bluuebunny/crossref_metadata_2025_split huggingface dataset:
Origin of rebound virus in chronically SIV-infected Rhesus monkeys following treatment discontinuation
Authors: Liu Po-Ting , Keele Brandon F. , Abbink Peter , Mercado Noe B. , Liu Jinyan , Bondzie Esther A. , Chandrashekar Abishek , Borducchi Erica N. , Hesselgesser Joseph , Mish Michael , Chin Gregory , Bekerman Elena , Geleziunas Romas , Barouch Dan H. 
Published: October 2020

AbstractViral rebound following antiretroviral therapy (ART) discontinuation in HIV-1-infected individuals is believed to originate from a small pool of CD4+ T cells harboring replication-competent provirus. However, the origin and nature of the rebound virus has remained unclear. Recent studies have suggested that rebound virus does not originate directly from individual latent proviruses but rather from recombination events involving multiple proviruses. Here we evaluate the origin of rebound virus in 16 ART-suppressed, chronically SIV-infected rhesus monkeys following ART discontinuation. We sequence viral RNA and viral DNA in these animals prior to ART initiation, during ART suppression, and following viral rebound, and we compare rebound viral RNA after ART discontinuation with near full-length viral DNA from peripheral blood and lymph node mononuclear cells (PBMC and LNMC) during ART suppression. Sequences of initial rebound viruses closely match viral DNA sequences in PBMC and LNMC during ART suppression. Recombinant viruses are rare in the initial rebound virus populations but arise quickly within 2–4 weeks after viral rebound. These data suggest that intact proviral DNA in PBMC and LNMC during ART suppression is likely the direct origin of viral rebound in chronically SIV-infected rhesus monkeys following ART discontinuation.
Maternal DNMT3A-dependent de novo methylation of the paternal genome inhibits gene expression in the early embryo
Authors: Richard Albert Julien , Au Yeung Wan Kin , Toriyama Keisuke , Kobayashi Hisato , Hirasawa Ryutaro , Brind’Amour Julie , Bogutz Aaron , Sasaki Hiroyuki , Lorincz Matthew 
Published: October 2020

AbstractDe novo DNA methylation (DNAme) during mammalian spermatogenesis yields a densely methylated genome, with the exception of CpG islands (CGIs), which are hypomethylated in sperm. While the paternal genome undergoes widespread DNAme loss before the first S-phase following fertilization, recent mass spectrometry analysis revealed that the zygotic paternal genome is paradoxically also subject to a low level of de novo DNAme. However, the loci involved, and impact on transcription were not addressed. Here, we employ allele-specific analysis of whole-genome bisulphite sequencing data and show that a number of genomic regions, including several dozen CGI promoters, are de novo methylated on the paternal genome by the 2-cell stage. A subset of these promoters maintains DNAme through development to the blastocyst stage. Consistent with paternal DNAme acquisition, many of these loci are hypermethylated in androgenetic blastocysts but hypomethylated in parthenogenetic blastocysts. Paternal DNAme acquisition is lost following maternal deletion of Dnmt3a, with a subset of promoters, which are normally transcribed from the paternal allele in blastocysts, being prematurely transcribed at the 4-cell stage in maternal Dnmt3a knockout embryos. These observations uncover a role for maternal DNMT3A activity in post-fertilization epigenetic reprogramming and transcriptional silencing of the paternal genome.
Diffusion of lithium ions in Lithium-argyrodite solid-state electrolytes
Authors: Baktash Ardeshir , Reid James C. , Roman Tanglaw , Searles Debra J. 
Published: October 2020

AbstractThe use of solid-state electrolytes to provide safer, next-generation rechargeable batteries is becoming more feasible as materials with greater stability and higher ionic diffusion coefficients are designed. However, accurate determination of diffusion coefficients in solids is problematic and reliable calculations are highly sought-after to understand how their structure can be modified to improve their performance. In this paper we compare diffusion coefficients calculated using nonequilibrium and equilibrium ab initio molecular dynamics simulations for highly diffusive solid-state electrolytes, to demonstrate the accuracy that can be obtained. Moreover, we show that ab initio nonequilibrium molecular dynamics can be used to determine diffusion coefficients when the diffusion is too slow for it to be feasible to obtain them using ab initio equilibrium simulations. Thereby, using ab initio nonequilibrium molecular dynamics simulations we are able to obtain accurate estimates of the diffusion coefficients of Li ions in Li6PS5Cl and Li5PS4Cl2, two promising electrolytes for all-solid-state batteries. Furthermore, these calculations show that the diffusion coefficient of lithium ions in Li5PS4Cl2 is higher than many other potential all-solid-state electrolytes, making it promising for future technologies. The reasons for variation in conductivities determined using computational and experimental methods are discussed. It is demonstrated that small degrees of disorder and vacancies can result in orders of magnitude differences in diffusivities of Li ions in Li6PS5Cl, and these factors are likely to contribute to inconsistencies observed in experimentally reported values. Notably, the introduction of Li-vacancies and disorder can enhance the ionic conductivity of Li6PS5Cl.
Towards the standardization of quantum state verification using optimal strategies
Authors: Jiang Xinhe , Wang Kun , Qian Kaiyi , Chen Zhaozhong , Chen Zhiyu , Lu Liangliang , Xia Lijun , Song Fangmin , Zhu Shining , Ma Xiaosong 
Published: October 2020

AbstractQuantum devices for generating entangled states have been extensively studied and widely used. As so, it becomes necessary to verify that these devices truly work reliably and efficiently as they are specified. Here we experimentally realize the recently proposed two-qubit entangled state verification strategies using both local measurements (nonadaptive) and active feed-forward operations (adaptive) with a photonic platform. About 3283/536 number of copies (N) are required to achieve a 99% confidence to verify the target quantum state for nonadaptive/adaptive strategies. These optimal strategies provide the Heisenberg scaling of the infidelity $${\it{\epsilon }}$$
ϵ
as a function of N ($${\it{\epsilon }}\sim N^{r}$$

ϵ
~

N

r

) with the parameter r = −1, exceeding the standard quantum limit with r = −0.5. We experimentally obtain the scaling parameters of r = −0.88 ± 0.03 and −0.78 ± 0.07 for nonadaptive and adaptive strategies, respectively. Our experimental work could serve as a standardized procedure for the verification of quantum states.
Very low overhead fault-tolerant magic state preparation using redundant ancilla encoding and flag qubits
Authors: Chamberland Christopher , Noh Kyungjoo 
Published: October 2020

AbstractFault-tolerant quantum computing promises significant computational speedup over classical computing for a variety of important problems. One of the biggest challenges for realizing fault-tolerant quantum computing is preparing magic states with sufficiently low error rates. Magic state distillation is one of the most efficient schemes for preparing high-quality magic states. However, since magic state distillation circuits are not fault-tolerant, all the operations in the distillation circuits must be encoded in a large distance error-correcting code, resulting in a significant resource overhead. Here, we propose a fault-tolerant scheme for directly preparing high-quality magic states, which makes magic state distillation unnecessary. In particular, we introduce a concept that we call redundant ancilla encoding. The latter combined with flag qubits allows for circuits to both measure stabilizer generators of some code, while also being able to measure global operators to fault-tolerantly prepare magic states, all using nearest neighbor interactions. We apply such schemes to a planar architecture of the triangular color code family and demonstrate that our scheme requires at least an order of magnitude fewer qubits and space–time overhead compared to the most competitive magic state distillation schemes. Since our scheme requires only nearest-neighbor interactions in a planar architecture, it is suitable for various quantum computing platforms currently under development.
Energy band alignment at the heterointerface between CdS and Ag-alloyed CZTS
Authors: Gansukh Mungunshagai , Li Zheshen , Rodriguez Moises Espindola , Engberg Sara , Martinho Filipe Mesquita Alves , Mariño Simon López , Stamate Eugen , Schou Jørgen , Hansen Ole , Canulescu Stela 
Published: October 2020

AbstractEnergy band alignment at the heterointerface between CdS and kesterite Cu2ZnSnS4 (CZTS) and its alloys plays a crucial role in determining the efficiency of the solar cells. Whereas Ag alloying of CZTS has been shown to reduce anti-site defects in the bulk and thus rise the efficiency, the electronic properties at the interface with the CdS buffer layer have not been extensively investigated. In this work, we present a detailed study on the band alignment between n-CdS and p-CZTS upon Ag alloying by depth-profiling ultraviolet photoelectron spectroscopy (UPS) and X-ray photoelectron spectroscopy (XPS). Our findings indicate that core-level peaks and the valence band edge of CdS exhibit a significant shift to a lower energy (larger than 0.4 eV) upon the etching of the CdS layer, which can be assigned due to band bending and chemical shift induced by a change in the chemical composition across the interface. Using a simplified model based on charge depletion layer conservation, a significantly larger total charge region depletion width was determined in Ag-alloyed CZTS as compared to its undoped counterpart. Our findings reveal a cliff-like band alignment at both CdS/CZTS and CdS/Ag-CZTS heterointerfaces. However, the conduction-band offset decreases by more than 0.1 eV upon Ag alloying of CZTS. The approach demonstrated here enables nanometer-scale depth profiling of the electronic structure of the p–n junction and can be universally applied to study entirely new platforms of oxide/chalcogenide heterostructures for next-generation optoelectronic devices.
Transition from a uni- to a bimodal interfacial charge distribution in $$\hbox {LaAlO}_3$$/$$\hbox {SrTiO}_3$$ upon cooling
Authors: Zwiebler M. , Di Gennaro E. , Hamann-Borrero J. E. , Ritschel T. , Green R. J. , Sawatzky G. A. , Schierle E. , Weschke E. , Leo A. , Granozio F. Miletto , Geck J. 
Published: October 2020

AbstractWe present a combined resonant soft X-ray reflectivity and electric transport study of $$\hbox {LaAlO}_3$$

LaAlO
3

/$$\hbox {SrTiO}_3$$

SrTiO
3

field effect devices. The depth profiles with atomic layer resolution that are obtained from the resonant reflectivity reveal a pronounced temperature dependence of the two-dimensional electron liquid at the $$\hbox {LaAlO}_3$$

LaAlO
3

/$$\hbox {SrTiO}_3$$

SrTiO
3

interface. At room temperature the corresponding electrons are located close to the interface, extending down to 4 unit cells into the $$\hbox {SrTiO}_3$$

SrTiO
3

substrate. Upon cooling, however, these interface electrons assume a bimodal depth distribution: They spread out deeper into the $$\hbox {SrTiO}_3$$

SrTiO
3

and split into two distinct parts, namely one close to the interface with a thickness of about 4 unit cells and another centered around 9 unit cells from the interface. The results are consistent with theoretical predictions based on oxygen vacancies at the surface of the $$\hbox {LaAlO}_3$$

LaAlO
3

film and support the notion of a complex interplay between structural and electronic degrees of freedom.
Reliability of quantitative transverse relaxation time mapping with $${\text{T}}_{{2}}$$-prepared whole brain pCASL
Authors: Schidlowski Martin , Stirnberg Rüdiger , Stöcker Tony , Rüber Theodor 
Published: October 2020

AbstractArterial spin labeling (ASL) is increasingly applied for cerebral blood flow mapping, but $${\text{T}}_{{2}}$$

T
2

relaxation of the ASL signal magnetization is often ignored, although it may be clinically relevant. To investigate the extent, to which quantitative $${\text{T}}_{{2}}$$

T
2

values in gray matter (GM) obtained by pseudocontinuous ASL (pCASL) perfusion MRI can be reproduced, are reliable and a potential neuroscientific biomarker, a prospective study was performed with ten healthy volunteers (5F,28 ± 3y) at a 3 T scanner. A $${\text{T}}_{{2}}$$

T
2

-prepared pCASL sequence enabled the measurement of quantitative $${\text{T}}_{{2}}$$

T
2

and perfusion maps. $${\text{T}}_{{2}}$$

T
2

times were modeled per voxel and analyzed within four GM-regions-of-interest (ROI). The intraclass correlation coefficients (ICCs) of the quantified ASL-$${\text{T}}_{{2}}$$

T
2

varied across brain regions. When averaged across subjects and postlabeling delays (PLDs), the ICCs ranged from reasonable values in parietal regions (ICC = 0.56) to smaller values in frontal regions (ICC = 0.36). Corresponding subject-averaged within-subject coefficients of variation (WSCVs) showed good test–retest measurement precision ($${\text{WSCV}}_{{{\text{PLD}}}} \le 0.14$$

WSCV
PLD

≤
0.14

for all PLDs), but more pronounced inter-subject variance. Reliability and precision of quantified ASL-$${\text{T}}_{{2}}$$

T
2

were region-, PLD- and subject-specific, showing fair to robust results in occipital, parietal and temporal ROIs. The results give rise to consider the method for future cerebral studies, where variable perfusion or altered $${\text{T}}_{{2}}$$

T
2

times are suspected.
Migration-induced transition in social structures: a view through the Sakoda model of social interactions
Authors: Goles Eric , Mascareño Aldo , Medina Pablo , Rica Sergio 
Published: October 2020

AbstractWe study the dynamics of three populations evolving in a two-dimensional discrete grid according to rules of attraction, rejection, or indifference following the framework of the seminal model by Sakoda and we apply it to migration phenomena. An interesting feature of the Sakoda model is the existence of a Potts-like energy which, as a common principle, decreases as time passes by. Here we consider the evolution of two populations until stabilization, then, we perturb this attractor by the inclusion of a third arrival: the immigrants. We show the conditions under which this irruption does not alter significantly the previous attractor (a sociological morphostatic behaviour) or it is dramatically changed (morphogenetic behaviour). We observe empirically that for a morphostatic behaviour the energy decreases while for morphogenesis this energy increases, revealing an escalation of social tension.
Pancreatic duct ligation reduces premalignant pancreatic lesions in a Kras model of pancreatic adenocarcinoma in mice
Authors: Cáceres Marta , Quesada Rita , Iglesias Mar , Real Francisco X. , Villamonte Maria , de Villarreal Jaime Martinez , Pérez Mónica , Andaluz Ana , Moll Xavier , Berjano Enrique , Dorcaratto Dimitri , Sánchez-Velázquez Patricia , Grande Luís , Burdío Fernando 
Published: October 2020

AbstractPancreatic duct ligation (PDL) in the murine model has been described as an exocrine pancreatic atrophy-inducing procedure. However, its influence has scarcely been described on premalignant lesions. This study describes the histological changes of premalignant lesions and the gene expression in a well-defined model of pancreatic ductal adenocarcinoma by PDL. Selective ligation of the splenic lobe of the pancreas was performed in Ptf1a-Cre(+/ki); K-ras LSLG12Vgeo(+/ki) mice (PDL-Kras mice). Three experimental groups were evaluated: PDL group, controls and shams. The presence and number of premalignant lesions (PanIN 1–3 and Atypical Flat Lesions—AFL) in proximal (PP) and distal (DP) pancreas were studied for each group over time. Microarray analysis was performed to find differentially expressed genes (DEG) between PP and PD. Clinical human specimens after pancreaticoduodenectomy with ductal occlusion were also evaluated. PDL-Kras mice showed an intense pattern of atrophy in DP which was shrunk to a minimal portion of tissue. Mice in control and sham groups had a 7 and 10-time increase respectively of risk of high-grade PanIN 2 and 3 and AFL in their DP than PDL-Kras mice. Furthermore, PDL-Kras mice had significantly less PanIN 1 and 2 and AFL lesions in DP compared to PP. We identified 38 DEGs comparing PP and PD. Among them, several mapped to protein secretion and digestion while others such as Nupr1 have been previously associated with PanIN and PDAC. PDL in Ptf1a-Cre(+/ki); K-ras LSLG12Vgeo(+/ki) mice induces a decrease in the presence of premalignant lesions in the ligated DP. This could be a potential line of research of interest in some cancerous risk patients.
Gene expression analysis in formalin fixed paraffin embedded melanomas is associated with density of corresponding immune cells in those tissues
Authors: Kwak Minyoung , Erdag Gulsun , Slingluff Craig L. 
Published: October 2020

AbstractImmune cell infiltrates in melanoma have important prognostic value. Gene expression analysis may simultaneously quantify numbers and function of multiple immune cell subtypes in formalin-fixed paraffin-embedded (FFPE) tissues. Prior studies report single gene expression can represent individual immune cell subtypes, but this has not been shown in FFPE melanomas. We hypothesized that gene expression profiling of human melanomas using a new RNA expression technology in FFPE tissue would correlate with the same immune cells identified by immunohistochemistry (IHC). This retrospective study included melanoma specimens analyzed by IHC on tumor tissue microarray (TMA) cores and by gene expression profiling with EdgeSeq Immuno-Oncology Assay using qNPA technology on the corresponding tumors. Standardized gene expression levels were analyzed relative to enumerated cells by IHC using Spearman rank test to calculate r-values. Multivariate analysis was performed by Kruskal–Wallis test. 119 melanoma specimens had both IHC and gene expression information available. There were significant associations between the level of gene expression and its quantified IHC cell marker for CD45+, CD3+, CD8+, CD4+, and CD20+cells (allp < 0.001). There were also significant associations with exhaustion markers FoxP3+, PD-1+, and PD-L1+(allp ≤ 0.0001). This new qNPA technology is useful to quantify intratumoral immune cells on FFPE specimens through RNA gene expression in metastatic melanoma. As previous studies have shown on other solid human tumors, we also confirm that the expression level of a single gene may be used to represent a single IHC immune cell marker in melanoma.
Bi2WO6–BiOCl heterostructure with enhanced photocatalytic activity for efficient degradation of oxytetracycline
Authors: Guo Mengfan , Zhou Zhaobo , Yan Shengnan , Zhou Pengfei , Miao Feng , Liang Shijun , Wang Jinlan , Cui Xinyi 
Published: October 2020

AbstractThe application of BiOCl in photocatalysis has been restricted by its low utilization of solar energy and fast recombination of charge carriers. In this study, zero-dimensional (0D) Bi2WO6 nanoparticles/two-dimensional (2D) layered BiOCl heterojunction composite was successfully constructed by facile hydrothermal and solvothermal methods. The most favorable sunlight photocatalytic activity was achieved for the as-prepared Bi2WO6–BiOCl composites with a ratio of 1%. The photocatalytic rate and mineralization efficiency of one typical antibiotic (i.e., oxytetracycline) over 1% Bi2WO6–BiOCl was about 2.7 and 5.3 times as high as that of BiOCl. Both experimental characterizations and density functional theory (DFT) calculations confirmed that the excellent photocatalytic performance mainly arised from the effective charge separation along the Bi2WO6 and BiOCl heterojunction interface. The effective electron transfer was driven by the internal electric field at the interfacial junction. In addition, 1% Bi2WO6–BiOCl exhibited excellent stability, and no apparent deactivation was observed after 4 test cycles. Therefore, the 0D/2D Bi2WO6–BiOCl heterojunction showed a great potential for the photocatalytic degradation of emerging organic pollutants.
Integrin alpha V (ITGAV) expression in esophageal adenocarcinoma is associated with shortened overall-survival
Authors: Loeser Heike , Scholz Matthias , Fuchs Hans , Essakly Ahlem , Damanakis Alexander Iannos , Zander Thomas , Büttner Reinhard , Schröder Wolfgang , Bruns Christiane , Quaas Alexander , Gebauer Florian 
Published: October 2020

AbstractValid biomarkers for a better prognostic prediction of the clinical course in esophageal adenocarcinoma (EAC) are still not implemented. Integrin alpha V (ITGAV), a transmembrane glycoprotein responsible for cell-to-matrix binding has been found to enhance tumor progression in several tumor entities. The expression pattern and biological role of ITGAV expression in esophageal adenocarcinoma (EAC) has not been analyzed so far. Aim of the study is to evaluate the expression level of ITGAV in a very large collective of EAC and its impact on individual patients´ prognosis. 585 patients with esophageal adenocarcinoma were analyzed immunohistochemically for ITGAV. The data was correlated with clinical, pathological and molecular data (TP53, HER2/neu, c-myc, GATA6, PIK3CA and KRAS). A total of 85 patients (14.3%) out of 585 analyzable tumors showed an ITGAV expression and intratumoral heterogeneity was low. ITGAV expression was correlated with a shortened overall-survival in the patients´ group that underwent primary surgery (p = 0.014) but not in the group of patients that received neoadjuvant treatment before surgery. No correlation between any of the analyzed molecular marker (mutations or amplifications) (TP53, HER2, c-myc, GATA6, PIK3CA and KRAS) and ITGAV expression could be observed. A multivariate cox-regression model was performed which showed tumor stage, lymph node metastasis and ITGAV expression as independent prognostic markers for overall-survival in the group of patients without neoadjuvant treatment. ITGAV expression is correlated with an impaired patient outcome in the group of patients without neoadjuvant therapy and serves as a prognostic factor in EAC.
A nanocomposite hydrogel with catalytic properties for trace-element detection in real-world samples
Authors: Bertolacci Laura , Valentini Paola , Pompa Pier Paolo 
Published: October 2020

AbstractA nanocomposite material characterized by peroxidase-like properties was developed through the dispersion of platinum nanoparticles (PtNPs) inside a hydrogelic matrix. The integration of the PtNP catalysts within the matrix resulted in their stabilization, preventing aggregation and precipitation in media of environmental interest, characterized by high ionic strength and by the presence of organic solutes. A thorough optimization of the matrix design was aimed at granting optimal diffusion of the reagents, in order to maintain the efficiency of the catalytic action. Such combined features allowed the implementation and prototyping of a colorimetric method for the detection of mercury in environmental water samples. The assay was based on a chromogenic reaction catalyzed by the peroxidase-like activity of PtNPs and its specific inhibition caused by trace amounts of mercury.