gebhart/patrepeval huggingface dataset:
A Tracking Framework for Accurate Face Localization (2006)

This paper proposes a complete framework for accurate face localization on video frames. Detection and forward tracking are first combined according to predefined rules to get a first set of face candidates. Backward tracking is then applied to provide another set of pos-sible localizations. Finally a dynamic programming algorithm is used to select the candidates that minimize a specific cost function. This method was designed to handle different scale, pose and lighting conditions. The experiments show that it improves the face detection rate compared to a frame-based detector and provides a higher precision than a forward information-based tracker.
Molecular cloning of ten distinct hypervariable regions from the cellulose synthase gene superfamily in aspen trees (2004)

Recent molecular genetic data suggest that cellulose synthase (CesA) genes coding for the enzymes that catalyze cellulose biosynthesis (CESAs) in Arabidopsis and other herbaceous plants belong to a large gene family. Much less is known about CesA genes from forest trees. To isolate new CesA genes from tree species, discriminative but easily obtainable homologous DNA probes are required. Hypervariable regions (HVRII) of CesA genes represent highly divergent DNA sequences that can be used to examine structural, expressional and functional relationships among CesA genes. We used a reverse transcriptase-polymerase chain reaction (RT-PCR)-based technique to identify HVRII regions from eight types of CesA genes and two types of CesA-like D (CslD) genes in quaking aspen (Populus tremuloides Michx.). Comparison of these aspen CESA/CSLD HVRII regions with the predicted proteins from eight full-length CesA/CslD cDNAs available in our laboratory and with searches for aspen CesA/CslD homologs in the recently released Populus trichocarpa Torr. & A. Gray. genome confirmed the utility of this approach in identifying several CesA/CslD gene members from the Populus genome. Phylogenetic analysis of 56 HVRII domains from a variety of plant species suggested that at least six distinct classes of CESAs exist in plants, supporting a previous proposal for renaming HVRII regions as class-specific regions (CSR). This method of CSR cloning could be applied to other crop plants and tree species, especially softwoods, for which the whole genome sequence is unlikely to become available in the near future because of the large size of these genomes.
Prediction of post‐translational glycosylation and phosphorylation of proteins from the amino acid sequence (2004)

Post-translational modifications (PTMs) occur on almost all proteins analyzed to date. The function of a modified protein is often strongly affected by these modifications and therefore increased knowledge about the potential PTMs of a target protein may increase our understanding of the molecular processes in which it takes part. High-throughput methods for the identification of PTMs are being developed, in particular within the fields of proteomics and mass spectrometry. However, these methods are still in their early stages, and it is indeed advantageous to cut down on the number of experimental steps by integrating computational approaches into the validation procedures. Many advanced methods for the prediction of PTMs exist and many are made publicly available. We describe our experiences with the development of prediction methods for phosphorylation and glycosylation sites and the development of PTM-specific databases. In addition, we discuss novel ideas for PTM visualization (exemplified by kinase landscapes) and improvements for prediction specificity (by using ESS--evolutionary stable sites). As an example, we present a new method for kinase-specific prediction of phosphorylation sites, NetPhosK, which extends our earlier and more general tool, NetPhos. The new server, NetPhosK, is made publicly available at the URL http://www.cbs.dtu.dk/services/NetPhosK/. The issues of underestimation, over-prediction and strategies for improving prediction specificity are also discussed.
Thermal conductivity of coated filler composites (1986)

The temperature field and thermal conductivity of a coated-fiber composite were studied analytically. The analytical model is based on the classical separation of variables and equivalent-inclusion method. Closed-form solutions are given for the thermal conductivity of a coated-fiber composite. The present results on the temperature gradient in a thin coating were compared with those based on the thin-coating model by Walpole, resulting in a complete agreement when the thickness of the coating approaches zero. Then, a parametric study was conducted to study the effect of coating properties and other parameters on the thermal conductivity of the composite. It was found in this parametric study that the use of highly conductive (or resistive) coating, even if its thickness is small, is quite effective in enhancing the overall thermal conductivity (or resistivity) of the composite.
Visualization of blood cell contrast in nailfold capillaries with high-speed reverse lens mobile phone microscopy (2020)

Quantification of optical absorption gaps in nailfold capillaries has recently shown promise as a non-invasive technique for neutropenia screening. Here we demonstrate a low-cost, portable attachment to a mobile phone that can resolve optical absorption gaps in nailfold capillaries using a reverse lens technique and oblique 520nm illumination. Resolution <4<i>μ</i>m within a 1mm<sup>2</sup> on-axis region is demonstrated, and wide field of view (3.5mm × 4.8mm) imaging is achieved with resolution <6<i>μ</i>m in the periphery. Optical absorption gaps (OAGs) are visible in superficial capillary loops of a healthy human participant by an ∼8-fold difference in contrast-to-noise ratio with respect to red blood cell absorption contrast. High speed video capillaroscopy up to 240 frames per second (fps) is possible, though 60fps is sufficient to resolve an average frequency of 37 OAGs/minute passing through nailfold capillaries. The simplicity and portability of this technique may enable the development of an effective non-invasive tool for white blood cell screening in point-of-care and global health settings.
Anti-Aβ Autoantibodies in Amyloid Related Imaging Abnormalities (ARIA): Candidate Biomarker for Immunotherapy in Alzheimer’s Disease and Cerebral Amyloid Angiopathy (2015)

Amyloid-related imaging abnormalities (ARIA) represent the major severe side effect of amyloid-beta (Aβ) immunotherapy for Alzheimer's disease (AD). Early biomarkers of ARIA represent an important challenge to ensure safe and beneficial effects of immunotherapies, given that different promising clinical trials in prodromal and subjects at risk for AD are underway. The recent demonstration that cerebrospinal fluid (CSF) anti-Aβ autoantibodies play a key role in the development of the ARIA-like events characterizing cerebral amyloid angiopathy-related inflammation generated great interest in the field of immunotherapy. Herein, we critically review the growing body of evidence supporting the monitoring of CSF anti-Aβ autoantibody as a promising candidate biomarker for ARIA in clinical trials.
A translational multiplex serology approach to profile the prevalence of anti-SARS-CoV-2 antibodies in home-sampled blood (2020)

Abstract The COVID-19 pandemic has posed a tremendous challenge for the global community. We established a translational approach combining home blood sampling by finger-pricking with multiplexed serology to assess the exposure to the SARS-CoV-2 virus in a general population. The developed procedure determines the immune response in multiplexed assays against several spike (S, here denoted SPK), receptor binding domain (RBD) and nucleocapsid (NCP) proteins in eluates from dried capillary blood. The seroprevalence was then determined in two study sets by mailing 1000 blood sampling kits to random households in urban Stockholm during early and late April 2020, respectively. After receiving 55% (1097/2000) of the cards back within three weeks, 80% (878/1097) were suitable for the analyses of IgG and IgM titers. The data revealed diverse pattern of immune response, thus seroprevalence was dependent on the antigen, immunoglobulin class, stringency to include different antigens, as well as the required analytical performance. Applying unsupervised dimensionality reduction to the combined IgG and IgM data, 4.4% (19/435; 95% CI: 2.4%-6.3%) and 6.3% (28/443; 95% CI: 4.1%-8.6%) of the samples clustered with convalescent controls. Using overlapping scores from at least two SPK antigens, prevalence rates reached 10.1% (44/435; 95% CI: 7.3%-12.9%) in study set 1 and 10.8% (48/443; 95% CI: 7.9%-13.7%). Measuring the immune response against several SARS-CoV-2 proteins in a multiplexed workflow can provide valuable insights about the serological diversity and improve the certainty of the classification. Combining such assays with home-sampling of blood presents a viable strategy for individual-level diagnostics and towards an unbiased assessment of the seroprevalence in a population and may serve to improve our understanding about the diversity of COVID-19 etiology. One Sentence Summary A multiplexed serology assay was developed to determine antibodies against SARS-CoV-2 proteins in home-sampled dried blood spots collected by finger pricking.
Fabrication of Three‐Dimensional Photonic Crystals Using Multibeam Interference Lithography and Electrodeposition (2009)

High-quality 3D photonic crystals are fabricated through electrodeposition into a polymer template created by multibeam interference lithography. Complete infilling of the template is achieved through electrodeposition of Cu2O, and subsequent etching of the template results in a Cu2O/air photonic crystal with the exact inverse structure of the template (see figure). The resultant photonic crystal shows a high peak reflectance at theoretically predicted wavelength.
Mechanism of integrating foreign DNA during transformation of Bacillus subtilis. (1978)

Genes encoding thymidylate synthetase from Bacillus subtilis bacteriophages were cloned in Escherichia coli. Chimeric plasmids pCD1 and pCD3 were constructed from site-specific endonuclease digests of bacteriophage phi3T DNA cloned in pMB9 in E. coli. Similar cloning techniques with bacteriophage beta22 DNA yielded chimeric plasmids pCD4, pCD5, and pCD6. Endonuclease digests of DNA from pCD1 and pCD3 propagated in E. coli or from DNA isolated from bacteriophage phi3T propagated in B. subtilis transformed B. subtilis from Thy- to Thy+. Intact DNA from bacteriophage beta22, endonuclease digests of beta22 DNA, and a chimeric plasmid (pCD5) composed only of the thybeta22 gene and pMB9 did not transform B. subtilis from Thy- to Thy+ even though pCD5 could transform Thy- E. coli to Thy+. However, if the thybeta22 fragment from pCD5 was introduced into another chimeric plasmid, pCD2, that contains a region of homology to the chromosome of B. subtilis in addition to pMB9, transformation of Thy- clones of B. subtilis was possible. Furthermore, Southern hybridization analyses of the digests of chromosomal DNA from the Thy+ transformants established that the entire chimeric plasmid was incorporated into the chromosome of B. subtilis. Treatment of these plasmids with site-specific endonucleases abolished transformation. These results indicated that the entire chimeric plasmid can be incorporated into the chromosome of B. subtilis by a Campbell-like model. Therefore, an additional mechanism for transformation exists whereby plasmids can be integrated if sufficient chromosomal homology is maintained.
A new stratified crossed stacked spiral inductor with improved self-resonance frequency (2011)

A new stratified crossed structure to decrease the parasitic capacitance of stacked spiral inductor is proposed. By shifting the neighbor trace at same layer to the adjacent, the capacitances between the inductor's strips are effectively compressed. Hence, its self-resonance frequency and quality factor can be improved. In order to evaluate the performance of the proposed inductor, both the conventional and the proposed stacked spiral inductors have been simulated and compared by Ansoft <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">™</sup> HFSS. The results show that the self-resonant frequency (f <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">SR</sub> ) and maximum quality factor (Q) of the proposed 3.4-nH inductor have 87% and 15% improvements, respectively, compared with those of the conventional inductor. Meanwhile, the presented stratified crossed structure can be integrated into RF circuits based on conventional CMOS process. All analysis and results are valuable for optimizing on-chip stacked spiral inductors, especially for their application on high frequency circuits.
Improving Outcomes through the Use of Surgical Sealants for Anastomotic Sealing during Cardiovascular Surgery (2009)

The continued need to minimize blood product usage both during and after cardiac surgical procedures has been challenged by a changing patient population, and most recently by the withdrawal of the antifibrinolytic aprotinin (Trasylol, Bayer Pharmaceuticals, West Haven, CT, USA) from the market. To meet these challenges, a variety of topical hemostatic tools have continued to emerge in the surgical armamentarium. These include hemostatic agents, adhesives, and sealants designed to control perioperative bleeding and decrease blood product utilization. Optimal application of novel topical adjuncts can be limited due to the lack of clarity on how to differentiate between these adjunctive hemostatic products and their appropriate uses. This paper will review the classes of these products, how and where such products can be used during cardiovascular surgery for achieving hemostasis, and the potential for improved outcomes through the appropriate selection and use of these agents.
Phosphor-Free Monolithic White-Light LED (2009)

<para xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink"> Phosphor-free monolithic InGaN-based white-light LED has the advantages of simpler device process and potentially higher efficiency. Several techniques have been developed for implementing such white-light LEDs. Among them, the key issue is the growth of a high-quality high-indium InGaN/GaN quantum well (QW). An underlying InGaN layer growth technique is introduced for enhancing the crystal quality of a high-indium QW. To demonstrate the superior properties of a QW grown with this technique, a green LED is fabricated based on the underlying growth technique to compare with another LED of the same emission wavelength based on the conventional growth method. Then, the underlying growth technique is used to grow three yellow-emitting QWs of high efficiency. The yellow photons mix with blue light from an overgrown blue-emitting QW to produce white light. The improved properties of the phosphor-free monolithic white-light LED are discussed in detail. </para>
Production of germline chimeric chickens following the administration of a busulfan emulsion (2005)

Busulfan (1,4-butanediol dimethanesulfonate) was used to deplete endogenous germ cells for the enhanced production of chicken germline chimeras. Utilizing immunohistochemical identification of primordial gem cells (PGCs) in Stage 27 chicken embryos, two delivery formulations were compared relative to the degree of endogenous PGC depletion, a busulfan suspension (BS) and a solublized busulfan emulsion (SBE). Both busulfan treatments resulted in a significant reduction in PGCs when compared to controls. However, the SBE resulted in a more consistent and extensive depletion of PGCs than that observed with the BS treatment. Repopulation of SBE-treated embryos with exogenous PGCs resulted in a threefold increase of PGCs in Stage 27 embryos. Subsequently, germline chimeras were produced by the transfer of male gonadal PGCs from Barred Plymouth Rock embryos into untreated and SBE-treated White Leghorn embryos. Progeny testing of the presumptive chimeras with adult Barred Plymouth Rock chickens was performed to evaluate the efficiency of germline chimera production. The frequency of germline chimerism in SBE-treated recipients increased fivefold when compared to untreated recipients. The number of donor-derived offspring from the germline chimeras also increased eightfold following SBE-treatment of the recipient embryos. These results demonstrated that the administration of a busulfan emulsion into the egg yolk of unincubated eggs improved the depletion of endogenous PGCs in the embryo and enhanced the efficiency of germline chimera production.
Graphene Epitaxy by Chemical Vapor Deposition on SiC (2011)

We demonstrate the growth of high quality graphene layers by chemical vapor deposition (CVD) on insulating and conductive SiC substrates. This method provides key advantages over the well-developed epitaxial graphene growth by Si sublimation that has been known for decades. (1) CVD growth is much less sensitive to SiC surface defects resulting in high electron mobilities of ∼1800 cm(2)/(V s) and enables the controlled synthesis of a determined number of graphene layers with a defined doping level. The high quality of graphene is evidenced by a unique combination of angle-resolved photoemission spectroscopy, Raman spectroscopy, transport measurements, scanning tunneling microscopy and ellipsometry. Our measurements indicate that CVD grown graphene is under less compressive strain than its epitaxial counterpart and confirms the existence of an electronic energy band gap. These features are essential for future applications of graphene electronics based on wafer scale graphene growth.
Percentile reference values for anthropometric body composition indices in European children from the IDEFICS study (2014)

The presented percentile curves may aid a differentiated assessment of total and abdominal adiposity in European children.
Vacuolar-type H(+)-ATPases are functionally expressed in plasma membranes of human tumor cells (1993)

Mammalian cells generally regulate their intracellular pH (pHi) via collaboration between Na(+)-H+ exchanger and HCO3- transport. In addition, a number of normal mammalian cells have been identified that express H(+)-adenosinetriphosphatases (ATPases) in their plasma membranes. Because tumor cells often maintain a high pHi, we hypothesized that they might functionally express H(+)-ATPases in their plasma membranes. In the first phase of the present study, we screened 19 normal and tumorigenic human cell lines for the presence of plasmalemmal H(+)-ATPase activity using bafilomycin A1 to inhibit V-type H(+)-ATPase and Sch-28080 to inhibit P-type H(+)-K(+)-ATPase. Bafilomycin A1 decreased pHi in the six tumor cell lines with the highest resting pHi in the absence of HCO3-. Sch-28080 did not affect pHi in any of the human cells. Simultaneous measurement of pH in the cytoplasm and in the endosomes/lysosomes localized the activity of bafilomycin to the plasma membrane in three cell lines. In the second phase of this study, these three cell lines were shown to recover from NH4(+)-induced acid loads in the absence of Na+. This recovery was inhibited by N-ethylmaleimide, bafilomycin A1, and ATP depletion and was not significantly affected by vanadate, Sch-28080, or hexamethyl amiloride. These results indicate that a vacuolar type H(+)-ATPase is expressed in the plasma membrane of some tumor cells.
A 20 MHz 6th order BiCMOS programmable filter using parasitic-insensitive integrators (2003)

A fast parasitic-insensitive continuous-time filter that uses an active integrating-capacitor is described. The filter IC consists of a sixth-order Bessel lowpass and a second-order cosine-equalizer stage. It is made up of three biquads with lowpass and bandpass outputs. Both outputs of the last stage are available with matched group-delay characteristics. The corner frequency is digitally programmable through the digital serial interface to 64 values over a 4 to 1 range. Techniques for excess-phase nulling and Gm-setting independent of supply and temperature are described. This 20 MHz, 5 V equalizer has 0.24% of total harmonic distortion with 2 Vp-p signals and is built in 1.5 mu m/4 GHz BiCMOS.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
TARGETING CANCER THERAPY: USING PROTEASE CLEAVAGE SEQUENCES TO DEVELOP MORE SELECTIVE AND EFFECTIVE CANCER TREATMENTS (2012)

This paper describes two methods for utilizing cancer associated proteases for targeting cancer therapy to the tumor. The first method is designing a drug delivery system based on liposomes that are sensitive to cancer associated proteases. Upon contact with the protease, the liposome releases its contents. The second method is designing a prodrug that is based on a porin isolated from Mycobacterium smegmatis. The porin is modified with protease consensus sequences, inhibiting its toxicity. Upon contact with the protease, the drug is activated. Protease sensitive liposomes were synthesized that were sensitive to urokinase plasminogen activator. This was done by synthesizing a cholesterol-anchored, uPA consensus – sequence-containing, acrylic acid block copolymer and using it to form a covalently bound polymer cage around the outside of a hypertonic liposome. Liposomes were synthesized that had a diameter of 136 nm. Upon addition of the polymer the diameter increased by 2.69 nm, indicating it had successfully embedded into the liposome membrane. After crosslinking with either a short peptide containing a lysine (so that it is a diamine) or ethylenediamine, the diameter increased between 5.33 nm and 14.1 nm (depending on the type and amount of the
Polished TFT's: surface roughness reduction and its correlation to device performance improvement (1997)

Chemical-mechanical polishing (CMP) has been applied to the fabrication of n-channel polysilicon thin film transistors (poly-Si TFT's). Three different polishing conditions are compared: (1) polishing before; (2) polishing after; and (3) both polishing before and after the a-Si recrystallization. Devices with no polishing act as control samples. Experiments consistently reveal that devices with post-anneal polishing exhibit the best performance, Two-fold improvement of drain current is attributed to the smoother active polysilicon surface. The electrical characteristics of a post-anneal polished TFT in terms of field effect mobility /spl mu//sub FE/, threshold voltage V/sub T/, and subthreshold swing S can be further improved if hydrogenation is employed. It is also found that a large decrease in the poly-Si surface roughness leads to higher dielectric breakdown strength and improved short-channel effects. Atomic force microscopy (AFM) and transmission electron microscopy (TEM) results are presented and correlated with electrical results.