bluuebunny/crossref_metadata_2025_split huggingface dataset:
Epigenetic conflict on a degenerating Y chromosome increases mutational burden in Drosophila males
Authors: Wei Kevin H.-C. , Gibilisco Lauren , Bachtrog Doris 
Published: November 2020

AbstractLarge portions of eukaryotic genomes consist of transposable elements (TEs), and the establishment of transcription-repressing heterochromatin during early development safeguards genome integrity in Drosophila. Repeat-rich Y chromosomes can act as reservoirs for TEs (‘toxic’ Y effect), and incomplete epigenomic defenses during early development can lead to deleterious TE mobilization. Here, we contrast the dynamics of early TE activation in two Drosophila species with vastly different Y chromosomes of different ages. Zygotic TE expression is elevated in male embryos relative to females in both species, mostly due to expression of Y-linked TEs. Interestingly, male-biased TE expression diminishes across development in D. pseudoobscura, but remains elevated in D. miranda, the species with the younger and larger Y chromosome. The repeat-rich Y of D. miranda still contains many actively transcribed genes, which compromise the formation of silencing heterochromatin. Elevated TE expression results in more de novo insertions of repeats in males compared to females. This lends support to the idea that the ‘toxic’ Y chromosome can create a mutational burden in males when genome-wide defense mechanisms are compromised, and suggests a previously unappreciated epigenetic conflict on evolving Y chromosomes between transcription of essential genes and silencing of selfish DNA.
Divergent architecture of the heterotrimeric NatC complex explains N-terminal acetylation of cognate substrates
Authors: Grunwald Stephan , Hopf Linus V. M. , Bock-Bierbaum Tobias , Lally Ciara C. M. , Spahn Christian M. T. , Daumke Oliver 
Published: November 2020

AbstractThe heterotrimeric NatC complex, comprising the catalytic Naa30 and the two auxiliary subunits Naa35 and Naa38, co-translationally acetylates the N-termini of numerous eukaryotic target proteins. Despite its unique subunit composition, its essential role for many aspects of cellular function and its suggested involvement in disease, structure and mechanism of NatC have remained unknown. Here, we present the crystal structure of the Saccharomyces cerevisiae NatC complex, which exhibits a strikingly different architecture compared to previously described N-terminal acetyltransferase (NAT) complexes. Cofactor and ligand-bound structures reveal how the first four amino acids of cognate substrates are recognized at the Naa30–Naa35 interface. A sequence-specific, ligand-induced conformational change in Naa30 enables efficient acetylation. Based on detailed structure–function studies, we suggest a catalytic mechanism and identify a ribosome-binding patch in an elongated tip region of NatC. Our study reveals how NAT machineries have divergently evolved to N-terminally acetylate specific subsets of target proteins.
Construction of a complete set of Neisseria meningitidis mutants and its use for the phenotypic profiling of this human pathogen
Authors: Muir Alastair , Gurung Ishwori , Cehovin Ana , Bazin Adelme , Vallenet David , Pelicic Vladimir 
Published: November 2020

AbstractThe bacterium Neisseria meningitidis causes life-threatening meningitis and sepsis. Here, we construct a complete collection of defined mutants in protein-coding genes of this organism, identifying all genes that are essential under laboratory conditions. The collection, named NeMeSys 2.0, consists of individual mutants in 1584 non-essential genes. We identify 391 essential genes, which are associated with basic functions such as expression and preservation of genome information, cell membrane structure and function, and metabolism. We use this collection to shed light on the functions of diverse genes, including a gene encoding a member of a previously unrecognised class of histidinol-phosphatases; a set of 20 genes required for type IV pili function; and several conditionally essential genes encoding antitoxins and/or immunity proteins. We expect that NeMeSys 2.0 will facilitate the phenotypic profiling of a major human bacterial pathogen.
LncRNA DILA1 inhibits Cyclin D1 degradation and contributes to tamoxifen resistance in breast cancer
Authors: Shi Qianfeng , Li Yudong , Li Shunying , Jin Liang , Lai Hongna , Wu Yanqing , Cai Zijie , Zhu Mengdi , Li Qian , Li Ying , Wang Jingru , Liu Yujie , Wu Zongqi , Song Erwei , Liu Qiang 
Published: November 2020

AbstractCyclin D1 is one of the most important oncoproteins that drives cancer cell proliferation and associates with tamoxifen resistance in breast cancer. Here, we identify a lncRNA, DILA1, which interacts with Cyclin D1 and is overexpressed in tamoxifen-resistant breast cancer cells. Mechanistically, DILA1 inhibits the phosphorylation of Cyclin D1 at Thr286 by directly interacting with Thr286 and blocking its subsequent degradation, leading to overexpressed Cyclin D1 protein in breast cancer. Knocking down DILA1 decreases Cyclin D1 protein expression, inhibits cancer cell growth and restores tamoxifen sensitivity both in vitro and in vivo. High expression of DILA1 is associated with overexpressed Cyclin D1 protein and poor prognosis in breast cancer patients who received tamoxifen treatment. This study shows the previously unappreciated importance of post-translational dysregulation of Cyclin D1 contributing to tamoxifen resistance in breast cancer. Moreover, it reveals the novel mechanism of DILA1 in regulating Cyclin D1 protein stability and suggests DILA1 is a specific therapeutic target to downregulate Cyclin D1 protein and reverse tamoxifen resistance in treating breast cancer.
On-surface lithium donor reaction enables decarbonated lithium garnets and compatible interfaces within cathodes
Authors: Yang Ya-Nan , Li Ying-Xiang , Li Yi-Qiu , Zhang Tao 
Published: November 2020

AbstractLithium garnets have been widely studied as promising electrolytes that could enable the next-generation all-solid-state lithium batteries. However, upon exposure to atmospheric moisture and carbon dioxide, insulating lithium carbonate forms on the surface and deteriorates the interfaces within electrodes. Here, we report a scalable solid sintering method, defined by lithium donor reaction that allows for complete decarbonation of Li6.4La3Zr1.4Ta0.6O12 (LLZTO) and yields an active LiCoO2 layer for each garnet particle. The obtained LiCoO2 coated garnets composite is stable against air without any Li2CO3. Once working in a solid-state lithium battery, the LiCoO2-LLZTO@LiCoO2 composite cathode maintains 81% of the initial capacity after 180 cycles at 0.1 C. Eliminating CO2 evolution above 4.0 V is confirmed experimentally after transforming Li2CO3 into LiCoO2. These results indicate that Li2CO3 is no longer an obstacle, but a trigger of the intimate solid-solid interface. This strategy has been extended to develop a series of LLZTO@active layer materials.
Developing a pathway-independent and full-autonomous global resource allocation strategy to dynamically switching phenotypic states
Authors: Wu Junjun , Bao Meijiao , Duan Xuguo , Zhou Peng , Chen Caiwen , Gao Jiahua , Cheng Shiyao , Zhuang Qianqian , Zhao Zhijun 
Published: November 2020

AbstractA grand challenge of biological chemical production is the competition between synthetic circuits and host genes for limited cellular resources. Quorum sensing (QS)-based dynamic pathway regulations provide a pathway-independent way to rebalance metabolic flux over the course of the fermentation. Most cases, however, these pathway-independent strategies only have capacity for a single QS circuit functional in one cell. Furthermore, current dynamic regulations mainly provide localized control of metabolic flux. Here, with the aid of engineering synthetic orthogonal quorum-related circuits and global mRNA decay, we report a pathway-independent dynamic resource allocation strategy, which allows us to independently controlling two different phenotypic states to globally redistribute cellular resources toward synthetic circuits. The strategy which could pathway-independently and globally self-regulate two desired cell phenotypes including growth and production phenotypes could totally eliminate the need for human supervision of the entire fermentation.
Next-generation sequencing analysis of circulating micro-RNA expression in response to parabolic flight as a spaceflight analogue
Authors: Jirak Peter , Wernly Bernhard , Lichtenauer Michael , Franz Marcus , Knost Thorben , Abusamrah Thaer , Kelm Malte , Bimpong-Buta Nana-Yaw , Jung Christian 
Published: November 2020

AbstractUnderstanding physiologic reactions to weightlessness is an indispensable requirement for safe human space missions. This study aims to analyse changes in the expression of circulating miRNAs following exposure to gravitational changes. Eight healthy volunteers (age: 24.5 years, male: 4, female: 4) were included. Each subject underwent 31 short-term phases of weightlessness and hypergravity induced by parabolic flight as a spaceflight analogue. At baseline, 1 and 24 h after parabolic flight, venous blood was withdrawn. Analysis of circulating miRNAs in serum was conducted by means of next generation sequencing. In total, 213 miRNAs were robustly detected (TPM > 5) by small RNA sequencing in all 24 samples. Four miRNAs evidenced a significant change in expression after adjusting for multiple testing. Only miR-223-3p showed a consistent significant decrease 24 h after parabolic flight compared to baseline values and values at 1 h after parabolic flight. miR-941 and miR-24-3p showed a significant decrease 24 h after parabolic flight compared to 1 h after parabolic flight but not to baseline values. miR-486-5p showed a significant increase 24 h after parabolic flight compared to 1 h after parabolic flight but not to baseline values. A target network analysis identified genes of the p53 signaling pathway and the cell cycle highly enriched among the targets of the four microRNAs. Our findings suggest cellular adaption to gravitational changes at the post-transcriptional level. Based on our results, we suggest a change in cell cycle regulation as potential explanation for adaptational changes observed in space missions.
Deconfinement of Mott localized electrons into topological and spin–orbit-coupled Dirac fermions
Authors: Pizarro José M. , Adler Severino , Zantout Karim , Mertz Thomas , Barone Paolo , Valentí Roser , Sangiovanni Giorgio , Wehling Tim O. 
Published: November 2020

AbstractThe interplay of electronic correlations, spin–orbit coupling and topology holds promise for the realization of exotic states of quantum matter. Models of strongly interacting electrons on honeycomb lattices have revealed rich phase diagrams featuring unconventional quantum states including chiral superconductivity and correlated quantum spin Hall insulators intertwining with complex magnetic order. Material realizations of these electronic states are, however, scarce or inexistent. In this work, we propose and show that stacking 1T-TaSe2 into bilayers can deconfine electrons from a deep Mott insulating state in the monolayer to a system of correlated Dirac fermions subject to sizable spin–orbit coupling in the bilayer. 1T-TaSe2 develops a Star-of-David charge density wave pattern in each layer. When the Star-of-David centers belonging to two adyacent layers are stacked in a honeycomb pattern, the system realizes a generalized Kane–Mele–Hubbard model in a regime where Dirac semimetallic states are subject to significant Mott–Hubbard interactions and spin–orbit coupling. At charge neutrality, the system is close to a quantum phase transition between a quantum spin Hall and an antiferromagnetic insulator. We identify a perpendicular electric field and the twisting angle as two knobs to control topology and spin–orbit coupling in the system. Their combination can drive it across hitherto unexplored grounds of correlated electron physics, including a quantum tricritical point and an exotic first-order topological phase transition.
Olive oil from the 79 A.D. Vesuvius eruption stored at the Naples National Archaeological Museum (Italy)
Authors: Sacchi Raffaele , Cutignano Adele , Picariello Gianluca , Paduano Antonello , Genovese Alessandro , Siano Francesco , Nuzzo Genoveffa , Caira Simonetta , Lubritto Carmine , Ricci Paola , D’Auria Alessia , Di Pasquale Gaetano , Motta Andrea , Addeo Francesco 
Published: November 2020

AbstractUsing a range of chromatographic, spectroscopic, and mass spectrometric analytical techniques, we characterized one of the “edible items” found at the Vesuvius archeological sites and guarded at the National Archaeological Museum of Naples (MANN) in Naples, Italy. We authenticated the specimen contained in a glass bottle (Mann-S1 sample) as originally olive oil and mapped the deep evolution throughout its 2000 years of storage. Triacylglycerols were completely hydrolyzed, while the resulting (hydroxy) fatty acids had partly condensed into rarely found estolides. A complex pattern of volatile compounds arose mainly from breakdown of oleic acid. With excellent approximation, radiocarbon dating placed the find at the time of the Plinian Mount Vesuvius eruption in 79 A.D., indicating that Mann-S1 is probably the oldest residue of olive oil in the world found in bulk amount (nearly 0.7 L).
Collective dynamics of dark web marketplaces
Authors: ElBahrawy Abeer , Alessandretti Laura , Rusnac Leonid , Goldsmith Daniel , Teytelboym Alexander , Baronchelli Andrea 
Published: November 2020

AbstractDark web marketplaces are websites that facilitate trade in illicit goods, mainly using Bitcoin. Since dark web marketplaces are unregulated, they do not offer any user protection, so police raids and scams regularly cause large losses to marketplace participants. However, the uncertainty has not prevented the proliferation of dark web marketplaces. Here, we investigate how the dark web marketplace ecosystem reorganises itself following marketplace closures. We analyse 24 separate episodes of unexpected marketplace closure by inspecting 133 million Bitcoin transactions among 38 million users. We focus on “migrating users” who move their trading activity to a different marketplace after a closure. We find that most migrating users continue their trading activity on a single coexisting marketplace, typically the one with the highest trading volume. User migration is swift and trading volumes of migrating users recover quickly. Thus, although individual marketplaces might appear fragile, coordinated user migration guarantees overall systemic resilience.
An empirical model to evaluate the effects of environmental humidity on the formation of wrinkled, creased and porous fibre morphology from electrospinning
Authors: Zhang Duo , Davoodi Pooya , Li Xia , Liu Ye , Wang Wenyu , Huang Yan Yan Shery 
Published: November 2020

AbstractControlling environmental humidity level and thus moisture interaction with an electrospinning solution jet has led to a fascinating range of polymer fibre morphological features; these include surface wrinkles, creases and surface/internal porosity at the individual fibre level. Here, by cross-correlating literature data of far-field electrospinning (FFES), together with our experimental data from near-field electrospinning (NFES), we propose a theoretical model, which can account, phenomenologically, for the onset of fibre microstructures formation from electrospinning solutions made of a hydrophobic polymer dissolved in a water-miscible or polar solvent. This empirical model provides a quantitative evaluation on how the evaporating solvent vapour could prevent or disrupt water vapor condensation onto the electrospinning jet; thus, on the condition where vapor condensation does occur, morphological features will form on the surface, or bulk of the fibre. A wide range of polymer systems, including polystyrene, poly(methyl methacrylate), poly-l-lactic acid, polycaprolactone were tested and validated. Our analysis points to the different operation regimes associated FFES versus NFES, when it comes to the system’s sensitivity towards environmental moisture. Our proposed model may further be used to guide the process in creating desirable fibre microstructure.
Resveratrol attenuates TLR-4 mediated inflammation and elicits therapeutic potential in models of sepsis
Authors: Wang Binbin , Bellot Gregory Lucien , Iskandar Kartini , Chong Tsung Wen , Goh Fera Yiqian , Tai June Jingyi , Schwarz Herbert , Wong Siew Cheng , Pervaiz Shazib 
Published: November 2020

AbstractSepsis is a potentially fatal condition triggered by systemic inflammatory response to infection. Due to the heightened immune reactivity and multi-organ pathology, treatment options are limited and several clinical trials have not produced the desired outcome, hence the interest in the discovery of novel therapeutic strategies. The polyphenol resveratrol (RSV) has shown promise against several pathological states, including acute and chronic inflammation. In this study, we evaluated its therapeutic potential in a murine model of sepsis and in patients undergoing transrectal ultrasound biopsy. RSV was able to inhibit lipopolysaccharide (LPS) stimulated inflammatory responses through blocking Phospholipase D (PLD) and its downstream signaling molecules SphK1, ERK1/2 and NF-κB. In addition, RSV treatment resulted in the downregulation of MyD88, an adaptor molecule in the TLR4 signaling pathway, and this effect at least in part, involved RSV-induced autophagy. Notably, RSV protected mice against polymicrobial septic shock induced upon cecal ligation and puncture, and inhibited pro-inflammatory cytokine production by human monocytes from transrectal ultrasound (TRUS) biopsy patients. Together, these findings demonstrate the immune regulatory activity of RSV and highlight its therapeutic potential in the management of sepsis.
Motion around triangular points in the restricted three-body problem with radiating heterogeneous primaries surrounded by a belt
Authors: Singh Jagadish , Haruna Sunusi 
Published: November 2020

AbstractThe present paper studies the locations and linear stability of the triangular equilibrium points when both primaries are radiating and considered as heterogeneous spheroid with three layers of different densities. Additionally, we include the effects of small perturbations in the Coriolis and centrifugal forces and potential from a belt (circumbinary disc). It is observed that the positions of the triangular equilibrium points are substantially affected by all parameters (except a perturbation in Coriolis force) involved in the system.The stabilty of motion is found only when $$0 < \mu < \mu_{c}$$

0
<
μ
<

μ
c

, where $$\mu_{c}$$

μ
c

is the critical mass value which depends on the combined effect of radiation pressures and heterogeneity of the primaries, small perturbations and the potential from a belt.It is also seen that the Coriolis force and the belt have stabilizing effect,while the centrifugal force, radiation and heterogeineity of the primaries have destabilizing behaviour.The net effect is that the size of the region of stability decreases when the value of these parameters increases where $$\mu$$
μ
is the mass ratio and $$k_{1} ,k_{2}$$

k
1

,

k
2

characterize heterogeneity of both primaries. A practical application of this model could be the study of motion of a dust grain near the heterogeneous and luminous binary stars surrounded by a belt.Finally, we carried out and discuss numerical experiments aiming at computing the positions of triangular points and critical masses of three binary systems: Archid, Xi Booties and Kruger 60.
Antifungal and anti-inflammatory potential of the endangered aromatic plant Thymus albicans
Authors: Roxo Mariana , Zuzarte Mónica , Gonçalves Maria José , Alves-Silva Jorge M. , Cavaleiro Carlos , Cruz Maria Teresa , Salgueiro Lígia 
Published: November 2020

AbstractThymus albicans is an endemic species of the Iberian Peninsula with a vulnerable conservation status. In an attempt to contribute to the valorization of this species, the present study brings new insights on the antifungal and anti-inflammatory mechanism of action of T. albicans essential oil. The antifungal activity of the oil and its major compounds was assessed for the first time against standard and clinically isolated strains of yeasts and filamentous fungi. The effect on the two major virulence factors of Candida albicans (germ tube formation and biofilm disruption) was considered in more detail. At 0.08 μL/mL, the oil inhibited C. albicans germ tube formation by more than 40% and decreased biofilm biomass at MIC values, thus pointing out its antivirulent potential. The anti-inflammatory activity of the essential oil was investigated on LPS-stimulated mouse macrophages (RAW 264.7) by evaluating the levels of several pro-inflammatory mediators, namely nitric oxide (NO), inducible nitric oxide synthase (iNOS) and cyclooxygenase-2 (COX-2). T. albicans oil reduced the production of nitrites, a NO derived sub-product, at non-cytotoxic concentrations of 0.32 and 0.64 μL/mL, by 27 and 41%, respectively. In addition, the iNOS protein levels of essential oil pre-treated cells were reduced by 14%. Overall, the high essential oil yield of T. albicans as well as its bioactive effects at concentrations without cytotoxicity, encourage further studies on the potential pharmacological applications of this species. Furthermore, these results raise awareness for the need to preserve endangered species that may hold relevant medicinal value.
A variable structure pneumatic soft robot
Authors: Huang Wenkai , Xiao Junlong , Xu Zhipeng 
Published: November 2020

AbstractIn this paper, a variable structure pneumatic soft robot is proposed. Its structure is variable in that when it grasps irregular objects, it can adapt to different sizes by active expansion or contraction. Its expansion range is from diameter 200 to 300 mm, its four soft pneumatic actuators (SPAs) can be rotated independently to adapt to different shapes, and it has high flexibility. The active compliant grasping method enables it to capture at the best position, which can improve the success rate of capture and reduce damage to the object being grasped. The experiment proves the effectiveness of the variable structure mechanism, and the proposed soft robot has low cost and a simple manufacturing process, so the mechanism has great application prospects.
Computational methods for visualizing and measuring verapamil efficacy for cerebral vasospasm
Authors: Abumoussa Andrew , Flores Alex , Ho James , Niethammer Marc , Sasaki-Adams Deanna , Lee Yueh Z. 
Published: November 2020

AbstractCerebral vasospasm is a dreaded sequelae of aneurysmal subarachnoid hemorrhage (aSAH), requiring timely intervention with therapeutic goals of improving brain perfusion. There are currently no standardized real-time, objective assessments of the interventional procedures performed to treat vasospasm. Here we describe real-time techniques to quantify cerebral perfusion during interventional cerebral angiography. We retrospectively analyzed 39 consecutive cases performed to treat clinical vasospasm and quantified the changes in perfusion metrics between pre- and post- verapamil administrations. With Digital Subtraction Angiography (DSA) perfusion analysis, we are able to identify hypoperfused territories and quantify the exact changes in cerebral perfusion for each individual case and vascular territory. We demonstrate that perfusion analysis for DSA can be performed in real time. This provides clinicians with a colorized map which directly visualizes hypoperfused tissue, combined with associated perfusion statistics. Quantitative thresholds and analysis based on DSA perfusion may assist with real-time dosage estimation and help predict response to treatment, however future prospective analysis is required for validation.