bluuebunny/crossref_metadata_2025_split huggingface dataset:
An empirical expression for on the axis of a slightly heated turbulent round jet
Authors: Lemay J. , Djenidi L. , Antonia R. A. , Benaïssa A. 
Published: March 2019

Self-preservation analyses of the equations for the mean temperature and the second-order temperature structure function on the axis of a slightly heated turbulent round jet are exploited in an attempt to develop an analytical expression for$\unicode[STIX]{x1D716}_{\unicode[STIX]{x1D703}}$, the mean dissipation rate of$\overline{\unicode[STIX]{x1D703}^{2}}/2$, where$\overline{\unicode[STIX]{x1D703}^{2}}$is the temperature variance. The analytical approach follows that of Thiessetet al.(J. Fluid Mech., vol. 748, 2014, R2) who developed an expression for$\unicode[STIX]{x1D716}_{k}$, the mean turbulent kinetic energy dissipation rate, using the transport equation for$\overline{(\unicode[STIX]{x1D6FF}u)^{2}}$, the second-order velocity structure function. Experimental data show that complete self-preservation for all scales of motion is very well satisfied along the jet axis for streamwise distances larger than approximately 30 times the nozzle diameter. This validation of the analytical results is of particular interest as it provides justification and confidence in the analytical derivation of power laws representing the streamwise evolution of different physical quantities along the axis, such as:$\unicode[STIX]{x1D702}$,$\unicode[STIX]{x1D706}$,$\unicode[STIX]{x1D706}_{\unicode[STIX]{x1D703}}$,$R_{U}$,$R_{\unicode[STIX]{x1D6E9}}$(all representing characteristic length scales), the mean temperature excess$\unicode[STIX]{x1D6E9}_{0}$, the mixed velocity–temperature moments$\overline{u\unicode[STIX]{x1D703}^{2}}$,$\overline{v\unicode[STIX]{x1D703}^{2}}$and$\overline{\unicode[STIX]{x1D703}^{2}}$and$\unicode[STIX]{x1D716}_{\unicode[STIX]{x1D703}}$. Simple models are proposed for$\overline{u\unicode[STIX]{x1D703}^{2}}$and$\overline{v\unicode[STIX]{x1D703}^{2}}$in order to derive an analytical expression for$A_{\unicode[STIX]{x1D716}_{\unicode[STIX]{x1D703}}}$, the prefactor of the power law describing the streamwise evolution of$\unicode[STIX]{x1D716}_{\unicode[STIX]{x1D703}}$. Further, expressions are also derived for the turbulent Péclet number and the thermal-to-mechanical time scale ratio. These expressions involve global parameters that are most likely to be influenced by the initial and/or boundary conditions and are therefore expected to be flow dependent.
Insulin-like growth factor I, binding proteins -1 and -3, risk of type 2 diabetes and macronutrient intakes in men
Authors: Similä Minna E. , Kontto Jukka P. , Virtamo Jarmo , Hätönen Katja A. , Valsta Liisa M. , Sundvall Jouko , Männistö Satu 
Published: March 2019

AbstractThe insulin-like growth factor (IGF) axis may be involved in the development of type 2 diabetes. We examined the associations of IGF-I and IGF binding proteins (IGFBP)-1 and -3 with diabetes risk and evaluated macronutrient intakes related to the observed associations. In a nested case–control study of the Alpha-Tocopherol, Beta-Carotene Cancer Prevention Study of Finnish male smokers aged 50–69 years, the IGF variables were measured from baseline serum samples for a random sample of 310 men with diabetes diagnosed during a 12-year follow-up and for 310 controls matched by age, recruitment day and intervention group. Diet at baseline was assessed using a validated FFQ. The associations of IGF proteins with diabetes risk were estimated using conditional logistic regression and the associations with macronutrient intakes using linear regression. IGF-I and IGFBP-3 were not associated with the incidence of diabetes. Higher IGFBP-1 was associated with lower diabetes risk in an unadjusted crude model (OR 0·25; 95 % CI 0·15, 0·42 in the highest quartile compared with the lowest), but not after adjustment for BMI (corresponding OR 0·76; 95 % CI 0·41, 1·40). Intakes of carbohydrates, plant protein and milk protein associated positively and intake of meat protein and fat negatively with IGFBP-1 (P<0·005). IGFBP-1 was inversely associated with diabetes risk, but the association was substantially dependent on BMI. The associations between macronutrient intakes and IGFBP-1 may reflect influences of nutrients or foods on insulin concentrations.
Universal properties for universal types in bifibrational parametricity
Authors: Ghani Neil , Forsberg Fredrik Nordvall , Orsanigo Federico 
Published: March 2019

AbstractIn the 1980s, John Reynolds postulated that a parametrically polymorphic function is an ad-hoc polymorphic function satisfying a uniformity principle. This allowed him to prove that his set-theoretic semantics has a relational lifting which satisfies the Identity Extension Lemma and the Abstraction Theorem. However, his definition (and subsequent variants) has only been given for specific models. In contrast, we give a model-independent axiomatic treatment by characterising Reynolds’ definition via a universal property, and show that the above results follow from this universal property in the axiomatic setting.
Fluorinated MOF platform for selective removal and sensing of SO2 from flue gas and air
Authors: Tchalala M. R. , Bhatt P. M. , Chappanda K. N. , Tavares S. R. , Adil K. , Belmabkhout Y. , Shkurenko A. , Cadiau A. , Heymans N. , De Weireld G. , Maurin G. , Salama K. N. , Eddaoudi M. 
Published: March 2019

AbstractConventional SO2 scrubbing agents, namely calcium oxide and zeolites, are often used to remove SO2 using a strong or irreversible adsorption-based process. However, adsorbents capable of sensing and selectively capturing this toxic molecule in a reversible manner, with in-depth understanding of structure–property relationships, have been rarely explored. Here we report the selective removal and sensing of SO2 using recently unveiled fluorinated metal–organic frameworks (MOFs). Mixed gas adsorption experiments were performed at low concentrations ranging from 250 p.p.m. to 7% of SO2. Direct mixed gas column breakthrough and/or column desorption experiments revealed an unprecedented SO2 affinity for KAUST-7 (NbOFFIVE-1-Ni) and KAUST-8 (AlFFIVE-1-Ni) MOFs. Furthermore, MOF-coated quartz crystal microbalance transducers were used to develop sensors with the ability to detect SO2 at low concentrations ranging from 25 to 500 p.p.m.
iRGD synergizes with PD-1 knockout immunotherapy by enhancing lymphocyte infiltration in gastric cancer
Authors: Ding Naiqing , Zou Zhengyun , Sha Huizi , Su Shu , Qian Hanqing , Meng Fanyan , Chen Fangjun , Du Shiyao , Zhou Shujuan , Chen Hong , Zhang Lianru , Yang Ju , Wei Jia , Liu Baorui 
Published: March 2019

AbstractPoor infiltration of activated lymphocytes into tumors represents a fundamental factor limiting the therapeutic effect of adoptive cell immunotherapy. A tumor-penetrating peptide, iRGD, has been widely used to deliver drugs into tumor tissues. In this study, we demonstrate for the first time that iRGD could also facilitate the infiltration of lymphocytes in both 3D tumor spheroids and several xenograft mouse models. In addition, combining iRGD modification with PD-1 knockout lymphocytes reveals a superior anti-tumor efficiency. Mechanistic studies demonstrate that the binding of iRGD to neuropilin-1 results in tyrosine phosphorylation of the endothelial barrier regulator VE-cadherin, which plays a role in the opening of endothelial cell contacts and the promotion of transendothelial lymphocyte migration. In summary, these results demonstrate that iRGD modification could promote tumor-specific lymphocyte infiltration, and thereby overcome the bottleneck associated with adoptive immune cell therapy in solid tumors.
Compressive three-dimensional super-resolution microscopy with speckle-saturated fluorescence excitation
Authors: Pascucci M. , Ganesan S. , Tripathi A. , Katz O. , Emiliani V. , Guillon M. 
Published: March 2019

AbstractNonlinear structured illumination microscopy (nSIM) is an effective approach for super-resolution wide-field fluorescence microscopy with a theoretically unlimited resolution. In nSIM, carefully designed, highly-contrasted illumination patterns are combined with the saturation of an optical transition to enable sub-diffraction imaging. While the technique proved useful for two-dimensional imaging, extending it to three-dimensions is challenging due to the fading of organic fluorophores under intense cycling conditions. Here, we present a compressed sensing approach that allows 3D sub-diffraction nSIM of cultured cells by saturating fluorescence excitation. Exploiting the natural orthogonality of speckles at different axial planes, 3D probing of the sample is achieved by a single two-dimensional scan. Fluorescence contrast under saturated excitation is ensured by the inherent high density of intensity minima associated with optical vortices in polarized speckle patterns. Compressed speckle microscopy is thus a simple approach that enables 3D super-resolved nSIM imaging with potentially considerably reduced acquisition time and photobleaching.
Using a Novel Transfer Learning Method for Designing Thin Film Solar Cells with Enhanced Quantum Efficiencies
Authors: Kaya Mine , Hajimirza Shima 
Published: March 2019

AbstractIn this study a new method for design optimization is proposed that is based on “transfer learning”. The proposed framework improves the accuracy and efficiency of surrogate-based optimization. A surrogate model is an approximation to a costly black-box function that can be used for more efficient search of optimal points. When design specifications change, the objective function changes too. Therefore, there is a need for a new surrogate model. However, the concept of transfer learning can be applied to refit the new surrogate more efficiently. In other words insights from previous experiences can be applied to learning and optimizing the new function. We use the proposed method in a particular problem pertaining to the design of “thin film multilayer solar cells”, where the goal is to maximize the external quantum efficiency of photoelectric conversion. The results show that the accuracy of the surrogate model is improved by 2–3 times using the transfer learning approach, using only half as many training data points as the original model. In addition, by transferring the design knowledge from one particular set of materials to another similar set of materials in the thin film structure, the surrogate-based optimization is improved, and is it obtained with far less computational time.
Novel genetic tools that enable highly pure protein production in Trichoderma reesei
Authors: Rantasalo Anssi , Vitikainen Marika , Paasikallio Toni , Jäntti Jussi , Landowski Christopher P. , Mojzita Dominik 
Published: March 2019

AbstractTrichoderma reesei is an established protein production host with high natural capacity to secrete enzymes. The lack of efficient genome engineering approaches and absence of robust constitutive gene expression systems limits exploitation of this organism in some protein production applications. Here we report engineering of T. reesei for high-level production of highly enriched lipase B of Candida antarctica (calB) using glucose as a carbon source. Multiplexed CRISPR/Cas9 in combination with the use of our recently established synthetic expression system (SES) enabled accelerated construction of strains, which produced high amounts of highly pure calB. Using SES, calB production levels in cellulase-inducing medium were comparable to the levels obtained by using the commonly employed inducible cbh1 promoter, where a wide spectrum of native enzymes were co-produced. Due to highly constitutive expression provided by the SES, it was possible to carry out the production in cellulase-repressing glucose medium leading to around 4 grams per liter of fully functional calB and simultaneous elimination of unwanted background enzymes.
Myc-driven chromatin accessibility regulates Cdc45 assembly into CMG helicases
Authors: Nepon-Sixt Brook S. , Bryant Victoria L. , Alexandrow Mark G. 
Published: March 2019

AbstractMyc-driven tumorigenesis involves a non-transcriptional role for Myc in over-activating replication origins. We show here that the mechanism underlying this process involves a direct role for Myc in activation of Cdc45-MCM-GINS (CMG) helicases at Myc-targeted sites. Myc induces decondensation of higher-order chromatin at targeted sites and is required for chromatin access at a chromosomal origin. Myc-driven chromatin accessibility promotes Cdc45/GINS recruitment to resident MCMs, and activation of CMGs. Myc-Box II, which is necessary for Myc-driven transformation, is required for Myc-induced chromatin accessibility, Cdc45/GINS recruitment, and replication stimulation. Myc interactors GCN5, Tip60, and TRRAP are essential for chromatin unfolding and recruitment of Cdc45, and co-expression of GCN5 or Tip60 with MBII-deficient Myc rescues these events and promotes CMG activation. Finally, Myc and Cdc45 interact and physiologic conditions for CMG assembly require the functions of Myc, MBII, and GCN5 for Cdc45 recruitment and initiation of DNA replication.
Soliton collision induced explosions in a mode-locked fibre laser
Authors: Peng Junsong , Zeng Heping 
Published: March 2019

AbstractSoliton explosion refers to a striking nonlinear dynamics in dissipative systems. In this state, a dissipative soliton collapses but returns back to its original state afterwards. Yet, the origin of such exotic soliton dynamics remains elusive. Here it is revealed that soliton collision can induce soliton explosions in a mode-locked fibre laser, benefiting from synchronous measurements of the spatio-temporal intensity evolution and the real-time spectra evolution using dispersive Fourier transform. Up to seven nonlinear regimes are observed successively in the laser by increasing the pump power only, including single-pulse mode locking, standard soliton explosions, noise-like mode locking, stable double pulsing, soliton collision induced explosions, soliton molecules, and double-pulse noise-like mode locking. These experimental findings are conducive to understand complex soliton dynamics in many nonlinear dissipative systems.
Carbon Nanomaterials in Hydrogenation Catalysis
Authors: Furimsky Edward 
Published: March 2019

Hydrogenation is a key reaction in both the food and petrochemical industries, where it is used to reduce carbon–carbon double bonds. Without a catalyst, hydrogenation reactions require extreme temperatures to occur, meaning catalysts are essential for the reaction to be industrially useful. During the past decade, the properties of many carbon nanomaterials that are relevant to hydrogenation catalysis have been described, including carbon nanotubes (CNTs), carbon nanofibers (CNFs), carbon nanohorns (CNHs), graphene oxide (GO), reduced graphene oxides (rGO) and fullerenes, that are relevant to hydrogenation catalysis, have been described. For many of these the production methods have advanced to the commercial stage. Numerous studies on the development of catalysts on carbon nano-supports have appeared in the scientific literature and these catalysts have shown remarkable activity and specificity.
Carbon Nanomaterials in Hydrogenation Catalysis is a valuable reference for researchers and chemical engineers working on improving hydrogenation processes and those interested in applications for carbon nanomaterials. Covering their production, modification and applications as a catalyst support this book provides an in-depth review of the current state-of-the art in using carbon nanomaterials for hydrogenation reactions.
Biochemical analysis of antimicrobial peptides in two different Capsicum genotypes after fruit infection by Colletotrichum gloeosporioides
Authors: Maracahipes Álan C. , Taveira Gabriel B. , Mello Erica O. , Carvalho André O. , Rodrigues Rosana , Perales Jonas , Teixeira-Ferreira André , Silva Marciele S. , Rocha Gustavo L. , Fernandes Kátia Valevski Sales , Gomes Valdirene M. 
Published: March 2019

Abstract
There are several phytosanitary problems that have been causing serious damage to the Capsicum crops, including anthracnose. Upon attack by certain pathogens, various protein molecules are produced, which are known as proteins related to pathogenesis (PR proteins), including antimicrobial peptides such as protease inhibitors, defensins and lipid transfer proteins (LTPs). The objective of this work is to identify antimicrobial proteins and/or peptides of two genotypes from Capsicum annuum fruits infected with Colletotrichum gloeosporioides. The fungus was inoculated into Capsicum fruits by the deposition of a spore suspension (106 conidia ml−1), and after 24 and 48 h intervals, the fruits were removed from the humid chamber and subjected to a protein extraction process. Protein analysis of the extracts was performed by tricine gel electrophoresis and Western blotting. The distinctive bands between genotypes in the electrophoresis profiles were subjected to mass spectrometry sequencing. Trypsin inhibition assays, reverse zymographic detection of protease inhibition and β-1,3-glucanase activity assays were also performed and extracts were also tested for their ability to inhibit the growth of C. gloeosporioides fungi ‘in vitro’. There were several low molecular weight proteins in all treated samples, and some treatments in which antimicrobial peptides such as defensin, lipid transfer protein (LTP) and protease inhibitor have been identified. It was shown that the green fruits are more responsive to infection, showing the production of antimicrobial peptides in response to injury and inoculation of the fungus, what did not occur in ripe fruits under any treatment.
Association between polymorphism in the promoter region of lncRNA GAS5 and the risk of colorectal cancer
Authors: Wang Yajie , Wu Shenshen , Yang Xi , Li Xiaobo , Chen Rui 
Published: March 2019

Abstract
The growth arrest special 5 (GAS5), as a research hotspot of long noncoding RNAs (lncRNAs), has been reported to be associated with colorectal cancer (CRC). However, the association between polymorphisms in GAS5 and the risk of CRC was not clear. In the present study, a case–control study in 1078 CRC patients and 1175 matched healthy controls was performed to evaluate the association between the potential functional genetic variants in GAS5 and the risk of CRC. PCR-TaqMan, qPCR, dual-luciferase assay, electrophoretic mobility shift assay (EMSA), flow cytometry, migration and invasion assays were performed to evaluate the function of polymorphism. Results showed that subjects carrying the rs55829688 CT/TT genotypes had a significantly higher risk of CRC when compared with the CC genotype. Further qPCR assay confirmed that the CRC tissues with rs55829688 CT/TT genotypes had a higher GAS5 mRNA expression level. The dual-luciferase assay, qPCR and EMSA assay revealed that rs55829688 T&gt;C polymorphism could decrease the expression level of GAS5 by impacting the binding ability of the transcription factor Yin Yang-1 (YY1) to the GAS5 promoter region. The expression of apoptosis-related proteins were detected by Western blot. Further, flow cytometry, migration, and invasion experiments showed that GAS5 repressed apoptosis and increased invasion and migration capability of CRC cells. Taken together, our findings provided evidence that the rs55829688 variant in the GAS5 promoter was associated with the risk of CRC and decreased expression of GAS5 by affecting the binding affinity of the transcription factors YY1 to GAS5.
Chromatin structures condensed by linker histones
Authors: Zhou Bing-Rui , Bai Yawen 
Published: March 2019

Abstract
In eukaryotic cells, genomic DNA exists in the form of chromatin through association with histone proteins, which consist of four core histone (H2A, H2B, H3, and H4) families and one linker histone (H1) family. The core histones bind to DNA to form the nucleosome, the recurring structural unit of chromatin. The linker histone binds to the nucleosome to form the next structural unit of chromatin, the chromatosome, which occurs dominantly in metazoans. Linker histones also play an essential role in condensing chromatin to form higher order structures. Unlike the core histones in the formation of the nucleosome, the role of linker histone in the formation of the chromatosome and high-order chromatin structure is not well understood. Nevertheless, exciting progress in the structural studies of chromatosomes and nucleosome arrays condensed by linker histones has been made in the last several years. In this mini-review, we discuss these recent experimental results and provide some perspectives for future studies.
One ring to bind them – Cohesin’s interaction with chromatin fibers
Authors: Moronta-Gines Macarena , van Staveren Thomas R.H. , Wendt Kerstin S. 
Published: March 2019

AbstractIn the nuclei of eukaryotic cells, the genetic information is organized at several levels. First, the DNA is wound around the histone proteins, to form a structure termed as chromatin fiber. This fiber is then arranged into chromatin loops that can cluster together and form higher order structures. This packaging of chromatin provides on one side compaction but also functional compartmentalization. The cohesin complex is a multifunctional ring-shaped multiprotein complex that organizes the chromatin fiber to establish functional domains important for transcriptional regulation, help with DNA damage repair, and ascertain stable inheritance of the genome during cell division. Our current model for cohesin function suggests that cohesin tethers chromatin strands by topologically entrapping them within its ring. To achieve this, cohesin’s association with chromatin needs to be very precisely regulated in timing and position on the chromatin strand. Here we will review the current insight in when and where cohesin associates with chromatin and which factors regulate this. Further, we will discuss the latest insights into where and how the cohesin ring opens to embrace chromatin and also the current knowledge about the ‘exit gates’ when cohesin is released from chromatin.