julilili42/papers huggingface dataset:
“I am thou… Thou art I…”—How Persona 4’s Young Adult Fiction Communicates Japanese Values
2017-06-21

Life is Strange, INSIDE, Oxenfree—all these video games represent a seemingly entirely new genre. Young Adult videogames diverge from the male, gloomy grown-up stereotypes and replace them with adolescent protagonists in their coming of age stories. Their commercial success seem to validate their endeavors. However, YA narratives are hidden in plain sights for many years within JRPGs. Shin Megami Tensei – Persona 4 (short Persona 4 or P4) is a cultural ambassador. This paper examines how the game’s procedural rhetoric in combination with its Young Adult story advocate in favor of specific Japanese values. The time structure of P4 reinforces a longterm orientation and requires strategic planning as well as tactical flexibility. So-called “Social Links” represents Japan unique take on collectivism. Each link encapsulates a small YA narrative and offers different benefits to social-active protagonist. Finally, grinding mechanics reflect the notion of repetition-based learning. Japanese schools teach through engaging with developing several solutions to a singular problem. The same holds true for the grinding process. All these elements combined create a game rhetoric promoting these aspects of Japanese culture.
Penetrance estimate of LRRK2 p.G2019S mutation in individuals of non‐Ashkenazi Jewish ancestry
2017-06-22

ABSTRACT Background Penetrance estimates of the leucine‐rich repeat kinase 2 ( LRRK2 ) p.G2019S mutation for PD vary widely (24%‐100%). The p.G2019S penetrance in individuals of Ashkenazi Jewish ancestry has been estimated as 25%, adjusted for multiple covariates. It is unknown whether penetrance varies among different ethnic groups. The objective of this study was to estimate the penetrance of p.G2019S in individuals of non‐Ashkenazi Jewish ancestry and compare penetrance between Ashkenazi Jews and non‐Ashkenazi Jews to age 80. Methods The kin‐cohort method was used to estimate penetrance in 474 first‐degree relatives of 69 non‐Ashkenazi Jewish LRRK2 p.G2019S carrier probands at 8 sites from the Michael J. Fox LRRK2 Cohort Consortium. An identical validated family history interview was administered to assess age at onset of PD, current age, or age at death for relatives in different ethnic groups at each site. Neurological examination and LRRK2 genotype of relatives were included when available. Results Risk of PD in non‐Ashkenazi Jewish relatives who carry a LRRK2 p.G2019S mutation was 42.5% (95% confidence interval [CI]: 26.3%‐65.8%) to age 80, which is not significantly higher than the previously estimated 25% (95% CI: 16.7%‐34.2%) in Ashkenazi Jewish carrier relatives. The penetrance of PD to age 80 in LRRK2 p.G2019S mutation carrier relatives was significantly higher than the noncarrier relatives, as seen in Ashkenazi Jewish relatives. Conclusions The similar penetrance of LRRK2 p.G2019S estimated in Ashkenazi Jewish carriers and non‐Ashkenazi Jewish carriers confirms that p.G2019S penetrance is 25% to 42.5% at age 80 in all populations analyzed. © 2017 International Parkinson and Movement Disorder Society
Transcriptome-Wide Identification of Novel UV-B- and Light Modulated Flavonol Pathway Genes Controlled by VviMYBF1
2017-06-22

Flavonols constitute a group of flavonoids with important photoprotective roles in plants. In addition, flavonol content and composition greatly influences fruit quality. We previously demonstrated that the grapevine R2R3-MYB transcription factor (TF) VviMYBF1 promotes flavonol accumulation by inducing the expression of flavonol synthase (<i>VviFLS1/VviFLS4</i>), a key step of the initial flavonol pathway. Despite this, gene networks underlying flavonol modification in grapevine including both structural and regulatory genes remain poorly understood. In order to identify flavonol modifying genes and TFs acting downstream of VviMYBF1 a microarray-based transcriptome analysis was performed on grapevine hairy roots ectopically expressing <i>VviMYBF1</i> or a Green Fluorescent Protein as control. <i>VviFLS1</i> was induced in VviMYBF1 transgenic roots and glycosylated flavonols accumulated significantly compared with control lines. Among the differentially expressed genes, potential flavonol-modifying enzymes with predicted rhamnosyltransferase (e.g., RhaT1) or glycosyltransferase (e.g., GT3) activities were identified. In addition, important TFs of the MYB and bZIP families such as the proanthocyanidin regulator VviMYBPA1 and the UV-B light responsive HY5 homolog VviHYH were significantly altered in their expression pattern by overexpression of VviMYBF1. Co-temporal expression analysis demonstrated positive correlation of <i>VviMYBF1</i> with <i>VviFLS1</i>, <i>VviGT3</i>, and <i>VviRhaT1</i> during berry development and in fruits ripened with different light and UV-B radiation conditions at field. These results show that VviMYBF1 overexpression led to the identification of novel genes of the flavonol pathway and that the flavonol modifying machinery can be influenced by agricultural practices to optimize flavonol composition in grapes.
Chapter 1: Standard Model Processes
2017-06-22

This chapter documents the production rates and typical distributions for a number of benchmark Standard Model processes, and discusses new dynamical phenomena arising at the highest energies available at this collider. We discuss the intrinsic physics interest in the measurement of these Standard Model processes, as well as their role as backgrounds for New Physics searches.
Neurogenic bowel dysfunction: Clinical management recommendations of the Neurologic Incontinence Committee of the Fifth International Consultation on Incontinence 2013
2017-06-22

Background Evidence‐based guidelines for the management of neurological disease and lower bowel dysfunction have been produced by the International Consultations on Incontinence (ICI). These are comprehensive guidelines, and were developed to have world‐wide relevance. Aims To update clinical management of neurogenic bowel dysfunction from the recommendations of the 4th ICI, 2009. Materials and Methods A series of evidence reviews and updates were performed by members of the working group. The resulting guidelines were presented at the 2012 meeting of the European Association of Urology for consultation, and modifications applied to deliver evidence based conclusions and recommendations for the scientific report of the 5th edition of the ICI in 2013. Results The current review is a synthesis of the conclusions and recommendations, including the algorithms for initial and specialized management of neurogenic bowel dysfunction. The pathophysiology is described in terms of spinal cord injury, multiple sclerosis, and Parkinson's disease. Assessment requires detailed history and clinical assessment, general investigations, and specialized testing, if required. Treatment primarily focuses on optimizing stool consistency and regulating bowel evacuation to improve quality of life. Symptom management covers conservative and interventional measures to promote good habits and assist stool evacuation, along with prevention of incontinence. Education is essential to achieving optimal bowel management. Discussion The review offers a pragmatic approach to management in the context of complex pathophysiology and varied evidence base.
Next generation sequencing of the clonal IGH rearrangement detects ongoing mutations and interfollicular trafficking in in situ follicular neoplasia
2017-06-22

Follicular lymphoma (FL) is characterized genetically by a significant intraclonal diversity of rearranged immunoglobulin heavy chain (IGH) genes and a substantial cell migration activity (follicular trafficking). Recently, in situ follicular neoplasia (ISFN), characterized by accumulations of immunohistochemically strongly BCL2-positive, t(14;18)+ clonal B cells confined to germinal centers in reactive lymph nodes, has been identified as a precursor lesion of FL with low risk of progression to manifest FL. The extent of ongoing somatic hypermutation of rearranged IGH genes and interfollicular trafficking in ISFN is not known. In this study we performed an in depth analysis of clonal evolution and cell migration patterns in a case of pure ISFN involving multiple lymph nodes. Using laser microdissection and next generation sequencing (NGS) we documented significant intraclonal diversity of the rearranged IGH gene and extensive interfollicular migration between germinal centers of the same lymph node as well as between different lymph nodes. Furthermore, we identified N-glycosylation motifs characteristic for FL in the CDR3 region.
Evidential adverbs in German
2017-06-22

Abstract This article addresses the semantic and morphosyntactic development of the German evidential adverbs offensichtlich, offenbar, anscheinend , and scheinbar ‘obviously’/‘apparently’/‘seemingly’ and their meaning contribution in present-day German. It will be argued that these expressions, most of which are historically derived from adjectives, innovated separate lexical entries as sentence adverbs in New High German resulting from a morphosyntactic reanalysis of an ambiguous surface structure. This reanalysis was accompanied by a profound semantic change, as a result of which the expressions acquired a wide-scope reading of the type ‘there is (clear) evidence that p’. The diachronic results are corroborated by experimental data from Present-Day German that show that these evidential sentence adverbs are underspecified with respect to evidence type (inference and report). The diachronic and synchronic findings are furthermore discussed in the light of grammaticalization and subjectification theory.
Early stages in the biogenesis of eukaryotic β‐barrel proteins
2017-06-22

The endosymbiotic organelles mitochondria and chloroplasts harbour, similarly to their prokaryotic progenitors, β‐barrel proteins in their outer membrane. These proteins are encoded on nuclear DNA , translated on cytosolic ribosomes and imported into their target organelles by a dedicated machinery. Recent studies have provided insights into the import into the organelles and the membrane insertion of these proteins. Although the cytosolic stages of their biogenesis are less well defined, it is speculated that upon their synthesis, chaperones prevent β‐barrel proteins from aggregation and keep them in an import‐competent conformation. In this Review, we summarize the current knowledge about the biogenesis of β‐barrel proteins, focusing on the early stages from the translation on cytosolic ribosomes to the recognition on the surface of the organelle.
Physics at a 100 TeV pp Collider: Standard Model Processes
2017-06-22

This report summarises the properties of Standard Model processes at the 100 TeV pp collider. We document the production rates and typical distributions for a number of benchmark Standard Model processes, and discuss new dynamical phenomena arising at the highest energies available at this collider. We discuss the intrinsic physics interest in the measurement of these Standard Model processes, as well as their role as backgrounds for New Physics searches.
The Braking Index of Millisecond Magnetars
2017-06-23

Abstract We make the first measurement of the braking index n of two putative millisecond magnetars born in short gamma-ray bursts. We measure and for millisecond magnetars born in GRB 130603B and GRB 140903A, respectively. The neutron star born in GRB 130603B has the only known a braking index consistent with the fiducial n = 3 value. This value is ruled out with 99.95% confidence for GRB 140903A. We discuss possible causes of braking indices in millisecond magnetars, showing that several models can account for the measurement of the braking index in GRB 140903A, while it is more difficult to account for a braking index consistent with n = 3.
Doxorubicin Effect on Myocardial Metabolism as a Prerequisite for Subsequent Development of Cardiac Toxicity: A Translational 18F-FDG PET/CT Observation
2017-06-23

The present translational study aimed to verify whether serial 18FFDG PET/CT predicts doxorubicin cardiotoxicity. Methods: Fifteen athymic mice were treated intravenously with saline (n = 5) or with 5 or 7.5 mg of doxorubicin per kilogram (n = = each) and underwent dynamic small-animal PET beforehand and afterward to estimate left ventricular (LV) metabolic rate of glucose (MRGlu). Thereafter, we retrospectively identified 69 patients who had been successfully treated with a regimen of doxorubicin, bleomycin, vinblastine, and dacarbazine for Hodgkin disease (HD) and had undergone 4 consecutive 18F-FDG PET/CT scans. Volumes of interest were drawn on LV myocardium to quantify mean SUV. All patients were subsequently interviewed by telephone (median follow-up, 30 mo); 36 of them agreed to undergo electrocardiography and transthoracic echocardiography. Results: In mice, LV MRGlu was 17.9 ± 4.4 nmol • min21 × g21 at baseline. Doxorubicin selectively and dose-dependently increased this value in the standard-dose (27.9 ± 9 nmol × min21 × g-1, P &amp;lt; 0.05 vs. controls) and high-dose subgroups (37.2 6 7.8 nmol × min21 × g-1, P &amp;lt; 0.01 vs. controls, P &amp;lt; 0.05 vs. standard-dose). In HD patients, LV SUV showed a progressive increase during doxorubicin treatment that persisted at follow-up. New-onset cardiac abnormalities appeared in 11 of 36 patients (31%). In these subjects, pretherapy LV SUV was markedly lower with respect to the remaining patients (1.53 ± 0.9 vs. 3.34 ± 2.54, respectively, P &amp;lt; 0.01). Multivariate analysis confirmed the predictive value of baseline LV SUV for subsequent cardiac abnormalities. Conclusion: Doxorubicin dosedependently increases LV MRGlu, particularly in the presence of low baseline 18F-FDG uptake. These results imply that low myocardial 18F-FDG uptake before the initiation of doxorubicin chemotherapy in HD patients may predict the development of chemotherapy-induced cardiotoxicity, suggesting that prospective clinical trials are warranted to test this hypothesis.
Planet-disc interaction in laminar and turbulent discs
2017-06-23

In weakly ionized discs turbulence can be generated through the vertical shear instability (VSI). Embedded planets feel a stochastic component in the torques acting on them which can impact their migration. In this work we study the interplay between a growing planet embedded in a protoplanetary disc and the VSI-turbulence. We performed a series of three-dimensional hydrodynamical simulations for locally isothermal discs with embedded planets in the mass range from 5 to 100 Earth masses. We study planets embedded in an inviscid disc that is VSI unstable, becomes turbulent and generates angular momentum transport with an effective . This is compared to the corresponding viscous disc using exactly this -value. In general we find that the planets have only a weak impact on the disc turbulence. Only for the largest planet ( ) the turbulent activity becomes enhanced inside of the planet. The depth and width of a gap created by the more massive planets ( ) in the turbulent disc equal exactly that of the corresponding viscous case, leading to very similar torque strengths acting on the planet, with small stochastic fluctuations for the VSI disc. At the gap edges vortices are generated that are stronger and longer lived in the VSI disc. Low mass planets (with ) do not open gaps in the disc in both cases but generate for the turbulent disc an over-density behind the planet that exerts a significant negative torque. This can boost the inward migration in VSI turbulent discs well above the Type I rate. Due to the finite turbulence level in realistic three-dimensional discs the gap depth will always be limited and migration will not stall in inviscid discs.
Electrophysiological alterations in a murine model of chronic coxsackievirus B3 myocarditis
2017-06-23

In CVB3+ mice, prolonged ventricular refractoriness and hyperpolarized resting membrane potentials in presence of unchanged APD were observed, suggesting that low level CVB3 expression does not promote VA by altered cardiac electrophysiology in this type of chronic myocarditis. These findings may suggest that other mechanisms such as chronic myocardial inflammation or fibrosis may account for arrhythmias observed in patients with chronic enteroviral myocarditis.
Facile Reversible Benzophenone Insertion into Rare‐Earth Metal Pyrazolate Complexes
2017-06-23

Treatment of the homoleptic Ce IV pyrazolate complex [Ce(Me 2 pz) 4 ] 2 (Me 2 pz = 3,5‐dimethylpyrazolato) with benzophenone (bp) led to the formation of an Me 2 pz‐substituted diphenylmethoxy‐( N ,O)‐chelating ligand (pdpm), possibly metal‐templated through initial coordination of bp to the cerium atom and subsequent bp insertion into the Ce–N(Me 2 pz) bond. This coordination/insertion process was shown to be reversible, leading to a complex sequence of equilibria involving multiple degrees of insertion/de‐insertion and association/dissociation. The dependency on temperature and the amount of bp of all equilibria was revealed, with insertion/association of bp being favored at low temperatures and de‐insertion/dissociation preferentially occurring at elevated temperatures. Such sets of equilibria were also observed for the treatment of trivalent complexes [Ln(Me 2 pz) 3 (thf)] 2 (Ln = La, Ce, Lu) with bp. Through structural analysis, the trivalent complexes were shown to be less effective in the bp‐to‐pdpm conversion than the Ce IV derivative, giving direct evidence of how an increase in rare‐earth Lewis acidity aids in ketone anchorage and concomitant conversion. The observed equilibria seem to also apply to the more illustrious organocerium systems. The conversion of bp into the corresponding tertiary alcohol by the routinely employed reagent CeCl 3 / n BuLi is the most selective when termination of the reaction by hydrolysis is performed at lower temperatures, with a reagent ratio bp/CeCl 3 / n BuLi of 1:1:1.
The influence of disulfide bonds on the mechanical stability of proteins is context dependent
2017-06-24

Disulfide bonds play a crucial role in proteins, modulating their stability and constraining their conformational dynamics. A particularly important case is that of proteins that need to withstand forces arising from their normal biological function and that are often disulfide bonded. However, the influence of disulfides on the overall mechanical stability of proteins is poorly understood. Here, we used single-molecule force spectroscopy (smFS) to study the role of disulfide bonds in different mechanical proteins in terms of their unfolding forces. For this purpose, we chose the pilus protein FimG from Gram-negative bacteria and a disulfide-bonded variant of the I91 human cardiac titin polyprotein. Our results show that disulfide bonds can alter the mechanical stability of proteins in different ways depending on the properties of the system. Specifically, disulfide-bonded FimG undergoes a 30% increase in its mechanical stability compared with its reduced counterpart, whereas the unfolding force of I91 domains experiences a decrease of 15% relative to the WT form. Using a coarse-grained simulation model, we rationalized that the increase in mechanical stability of FimG is due to a shift in the mechanical unfolding pathway. The simple topology-based explanation suggests a neutral effect in the case of titin. In summary, our results indicate that disulfide bonds in proteins act in a context-dependent manner rather than simply as mechanical lockers, underscoring the importance of considering disulfide bonds both computationally and experimentally when studying the mechanical properties of proteins.
Low‐thrombogenic fibrin‐heparin coating promotes in vitro endothelialization
2017-06-24

Abstract Long‐term performance of implanted cardiovascular grafts can be ensured if living endothelium overgrows their surface. Surface modifications to implants are therefore being sought that can encourage endothelialization while preventing thrombus formation until the natural endothelium is formed. In the present study, heparin was covalently attached to a fibrin mesh grown from a polyvinyl chloride (PVC) substrate surface by the catalytic action of surface immobilized thrombin on a fibrinogen solution. The coating prevented platelet activation, thrombin generation and clot formation, and reduced inflammatory reactions when exposed to fresh human whole blood circulating in a Chandler loop model. In addition, in vitro seeded human umbilical vein and human saphenous vein endothelial cells showed considerably enhanced attachment and proliferation on the coating. © 2017 Wiley Periodicals, Inc. J Biomed Mater Res Part A: 105A: 2995–3005, 2017.
Comparative performance of the BGISEQ-500 vs Illumina HiSeq2500 sequencing platforms for palaeogenomic sequencing
2017-06-26

Abstract Ancient DNA research has been revolutionized following development of next-generation sequencing platforms. Although a number of such platforms have been applied to ancient DNA samples, the Illumina series are the dominant choice today, mainly because of high production capacities and short read production. Recently a potentially attractive alternative platform for palaeogenomic data generation has been developed, the BGISEQ-500, whose sequence output are comparable with the Illumina series. In this study, we modified the standard BGISEQ-500 library preparation specifically for use on degraded DNA, then directly compared the sequencing performance and data quality of the BGISEQ-500 to the Illumina HiSeq2500 platform on DNA extracted from 8 historic and ancient dog and wolf samples. The data generated were largely comparable between sequencing platforms, with no statistically significant difference observed for parameters including level (P = 0.371) and average sequence length (P = 0718) of endogenous nuclear DNA, sequence GC content (P = 0.311), double-stranded DNA damage rate (v. 0.309), and sequence clonality (P = 0.093). Small significant differences were found in single-strand DNA damage rate (ΔS; slightly lower for the BGISEQ-500, P = 0.011) and the background rate of difference from the reference genome (Θ; slightly higher for BGISEQ-500, P = 0.012). This may result from the differences in amplification cycles used to polymerase chain reaction–amplify the libraries. A significant difference was also observed in the mitochondrial DNA percentages recovered (P = 0.018), although we believe this is likely a stochastic effect relating to the extremely low levels of mitochondria that were sequenced from 3 of the samples with overall very low levels of endogenous DNA. Although we acknowledge that our analyses were limited to animal material, our observations suggest that the BGISEQ-500 holds the potential to represent a valid and potentially valuable alternative platform for palaeogenomic data generation that is worthy of future exploration by those interested in the sequencing and analysis of degraded DNA.