA and DHA in mud crab has shown the increased results when giving the smallest dose, 2% of CFO at P1 treatment, but when the dose was increased again to 4%, 6% and even 8% the results did not show any significant difference.
Depressive Symptoms Among Rural “Left-Behind” Older Adults: A Test of the High Outmigration Penalty Hypothesis
Authors: Song Qian , Wang Haowei , Burr Jeffery A 
Published: March 2021

Abstract

Objectives
We investigated whether there was a “high outmigration penalty” for psychological health among older adults in rural China by assessing 2 potential community stressors associated with major sociodemographic changes in the community—increased outmigration and older adult density. We also investigated whether disparities in community economic conditions moderated the association between community stressors and depressive symptoms.

Methods
We employed 3 waves of data from the China Health and Retirement Longitudinal Study (2011–2015), using multilevel negative binomial models to address our research questions.

Results
Our results supported the “high outmigration penalty” hypothesis. Older adults living in low-income rural communities may experience an aggravated mental health penalty compared to those living in high-income rural communities. Higher older adult density was also associated with more depressive symptoms but only in less wealthy communities. Community differences in economic conditions were key factors buffering the high outmigration disadvantage associated with the psychological health of older Chinese adults.

Discussion
Rural outmigration may have deepened existing intercommunity health disparities among older adults. Policies should be developed to address community-level factors negatively associated with the well-being of older Chinese adults living in high outmigration and less wealthy rural communities.
Article 3: Market Share Threshold
Authors: Wijckmans Frank , Tuytschaever Filip 
Published: March 2021

Abstract
This chapter discusses the market share limits that determine the applicability of Regulation 330/2010. Each of the supplier and the buyer must in principle remain below an individual limit of 30 per cent. In order to assess the market share limits, the chapter addresses the following steps of the analysis: (i) ninth step: definition of the relevant market; and (ii) tenth step: calculation of the market shares. It concludes by addressing the concrete and practical application of the market share limits in accordance with Regulation 330/2010 and offers easy-to-read overview tables illustrating the effect of changes in the market share levels over time.
Automatic detection of pituitary microadenoma from magnetic resonance imaging using deep learning algorithms
Authors: Li Qingling , Zhu Yanhua , Chen Minglin , Guo Ruomi , Hu Qingyong , Deng Zhenghui , Deng Songqing , Wen Huiquan , Gao Rong , Nie Yuanpeng , Li Haicheng , Zhang Tiecheng , Chen Jianning , Shi Guojun , Shen Jun , Cheung Wai Wilson , Guo Yulan , Chen Yanming 
Published: March 2021

ABSTRACTPituitary microadenoma (PM) is often difficult to detect by MR imaging alone. We employed a computer-aided PM diagnosis (PM-CAD) system based on deep learning to assist radiologists in clinical workflow. We enrolled 1,228 participants and stratified into 3 non-overlapping cohorts for training, validation and testing purposes. Our PM-CAD system outperformed 6 existing established convolutional neural network models for detection of PM. In test dataset, diagnostic accuracy of PM-CAD system was comparable to radiologists with > 10 years of professional expertise (94% versus 95%). The diagnostic accuracy in internal and external dataset was 94% and 90%, respectively. Importantly, PM-CAD system detected the presence of PM that had been previously misdiagnosed by radiologists. This is the first report showing that PM-CAD system is a viable tool for detecting PM. Our results suggest that PM-CAD system is applicable to radiology departments, especially in primary health care institutions.
Total nodule number is an independent prognostic factor in resected stage III non-small cell lung cancer: a deep learning powered study
Authors: Chen Xiuyuan , Qi Qingyi , Sun Zewen , Wang Dawei , Sun Jinlong , Tan Weixiong , Liu Xianping , Liu Taorui , Hong Nan , Yang Fan 
Published: March 2021

ABSTRACTAlmost every lung cancer patient has multiple pulmonary nodules while the significance of nodule multiplicity in locally advanced non-small cell lung cancer (NSCLC) remained unclear. This study explores the relationship between deep learning detected total nodule number (TNN) and survival outcomes in patients with surgical resected stage I-III NSCLC. Patients who underwent surgical resection for stage I-III NSCLC with accessible preoperative chest CT scan from 2005 to 2018 were identified from our database. Deep learning-based AI algorithms using convolutional neural networks (CNN) was applied for pulmonary nodule (PN) detection and classification. Of the 2126 patients, a total number of 33410 PNs were detected by AI. Median TNN detected per person was 12 (IQR 7-20). AI-detected TNN (analyzed as continuous variable) was independent prognostic factor for both RFS (HR 1.012, 95% CI 1.002-1.022, p = 0.021) and OS (HR 1.013, 95% CI 1.002-1.025, p = 0.021) in multivariate analyses of stage III cohort; while it was not significantly associated with survival in stage I and II cohorts. In terms of nodule categories, the numbers of upper-lobe nodule, same-side nodule, other-side nodule, solid nodule, and even solid nodule at small size (≤ 6mm) were independent prognostic factors; while the numbers of middle/lower-lobe nodule, same-lobe nodule, subsolid nodule, calcific nodule and perifissural nodule were not associated with survival. In survival tree analysis, rather than using traditional IIIA and IIIB classification, the model grouped cases by AI-detected TNN (lower vs. higher: log-rank p < 0.001), which showed superior discrimination of survival in stage III cohort. In conclusion, AI-detected TNN was significantly associated with survival in patients with surgical resected stage III NSCLC. Lower TNN detected on preoperative CT scan indicated better prognosis in patients who underwent complete surgical resection.
N6-methyladenosine RNA modification regulates strawberry fruit ripening in an ABA-dependent manner
Authors: Zhou Leilei , Tang Renkun , Li Xiaojing , Tian Shiping , Li Bingbing , Qin Guozheng 
Published: March 2021

AbstractBackgroundEpigenetic marks, such as DNA methylation, play pivotal roles in regulating ripening of both climacteric and non-climacteric fruits. However, it remains unclear whether mRNA m6A methylation, the epitranscriptome, is functionally conserved for ripening control.ResultsHere we show that m6A methylation, which has been revealed to regulate ripening of tomato, a typical climacteric fruit, displays a dramatic change at ripening onset of strawberry, a classical non-climacteric fruit. The m6A modification in the coding sequence (CDS) regions appears to be ripening-specific and tends to stabilize the mRNAs, whereas m6A around the stop codons and within the 3’ untranslated regions is generally negatively correlated with the abundance of the mRNAs. We identified thousands of transcripts with m6A hypermethylation in the CDS regions, including those ofNCED5,ABAR, andAREB1in the abscisic acid (ABA) biosynthesis and signaling pathway. We demonstrated that the methyltransferases MTA and MTB are indispensable for normal ripening of strawberry fruit, and MTA-mediated m6A modification promotes mRNA stability ofNCED5andAREB1, while facilitates translation ofABAR.ConclusionOur findings uncover that m6A methylation regulates ripening of non-climacteric strawberry fruit by targeting ABA pathway, which is distinct from that in climacteric tomato fruit.
The memory B cell response to influenza vaccination is impaired in older persons
Authors: Carr Edward J , Wheatley Adam K , Hill Danika L , Linterman Michelle A 
Published: March 2021

AbstractInfluenza imparts an age-related increase in mortality and morbidity. The most effective countermeasure is vaccination; however, vaccines offer modest protection in older adults. To investigate how ageing impacts the memory B cell response we tracked haemagglutinin specific B cells by indexed flow sorting and single cell RNA sequencing in twenty healthy adults administered the trivalent influenza vaccine. We found age-related skewing in the memory B cell compartment six weeks after vaccination, with younger adults developing haemagglutinin specific memory B cells with anFCRL5+“atypical” phenotype, showing evidence of somatic hypermutation and positive selection, which happened to a lesser extent in older persons. We confirmed the germinal center ancestry of theseFCRL5+“atypical” memory B cells using scRNASeq from fine needle aspirates of influenza responding human lymph nodes and paired blood samples. Together, this study shows that the aged human germinal center reaction and memory B cell response following vaccination is defective.SummaryImmune responses to vaccination wane with age. Using single cell RNA sequencing of influenza vaccine specific B cells, this study delineates changes in B cell memory generation, antibody mutation and their subsequent selection in older persons.
Mature parvalbumin interneuron function in prefrontal cortex requires activity during a postnatal sensitive period
Authors: Canetta Sarah E. , Holt Emma S. , Benoit Laura J. , Teboul Eric , Sahyoun Gabriella M. , Ogden R. Todd , Harris Alexander Z. , Kellendonk Christoph 
Published: March 2021

SummaryIn their seminal findings, Hubel and Wiesel identified sensitive periods in which experience can exert lasting effects on adult visual cortical functioning and behavior via transient changes in neuronal activity during development. Whether comparable sensitive periods exist for non-sensory cortices, such as the prefrontal cortex, in which alterations in activity determine adult circuit function and behavior is still an active area of research. Here, we demonstrate that inhibition of prefrontal parvalbumin-expressing interneurons during the juvenile and adolescent period, results inpersistentimpairments in adult prefrontal circuit connectivity,in vivonetwork function and behavioral flexibility that can be reversed by targeted activation of parvalbumin interneurons in adulthood. In contrast, transient suppression of parvalbumin interneuron activity in adulthood produces no lasting effects. These findings identify an activity-dependent sensitive period for prefrontal circuit maturation and highlight how abnormal parvalbumin interneuron activity during development alters adult prefrontal circuit function and cognitive behavior.
Acyloxyacyl Hydrolase Modulates the Gut Microbiome Through Transcriptional Regulators of Corticotropin-Releasing Factor
Authors: Rahman-Enyart Afrida , Aguiniga Lizath M. , Yang Wenbin , Yaggie Ryan E. , White Bryan , Welge Michael , Auvil Loretta , Berry Matthew , Bushell Colleen , Schaeffer Anthony J. , Klumpp David J. 
Published: March 2021

ABSTRACTGut microbiome-host interactions play a crucial role in health and disease. Altered gut microbiome composition has been observed in patients with interstitial cystitis/bladder pain syndrome (IC/BPS), a disorder characterized by pelvic pain, voiding dysfunction, and often co-morbid with anxiety/depression. We recently showed that mice deficient for acyloxyacyl hydrolase (AOAH) mimic pelvic pain symptoms and comorbidities of IC/BPS and also exhibit gut dysbiosis. In addition, we previously identified that the conditional knockout (cKO) of two transcriptional regulators of the gene encoding corticotropin-releasing factor,Crf, that are downstream of AOAH, aryl hydrocarbon receptor (AhR) and peroxisome proliferator-activated receptor-γ(PPARγ), alleviate anxiety/depressive and voiding phenotypes of AOAH-deficient mice. Here, we examined the effects of AhR and PPARγin CRF-expressing cells on the dysbiosis of AOAH-deficiency. AOAH-deficient mice with cKO ofPPARγandAhR/PPARγexhibited reduced pelvic allodynia compared to AOAH-deficient mice, suggesting a role for PPARγin regulating pelvic pain. 16S rRNA sequencing of fecal stool from female AOAH-deficient mice with a cKO of AhR and/or PPARγin CRF-expressing cells identified altered gut microbiota distinct from AOAH-deficient stool. The cKO of AhR and PPARγshowed improved cecum barrier function in females compared to AOAH-deficient mice, whereas males were primarily affected by PPARγ, suggesting sex differences in gut responses. Pair-wise comparison of microbiota also suggested sex differences in response to AOAH-deficiency and conditional knockout ofAhRandPPARγ. Our findings suggest that the dysbiosis and leaky gut of AOAH deficiency is mediated by AhR and PPARγin CRF-expressing cells and reveal a novel mechanism and therapeutic targets for pelvic pain.
GroEL/S helps purge deleterious mutations and reduce genetic diversity during adaptive protein evolution
Authors: Iyengar Bharat Ravi , Wagner Andreas 
Published: March 2021

AbstractChaperones are proteins that help other proteins fold. They also affect the adaptive evolution of their client proteins by buffering deleterious mutations and increasing the genetic diversity of evolving proteins. We study how the bacterial chaperone GroE (GroEL + GroES) affects the evolution of green fluorescent protein (GFP). To this end we subjected GFP to multiple rounds of mutation and selection for its color phenotype in four replicateE. colipopulations, and studied its evolutionary dynamics through high-throughput sequencing and mutant engineering. We evolved GFP both under stabilizing selection for its ancestral (green) phenotype, and to directional selection for a new (cyan) phenotype,. We did so both under low and high expression of the chaperone GroE. In contrast to prevailing wisdom, we observe that GroE does not just buffer but also helps purge deleterious mutations from evolving populations. In doing so, GroE helps reduce the genetic diversity of evolving populations. In addition, it causes phenotypic heterogeneity in mutants with the same genotype, potentiating their effect in some cells, and buffering it in others. Our observations show that chaperones can affect adaptive evolution through more than one mechanism.HighlightsGroE reduces genetic diversityGroE potentiates the effect of deleterious mutationsGroE intensifies purifying selection and leads to higher activity of client proteins