gebhart/patrepeval huggingface dataset:
Multi-Band OFDM versus Single-Carrier DP-QPSK for 100 Gbps Long-Haul WDM Transmission (2012)

We experimentally compare the performance of coherent dual-polarization multi-band OFDM (DP-MB-OFDM) and coherent single-carrier dual-polarization QPSK (DP-QPSK) for 100 Gbps long-haul WDM transport. We show that, after transmission over 1000 km of DCF-free G.652 fiber line, DP-MB-OFDM and DP-QPSK have nearly the same performance at 100 Gbps.
Optimal Encoding of Contextuality in Polarization Entangled Photon States (2022)

It is shown that the simultaneous validity of seemingly contradictory statements about the linear and circular polarization of two photons is optimized by a careful adjustment of the balance between entanglement and local polarization.
Circle criteria in recursive identification (1997)

Positive real conditions and differential sector conditions have recently been shown to imply global convergence w.p. 1, for recursive identification schemes based on a class of single-input/single-output linear Wiener models. The models consist of linear dynamics followed by a static output nonlinearity. The model structure is hence closely related to that of the Lure problem in the stability theory of feedback systems. This paper proves that the conditions for convergence can be transformed to graphical circle criteria, depending on the sector conditions and on the Nyquist plot of a transfer function related to the prior knowledge of the poles of the identified system.
An Analytical View of Multiple CDNs Collaboration (2014)

Content Distribution Networks (CDN) are a well-known and accepted way to deliver content. Considering the ever growing number of users and also the growing number of small localized CDNs, there is a strong trend for collaboration among them. CDN collaboration may cause cost reduction for CDN providers and better quality of experience for the end user. However, CDN collaboration raises performance issues. This paper presents an analytical view of collaboration among CDNs. Our analytical approach provides studies of collaboration performance through metrics such as cache hit, latency, and number of caches. Then, we present a collaboration overhead representation, considering two collaboration request routing strategies. From our performance analyses, we show that CDN collaboration can reduce response time and could also help a primary CDN deal with a flash crowd event.
Pixel-Parallel Image-Matching Circuit Schemes for a Single-Chip Fingerprint Sensor and Identifier (2005)

This paper describes pixel-parallel image-matching circuit schemes that provide the optimal binarization, the high-speed low-power comparison, and the accurate matching of fingerprint images needed for fingerprint verification. Image binarizing is adjusted adaptively during the fingerprint sensing operation. The obtained image is compared with the template in the pixel array, and the results from all of the pixels are totaled by a variable-delay circuit at high speed and low power. For accurate matching, the image is scanned by shifting it in the pixel array while maintaining whole image. The experimental results demonstrate that the proposed schemes provide optimal binary images of most fingers under any condition and environment, 11-μs 147-μW totaling of results from 20,584 pixels, and wide-range image scanning and accurate matching for fingerprint images. These schemes are effective for fast and low-power fingerprint verification for a single-chip fingerprint sensor and identifier.
Identification of gene differences between dogs with poor periodontal scores compared dogs with good periodontal scores (2008)

Fifty‐six (&gt; 1 years of age) spayed/neutered beagles were identified for this study. Dogs were scored for periodontal lesions and fed commercially available adult foods. At the time around scoring, a blood sample was drawn into a PAXgene Blood RNA tube. RNA was extracted according to the procedures provided in the PAXgene Blood RNA Kit Handbook (Qiagen, Valencia, CA). RNA was hybridized to an Affymetrix GeneChip Canine‐2 Genome Arrays and normalized using Robust Multi‐Array Average. Transcripts having a P &lt; 0.01 (following a false discovery rate adjustment value of 0.1) and a fold change range of at least 1.2 were considered different among the two groups. Analysis of the RNA found differences in 284 genes between the dogs with poor periodontal scores and dogs with good periodontal scores. Of the genes identified, 157 were up‐regulated and 127 down‐regulated in dogs with poor periodontal scores and dogs with good periodontal scores. Genes associated with inflammation process and pain response were increased, while cell adhesion and attachment, heavy metal binding, glycoprotein synthesis, and cytoskeleton structure support were decreased in dogs with poor periodontal scores compared to dogs with good periodontal scores.
Identification of a CpG Island Methylator Phenotype that Defines a Distinct Subgroup of Glioma (2019)

We have profiled promoter DNA methylation alterations in 272 glioblastoma tumors in the context of The Cancer Genome Atlas (TCGA). We found that a distinct subset of samples displays concerted hypermethylation at a large number of loci, indicating the existence of a glioma-CpG island methylator phenotype (G-CIMP). We validated G-CIMP in a set of non-TCGA glioblastomas and low-grade gliomas. G-CIMP tumors belong to the proneural subgroup, are more prevalent among lower-grade gliomas, display distinct copynumber alterations, and are tightly associated with IDH1 somatic mutations. Patients with G-CIMP tumors are younger at the time of diagnosis and experience significantly improved outcome. These findings identify G-CIMP as a distinct subset of human gliomas on molecular and clinical grounds.
Incorporation in vivo of [32P]orthophosphate and [Me-3H]choline into rough microsomal, Golgi, and plasma membranes of rat liver (1977)

To study membrane biogenesis and to test the validity of the endomembrane flow hypothesis, incorporation of 32 P and [Me- 3 H]choline in vivo into membranes of the rat liver was followed. Rough microsomal, Golgi-rich, and plasma membrane fractions were monitored with marker enzyme assays and shown with morphometric analysis to contain 82% rough microsomes, at least 70% Golgi complexes, and 88% plasma membranes, respectively. Membrane subfractions from the rough microsomal and Golgi-rich fractions were prepared by sonic disruption.At 5 to 30 min after 32 P injection, the specific radioactivity of phosphatidylcholine was higher in the rough microsomal membranes than in the Golgi membranes. From 1 to 3 h, the specific activity of phosphatidylcholine in Golgi membranes became higher and reached the maximum at about 3 h. Although the plasma membrane had the lowest specific radioactivity throughout 0.25–3 h, it increased rapidly thereafter to attain the highest specific activity at 5 h. Both rough microsomal and plasma membranes reached their maxima at 5 h.The specific radioactivity of [ 32 P]phosphatidylethanolamine in the three membrane fractions was similar to that of [ 32 P]phosphatidylcholine except from 5 to 30 min, when the specific radioactivity of phosphatidylethanolamine in the Golgi membranes was similar to the rough microsomal membranes.At 15 min to 5 h after [Me- 3 H]choline injection, more than 90% of the radioactivity in all the membranes was acid-precipitable. The specific radioactivities of the acid-precipitated membranes, expressed as dpm per milligram protein, reached the maximum at 3 h. After [Me- 3 H]choline injection, the specific radioactivity of phosphatidylcholine separated from the lipid extract of the acid-precipitated membranes (dpm per micromole phosphorus) did not differ significantly in the three membrane fractions. The results indicated rapid incorporation of choline into membrane phosphatidylcholine by the rough endoplasmic reticulum, Golgi, and plasma membranes simultaneously.The data with both 32 P and [Me- 3 H]choline precursors did not support the endomembrane flow hypothesis. The Golgi complexes apparently synthesized phosphatidylethanolamine and incorporated choline into phosphatidylcholine as well as the endoplasmic reticulum. The results are discussed with relevance to current hypotheses on the biogenesis and transfer of membrane phospholipids.
Deprotonation and Cation Adsorption on the NiOOH/Water Interface: A Grand-Canonical First-Principles Investigation (2021)

Nickel-based oxides are highly active, cost effective materials for the oxygen evolution reaction in alkaline conditions. Recent experimental studies have revealed the importance of surface deprotonation and alkali metal cation adsorption on the activity of Ni oxide surfaces, in contact with aqueous alkaline electrolyte. As a first step to elucidate the role of the alkali adsorption for the activity, we performed first-principles electronic structure calculations to address the stable surface structures of beta-NiOOH(0001) as a function of the operating conditions in an electrochemical environment. We present a grand-canonical approach to compute the surface Pourbaix diagram of the beta-NiOOH/water interface for the processes of deprotonation and alkali metal cation adsorption. The results of this study emphasize the importance of double layer effects, including the adsorbate-induced change of surface dipole moments and the rearrangement of water molecules due to their strong interaction with the adsorbed species, for the most stable interface structure.
Construction of a Highly Active Xylanase Displaying Oleaginous Yeast: Comparison of Anchoring Systems (2014)

Three Yarrowia lipolytica cell wall proteins (YlPir, YlCWP1 and YlCBM) were evaluated for their ability to display the xylanase TxXYN from Thermobacillus xylanilyticus on the cell surface of Y. lipolytica. The fusion proteins were produced in Y. lipolytica JMY1212, a strain engineered for mono-copy chromosomal insertion, and enabling accurate comparison of anchoring systems. The construction using YlPir enabled cell bound xylanase activity to be maximised (71.6 U/g). Although 48% of the activity was released in the supernatant, probably due to proteolysis at the fusion zone, this system is three times more efficient for the anchoring of TxXYN than the YlCWP1 system formerly developed for Y. lipolytica. As far as we know it represents the best displayed xylanase activity ever published. It could be an attractive alternative anchoring system to display enzymes in Y. lipolytica.
In situ scanning tunneling microscopy observations of polycrystalline MgO(001) tunneling barriers grown on amorphous CoFeB electrode (2007)

Topological surface analysis using in situ scanning tunneling microscopy was performed for highly oriented polycrystalline (textured) MgO(001) tunneling barrier layers grown on amorphous CoFeB electrode layers. The microscopy revealed a MgO surface structure in which nanosized grains were dispersed on clusters that originated from the CoFeB underlayer. In situ annealing reduced this surface roughness. Local tunneling spectroscopy measurements revealed the formation of a nearly perfect and uniform tunneling barrier in spite of grain boundaries in the textured MgO(001) layer, which is consistent with the fact that textured CoFeB∕MgO∕CoFeB and fully epitaxial MgO-based magnetic tunnel junctions exhibit comparable spin-dependent tunneling properties.
Characterization and Modeling of UHF RFID Channels for Ranging and Localization (2012)

A comprehensive characterization and model of the UHF RFID channel is presented for narrowband through ultra-wideband tag localization systems. The analyses are based on ultra-wideband channel measurements in a warehouse portal, centered around 900 MHz. Measured scenarios include an electromagnetically transparent pallet and a pallet containing liquids, each for a portal shielded by metal backplanes and for a portal shielded by absorbing material. The presented analyses cover the individual channels to and from the tag, the feedback channel, and the backscatter channel, for bi- and monostatic reader setups. We find that the direct path is rarely dominant on the backscatter link despite clear line-of-sight conditions and directive reader antennas. The power ratio between the direct and all indirect paths ranges from -20 through 5 dB for the more common metal portal, and RMS delay spreads are in the range of 10-80 ns. Since only the direct (line-of-sight) path carries the correct distance/direction information, tag localization in such portals requires high robustness with respect to weak line-of-sight components. We also show that classical channel models in UHF RFID, despite predicting the incident power level at the tag accurately, produce far too optimistic estimates of channel parameters relevant to ranging and localization.
Molecular beam epitaxy and structural anisotropy of m-plane InN grown on free-standing GaN (2008)

This study reports on the growth of high-quality nonpolar m-plane [11¯00] InN films on free-standing m-plane GaN substrates by plasma-assisted molecular beam epitaxy. Optimized growth conditions (In/N ratio ∼1 and T=390–430 °C) yielded very smooth InN films with undulated features elongated along the [112¯0] orientation. This directionality is associated with the underlying defect structure shown by the anisotropy of x-ray rocking curve widths parallel to the [112¯0] (i.e., 0.24°–0.34°) and [0001] (i.e., 1.2°–2.7°) orientations. Williamson–Hall analysis and transmission electron microscopy identified the mosaic tilt and lateral coherence length and their associations with different densities of dislocations and basal-plane stacking faults. Ultimately, very low band gap energies of ∼0.67 eV were measured by optical absorption similar to the best c-plane InN.
Turnover of heparan sulfate proteoglycans from substratum adhesion sites of murine fibroblasts. (1984)

Substratum adhesion sites from murine Balb/c SVT2 fibroblasts are enriched in heparan sulfate proteoglycans which have been implicated in mediating adhesion of these cells to a fibronectin-adsorbed tissue culture substratum. Most of the heparan sulfate isolated from newly formed adhesion sites is found covalently attached to protein as proteoglycan while a significant portion of heparan sulfate from older sites has been identified as a single-chain species. This observation suggests that there may be catabolism of the heparan sulfate proteoglycan during the "maturation" of these adhesion sites at the cell's undersurface. Zwittergent 3-12 selectively extracts the single-chain class of heparan sulfate from either newly formed or "mature" adhesion sites while leaving the proteoglycan firmly bound in these sites. In an effort to further characterize the metabolism of these proteoglycans, substratum adhesion sites were isolated at various times after the cells had been pulse-radiolabeled using radioactive sulfate and subsequently chased. Greater than 80% of the sulfate-radiolabeled material is lost from the substratum-attached material within 24-48 h. Characterization of both the Zwittergent-soluble and -resistant heparan sulfate indicated that there was an initial accumulation followed by a rapid loss of a portion of the radiolabeled heparan sulfate as the single-chain Zwittergent-soluble class. However, most of the heparan sulfate proteoglycan was lost from the adhesion sites following approximately a 4-h time lag during the chase period without going through a smaller molecular weight intermediate. The turnover properties of the heparan sulfate proteoglycan in the EGTA-detachable cells were different from those in the substratum-attached fraction of the cell. The significance of these two different mechanisms of turnover of heparan sulfate proteoglycan in adhesion sites is discussed in relation to the role of this proteoglycan in mediating adhesion processes.
Mixed Frequency Excitation of an Electrostatically Actuated Resonator (2015)

We investigate experimentally and theoretically the dynamics of a capacitive resonator under mixed frequency excitation of two AC harmonic signals. The resonator is composed of a proof mass suspended by two cantilever beams. Experimental measurements are conducted using a laser Doppler vibrometer to reveal the interesting dynamics of the system when subjected to two-source excitation. A nonlinear single-degree-of-freedom model is used for the theoretical investigation. The results reveal combination resonances of additive and subtractive type, which are shown to be promising to increase the bandwidth of the resonator near primary resonance frequency. Our results also demonstrate the ability to shift the combination resonances to much lower or much higher frequency ranges. We also demonstrate the dynamic pull-in instability under mixed frequency excitation.
Chromatin-targeting small molecules cause class-specific transcriptional changes in pancreatic endocrine cells (2012)

Under the instruction of cell-fate-determining, DNA-binding transcription factors, chromatin-modifying enzymes mediate and maintain cell states throughout development in multicellular organisms. Currently, small molecules modulating the activity of several classes of chromatin-modifying enzymes are available, including clinically approved histone deacetylase (HDAC) and DNA methyltransferase (DNMT) inhibitors. We describe the genome-wide expression changes induced by 29 compounds targeting HDACs, DNMTs, histone lysine methyltransferases (HKMTs), and protein arginine methyltransferases (PRMTs) in pancreatic α- and β-cell lines. HDAC inhibitors regulate several hundred transcripts irrespective of the cell type, with distinct clusters of dissimilar activity for hydroxamic acids and orthoamino anilides. In contrast, compounds targeting histone methyltransferases modulate the expression of restricted gene sets in distinct cell types. For example, we find that G9a/GLP methyltransferase inhibitors selectively up-regulate the cholesterol biosynthetic pathway in pancreatic but not liver cells. These data suggest that, despite their conservation across the entire genome and in different cell types, chromatin pathways can be targeted to modulate the expression of selected transcripts.
High-resolution analysis of long-term serum antibodies in humans following convalescence of SARS-CoV-2 infection (2022)

Long-term antibody responses to SARS-CoV-2 have focused on responses to full-length spike protein, specific domains within spike, or nucleoprotein. In this study, we used high-density peptide microarrays representing the complete proteome of SARS-CoV-2 to identify binding sites (epitopes) targeted by antibodies present in the blood of COVID-19 resolved cases at 5 months post-diagnosis. Compared to previous studies that evaluated epitope-specific responses early post-diagnosis (< 60 days), we found that epitope-specific responses to nucleoprotein and spike protein have contracted, and that responses to membrane protein have expanded. Although antibody titers to full-length spike and nucleoprotein remain steady over months, taken together our data suggest that the population of epitope-specific antibodies that contribute to this reactivity is dynamic and evolves over time. Further, the spike epitopes bound by polyclonal antibodies in COVID-19 convalescent serum samples aligned with known target sites that can neutralize viral activity suggesting that the maintenance of these antibodies might provide rapid serological immunity. Finally, the most dominant epitopes for membrane protein and spike showed high diagnostic accuracy providing novel biomarkers to refine blood-based antibody tests. This study provides new insights into the specific regions of SARS-CoV-2 targeted by serum antibodies long after infection.
Information embedding in electrophotographic document forms through laser intensity modulation &#x2013; a communications systems perspective (2009)

Printed documents have been used as accessories to fraud, terrorist attacks, forgery, and extortion. Tracking down the printer that was used to produce such documents may be beneficial to law enforcement and military agents. Printer identification requires the extraction of a set of features or signatures that uniquely represent the printer. These signatures can be inherent or intrinsic to the printing process, or they can be artificially produced and embedded during the printing process. In this paper, the hidden information for an electrophotographic (EP) printer is generated by altering the laser beam intensity from scan line to scan line, which results in dot gain, and shift in the horizontal position of the dots. Techniques from digital communications are applied to this embedding signal to make it imperceptible, but reliably transmitted and recovered. The embedding signal is inserted in the frames or borders of security documents such as bank notes, statements, and event tickets. Such an embedding scheme offers a content-independent domain for marking the print compared to using text characters or halftone images.
Cross-Reactive Immunity to Mycobacterium tuberculosis DosR Regulon-Encoded Antigens in Individuals Infected with Environmental, Nontuberculous Mycobacteria (2009)

Mycobacterium tuberculosis DosR regulon-encoded antigens are highly immunogenic in M. tuberculosis-infected humans and are associated with latent tuberculosis infection. We have investigated the hypothesis that infection with or exposure to nontuberculous mycobacteria (NTM) can induce cross-reactive immunity to M. tuberculosis DosR regulon-encoded antigens since responsiveness has been observed in non-M. tuberculosis-exposed but purified protein derivative-responsive individuals. M. tuberculosis DosR regulon-encoded antigen-specific T-cell responses were studied in peripheral blood mononuclear cells (PBMCs) of NTM-infected/exposed individuals. BLASTP was used to determine the presence of M. tuberculosis DosR regulon-encoded protein orthologs among environmental mycobacteria and nonmycobacteria. Significant gamma interferon production was observed in PBMCs from NTM-infected/exposed individuals in response to M. tuberculosis DosR regulon-encoded antigens. DosR regulon-encoded protein orthologs were prominently present in tuberculous and environmental mycobacteria and surprisingly also in nonmycobacteria. The ubiquitous presence of the highly conserved DosR master regulator protein Rv3133c suggests that this is a general adaptive bacterial response regulator. We report a first series of M. tuberculosis antigens to which cross-reactive immunity is induced by NTM infection/exposure. The high conservation of M. tuberculosis DosR regulon-encoded antigens most likely enables them to induce cross-reactive T-cell responses.
Low-loss hybrid silicon tapers (2011)

Two types of hybrid silicon tapers are studied. Single taper loss is 0.3 - 0.5 dB, enabling integration of III/V actives on silicon-on-insulator passive circuitry with low loss.
Bogoliubov-like mode in the Tonks-Girardeau Gas (2005)

We reformulate 1D boson-fermion duality in path-integral terms. The result is a 1D counterpart of the boson-fermion duality in the 2D Chern-Simons gauge theory. The theory is consistent and enables, using standard resummation techniques, to obtain the long-wave-length asymptotics of the collective mode in 1D boson systems at the Tonks-Girardeau regime. The collective mode has the dispersion of Bogoliubov phonons: $ω(q)=q \sqrt{\barρU(q)/m}$, where $\barρ$ is the bosons density and $U(q)$ is a Fourier component of the two-body potential.