bluuebunny/crossref_metadata_2025_split huggingface dataset:
Reference gene selection for qRT-PCR analysis of season- and tissue-specific gene expression profiles in the honey bee Apis mellifera
Authors: Jeon Ji Hyang , Moon KyungHwan , Kim YeongHo , Kim Young Ho 
Published: August 2020

AbstractHoney bees are both important pollinators and model insects due to their highly developed sociality and colony management. To better understand the molecular mechanisms underlying honey bee colony management, it is important to investigate the expression of genes putatively involved in colony physiology. Although quantitative real-time PCR (qRT-PCR) can be used to quantify the relative expression of target genes, internal reference genes (which are stably expressed across different conditions) must first be identified to ensure accurate normalisation of target genes. To identify reliable reference genes in honey bee (Apis mellifera) colonies, therefore, we evaluated seven candidate genes (ACT, EIF, EF1, RPN2, RPS5, RPS18 and GAPDH) in samples collected from three honey bee tissue types (head, thorax and abdomen) across all four seasons using three analysis programmes (NormFinder, BestKeeper and geNorm). Subsequently, we validated various normalisation methods using each of the seven reference genes and a combination of multiple genes by calculating the expression of catalase (CAT). Although the genes ranked as the most stable gene were slightly different on conditions and analysis methods, our results suggest that RPS5, RPS18 and GAPDH represent optimal honey bee reference genes for target gene normalisation in qRT-PCR analysis of various honey bee tissue samples collected across seasons.
Thermodynamic efficiency, reversibility, and degree of coupling in energy conservation by the mitochondrial respiratory chain
Authors: Wikström Mårten , Springett Roger 
Published: August 2020

AbstractThe protonmotive mitochondrial respiratory chain, comprising complexes I, III and IV, transduces free energy of the electron transfer reactions to an electrochemical proton gradient across the inner mitochondrial membrane. This gradient is used to drive synthesis of ATP and ion and metabolite transport. The efficiency of energy conversion is of interest from a physiological point of view, since the energy transduction mechanisms differ fundamentally between the three complexes. Here, we have chosen actively phosphorylating mitochondria as the focus of analysis. For all three complexes we find that the thermodynamic efficiency is about 80–90% and that the degree of coupling between the redox and proton translocation reactions is very high during active ATP synthesis. However, when net ATP synthesis stops at a high ATP/ADP.Pi ratio, and mitochondria reach “State 4” with an elevated proton gradient, the degree of coupling drops substantially. The mechanistic cause and the physiological implications of this effect are discussed.
Mechanistic study of superlattice-enabled high toughness and hardness in MoN/TaN coatings
Authors: Hahn Rainer , Koutná Nikola , Wójcik Tomasz , Davydok Anton , Kolozsvári Szilárd , Krywka Christina , Holec David , Bartosik Matthias , Mayrhofer Paul H. 
Published: August 2020

AbstractMachining and forming tools exposed to challenging environments require protective coatings to extend their lifetime and reliability. Although transition metal nitrides possess excellent strength and resistance against chemical attacks, they lack ductility and are prone to premature failure. Here, by investigating structural and mechanical properties of MoN-TaN superlattices with different bilayer thickness, we develop coatings with high fracture toughness and hardness, stemming from the formation of a metastable tetragonally distorted phase of TaN up to layer thicknesses of 2.5 nm. Density functional theory calculations and experimental results further reveal a metal-vacancy stabilized cubic Ta0.75N phase with an increased Young’s modulus but significantly lower fracture toughness. We further discuss the influence of coherency strains on the fracture properties of superlattice thin films. The close interplay between our experimental and ab initio data demonstrates the impact of phase formation and stabilization on the mechanical properties of MoN-TaN superlattices.
Emerging roles for the IL-6 family of cytokines in pancreatic cancer
Authors: van Duijneveldt Gemma , Griffin Michael D.W. , Putoczki Tracy L. 
Published: August 2020

AbstractPancreatic cancer has one of the poorest prognoses of all malignancies, with little improvement in clinical outcome over the past 40 years. Pancreatic ductal adenocarcinoma is responsible for the vast majority of pancreatic cancer cases, and is characterised by the presence of a dense stroma that impacts therapeutic efficacy and drives pro-tumorigenic programs. More specifically, the inflammatory nature of the tumour microenvironment is thought to underlie the loss of anti-tumour immunity and development of resistance to current treatments. Inflammatory pathways are largely mediated by the expression of, and signalling through, cytokines, chemokines, and other cellular messengers. In recent years, there has been much attention focused on dual targeting of cancer cells and the tumour microenvironment. Here we review our current understanding of the role of IL-6, and the broader IL-6 cytokine family, in pancreatic cancer, including their contribution to pancreatic inflammation and various roles in pancreatic cancer pathogenesis. We also summarise potential opportunities for therapeutic targeting of these pathways as an avenue towards combating poor patient outcomes.
Making it or breaking it: DNA methylation and genome integrity
Authors: Sriraman Anusha , Debnath Turja K. , Xhemalce Blerta , Miller Kyle M. 
Published: August 2020

Abstract
Cells encounter a multitude of external and internal stress-causing agents that can ultimately lead to DNA damage, mutations and disease. A cascade of signaling events counters these challenges to DNA, which is termed as the DNA damage response (DDR). The DDR preserves genome integrity by engaging appropriate repair pathways, while also coordinating cell cycle and/or apoptotic responses. Although many of the protein components in the DDR are identified, how chemical modifications to DNA impact the DDR is poorly understood. This review focuses on our current understanding of DNA methylation in maintaining genome integrity in mammalian cells. DNA methylation is a reversible epigenetic mark, which has been implicated in DNA damage signaling, repair and replication. Sites of DNA methylation can trigger mutations, which are drivers of human diseases including cancer. Indeed, alterations in DNA methylation are associated with increased susceptibility to tumorigenesis but whether this occurs through effects on the DDR, transcriptional responses or both is not entirely clear. Here, we also highlight epigenetic drugs currently in use as therapeutics that target DNA methylation pathways and discuss their effects in the context of the DDR. Finally, we pose unanswered questions regarding the interplay between DNA methylation, transcription and the DDR, positing the potential coordinated efforts of these pathways in genome integrity. While the impact of DNA methylation on gene regulation is widely understood, how this modification contributes to genome instability and mutations, either directly or indirectly, and the potential therapeutic opportunities in targeting DNA methylation pathways in cancer remain active areas of investigation.
The Shikani HME: A New Tracheostomy Heat and Moisture Exchanger
Authors: Shikani Alan H. , Elamin Elamin M. , Miller Andrew C. 
Published: August 2020

Purpose

Tracheostomy patients face many adversities including loss of phonation and essential airway functions including air filtering, warming, and humidification. Heat and moisture exchangers (HMEs) facilitate humidification and filtering of inspired air. The Shikani HME (S-HME) is a novel turbulent airflow HME that may be used in-line with the Shikani Speaking Valve (SSV), allowing for uniquely preserved phonation during humidification. The aims of this study were to (a) compare the airflow resistance (
R
airflow
) and humidification efficiency of the S-HME and the Mallinckrodt Tracheolife II tracheostomy HME (M-HME) when dry (time zero) and wet (after 24 hr) and (b) determine if in-line application of the S-HME with a tracheostomy speaking valve significantly increases
R
airflow
over a tracheostomy speaking valve alone (whether SSV or Passy Muir Valve [PMV]).

Method

A prospective observational ex vivo study was conducted using a pneumotachometer lung simulation unit to measure airflow (
Q
) amplitude and
R
airflow
, as indicated by a pressure drop (
P
Drop
) across the device (S-HME, M-HME, SSV + S-HME, and PMV). Additionally,
P
Drop
was studied for the S-HME and M-HME when dry at time zero (T
0
) and after 24 hr of moisture testing (T
24
) at
Q
of 0.5, 1, and 1.5 L/s.

Results

R
airflow
was significantly less for the S-HME than M-HME (T
0
and T
24
).
R
airflow
of the SSV + S-HME in series did not significant increase
R
airflow
over the SSV or PMV alone. Moisture loss efficiency trended toward greater efficiency for the S-HME; however, the difference was not statistically significant.

Conclusions
The turbulent flow S-HME provides heat and moisture exchange with similar or greater efficacy than the widely used laminar airflow M-HME, but with significantly lower resistance. The S-HME also allows the innovative advantage of in-line use with the SSV, hence allowing concurrent humidification and phonation during application, without having to manipulate either device.
Induction motor fault detection based on multi‐sensory control and wavelet analysis
Authors: Abubakar Ukashatu , Mekhilef Saad , Gaeid Khalaf S. , Mokhlis Hazlie , Al Mashhadany Yousif I. 
Published: August 2020

Detection and fault‐tolerant control (FTC) of faults in the early stage is desirable in improving efficiency. An implementation strategy is proposed for the individual controllers that work collectively in induction motor (IM) drive by interswitching from one form of a control strategy to another. The interswitching occurs between voltage by frequency (V/f) open‐loop control, closed‐loop (V/f) control, sensorless vector control and sensor vector control. Optimal performance capabilities are attained with vector control, whereas V/f is a setup that is affordable but with increased speed. In this study, the faults are open and short circuits winding faults, speed sensor failures and stator winding faults. When the severity of the fault is high, an embedded protection entity interrupts the motor. Daubechies 10 wavelet is used due to its significant vanishing moments compared to the other types of Daubechies as fault index with the stator current of 1 kW IM. A novel enhanced model reference adaptive system is employed for sensorless vector control to assess the motor speed. Both the simulation and experiment (using the F28335 DSP controller) indicate that the framework is effective in detecting the fault, ensuring the robustness of the FTC scheme and proving the effectiveness of the proposed algorithm.
Den Umherschweifenden behandeln
Authors: Corts Magga 
Published: August 2020

SummaryDer Nervus (N.) vagus ist der längste Hirnnerv und reicht vom Gehirn bis zur linken Colonflexur. Grundsätzlich ist der N. vagus für einen ausgeglichenen Gemütszustand wichtig; er fördert Regeneration, Wachstum, Erholung und Ruhezustand. Verschiedene Behandlungstechniken ermöglichen, dass der N. vagus aktiviert oder Engpässe mobilisiert werden.
Regio- and Stereoselectivity in the 1,3-Dipolar Cycloaddition Reactions of Isoquinolinium Ylides with Cyclopenta[a]acenaphthylen-8-ones
Authors: Yavari Issa , Ravaghi Parisa , Safaei Maryam , Kayanian Jasmine 
Published: August 2020

AbstractA convenient regio- and diastereoselective synthesis of functionalized 5a,5b-dihydro-5H,13H-naphtho[1′′,8′′:4′,5′,6′]pentaleno[1′:3,4]pyrrolo[2,1-a]isoquinolin-5-ones via 1,3-dipolar cycloaddition reaction of 8H-cyclopenta[a]acenaphthylen-8-ones with carbonyl-stabilized isoquinolinium N-ylides, is described. Based on DFT calculations at b3lyp/6-311+g(d,p) level of theory, a nonconcerted mechanism is proposed to explain the regioselectivity of this reaction. The structure of a typical product was confirmed by X-ray crystallographic analysis.
Visible-Light-Mediated Photoredox Reactions in the Total Synthesis of Natural Products
Authors: Cordero-Vargas Alejandro , Mateus-Ruiz Jeferson B. 
Published: August 2020

In the last two decades, the field of photoredox catalysis (PRC) has grown impressively with reports of new synthetic methodologies and more efficient versions of known free-radical reactions. The impressive success of visible-light-mediated photoredox catalysis is, in great part, due to its low environmental impact, mild reaction conditions, clean reactions, and inexpensive methodologies. These features have allowed photoredox catalysis to emerge as a powerful tool in the synthesis of natural products; much excellent work was reported between 2011 and 2015. Since 2016, a number of more efficient and impressive total syntheses of natural products featuring photoredox catalysis have been reported. In this review, we summarize the recent synthetic applications of photoredox catalysis in the total synthesis of natural products between 2016 and 2020.1 Introduction2 Intermolecular Additions from Functionalized Substrates2.1 Intermolecular Additions from Alkyl Halides2.2 Intermolecular Additions from Alcohols and Carboxylic Acids3 Cyclizations from Functionalized Substrates3.1 Cyclizations of Carbon-Centered Radicals3.2 Cyclizations of Nitrogen-Centered Radicals4 Intramolecular Cyclization from Non-functionalized N–H Bonds4.1 Type I Radical Cascade4.2 Type II Radical Cascade4.3 Type III Radical Cascade5 Functionalization of Imines and Enamines6 Cycloadditions7 Miscellaneous7.1 Dehalogenation and Reductive Decarboxylation7.2 Thiyl Radical Promoted Cascade8 Conclusions and Perspectives
Adventures and Detours in the Synthesis of Hydropentalenes
Authors: Laschat Sabine , Deimling Max , Zens Anna , Park Natja , Hess Christine , Klenk Simon , Dilruba Zarfishan , Baro Angelika 
Published: August 2020

Functionalized hydropentalenes (i.e., bicyclo[3.3.0]octanones) constitute important building blocks for natural products and for ligands for asymmetric catalysis. The assembly and tailored functionalization of this convex roof-shaped scaffold is challenging and has motivated a variety of synthetic approaches including our own contributions, which will be presented in this account.1	Introduction2	Biosynthesis of Hydropentalenes3	Hydropentalenes through the Pauson–Khand Reaction4	Hydropentalenes through Transannular Oxidative Cyclization of Cycloocta-1,4-diene5	Functionalization of Bicyclo[3.3.0]octan-1,4-dione to Dodecahydrocyclopenta[a]indenes6	Functionalization of Bicyclo[3.3.0]octan-1,4-diones to Crown Ether Hybrids7	Functionalization of Bicyclo[3.3.0]octan-1,4-dione to Cylindramide8	Tandem Ring-Opening Metathesis/Ring-Closing Metathesis/Cross-Metathesis of Bicyclo[2.2.1]heptanes9	Functionalization of Bicyclo[3.3.0]octan-1,4-dione to Geodin A10	Hydropentalenes through Enantioselective Desymmetrization of Weiss Diketones11	Functionalization of Weiss Diketones by Carbonyl Ene Reactions12	Functionalization of the Weiss Diketone to Cylindramide and Geodin A Core Units13	Biological Properties of Bicyclo[3.3.0]octanes14	Hydropentalenes through Vinylcyclopropane Cyclopentene Rearrangement15	Functionalization of Bicyclo[3.3.0]octanes toward Chiral Dienes16	Miscellaneous Syntheses of Hydropentalenes17	Conclusion and Outlook
The objectivity illusion and voter polarization in the 2016 presidential election
Authors: Schwalbe Michael C. , Cohen Geoffrey L. , Ross Lee D. 
Published: August 2020

Significance
Political polarization increasingly threatens democratic institutions. The belief that “my side” sees the world objectively while the “other side” sees it through the lens of its biases contributes to this political polarization and accompanying animus and distrust. This conviction, known as the “objectivity illusion,” was strong and persistent among Trump and Clinton supporters in the weeks before the 2016 presidential election. We show that the objectivity illusion predicts subsequent bias and polarization, including heightened partisanship over the presidential debates. A follow-up study showed that both groups impugned the objectivity of a putative blog author supporting the opposition candidate and saw supporters of that opposing candidate as evil.
Uncovering targeting priority to yeast peroxisomes using an in-cell competition assay
Authors: Rosenthal Mira , Metzl-Raz Eyal , Bürgi Jérôme , Yifrach Eden , Drwesh Layla , Fadel Amir , Peleg Yoav , Rapaport Doron , Wilmanns Matthias , Barkai Naama , Schuldiner Maya , Zalckvar Einat 
Published: August 2020

SignificanceHalf of eukaryotic proteins reside in organelles to which they are directed by dedicated targeting pathways, each recognizing unique targeting signals. Multiple proteins compete for any targeting pathway and might have different priority of reaching an organelle. However, the proteins with targeting priority, and the mechanisms underlying it, have not been explored. We developed a systematic tool to study targeting priority. We expressed a competitor protein and examined how it affects the localization of all other proteins targeted by the same pathway. We found several proteins with high targeting priority, dissected the mechanism of priority, and suggest that priority is governed by different parameters. This approach can be modified to study targeting priority in various organelles, cell types, and organisms.
Global epigenomic analysis of KSHV-infected primary effusion lymphoma identifies functional
MYC
superenhancers and enhancer RNAs
Authors: Park Angela , Oh Soohwan , Jung Kyle L. , Choi Un Yung , Lee Hye-Ra , Rosenfeld Michael G. , Jung Jae U. 
Published: August 2020

Significance
Enhancers are crucial regulatory elements that dictate cellular processes by spatiotemporally controlling promoter activity. Recent studies have shown that active enhancers themselves generate noncoding enhancer RNAs (eRNAs) that play a critical role in fine tuning gene expression. Using genomic approaches, we demonstrate that oncogenic KSHV modulates host enhancer activity in PELs to control its lifecycle. During KSHV latency, expression levels of several key transcription factors and oncogenes are elevated by clusters of enhancers. Upon virus reactivation, global host enhancer activities are suppressed in order to facilitate viral replication. Our results indicate that better understanding and targeting host enhancer and eRNA functions may lead to novel therapeutics for PELs.
Genome-wide analyses reveal drivers of penguin diversification
Authors: Vianna Juliana A. , Fernandes Flávia A. N. , Frugone María José , Figueiró Henrique V. , Pertierra Luis R. , Noll Daly , Bi Ke , Wang-Claypool Cynthia Y. , Lowther Andrew , Parker Patricia , Le Bohec Celine , Bonadonna Francesco , Wienecke Barbara , Pistorius Pierre , Steinfurth Antje , Burridge Christopher P. , Dantas Gisele P. M. , Poulin Elie , Simison W. Brian , Henderson Jim , Eizirik Eduardo , Nery Mariana F. , Bowie Rauri C. K. 
Published: August 2020

SignificancePenguins have long been of interest to scientists and the general public, but their evolutionary history remains unresolved. Using genomes, we investigated the drivers of penguin diversification. We found that crown-group penguins diverged in the early Miocene in Australia/New Zealand and identifiedAptenodytes(emperor and king penguins) as the sister group to all other extant penguins. Penguins first occupied temperate environments and then radiated to cold Antarctic waters. The Antarctic Circumpolar Current’s (ACC) intensification 11.6 Mya promoted penguin diversification and geographic expansion. We detected interspecies introgression among penguins, in some cases following the direction of the ACC, and identified genes acting on thermoregulation, oxygen metabolism, and diving capacity that underwent adaptive evolution as they progressively occupied more challenging thermal niches.
Light-induced
psbA
translation in plants is triggered by photosystem II damage via an assembly-linked autoregulatory circuit
Authors: Chotewutmontri Prakitchai , Barkan Alice 
Published: August 2020

Significance
Photosystem II (PSII) harbors the water-splitting activity underlying oxygenic photosynthesis. The PSII reaction center protein D1 is subject to photodamage and must be replaced with nascent D1 to maintain photosynthetic activity. How new D1 synthesis is coordinated with D1 damage has been a long-standing question. Our results clarify the nature of the light-induced signal that activates D1 synthesis for PSII repair in plants, and suggest an autoregulatory mechanism in which degradation of damaged D1 relieves a repressive interaction between D1 and translational activators in a complex that functions in PSII assembly and repair. This proposed mechanism comprises a responsive switch that couples D1 synthesis to need for D1 during PSII biogenesis and repair.
Supernova triggers for end-Devonian extinctions
Authors: Fields Brian D. , Melott Adrian L. , Ellis John , Ertel Adrienne F. , Fry Brian J. , Lieberman Bruce S. , Liu Zhenghai , Miller Jesse A. , Thomas Brian C. 
Published: August 2020

The Late Devonian was a protracted period of low speciation resulting in biodiversity decline, culminating in extinction events near the Devonian–Carboniferous boundary. Recent evidence indicates that the final extinction event may have coincided with a dramatic drop in stratospheric ozone, possibly due to a global temperature rise. Here we study an alternative possible cause for the postulated ozone drop: a nearby supernova explosion that could inflict damage by accelerating cosmic rays that can deliver ionizing radiation for up to

∼
100

ky. We therefore propose that the end-Devonian extinctions were triggered by supernova explosions at

∼
20

pc

, somewhat beyond the “kill distance” that would have precipitated a full mass extinction. Such nearby supernovae are likely due to core collapses of massive stars; these are concentrated in the thin Galactic disk where the Sun resides. Detecting either of the long-lived radioisotopes

Sm

146

or

Pu

244

in one or more end-Devonian extinction strata would confirm a supernova origin, point to the core-collapse explosion of a massive star, and probe supernova nucleosynthesis. Other possible tests of the supernova hypothesis are discussed.
Characterization of mouse di-N-acetylchitobiase that can degrade chitin-oligosaccharides
Authors: Ohno Misa , Miyazaki Masao , Kimura Masahiro , Minowa Yusaku , Sakaguchi Masayoshi , Oyama Fumitaka , Yamashita Tetsuro 
Published: August 2020

Abstract
Di-N-acetylchitobiase (Ctbs) degrades β-1,4 glycoside bonds of the chitobiose core of free asparagine-linked glycan. This study examined whether Ctbs degrades chitin-oligosaccharides to GlcNAc in mammals. We analyzed Ctbs mRNA and protein expression in mouse tissues and characterized enzymatic activity using recombinant mouse Ctbs expressed in Escherichia coli. Ctbs mRNA and protein were expressed in various tissues of mouse, including the stomach. Optimal conditions for recombinant Ctbs were pH 3.0 and 45°C, and the recombinant enzyme was retained more than 94% activity after incubation at pH 3.0–7.0 and below 37°C. The recombinant Ctbs hydrolyzed (GlcNAc)3 and (GlcNAc)6 at pH 3.0 and produced GlcNAc. The Km of Ctbs was lowest with (GlcNAc)3 as a substrate. kcat/Km was fourfold as high with (GlcNAc)3 and (GlcNAc)4 as substrates than with (GlcNAc)2. These results suggest that Ctbs digests chitin-oligosaccharides or (GlcNAc)2 of reducing-end residues of oligosaccharides and produces GlcNAc in mouse tissues.