bluuebunny/crossref_metadata_2025_split huggingface dataset:
Rap1 and Cdc13 have complementary roles in preventing exonucleolytic degradation of telomere 5′ ends
Authors: Runnberg Rikard , Narayanan Saishyam , Cohn Marita 
Published: August 2017

AbstractTelomere DNA ends with a single-stranded 3′ overhang. Long 3′ overhangs may cause aberrant DNA damage responses and accelerate telomere attrition, which is associated with cancer and aging, respectively. Genetic studies have indicated several important players in preventing 5′ end hyper-resection, yet detailed knowledge about the molecular mechanism in which they act is still lacking. Here, we use an in vitro DNA 5′ end protection assay, to study how N. castellii Cdc13 and Rap1 protect against 5′ exonucleolytic degradation by λ-exonuclease. The homogeneous telomeric repeat sequence of N. castellii allows us to study their protection ability at exact binding sites relative to the 5′ end. We find efficient protection by both Cdc13 and Rap1 when bound close to the 5′ end. Notably, Rap1 provides protection when binding dsDNA at a distance from the 5′ end. The DNA binding domain of Rap1 is sufficient for 5′ end protection, and its wrapping loop region is essential. Intriguingly, Rap1 facilitates protection also when its binding site contains 2 nt of ssDNA, thus spanning across the ds-ss junction. These results highlight a role of Rap1 in 5′ end protection and indicate that Cdc13 and Rap1 have complementary roles in maintaining proper 3′ overhang length.
Monocyte infiltration and proliferation reestablish myeloid cell homeostasis in the mouse retina following retinal pigment epithelial cell injury
Authors: Ma Wenxin , Zhang Yikui , Gao Chun , Fariss Robert N. , Tam Johnny , Wong Wai T. 
Published: August 2017

AbstractAge-related macular degeneration (AMD), a leading contributor of vision loss, currently lacks comprehensive treatment. While AMD histopathology involves retinal pigment epithelium (RPE) injury associated with immune cell infiltration, the nature of immune cell responses to RPE injury remains undefined. We induced RPE injury pharmacologically and genetically in transgenic mouse models in which microglia and systemic monocytes were separately tagged, enabling a spatial and temporal dissection of the relative contributions of microglia vs. monocytes to post-injury changes. We found that myeloid cell responses to RPE injury occur in stages: (1) an early mobilization of endogenous microglia from the inner retina to the RPE layer, followed by (2) subsequent monocyte infiltration from the retinal vasculature into the inner retina that replenishes the local myeloid cell population in a CCR2-regulated manner. These altered distributions of myeloid cells post-injury were long-lived, with recruited monocytes acquiring the distribution, markers, and morphologies of neighboring endogenous microglia in a durable manner. These findings indicate the role played by infiltrating monocytes in maintaining myeloid cell homeostasis in the retina following AMD-relevant RPE injury and provide a foundation for understanding and therapeutically modulating immune aspects in retinal disease.
Stability in metabolic phenotypes and inferred metagenome profiles before the onset of colitis-induced inflammation
Authors: Glymenaki M. , Barnes A. , Hagan S. O’ , Warhurst G. , McBain A. J. , Wilson I. D. , Kell D. B. , Else K. J. , Cruickshank S. M. 
Published: August 2017

AbstractInflammatory bowel disease (IBD) is associated with altered microbiota composition and metabolism, but it is unclear whether these changes precede inflammation or are the result of it since current studies have mainly focused on changes after the onset of disease. We previously showed differences in mucus gut microbiota composition preceded colitis-induced inflammation and stool microbial differences only became apparent at colitis onset. In the present study, we aimed to investigate whether microbial dysbiosis was associated with differences in both predicted microbial gene content and endogenous metabolite profiles. We examined the functional potential of mucus and stool microbial communities in themdr1a−/−mouse model of colitis and littermate controls using PICRUSt on 16S rRNA sequencing data. Our findings indicate that despite changes in microbial composition, microbial functional pathways were stable before and during the development of mucosal inflammation. LC-MS-based metabolic phenotyping (metabotyping) in urine samples confirmed that metabolite profiles inmdr1a−/−mice were remarkably unaffected by development of intestinal inflammation and there were no differences in previously published metabolic markers of IBD. Metabolic profiles did, however, discriminate the colitis-pronemdr1a−/−genotype from controls. Our results indicate resilience of the metabolic network irrespective of inflammation. Importantly as metabolites differentiated genotype, genotype-differentiating metabolites could potentially predict IBD risk.
High-speed manufacturing of highly regular femtosecond laser-induced periodic surface structures: physical origin of regularity
Authors: Gnilitskyi Iaroslav , Derrien Thibault J.-Y. , Levy Yoann , Bulgakova Nadezhda M. , Mocek Tomáš , Orazi Leonardo 
Published: August 2017

AbstractHighly regular laser-induced periodic surface structures (HR-LIPSS) have been fabricated on surfaces of Mo, steel alloy and Ti at a record processing speed on large areas and with a record regularity in the obtained sub-wavelength structures. The physical mechanisms governing LIPSS regularity are identified and linked with the decay length (i.e. the mean free path) of the excited surface electromagnetic waves (SEWs). The dispersion of the LIPSS orientation angle well correlates with the SEWs decay length: the shorter this length, the more regular are the LIPSS. A material dependent criterion for obtaining HR-LIPSS is proposed for a large variety of metallic materials. It has been found that decreasing the spot size close to the SEW decay length is a key for covering several cm2 of material surface by HR-LIPSS in a few seconds. Theoretical predictions suggest that reducing the laser wavelength can provide the possibility of HR-LIPSS production on principally any metal. This new achievement in the unprecedented level of control over the laser-induced periodic structure formation makes this laser-writing technology to be flexible, robust and, hence, highly competitive for advanced industrial applications based on surface nanostructuring.
Giant pandas can discriminate the emotions of human facial pictures
Authors: Li Youxu , Dai Qiang , Hou Rong , Zhang Zhihe , Chen Peng , Xue Rui , Feng Feifei , Chen Chao , Liu Jiabin , Gu Xiaodong , Zhang Zejun , Qi Dunwu 
Published: August 2017

AbstractPrevious studies have shown that giant pandas (Ailuropoda melanoleuca) can discriminate face-like shapes, but little is known about their cognitive ability with respect to the emotional expressions of humans. We tested whether adult giant pandas can discriminate expressions from pictures of half of a face and found that pandas can learn to discriminate between angry and happy expressions based on global information from the whole face. Young adult pandas (5–7 years old) learned to discriminate expressions more quickly than older individuals (8–16 years old), but no significant differences were found between females and males. These results suggest that young adult giant pandas are better at discriminating emotional expressions of humans. We showed for the first time that the giant panda, can discriminate the facial expressions of humans. Our results can also be valuable for the daily care and management of captive giant pandas.
Pre-coincidence brain activity predicts the perceptual outcome of streaming/bouncing motion display
Authors: Zhao Song , Wang Yajie , Jia Lina , Feng Chengzhi , Liao Yu , Feng Wenfeng 
Published: August 2017

AbstractWhen two identical visual discs move toward each other on a two-dimensional visual display, they can be perceived as either “streaming through” or “bouncing off” each other after their coincidence. Previous studies have observed a strong bias toward the streaming percept. Additionally, the incidence of the bouncing percept in this ambiguous display could be increased by various factors, such as a brief sound at the moment of coincidence and a momentary pause of the two discs. The streaming/bouncing bistable motion phenomenon has been studied intensively since its discovery. However, little is known regarding the neural basis underling the perceptual ambiguity in the classic version of the streaming/bouncing motion display. The present study investigated the neural basis of the perception disambiguating underling the processing of the streaming/bouncing bistable motion display using event-related potential (ERP) recordings. Surprisingly, the amplitude of frontal central P2 (220–260 ms) that was elicited by the moving discs ~200 ms before the coincidence of the two discs was observed to be predictive of subsequent streaming or bouncing percept. A larger P2 amplitude was observed for streaming percept than the bouncing percept. These findings suggest that the streaming/bouncing bistable perception may have been disambiguated unconsciously ~200 ms before the coincidence of the two discs.
Schisandrin B reverses doxorubicin resistance through inhibiting P-glycoprotein and promoting proteasome-mediated degradation of survivin
Authors: Wang Shengpeng , Wang Anqi , Shao Min , Lin Ligen , Li Peng , Wang Yitao 
Published: August 2017

AbstractAcquired drug resistance poses a great challenge in cancer therapy. Drug efflux and anti-apoptotic processes are the most two common mechanisms that confer cancer drug resistance. In this study, we found that Schisandrin B (Sch B), one of the major dibenzocyclooctadiene derivatives extracted from Chinese herbal medicine Schisandrae Chinensis Fructus, could significantly enhance the sensitivity of doxorubicin (DOX)-resistant breast cancer and ovarian cancer cells to DOX. Our results showed that Sch B increased the intracellular accumulation of DOX through inhibiting expression and activity of P-glycoprotein (P-gp). Meanwhile, Sch B could markedly downregulate the expression of anti-apoptotic protein survivin. Overexpression of survivin attenuated the sensitizing effects of Sch B, while silencing of survivin enhanced Sch B-mediated sensitizing effects. Furthermore, Sch B preferentially promoted chymotryptic activity of the proteasome in a concentration-dependent manner, and the proteasome inhibitor MG-132 prevented Sch B-induced survivin downregulation. Taken together, our findings suggest that Sch B could be a potential candidate for combating drug resistant cancer via modulating two key factors that responsible for cancer resistance.
Metabolic Reconstruction and Modeling Microbial Electrosynthesis
Authors: Marshall Christopher W. , Ross Daniel E. , Handley Kim M. , Weisenhorn Pamela B. , Edirisinghe Janaka N. , Henry Christopher S. , Gilbert Jack A. , May Harold D. , Norman R. Sean 
Published: August 2017

AbstractMicrobial electrosynthesis is a renewable energy and chemical production platform that relies on microbial cells to capture electrons from a cathode and fix carbon. Yet despite the promise of this technology, the metabolic capacity of the microbes that inhabit the electrode surface and catalyze electron transfer in these systems remains largely unknown. We assembled thirteen draft genomes from a microbial electrosynthesis system producing primarily acetate from carbon dioxide, and their transcriptional activity was mapped to genomes from cells on the electrode surface and in the supernatant. This allowed us to create a metabolic model of the predominant community members belonging to Acetobacterium, Sulfurospirillum, and Desulfovibrio. According to the model, the Acetobacterium was the primary carbon fixer, and a keystone member of the community. Transcripts of soluble hydrogenases and ferredoxins from Acetobacterium and hydrogenases, formate dehydrogenase, and cytochromes of Desulfovibrio were found in high abundance near the electrode surface. Cytochrome c oxidases of facultative members of the community were highly expressed in the supernatant despite completely sealed reactors and constant flushing with anaerobic gases. These molecular discoveries and metabolic modeling now serve as a foundation for future examination and development of electrosynthetic microbial communities.
Dated phylogeny and dispersal history of the butterfly subfamily Nymphalinae (Lepidoptera: Nymphalidae)
Authors: Su Chengyong , Shi Qinghui , Sun Xiaoyan , Ma Junye , Li Chunxiang , Hao Jiasheng , Yang Qun 
Published: August 2017

AbstractThe origin and dispersal history of the large butterfly subfamily Nymphalinae are not fully understood, due to internal phylogenetic and time calibration issues. We conducted phylogenetic and dating analyses using mitochondrial and nuclear genes of biogeographically diverse groups of the Nymphalinae in order to resolve some controversial relationships and the paleobiogeographic pattern of the subfamily. Our results support the sister relationship of Vanessa (Tribe Nymphalini) and the Nymphalis-group, and the grouping of the three old-world genera (Rhinopalpa, Kallimoides and Vanessula) within Tribe Victorinini. Molecular dating analyses invoking two additional calibrations under the butterfly-host plant coevolutionary scenarios result in a relatively deeper divergence of the subfamily’s two major clades (Nymphalini and the Kallimoids), compatible with the Cretaceous floral turnover scenario during the so-called Cretaceous Terrestrial Revolution. Phylobiogeographic analyses reveal that the Oriental region is probably the center of early divergences for Nymphalinae after the Cretaceous-Paleogene (K-Pg) mass extinction, followed by repeated dispersals into the rest of the Old World and the New World during various periods beginning in Eocene. The biogeographic history indicates that temperature changes and host-plant diversification may have facilitated the dispersals of this butterfly subfamily, with accelerated global colonization during the middle to late Miocene.
Optimal Target Level of Low-density Lipoprotein Cholesterol for Vascular Function in Statin Naïve Individuals
Authors: Matsui Shogo , Kajikawa Masato , Hida Eisuke , Maruhashi Tatsuya , Iwamoto Yumiko , Iwamoto Akimichi , Oda Nozomu , Kishimoto Shinji , Hidaka Takayuki , Kihara Yasuki , Chayama Kazuaki , Goto Chikara , Aibara Yoshiki , Nakashima Ayumu , Yusoff Farina Binti Mohamad , Noma Kensuke , Higashi Yukihito 
Published: August 2017

AbstractWe investigated (1) the relationship between low-density lipoprotein cholesterol (LDL-C) and vascular function in patients receiving and those not receiving statin therapy and (2) optimal level of LDL-C for maintenance of vascular function. Flow-mediated vasodilation (FMD) and nitroglycerine-induced vasodilation (NID) were inversely correlated with LDL-C in the 957 statin naïve subjects but not in the 392 subjects receiving statin therapy. In statin naïve subjects, non-high LDL-C (≤100 mg/dL) was independently associated with a decrease in adjusted odds ratio of the low tertile of FMD (OR: 0.62, 95% CI: 0.45–0.85; P = 0.003) and NID (OR: 0.69, 95% CI: 0.50–0.96; P = 0.03). Adjusted odds ratio of the low tertile of FMD was significantly lower in the low LDL-C group (≤70 mg/dL) (OR: 0.47, 95% CI, 0.27–0.81; P = 0.006) and in the moderate LDL-C group (70.1–100 mg/dL) (OR: 0.66, 95% CI, 0.48–0.94; P = 0.02) than in the high LDL-C group (>100 mg/dL). There was no significant difference in FMD between the low LDL-C group and moderate LDL-C group. There were significant relationships of FMD and NID with LDL-C levels in statin naïve subjects. In a general population, LDL-C of ≤100 mg/dL may be the optimal target level for maintenance of endothelial function.
Detection of magnetized quark-nuggets, a candidate for dark matter
Authors: VanDevender J. Pace , VanDevender Aaron P. , Sloan T. , Swaim Criss , Wilson Peter , Schmitt Robert. G. , Zakirov Rinat , Blum Josh , Cross James L. , McGinley Niall 
Published: August 2017

AbstractQuark nuggets are theoretical objects composed of approximately equal numbers of up, down, and strange quarks and are also called strangelets and nuclearites. They have been proposed as a candidate for dark matter, which constitutes ~85% of the universe’s mass and which has been a mystery for decades. Previous efforts to detect quark nuggets assumed that the nuclear-density core interacts directly with the surrounding matter so the stopping power is minimal. Tatsumi found that quark nuggets could well exist as a ferromagnetic liquid with a ~1012-T magnetic field. We find that the magnetic field produces a magnetopause with surrounding plasma, as the earth’s magnetic field produces a magnetopause with the solar wind, and substantially increases their energy deposition rate in matter. We use the magnetopause model to compute the energy deposition as a function of quark-nugget mass and to analyze testing the quark-nugget hypothesis for dark matter by observations in air, water, and land. We conclude the water option is most promising.
Whole genome-based phylogeny of reptile-associated Helicobacter indicates independent niche adaptation followed by diversification in a poikilothermic host
Authors: Gilbert Maarten J. , Duim Birgitta , Timmerman Arjen J. , Zomer Aldert L. , Wagenaar Jaap A. 
Published: August 2017

AbstractReptiles have been shown to host a significant Helicobacter diversity. In order to survive, reptile-associated Helicobacter lineages need to be adapted to the thermally dynamic environment encountered in a poikilothermic host. The whole genomes of reptile-associated Helicobacter lineages can provide insights in Helicobacter host adaptation and coevolution. These aspects were explored by comparing the genomes of reptile-, bird-, and mammal-associated Helicobacter lineages. Based on average nucleotide identity, all reptile-associated Helicobacter lineages in this study could be considered distinct species. A whole genome-based phylogeny showed two distinct clades, one associated with chelonians and one associated with lizards. The phylogeny indicates initial adaptation to an anatomical niche, which is followed by an ancient host jump and subsequent diversification. Furthermore, the ability to grow at low temperatures, which might reflect thermal adaptation to a reptilian host, originated at least twice in Helicobacter evolution. A putative tricarballylate catabolism locus was specifically present in Campylobacter and Helicobacter isolates from reptiles. The phylogeny of reptile-associated Helicobacter parallels host association, indicating a high level of host specificity. The high diversity and deep branching within these clades supports long-term coevolution with, and extensive radiation within the respective reptilian host type.
Myosin isoform expressed in metastatic prostate cancer stimulates cell invasion
Authors: Maly Ivan V. , Domaradzki Tera M. , Gosy Victoria A. , Hofmann Wilma A. 
Published: August 2017

AbstractDuring metastasis, tumor cells migrate out of their original tissue to invade other organs. Secretion of exosomes and metalloproteases is essential for extracellular matrix remodeling, enabling migration through tissue barriers. Metastatic prostate cancer is differentiated by expression of the rare isoform A of the molecular motor myosin IC, however the function of this isoform remained unknown. Here we show that it contributes causatively to the invasive motility of prostate cancer cells. We found that the isoform associates with metalloprotease-containing exosomes and stimulates their secretion. While the data show that myosin IC is involved in prostate cancer cell migration, migration outside extracellular matrix in vitro proves little affected specifically by isoform A. Nevertheless, this isoform stimulates invasion through extracellular matrix, pointing to a critical role in secretion. Both the secretion and invasion depend on the integrity of the motor and lipid-binding domains of the protein. Our results demonstrate how myosin IC isoform A is likely to function in metastasis, driving secretion of exosomes that enable invasion of prostate cancer cells across extracellular matrix barriers. The new data identify a molecule suitable for a mechanistically grounded development into a marker and target for prognosis, detection, and treatment of invasive prostate cancer.
Unconventional fractional quantum Hall effect in bilayer graphene
Authors: Jacak Janusz Edward 
Published: August 2017

AbstractRecent experimental progress in Hall measurements in bilayer graphene in the so-called open-face configuration of boron nitride encapsulated samples, together with the earlier technique of suspended samples, allows for precise observation of the fractional quantum Hall effect (FQHE) in all 4 subbands of the Lowest Landau level (with n = 0 and n = 1) and in the next LL subbands (with n = 2) in the bilayer system. Many newly observed FQHE features do not agree with a conventional model of composite fermions and reveal a different hierarchy in comparison to monolayer graphene or GaAs 2DEG. We explain the peculiarity of the FQHE hierarchy in the bilayer system in the framework of a topological approach, which includes the composite fermion model as its special case. Inclusion of a topological effect caused by the hopping of electrons between the two sheets in the bilayer system allowed for an explanation of the FQHE hierarchy in the graphene bilayer in satisfactory accordance with the experimental observations.
Metabolomic and Lipidomic Profiling Identifies The Role of the RNA Editing Pathway in Endometrial Carcinogenesis
Authors: Altadill Tatiana , Dowdy Tyrone M. , Gill Kirandeep , Reques Armando , Menon Smrithi S. , Moiola Cristian P. , Lopez-Gil Carlos , Coll Eva , Matias-Guiu Xavier , Cabrera Silvia , Garcia Angel , Reventos Jaume , Byers Stephen W. , Gil-Moreno Antonio , Cheema Amrita K. , Colas Eva 
Published: August 2017

AbstractEndometrial cancer (EC) remains the most common malignancy of the genital tract among women in developed countries. Although much research has been performed at genomic, transcriptomic and proteomic level, there is still a significant gap in the metabolomic studies of EC. In order to gain insights into altered metabolic pathways in the onset and progression of EC carcinogenesis, we used high resolution mass spectrometry to characterize the metabolomic and lipidomic profile of 39 human EC and 17 healthy endometrial tissue samples. Several pathways including lipids, Kynurenine pathway, endocannabinoids signaling pathway and the RNA editing pathway were found to be dysregulated in EC. The dysregulation of the RNA editing pathway was further investigated in an independent set of 183 human EC tissues and matched controls, using orthogonal approaches. We found that ADAR2 is overexpressed in EC and that the increase in expression positively correlates with the aggressiveness of the tumor. Furthermore, silencing of ADAR2 in three EC cell lines resulted in a decreased proliferation rate, increased apoptosis, and reduced migration capabilities in vitro. Taken together, our results suggest that ADAR2 functions as an oncogene in endometrial carcinogenesis and could be a potential target for improving EC treatment strategies.