bluuebunny/crossref_metadata_2025_split huggingface dataset:
Transfer RNA Recognition and Aminoacylation by Synthetases
Authors: Giegé Richard , Eriani Gilbert 
Published: March 2021

AbstractFidelity of transfer ribonucleic acid (tRNA) charging by amino acids ensures correct translation of the genetic code into proteins. Charging is catalysed by a set of enzymes known as aminoacyl‐tRNA synthetases. Owing to the degeneracy of the genetic code, some of the different tRNAs have the same amino acids attached to them. Specificity of charging obeys universal rules and is ensured by positive elements, the identity determinants unique to each tRNA and responsible for its recognition by the cognate synthetase, and negative elements, the antideterminants that prevent false recognitions. To fulfil the aminoacylation specificity and prevent noncognate aminoacyl‐tRNA delivery to the ribosome, some synthetases also mediate proofreading reactions that increase fidelity of the tRNA charging. In such reactions, misactivated amino acids or mischarged tRNAs are checked in specific sites, and noncognate products are hydrolysed. However, mischarging is beneficial under certain stress circumstances or when catalysed by nondiscriminatory synthetases and represents a driving force in evolution.Key ConceptsTranslational expression of the genetic code refers to aminoacyl‐tRNA‐ and ribosome‐dependent decoding of genes into proteins, a process highly dependent on fidelity of tRNA aminoacylation by synthetases.The rules that account for the aminoacylation identity of tRNAs are referred to as the second genetic code.The RNA operational code is encoded in the acceptor stem of tRNA and is crucial for recognition by aminoacyl‐tRNA synthetases and specific aminoacylation.Allostery in tRNA–synthetase systems concerns long‐range transfer of chemical information (up to 75 Å) to the synthetase catalytic site (through the body of tRNA and/or synthetase) triggered by contacts of tRNA identity determinants with the synthetase.Engineering the identity of tRNA–synthetase systems allows reprogramming the genetic code.
Sauria (Lizards)
Authors: Benton Michael J 
Published: March 2021

AbstractLizards are generally small fast‐moving four‐legged slender terrestrial animals. The group of 6880 species of lizards, however, contains some exceptions: the large predatory Komodo dragon, the marine Galapagos iguana, the glidingDraco, various limbless forms and burrowers.Key ConceptsLizards are a large part of the Squamata, the clade comprising lizards, snakes and amphisbaenians.There are some 6880 species of lizards today.Lizards range in size from tiny geckos and chameleons only 2–3‐cm long to the Komodo monitor up to 2.6‐m long.Lizards have kinetic skulls with three extra joints, so they can open their mouth extra wide while feeding.Squamates fall into six major groups – the geckos, skinks, iguanas, anguimorphs (anguids, varanids), amphisbaenians and snakes.Lizards are all ectothermic, controlling their body temperatures by behavioural means.Lizards live mainly in tropical areas.The fossil history of lizards shows that they evolved in the Triassic and became more diverse in the Jurassic and Cretaceous. The Late Cretaceous mosasaurs were the largest lizards of all, marine predators that reached 3–10 m in length.
Evolutionary Ideas: The Eclipse of Darwinism
Authors: Bowler Peter J 
Published: March 2021

AbstractFollowing the acceptance of evolutionism, biologists tried – with limited success – to reconstruct the history of life on Earth and also debated the mechanism of evolution. Many alternatives to Darwinian natural selection were tried out, including a revived version of Lamarck's theory of the inheritance of acquired characters and evolution by saltations (which paved the way for Mendelian genetics).
Rhodosalinus
Authors: Guo Ling‐Yun , Du Zong‐Jun 
Published: March 2021

Abstract

Rho.do.sa.li'nus. Gr. neut. n.
rhodon
, the rose; L. masc. adj.
salinus
, saline; N.L. masc. n.
Rhodosalinus
, the red‐colored bacterium isolated from saline.

Proteobacteria / Alphaproteobacteria / Rhodobacterales / Rhodobacteraceae / Rhodosalinus

The genus
Rhodosalinus
contains moderately halophilic, facultatively anaerobic, and mesophilic bacteria. It currently includes two species,
Rhodosalinus sediminis
and
Rhodosalinus halophilus
, both isolated from marine salterns. Cells are Gram‐stain‐negative, motile, non‐spore‐forming, and rod shaped. Colonies of
Rhodosalinus
are circular and red or beige. The genomes of the
Rhodosalinus
species have a high G + C content, from 69.8% (genome sequencing) to 70.9% (HPLC). The sole respiratory ubiquinone is Q‐10. The major polar lipid profile contains phosphatidylglycerol, unidentified glycolipid, unidentified lipids, and unidentified phospholipids. The major fatty acids are C
18:1
ω7
c
, cyclo C
19:0
ω8
c
, and C
18:0
.

DNA G + C content (mol%)
: 69.8–70.9.

Type species
:
Rhodosalinus sediminis
Guo et al. 2017
VP
.
Eggerthellales
Authors: Gupta Radhey S. 
Published: March 2021

Abstract

Eg.ger.thel.la'les. N.L. fem. n.
Eggerthella
, type genus of the order; suff. ‐
ales
, ending to denote an order; N.L. fem. pl. n.
Eggerthellales
, the order of
Eggerthella
.

Actinobacteria / Coriobacteriia / Eggerthellales

The order contains the family
Eggerthellaceae
. The characteristics of this order are the same as that of the family
Eggerthellaceae
. The species of this order form a distinct clade in phylogenetic trees based on the concatenated sequences of different datasets of proteins. Additionally, the members of this order can be reliably distinguished from those of the order
Coriobacteriales
and other
Actinobacteria
, based on multiple molecular markers in the forms of conserved signature inserts/deletions in proteins that are exclusively present in the members of this order.

Type genus
:
Eggerthella
Wade et al. 1999
VP
.
On the reduction of aperture complexity in kidney SABR
Authors: Gaudreault Mathieu , Offer Keith , Kron Tomas , Siva Shankar , Hardcastle Nicholas 
Published: March 2021

AbstractBackgroundStereotactic ablative body radiotherapy (SABR) of primary kidney cancers is confounded by motion. There is a risk of interplay effect if the dose is delivered using volumetric modulated arc therapy (VMAT) and flattening filter‐free (FFF) dose rates due to target and linac motion. This study aims to provide an efficient way to generate plans with minimal aperture complexity.MethodsIn this retrospective study, 62 patients who received kidney SABR were reviewed. For each patient, two plans were created using internal target volume based motion management, on the average intensity projection of a four‐dimensional CT. In the first plan, optimization was performed using a knowledge‐based planning model based on delivered clinical plans in our institution. In the second plan, the optimization was repeated, with a maximum monitor unit (MU) objective applied in the optimization. Dose‐volume, conformity, and complexity metric (with the field edge metric and the modulation complexity score) were compared between the two plans. Results are shown in terms of median (first quartile — third quartile).ResultsSimilar dosimetry was obtained with and without the utilization of an objective on the MU. However, complexity was reduced by using the objective on the MUs (modulation complexity score = 0.55 (0.50–0.61) / 0.33 (0.29–0.36), P‐value < 10−10, with/without the MU objective). Reduction of complexity was driven by a larger aperture area (area aperture variability = 0.68 (0.64–0.73) / 0.42 (0.37–0.45), P‐value < 10−10, with/without the MU objective). Using the objective on the MUs resulted in a more spherical dose distribution (sphericity 50% isodose = 0.73 (0.69–0.75) / 0.64 (0.60–0.68), P‐value < 10−8, with/without the MU objective) reducing dose to organs at risk given respiratory motion.ConclusionsAperture complexity is reduced in kidney SABR by using an objective on the MU delivery with VMAT and FFF dose rate.
Commissioning cranial single‐isocenter multi‐target radiosurgery for the Versa HD
Authors: Knill Cory , Sandhu Raminder , Halford Robert , Snyder Michael , Seymour Zachary 
Published: March 2021

AbstractPurposeBrainlab’s Elements Multiple Brain Mets SRS (MBMS) is a dedicated treatment planning system for single‐isocenter multi‐target (SIMT) cranial stereotactic radiosurgery (SRS) treatments. The purpose of this study is to present the commissioning experience of MBMS on an Elekta Versa HD.MethodsMBMS was commissioned for 6 X, 6 FFF, and 10 FFF. Beam data collected included: output factors, percent depth doses (PDDs), diagonal profiles, collimator transmission, and penumbra. Beam data were processed by Brainlab and resulting parameters were entered into the planning system to generate the beam model. Beam model accuracy was verified for simple fields. MBMS plans were created on previously treated cranial SRS patient data sets. Plans were evaluated using Paddick inverse conformity (ICI), gradient indices (GI), and cumulative volume of brain receiving 12 Gy. Dosimetric accuracy of the MBMS plans was verified using microDiamond, Gafchromic film, and SRS Mapcheck measurements of absolute dose and dose profiles for individual targets. Finally, an end‐to‐end (E2E) test was performed with a MR‐CT compatible phantom to validate the accuracy of the simulation‐to‐delivery process.ResultsFor square fields, calculated scatter factors were within 1.0% of measured, PDDs were within 0.5% past dmax, and diagonal profiles were within 0.5% for clinically relevant off‐axis distances (<10 cm). MBMS produced plans with ICIs < 1.5 and GIs < 5.0 for targets > 10 mm. Average point doses of the MBMS plans, measured by microDiamond, were within 0.31% of calculated (max 2.84%). Average per‐field planar pass rates were 98.0% (95.5% minimum) using a 2%/1 mm/10% threshold relative gamma analysis. E2E point dose measurements were within 1.5% of calculated and Gafchromic film pass rates were 99.6% using a 5%/1 mm/10% threshold gamma analysis.ConclusionThe experience presented can be used to aid the commissioning of the Versa HD in the Brainlab MBMS treatment planning system, to produce safe and accurate SIMT cranial SRS treatments.
Interfacial Curvature in Confined Coculture Directs Stromal Cell Activity with Spatial Corralling of Pancreatic Cancer Cells
Authors: Nemec Stephanie , Lam Joey , Zhong Jingxiao , Heu Celine , Timpson Paul , Li Qing , Youkhana Janet , Sharbeen George , Phillips Phoebe A. , Kilian Kristopher A. 
Published: March 2021

AbstractInterfacial cues in the tumor microenvironment direct the activity and assembly of multiple cell types. Pancreatic cancer, along with breast and prostate cancers, is enriched with cancer‐associated fibroblasts (CAFs) that activate to coordinate the deposition of the extracellular matrix, which can comprise over 90% of the tumor mass. While it is clear that matrix underlies the severity of the disease, the relationship between stromal‐tumor cell assembly and cell‐matrix dynamics remains elusive. Micropatterned hydrogels deconstruct the interplay between matrix stiffness and geometric confinement, guiding heterotypic cell populations and matrix assembly in pancreatic cancer. Interfacial cues at the perimeter of microislands guide CAF migration and direct cancer cell assembly. Computational modeling shows curvature‐stress dependent cellular localization for cancer and CAFs in coculture. Regions of convex curvature enhance edge stress that activates a myofibroblast phenotype in the CAFs with migration and increased collagen I deposition, ultimately leading to a central “corralling” of cancer cells. Inhibiting mechanotransduction pathways decreases CAF activation and the associated corralling phenotype. Together, this work reveals how interfacial biophysical cues underpin aspects of stromal desmoplasia, a hallmark of disease severity and chemoresistance in the pancreatic, breast, and prostate cancers, thereby providing a tool to expand stroma‐targeting therapeutic strategies.
Tunable White Light Emission in a Zero‐Dimensional Organic–Inorganic Metal Halide Hybrid with Ultra‐High Color Rendering Index
Authors: Song Gaomin , Li Zhongyuan , Gong Pifu , Xie Rong‐Jun , Lin Zheshuai 
Published: March 2021

AbstractOrganic–inorganic metal halide hybrids (OIMHs) with broadband white light (WL) emission are considered as a new type of rare‐earth‐free phosphors. Herein, eco‐friendly and stable Sn(IV) is selected as the B‐site inorganic cation to synthesize a 0D lead‐free OIMH (C5N2H14)SnCl6, in which the isolated [SnCl6]2− octahedra are separated by large organic [C5N2H14]2+ cations. Under different excitations, this compound exhibits warm white emission with a tunable color rendering index (CRI) from 80 to 97, the highest value among all known OIMHs, owing to the synergistic effect of [C5N2H14]2+ and [SnCl6]2− octahedra. This work presents a new strategy toward the WL materials with ultra‐high CRI by co‐regulating organic cations and inorganic polyhedra.
A murine model of tuberculosis/type 2 diabetes comorbidity for investigating the microbiome, metabolome and associated immune parameters
Authors: Sathkumara Harindra D. , Eaton Janet L. , Field Matt A. , Govan Brenda L. , Ketheesan Natkunam , Kupz Andreas 
Published: March 2021

AbstractTuberculosis (TB) is one of the deadliest infectious diseases in the world. The metabolic disease type 2 diabetes (T2D) significantly increases the risk of developing active TB. Effective new TB vaccine candidates and novel therapeutic interventions are required to meet the challenges of global TB eradication. Recent evidence suggests that the microbiota plays a significant role in how the host responds to infection, injury and neoplastic changes. Animal models that closely reflect human physiology are crucial in assessing new treatments and to decipher the underlying immunological defects responsible for increased TB susceptibility in comorbid patients. In this study, using a diet‐induced murine T2D model that reflects the etiopathogenesis of clinical T2D and increased TB susceptibility, we investigated how the intestinal microbiota may impact the development of T2D, and how the gut microbial composition changes following a very low‐dose aerosol infection with Mycobacterium tuberculosis (Mtb). Our data revealed a substantial intestinal microbiota dysbiosis in T2D mice compared to non‐diabetic animals. The observed differences were comparable to previous clinical reports in TB patients, in which it was shown that Mtb infection causes rapid loss of microbial diversity. Furthermore, diversity index and principle component analyses demonstrated distinct clustering of Mtb‐infected non‐diabetic mice vs. Mtb‐infected T2D mice. Our findings support a broad applicability of T2D mice as a tractable small animal model for studying distinct immune parameters, microbiota and the immune‐metabolome of TB/T2D comorbidity. This model may also enable answers to be found to critical outstanding questions about targeted interventions of the gut microbiota and the gut‐lung axis.
High‐Performance Porous Ionic Liquids for Low‐Pressure CO2 Capture**
Authors: Avila Jocasta , Lepre L. Fernando , Santini Catherine C. , Tiano Martin , Denis‐Quanquin Sandrine , Chung Szeto Kai , Padua Agilio A. H. , Costa Gomes Margarida 
Published: March 2021

AbstractPorous ionic liquids are non‐volatile, versatile materials that associate porosity and fluidity. New porous ionic liquids, based on the ZIF‐8 metal–organic framework and on phosphonium acetate or levulinate salts, were prepared and show an increased capacity to absorb carbon dioxide at low pressures. Porous suspensions based on phosphonium levulinate ionic liquid absorb reversibly 103 % more carbon dioxide per mass than pure ZIF‐8 at 1 bar and 303 K. We show how the rational combination of MOFs with ionic liquids can greatly enhance low pressure CO2 absorption, paving the way towards a new generation of high‐performance, readily available liquid materials for effective low pressure carbon capture.
A Covalent Organic Framework Film for Three‐State Near‐Infrared Electrochromism and a Molecular Logic Gate
Authors: Hao Qing , Li Zhi‐Juan , Bai Bin , Zhang Xing , Zhong Yu‐Wu , Wan Li‐Jun , Wang Dong 
Published: March 2021

AbstractA Kagome structure covalent organic framework (COF) film with three‐state NIR electrochromic properties was designed and synthesized. The COFTPDA‐PDA film is composed of hexagonal nanosheets with high crystallinity and has three reversible color states at different applied potentials. It has high absorption spectra changes in the NIR region, ascribed to the strong intervalence charge transfer (IVCT) interaction of the Class III mixed‐valence systems of the conjugated triphenylamine species. The film showed sub‐second response time (1.3 s for coloring and 0.7 s for bleaching at 1050 nm) and long retention time in the NIR region. COFTPDA‐PDA film shows superior NIR electrochromic properties in term of response time and stability, attributed to the highly ordered porous structure and the π–π stacking structure of the COFTPDA‐PDA architecture. The COFTPDA‐PDA film was applied in mimicking a flip‐flop logic gate with optical memory function.
Interfering with Metabolic Profile of Triple‐Negative Breast Cancers Using Rationally Designed Metformin Prodrugs
Authors: Babak Maria V. , Chong Kai Ren , Rapta Peter , Zannikou Markella , Tang Hui Min , Reichert Lisa , Chang Meng Rui , Kushnarev Vladimir , Heffeter Petra , Meier‐Menches Samuel M. , Lim Zhi Chiaw , Yap Jian Yu , Casini Angela , Balyasnikova Irina V. , Ang Wee Han 
Published: March 2021

AbstractTriple‐negative breast cancer (TNBC) is the most aggressive subtype of breast cancer, characterized by an aberrant metabolic phenotype with high metastatic capacity, resulting in poor patient prognoses and low survival rates. We designed a series of novel AuIIIcyclometalated prodrugs of energy‐disrupting Type II antidiabetic drugs namely, metformin and phenformin. Prodrug activation and release of the metformin ligand was achieved by tuning the cyclometalated AuIIIfragment. The lead complex3metwas 6000‐fold more cytotoxic compared to uncoordinated metformin and significantly reduced tumor burden in mice with aggressive breast cancers with lymphocytic infiltration into tumor tissues. These effects was ascribed to3metinterfering with energy production in TNBCs and inhibiting associated pro‐survival responses to induce deadly metabolic catastrophe.
Assembly of a Metal–Organic Framework (MOF) Membrane on a Solid Electrocatalyst: Introducing Molecular‐Level Control Over Heterogeneous CO2 Reduction
Authors: Mukhopadhyay Subhabrata , Shimoni Ran , Liberman Itamar , Ifraemov Raya , Rozenberg Illya , Hod Idan 
Published: March 2021

AbstractElectrochemically active Metal‐Organic Frameworks (MOFs) have been progressively recognized for their use in solar fuel production schemes. Typically, they are utilized as platforms for heterogeneous tethering of exceptionally large concentration of molecular electrocatalysts onto electrodes. Yet so far, the potential influence of their extraordinary chemical modularity on electrocatalysis has been overlooked. Herein, we demonstrate that, when assembled on a solid Ag CO2 reduction electrocatalyst, a non‐catalytic UiO‐66 MOF acts as a porous membrane that systematically tunes the active site's immediate chemical environment, leading to a drastic enhancement of electrocatalytic activity and selectivity. Electrochemical analysis shows that the MOF membrane improves catalytic performance through physical and electrostatic regulation of reactants delivery towards the catalytic sites. The MOF also stabilizes catalytic intermediates via modulation of active site's secondary coordination sphere. This concept can be expanded to a wide range of proton‐coupled electrochemical reactions, providing new means for precise, molecular‐level manipulation of heterogeneous solar fuels systems.
Chemical Strategies for Making Strong Graphene Materials
Authors: Zhou Tianzhu , Cheng Qunfeng 
Published: March 2021

AbstractGraphene materials have been widely applied in various fields because of their remarkable mechanical and electrical properties. However, two obstacles arise during the assembly of graphene platelets into macroscale graphene materials and composites that impair the performance of the resultant graphene materials: 1) the voids between the graphene platelets, and 2) the wrinkling of the graphene platelets. In the past decade, several strategies have been developed to eliminate these obstacles. These strategies result in strong macroscale graphene materials, such as graphene fibers with tensile strengths of over 3.4 GPa and sheets with tensile strengths of over 1.5 GPa, which have many practical applications. This Minireview summarizes the effective strategies for assembling graphene materials and compares their advantages and drawbacks. The preparation processes as well as the resulting fundamental mechanical properties and wide spectrum of electrical and magnetic properties are also discussed. Finally, our outlook for the future of this field is presented.
Maternal ethnicity and the prevalence of British pregnancies affected by neural tube defects
Authors: Peake Jordana N. , Knowles Rachel L. , Shawe Jill , Rankin Judith , Copp Andrew J. 
Published: March 2021

AbstractBackgroundFew data are available on the prevalence of neural tube defects (NTDs) within different ethnic communities of the United Kingdom. This study aimed to calculate prevalence estimates for NTD‐affected pregnancies, classified by maternal ethnicity, and to explore why variations in prevalence might exist.MethodsA cross‐sectional study was performed with data from regional congenital anomaly registers in England and Wales, for NTD‐affected pregnancies between 2006 and 2011. Using binomial regression models, we examined NTD‐affected pregnancy prevalence estimates and rate ratios (PRRs), by maternal ethnicity.ResultsThe prevalence of NTDs was 12.14 per 10,000 births, with no differences between study years. Anencephaly, encephalocele and spina bifida occurred at 4.98, 1.37 and 5.80 per 10,000 births respectively. Mothers of Indian ethnicity were 1.84 times more likely (95% CI: 1.24, 2.73) and Bangladeshi mothers 2.86 times more likely (95% CI: 1.48, 5.53) than White mothers to have an NTD‐affected pregnancy, after adjusting for maternal deprivation and maternal age. The excess prevalence in Indian mothers was specifically for anencephaly (PRR 2.57; 95% CI: 1.52, 4.34), and in Bangladeshi mothers the trend was for increased spina bifida (PRR 3.86; 95% CI: 0.72, 8.69). Anencephaly in Indian mothers was especially associated with other congenital anomalies (non‐isolated NTDs).ConclusionsDifferent British ethnic groups vary in NTD prevalence. The excess prevalence of anencephaly as a non‐isolated NTD in pregnancies of Indian mothers could indicate involvement of genetic or other unmeasured behavioral factors. Future work is needed to seek etiological explanations for the ethnicity differences and to develop improved methods for primary prevention.