bluuebunny/crossref_metadata_2025_split huggingface dataset:
O‐GlcNAc Engineering on a Target Protein in Cells with Nanobody‐OGT and Nanobody‐splitOGA
Authors: Ramirez Daniel H. , Ge Yun , Woo Christina M. 
Published: May 2021

AbstractThe monosaccharide O‐linked N‐acetyl glucosamine (O‐GlcNAc) is an essential and dynamic post‐translational modification (PTM) that decorates thousands of nucleocytoplasmic proteins. Interrogating the role of O‐GlcNAc on a target protein is crucial yet challenging to perform in cells. We recently reported a pair of methods to selectively install or remove O‐GlcNAc on a target protein in cells using an engineered O‐GlcNAc transferase (OGT) or split O‐GlcNAcase (OGA) fused to a nanobody. Target protein O‐GlcNAcylation and de‐O‐GlcNAcylation complements methods to interrogate the role of O‐GlcNAc on a global scale or at individual glycosites. Herein, we describe a protocol for utilizing the nanobody‐OGT and nanobody‐splitOGA systems to screen for O‐GlcNAc functionality on a target protein. We additionally include associated protocols for the detection of O‐GlcNAc and cloning procedures to adapt the method for the user's target protein of interest. © 2021 Wiley Periodicals LLC.This article was corrected on 28 July 2022. See the end of the full text for details.Basic Protocol 1: Target protein O‐GlcNAcylation of JunB using nanobody‐OGTBasic Protocol 2: Target protein deglycosylation of Nup62 using nanobody‐splitOGAAlternate Protocol: Verification of the O‐GlcNAc state of a tagged target protein through chemoenzymatic labelingSupport Protocol: Cloning of new nanobody‐OGT/nanobody‐splitOGA and target protein pairs
Immunohistochemical and Genetic Labeling of Hairy and Glabrous Skin Innervation
Authors: Pomaville Matthew B. , Wright Kevin M. 
Published: May 2021

AbstractCutaneous innervation is an essential component of the mammalian sensory nervous system. During development, genetically and morphologically diverse subtypes of sensory neurons use distinct molecular pathways to innervate end organs or form free nerve endings in glabrous and hairy skin. Peripheral neurons can be damaged by acute injury or degenerate due to chronic conditions including diabetes and chemotherapy, leading to peripheral neuropathy. The analysis of skin and cutaneous innervation can be applied to many research endeavors, from developmental neuroscience to pharmaceutical testing. Due to the natural hydrophobicity and heterogenous makeup of the skin (dense, keratinized cells as well as sparse, extracellular‐matrix‐bound cells), its histological analysis presents unique challenges compared to that of many other tissues. This series of protocols describes histological methods for generalized immunohistochemistry and subtype‐specific genetic labeling of sensory neurons in mouse skin in both whole‐mount and section formats. We provide detailed methodology of tissue preparation for hairy and glabrous skin, several types of labeling, and counting of hair follicles in flat‐mounted mouse skin. © 2021 Wiley Periodicals LLC.Basic Protocol 1: Cryosectioning and immunostaining of mouse hairy skinAlternate Protocol 1: Alternate method for preparation and fixation of mouse hairy skinBasic Protocol 2: Sectioning of mouse paw glabrous skinBasic Protocol 3: Whole‐mount immunolabeling of mouse skinBasic Protocol 4: Sparse labeling of skin‐innervating neurons with a Cre‐dependent membrane‐bound alkaline phosphatase reporterAlternate Protocol 2: Sparse labeling of skin‐innervating neurons with a Cre‐dependent fluorescent reporterBasic Protocol 5: Oil Red O staining of skin
Learning‐dependent dendritic spine plasticity is impaired in spontaneous autoimmune encephalomyelitis
Authors: Huang Lianyan , Lafaille Juan J. , Yang Guang 
Published: May 2021

AbstractCognitive impairment is often observed in multiple sclerosis and its animal models, experimental autoimmune encephalomyelitis (EAE). Using mice with immunization‐induced EAE, we have previously shown that the stability of cortical synapses is markedly decreased before the clinical onset of EAE. In this study, we examined learning‐dependent structural synaptic plasticity in a spontaneous EAE model. Transgenic mice expressing myelin basic protein‐specific T cell receptor genes develop EAE spontaneously at around 8 weeks of age. Using in vivo two‐photon microscopy, we found that the elimination and formation rates of postsynaptic dendritic spines in somatosensory and motor cortices increased weeks before detectable signs of EAE and remained to be high during the disease onset. Despite the elevated basal spine turnover, motor learning‐induced spine formation was reduced in presymptomatic EAE mice, in line with their impaired ability to retain learned motor skills. Additionally, we found a substantial elevation of IFN‐γ mRNA in the brain of 4‐week‐old presymptomatic mice, and treatment of anti‐IFN‐γ antibody reduced dendritic spine elimination in the cortex. Together, these findings reveal synaptic instability and failure to form new synapses after learning as early brain pathology of EAE, which may contribute to cognitive and behavioral deficits seen in autoimmune diseases.
Revisiting institutional stability: A systematic review and distillations of dominant modes
Authors: Galik Christopher S. , Chelbi Leila 
Published: May 2021

AbstractThe concept of institutional stability has been explored from multiple disciplinary lenses and is associated with a variety of theories and frameworks, masking important variation in the mechanisms and modes of institutional stability, and complicating our understanding of how and why institutions are maintained over time. This is particularly salient to questions of environmental governance, where the recent pace and magnitude of both political and environmental change necessitates more careful attention to the capacity of existing institutions to persist or adapt. Here, we conduct a systematic review to examine the treatment of institutional stability in the literature to determine whether dominant or consistent conceptualizations of institutional stability are present. Beginning with a list of 21 synonyms for stability as used in the literature, we assembled a raw dataset of 23,379 manuscripts in print or published between 1976 and August 2019. Papers were then screened to ensure a theoretical or empirical analysis of institutional stability, resulting in a final dataset of 165 unique manuscripts. From our review, we propose two separate axes—directionality and intentionality—upon which four separate modes of stability may be arrayed. Termed passive stability, active stability, intended inaction, and failed action, we find that each is characterized by distinct mechanisms and captures specific concepts detailed in the extant literature. Though we believe our typology to have the potential to provide for a more precise analysis of institutional stability and associated policy and resource outcomes, further research is necessary to demonstrate its applicability.
Chromatin assembly factor 1B critically controls the early development but not function acquisition of invariant natural killer T cells in mice
Authors: Xu Yu , Ma Junwei , Luo Haorui , Shi Yaohuang , Liu Haifeng , Sun Ao , Xu Chenqi , Ji Hongbin , Liu Xiaolong 
Published: May 2021

AbstractCD4+CD8+ double‐positive thymocytes give rise to both conventional TCRαβ+ T cells and invariant natural killer T cells (iNKT cells), but these two kinds of cells display different characteristics. The molecular mechanism underlying iNKT cell lineage development and function acquisition remain to be elucidated. We show that the loss of chromatin assembly factor 1B (CHAF1b) maintains the normal development of conventional TCRαβ+ T cells but severely impairs early development of iNKT cells. This dysregulation is accompanied by the impairment in chromatin activation and gene transcription at Vα14‐Jα18 locus. Notably, ectopic expression of a Vα14‐Jα18 TCR rescues Chaf1b‐deficient iNKT cell developmental defects. Moreover, cytokine secretion and antitumor activity are substantially maintained in Vα14‐Jα18 TCR transgene‐rescued Chaf1b‐deficient iNKT cells. Our study identifies CHAF1b as a critical factor that controls the early development but not function acquisition of iNKT cells via lineage‐ and stage‐specific regulation.
Autosomal deletion/insertion polymorphisms for global stratification analyses and ancestry origin inferences of different continental populations by machine learning methods
Authors: Jin Xiaoye , Liu Yuluo , Zhang Yuanyuan , Li Yongle , Chen Chuanliang , Wang Hongdan 
Published: May 2021

AbstractA lot of population data of 30 deletion/insertion polymorphisms (DIPs) of the Investigator DIPplex kit in different continental populations have been reported. Here, we assessed genetic distributions of these 30 DIPs in different continental populations to pinpoint candidate ancestry informative DIPs. Besides, the effectiveness of machine learning methods for ancestry analysis was explored. Pairwise informativeness (In) values of 30 DIPs revealed that six loci displayed relatively high In values (>0.1) among different continental populations. Besides, more loci showed high population‐specific divergence (PSD) values in African population. Based on the pairwise In and PSD values of 30 DIPs, 17 DIPs in the Investigator DIPplex kit were selected to ancestry analyses of African, European, and East Asian populations. Even though 30 DIPs provided better ancestry resolution of these continental populations based on the results of PCA and population genetic structure, we found that 17 DIPs could also distinguish these continental populations. More importantly, these 17 DIPs possessed more balanced cumulative PSD distributions in these populations. Six machine learning methods were used to perform ancestry analyses of these continental populations based on 17 DIPs. Obtained results revealed that naïve Bayes manifested the greatest performance; whereas, k nearest neighbor showed relatively low performance. To sum up, these machine learning methods, especially for naïve Bayes, could be used as the valuable tool for ancestry analysis.
Energy and exergy assessment with updated Reistad estimates: A case study in the transportation sector of Bangladesh
Authors: Chowdhury Hemal , Chowdhury Tamal , Rashedi Ahmad , Banik Sajal Chandra , Khanam Taslima , Saidur Rahman , Sait Sadiq M. , Rosen Marc A. 
Published: May 2021

AbstractTransportation sector is one of the core parts of modern civilization. Proper utilization of energy and exergy in this sector is necessary to ensure energy loss and environmental sustainability. Increasing exergy efficiency will reduce carbon emissions from this sector. Since 1970, Reistad estimates have been widely used to determine the energy and exergy efficiencies of this sector. However, the modern transport sector has undergone significant changes in recent decades. Hence, it is necessary to apply new Reistad estimates in determining the energy and exergy efficiencies. This is the first study to apply updated Reistad estimates to explore the energy and exergy efficiencies in the transportation sector of Bangladesh based on the data from 2000 to 2017. The overall exergy efficiency is significantly lower than the energy efficiencies as it ranges from 27.7% to 30.0%. Efficiencies are lower as the maximum portion of input exergy is lost to the environment. The road subsector needs major improvements as it is responsible for major amount of exergy loss. A comparison is made between conventional and updated estimates which highlights that the updated estimates provide more accurate results. Thus, it is recommended to apply updated Reistad estimates in determining the energy and exergy efficiencies of the transport sector.
Response of transient rock uplift and base level knickpoints to erosional efficiency contrasts in bedrock streams
Authors: Wolpert Joshua A. , Forte Adam M. 
Published: May 2021

AbstractKnickpoints in bedrock streams are often interpreted as transient features generated by a change in boundary conditions. It is typically assumed that knickpoints propagate upstream with constant vertical velocities, though this relies on a stream being in erosional steady state (erosion rate equals rock uplift rate) prior to the knickpoint's formation. Recent modeling and field studies suggest that along‐stream contrasts in rock erodibility perturb streams from erosional steady state. To evaluate how contrasts in rock erodibility might impact knickpoint interpretations, we test parameter space (rock erodibility, rock contact dip angle, change in rock uplift rate) in a one‐dimensional (1D) bedrock stream model that has variable rock erodibility and produces a knickpoint with a sudden change in rock uplift rate. Upstream of a rock contact, the vertical velocity of a knickpoint generated by a change in rock uplift rate is strongly correlated with how the rock contact has previously perturbed erosion rates. These knickpoints increase vertical velocity upon propagating upstream of a hard over soft contact and decrease vertical velocity upon propagating upstream of a soft over hard contact. However, interactions with other transient perturbations produced by rock contacts make for nuances in knickpoint behavior. Rock contacts also influence the geometry of knickpoints, which can become particularly difficult to identify upstream of soft over hard rock contacts. Using our simulations, we demonstrate how a contact's along‐stream horizontal migration rate and cross‐contact change in rock strength control how much an upstream reach is perturbed from erosional steady state. When simulations include multiple contacts, the knickpoint is particularly prone to colliding with other transient perturbations and can even disappear altogether if rock contact dips are sufficiently shallow. Caution should be taken when analyzing stream profiles in areas with significant changes in rock strength, especially when rock contact dip angles are near the stream's slope.
Rapid non‐destructive analysis of lignin using NIR spectroscopy and chemo‐metrics
Authors: Wu Xin , Li Guanglin , Liu Xuwen , He Fengyun 
Published: May 2021

AbstractLignin plays an important role in the formation of stone cells in pears. However, the accumulation of lignin had adverse impact on the flavor and quality of the fruit. A rapid and accurate method for measuring the lignin content of pears is therefore required. An improved variables selection method called ‘the bootstrapping soft shrinkage combined with frequency and regression coefficient of variables (FRCBOSS)’ was therefore developed based on ‘the bootstrapping soft shrinkage (BOSS)’technique, to identify the characteristic wavelengths of near‐infrared (NIR) spectra for non‐destructive and rapid analysis of lignin. Sub‐models were generated by weighted bootstrap sampling (WBS) in the FRCBOSS method. For the BOSS method, the new weights of variables were determined only as the absolute values of regression coefficients of variables in each iteration. In contrast, the FRCBOSS method also considers the frequency of variables in variable space. Moreover, the FRCBOSS algorithm overcomes the disadvantage of BOSS in selecting variables, which could incorporate useful wavelengths that would otherwise be removed by the BOSS method. In addition, a range of different pre‐treatment methods were used for comparison in the detection of lignin in the Snow pears. These include Savitzky–Golay Smoothing (SG), Normalization (NORM), Standard Normal Variate (SNV), and 1st Derivative (D1), as well as a combination of these methods and the different variables selection method (SiPLS, SiPLS‐SPA, SiPLS‐CARS, SiPLS‐BOSS, and SiPLS‐FRCBOSS). The number of variables selected by FRCBOSS was a little larger than that selected by BOSS. The partial least square regression (PLSR) model based on the 19 variables selected by SiPLS‐FRCBOSS method had the best prediction ability, with a Rp value of prediction of 0.880 and a RMSEP value of 1.004%. We conclude that NIR diffuse reflectance spectroscopy technology combined with FRC‐BOSS is an accurate and useful tool for the non‐destructive and rapid determination of pear lignin contents.
Behavior of Cucumis sativus L. in presence of aluminum stress: Germination, plant growth, and antioxidant enzymes
Authors: Kouki Rim , Ayachi Rim , Ferreira Renata , Sleimi Noomene 
Published: May 2021

AbstractAluminum (Al) is an ubiquitously present element in soil; it is considered as a major problem in crop production that affects plant growth and development on acid soils. The aim of this work was to determine the germination parameters, to quantify the water status and growth, to assess the Al accumulation, and antioxidant enzyme activities in plants to evaluate the stress exerted by aluminum in Cucumis sativus L. For germination test, increasing doses of Al were used (0, 200, 500, 1,000, and 2,000 μM). Results showed that germination was stimulated with 500 of Al. Aluminum effects on development were studied by treating the plants with different concentrations of Al (100, 200, 300, and 500 µM, Al) during 45 days. As regards to the plant's growth, water content, and dry biomass production there was a slight increase. On the other hand, the activities of the antioxidant enzymes were disturbed by aluminum stress. Data indicate that the catalase (CAT) activity showed a decrease in the different parts of the plant. However, guaiacol peroxidase (GPX) and ascorbate peroxidase (APX) activities were significantly stimulated. Studying the effects of Al‐induced stress allowed us to conclude that cucumber has a high ability to accumulate this element in the roots.
Mechanical, sensory, and consumer evaluation of ketogenic, gluten‐free breads
Authors: Gillespie Rachel , Ahlborn Gene J. 
Published: May 2021

AbstractKetogenic, gluten‐free breads comprised of almond flour, oat bran fiber, or combinations of both were compared. The textural properties, sensory attributes, and consumer acceptance were analyzed on each bread containing 100% almond flour (AF), 66.7% almond flour with 33.3% oat bran fiber (AOB), 66.7% oat bran fiber with 33.3% almond flour (OBA), and 100% oat bran fiber (OB). AF and AOB breads had a more open crumb structure composed of cells between 1–4 mm2. OBA and OB had a significantly dense crumb pattern made up of more cells less than one millimeter squared. Quantitative–descriptive analysis (QDA) and consumer acceptance testing was conducted 24 hr after baking and mechanical endpoints were evaluated 24, 72, and 120 hr after baking. AF and AOB breads were preferred over OBA and OB breads in QDA evaluation and consumer acceptance scores. Greater percentages of oat bran fiber resulted in a bread that was less moist, firmer in texture, and chewier with trained panelists. In both sensory evaluations, higher amounts of almond flour resulted in higher values in eggy flavor while increased amounts of oat bran fiber correlated with higher values in earthy flavor. Mechanical testing identified higher percentages of almond flour resulted in bread that was less firm and less chewy. Over time, all variations with almond flour became softer and less chewy, while the OB bread increased in firmness. Sensory cohesiveness did not correlate with the mechanical equivalent, identifying a need to re‐evaluate the parameters used to calculate this objective endpoint.
Nanotechnology: A novel tool to enhance the bioavailability of micronutrients
Authors: Arshad Rizwan , Gulshad Lubaba , Haq Iahtisham‐Ul‐ , Farooq Muhammad Adil , Al‐Farga Ammar , Siddique Rabia , Manzoor Muhammad Faisal , Karrar Emad 
Published: May 2021

AbstractNanotechnology has revolutionized the field of food systems, diagnostics, therapeutics, pharmaceuticals, the agriculture sector, and nutraceuticals. Nanoparticles are playing important role in giving the solution to enhance bioavailability of oral delivery of bioactive compounds. This review revealed that nanoparticles can improve the bioavailability of micronutrients, for example, vitamin B12, vitamin A, folic acid, and iron. However, toxicity associated with nanoparticle‐based delivery systems is still a major concern after ingestion of nano‐based supplements. The mode of the mechanism of nanomaterial along with bioactive components in different physiological conditions of the human body is also a major gap in the field of nanoceuticals. In the future, more evidence‐based clinical investigations are needed to confirm the exact approach to physiological changes in the human body.
High‐resolution multibeam sonar bathymetry of the deepest place in each ocean
Authors: Bongiovanni Cassandra , Stewart Heather A. , Jamieson Alan J. 
Published: May 2021

AbstractOver the course of 10 months, the global Five Deeps Expedition (2018–2019) mapped ~550,000 km2 of seafloor of which 61% comprised new coverage over areas never before surveyed and ~30% was acquired from some of the ocean's deepest trenches and fracture zones. The deepest points of each ocean were mapped using a latest‐generation, full‐ocean depth Kongsberg EM 124 multibeam echosounder. These extreme depths were corrected using Conductivity, Temperature and Depth (CTD) data from sea surface to full ocean depth. The deepest place in each ocean were identified as the Brownson Deep, Puerto Rico Trench in the Atlantic Ocean (8,378 ± 5 m), an unnamed deep within the South Sandwich Trench in the Southern Ocean (7,432 ± 13 m), an unnamed deep within the Java Trench in the Indian Ocean (7,187 ± 13 m), Challenger Deep within the Mariana Trench in the Pacific Ocean (10,924 ± 15 m), and the Molloy Hole in the Arctic Ocean (5,551 ± 14 m). As part of the overarching mission of the Five Deeps Expedition, and to clarify beyond doubt the deepest point in the Indian, Pacific and Southern oceans, other sites were visited that had been postulated as potential deepest locations. This study has confirmed that the Horizon Deep within the Tonga Trench is the second deepest point in the Pacific Ocean (10,816 ± 16 m), the Dordrecht Deep within the Diamantina Fracture Zone is not the deepest point in the Indian Ocean (7,019 ± 17 m) and that in accordance with the guidelines of the Antarctic Treaty and International Hydrographic Organisation, although the Meteor Deep is the deepest point in the South Sandwich Trench (8,265 ± 13 m) it is located within the waters of the Atlantic Ocean and not the Southern Ocean.