gebhart/patrepeval huggingface dataset:
Wash-free paper diagnostics for the rapid detection of blood type antibodies (2021)

Identification of specific antibodies in patient plasma is an essential part of many diagnostic procedures and is critical for safe blood transfusion. Current techniques require laboratory infrastructure and long turnaround times which limits access to those nearby tertiary healthcare providers. Addressing this challenge, a novel and rapid paper-based antibody test is reported. We validate antibody detection with reverse blood typing using IgM antibodies and then generalise the validity by adapting to detect SARS CoV-2 (COVID-19) antibodies in patient serum samples. Reagent red blood cells (RBC) are first combined with the patient plasma containing the screened antibody and a droplet of the mixture is then deposited onto paper. The light intensity profile is analyzed to identify test results, which can be detected by eye and/or with image processing to allow full automation. The efficacy of this test to perform reverse blood typing is demonstrated and the performance and sensitivity of this test using different paper types and RBC reagents was investigated using clinical samples. As an example of the flexibility of this approach, we labeled the RBC reagent with an antibody-peptide conjugate to detect SARS CoV-2 (COVID-19) antibodies in patient serum samples. This concept could be generalized to any agglutination-based antibody diagnostics with blood plasma.
Transoral gastroplasty is safe, feasible, and induces significant weight loss in morbidly obese patients: results of the second human pilot study (2008)

This second pilot trial confirmed the feasibility and safety of transoral gastroplasty. The early results and technical improvements reported in the present study are encouraging in terms of safety, early weight loss, and quality of life, and clearly allowed multicenter trials, which are planned to start soon.
[Poster] Device vs. user perspective rendering in google glass AR applications (2014)

According to Gartner's 2013 Hype Cycle for Emerging Technologies, Augmented Reality will reach its Plateu of Productivity before Wearable User Interfaces. In this work, device and user-perspective rendering are compared regarding their applicability to AR-based solutions for Google Glass. The conducted experiment measured and evaluated the advantages and drawbacks on each method and also got positive and negative feedbacks given by users. The tests showed that users preferred the device-perspective approach.
Gate-Based High Fidelity Spin Read-out in a CMOS Device (2018)

The engineering of electron spin qubits in a compact unit cell embedding all quantum functionalities is mandatory for large scale integration. In particular, the development of a high-fidelity and scalable spin readout method remains an open challenge. Here we demonstrate high-fidelity and robust spin readout based on gate reflectometry in a CMOS device comprising one qubit dot and one ancillary dot coupled to an electron reservoir to perform readout. This scalable method allows us to read out a spin with a fidelity above 99% for 1 ms integration time. To achieve such fidelity, we exploit a latched spin blockade mechanism that requires electron exchange between the ancillary dot and the reservoir. We show that the demonstrated high read-out fidelity is fully preserved up to 0.5 K. This results holds particular relevance for the future co-integration of spin qubits and classical control electronics.
Influence of Variables on Hemoglobin A1c Values and Nonheterogeneity of Hemoglobin A1c Reference Ranges (2009)

Age, sex, and smoking status influence HbA1c values. Despite standardization of HbA1c methods and published recommendations, there is wide heterogeneity in HbA1c reference ranges in the United States.
Tumor-specific peptides in cutaneous T-cell lymphoma: Association with class I major histocompatibility complex and possible derivation from the clonotypic T-cell receptor (1998)

We wished to identify and characterize tumor-associated class I peptides which could potentially serve as immunogens for an immunoprotective CD8 response in cutaneous T-cell lymphoma (CTCL). Candidate idiotypic peptides were identified from the third complementarity determining region (CDR3) of the clonotypic T-cell receptor (TCR) expressed on malignant T cells and native class I peptides were identified from CTCL cells. Idiotypic peptides were designed by sequencing of patients' CDR3 and identifying 9 amino acid peptides that could be accommodated in the peptide-binding motif of the class I alleles. Three candidate idiotypic peptides were synthesized and tested by measuring release of tumor necrosis factor-alpha (TNF-alpha) from autologous CD8 cells. Native peptides were acid-eluted from class I molecules on CTCL lymphocytes, fractionated, tested in the TNF-alpha assay and sequenced. Two unique idiotypic peptides were specifically recognized by autologous CD8 cells from CTCL patients. In addition, a native peptide eluted from class I molecules of CTCL tumor cells was identified, in the protein data base, as a novel molecule with partial sequence homology to the conserved portion of the patient's TCR. This homology was used to construct an extended native peptide sequence that was immunogenic for CD8 cells from both CTCL patients. Our results demonstrate that peptides derived from the TCR can be used as tumor-specific immunogens that are recognized by CD8 cells. Moreover, novel class I peptides isolated from the tumor cell also serve as immunogens. These peptides might form the basis of an anti-tumor vaccine for immunotherapy of CTCL.
Low-Calcium Serum-Free Defined Medium Selects for Growth of Normal Prostatic Epithelial Stem Cells (2006)

Stage-specific differentiation markers were used to evaluate the cellular composition and the origin of nonimmortalized (PrEC) and immortalized (PZ-HPV7, CA-HPV10, RWPE-1, and 957E/hTERT) human prostate cell lines. These studies documented that immortalized and nonimmortalized prostate epithelial cells established and maintained in low (i.e., <300 micromol/L) Ca(2+) serum-free defined (SFD) medium were all derived from normal nonmalignant prostate tissues and contain CD133(+)/ABCG2(+)/alpha(2)beta(1)(Hi)/p63(-)/PSCA(-)/AR(-)/PSA(-) prostate stem cells. In these cultures, prostate stem cells are able to self-renew and generate two distinct cell lineages: the minor proliferatively quiescent neuroendocrine lineage and the major transit-amplifying cell lineage. Subsequently, CD133(-)/ABCG2(-)/alpha(2)beta(1)(Hi)/p63(+)/PSCA(-)/AR(-)/PSA(-) transit-amplifying cells proliferate frequently and eventually mature into proliferatively quiescent CD133(-)/ABCG2(-)/alpha(2)beta(1)(Lo)/p63(-)/PSCA(+)/AR(-)/PSA(-) intermediate cells. Such proliferatively quiescent intermediate cells, however, do not complete their full maturation into CD133(-)/ABCG2(-)/alpha(2)beta(1)(Lo)/p63(-)/PSCA(-)/AR(+)/PSA(+) luminal-secretory cells in low Ca(2+) SFD medium. Addition of universal type I IFN and synthetic androgen (R1881) to culture medium resulted in up-regulation of androgen receptor protein expression. However, it failed to induce full differentiation of intermediate cells into AR(+)/PSA(+) luminal-secretory cells. Our results indicate that such inability of prostate epithelial cells to complete their differentiation is due to continuous expression of Notch-1 receptor and its downstream effector, Hey-1 protein, which actively suppresses differentiation via its ability to transcriptionally repress a series of genes, including the GATA family of transcription factors.
Identification of two reduction products of glyoxal bis(2-mercaptoanil)nickel. Characterization of the one-electron reduction product and the partially hydrogenated anion (1967)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTIdentification of two reduction products of glyoxal bis(2-mercaptoanil)nickel. Characterization of the one-electron reduction product and the partially hydrogenated anionF. Lalor, M. Frederick. Hawthorne, August H. Maki, K. Darlington, Alan. Davison, Harry B. Gray, Zvi. Dori, and Edward I. StiefelCite this: J. Am. Chem. Soc. 1967, 89, 10, 2278–2281Publication Date (Print):May 1, 1967Publication History Published online1 May 2002Published inissue 1 May 1967https://pubs.acs.org/doi/10.1021/ja00986a008https://doi.org/10.1021/ja00986a008research-articleACS PublicationsRequest reuse permissionsArticle Views104Altmetric-Citations21LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-Alertsclose Get e-Alerts
Characterization of a Human H5N1 Influenza A Virus Isolated in 2003 (2005)

In 2003, H5N1 avian influenza virus infections were diagnosed in two Hong Kong residents who had visited the Fujian province in mainland China, affording us the opportunity to characterize one of the viral isolates, A/Hong Kong/213/03 (HK213; H5N1). In contrast to H5N1 viruses isolated from humans during the 1997 outbreak in Hong Kong, HK213 retained several features of aquatic bird viruses, including the lack of a deletion in the neuraminidase stalk and the absence of additional oligosaccharide chains at the globular head of the hemagglutinin molecule. It demonstrated weak pathogenicity in mice and ferrets but caused lethal infection in chickens. The original isolate failed to produce disease in ducks but became more pathogenic after five passages. Taken together, these findings portray the HK213 isolate as an aquatic avian influenza A virus without the molecular changes associated with the replication of H5N1 avian viruses in land-based poultry such as chickens. This case challenges the view that adaptation to land-based poultry is a prerequisite for the replication of aquatic avian influenza A viruses in humans.
Improved Vertical Carrier Transport for Green III-Nitride LEDs Using (In,Ga)N Alloy Quantum Barriers (2022)

We report on experimental and simulation-based results using $(\mathrm{In},\mathrm{Ga})\mathrm{N}$ alloy quantum barriers in c-plane green light-emitting diode (LED) structures as a means to improve vertical carrier transport and reduce forward voltage $({V}_{F})$. Three-dimensional device simulations that include random alloy fluctuations are used to understand carrier behavior in a disordered potential. The simulated current density--voltage (J-V) characteristics and modified electron-hole overlap $|{F}_{\mathrm{mod}}{|}^{2}$ indicate that increasing the indium fraction in the $(\mathrm{In},\mathrm{Ga})\mathrm{N}$ quantum barriers leads to a reduced polarization discontinuity at the interface between the quantum barrier and quantum well, thereby reducing ${V}_{F}$ and improving $|{F}_{\mathrm{mod}}{|}^{2}$. Maps of electron and hole current through the device show a relatively homogenous distribution in the $XY$ plane for structures using $\mathrm{Ga}\mathrm{N}$ quantum barriers; in contrast, preferential pathways for vertical transport are identified in structures with $(\mathrm{In},\mathrm{Ga})\mathrm{N}$ barriers as regions of high and low current. A positive correlation between hole (electron) current in the p-side (n-side) barrier and indium fraction reveals that preferential pathways exist in regions of high indium content. Furthermore, a negative correlation between the strain ${\ensuremath{\epsilon}}_{zz}$ and indium fraction shows that high indium content regions have reduced strain-induced piezoelectric polarization in the Z direction due to the mechanical constraint of the surrounding lower indium content regions. Experimentally, multiple quantum well green LEDs with $(\mathrm{In},\mathrm{Ga})\mathrm{N}$ quantum barriers exhibit lower ${V}_{F}$ and blue-shifted wavelengths relative to LEDs with $\mathrm{Ga}\mathrm{N}$ quantum barriers, consistent with simulation data. These results can be used to inform heterostructure design of low ${V}_{F}$, long-wavelength LEDs and provide important insight into the nature of carrier transport in III-nitride alloy materials.
Probing the Acyl Carrier Protein-Enzyme Interactions within Terminal Alkyne Biosynthetic Machinery (2018)

Abstract The alkyne functionality has attracted much interest due to its diverse chemical and biological applications. We recently elucidated an acyl carrier protein (ACP)-dependent alkyne biosynthetic pathway, however, little is known about ACP interactions with the alkyne biosynthetic enzymes, an acyl-ACP ligase (JamA) and a membrane-bound bi-functional desaturase/acetylenase (JamB). Here, we showed that JamB has a more stringent interaction with ACP than JamA. In addition, site directed mutagenesis of a non-cognate ACP significantly improved its compatibility with JamB, suggesting a possible electrostatic interaction at the ACP-JamB interface. Finally, error-prone PCR and screening of a second non-cognate ACP identified hot spots on the ACP that are important for interacting with JamB and yielded mutants which were better recognized by JamB. Our data thus not only provide insights into the ACP interactions in alkyne biosynthesis, but it also potentially aids in future combinatorial biosynthesis of alkyne-tagged metabolites for chemical and biological applications. Topical Heading Biomolecular Engineering, Bioengineering, Biochemicals, Biofuels, and Food
Field-Tunable Interactions and Frustration in Underlayer-Mediated Artificial Spin Ice (2021)

Artificial spin ice systems have opened experimental windows into a range of model magnetic systems through the control of interactions among nanomagnet moments. This control has previously been enabled by altering the nanomagnet size and the geometry of their placement. Here we demonstrate that the interactions in artificial spin ice can be further controlled by including a soft ferromagnetic underlayer below the moments. Such a substrate also breaks the symmetry in the array when magnetized, introducing a directional component to the correlations. Using spatially resolved magneto-optical Kerr effect microscopy to image the demagnetized ground states, we show that the correlation of the demagnetized states depends on the direction of the underlayer magnetization. Further, the relative interaction strength of nearest and next-nearest neighbors varies significantly with the array geometry. We exploit this feature to induce frustration in an inherently unfrustrated square lattice geometry, demonstrating new possibilities for effective geometries in two-dimensional nanomagnetic systems.
Structure of the complete elongation complex of RNA polymerase II with basal factors (2017)

In the early stage of transcription, eukaryotic RNA polymerase II (Pol II) exchanges initiation factors with elongation factors to form an elongation complex for processive transcription. Here we report the structure of the Pol II elongation complex bound with the basal elongation factors Spt4/5, Elf1, and TFIIS. Spt4/5 (the Spt4/Spt5 complex) and Elf1 modify a wide area of the Pol II surface. Elf1 bridges the Pol II central cleft, completing a "DNA entry tunnel" for downstream DNA. Spt4 and the Spt5 NGN and KOW1 domains encircle the upstream DNA, constituting a "DNA exit tunnel." The Spt5 KOW4 and KOW5 domains augment the "RNA exit tunnel," directing the exiting nascent RNA. Thus, the elongation complex establishes a completely different transcription and regulation platform from that of the initiation complexes.
Cytotoxic compounds against cancer cells from Bombyx mori inoculated with Cordyceps militaris (2017)

Two compounds, 3'-deoxyinosine and cordycepin, were isolated from Bombyx mori inoculated with Cordyceps militaris. In the bioassay examining cytotoxicity against cancer cells, both compounds showed toxicity against A549, PANC-1, and MCF-7 cancer cells.
Paranom: A Parallel Anomaly Dataset Generator (2018)

In this paper, we present Paranom, a parallel anomaly dataset generator. We discuss its design and provide brief experimental results demonstrating its usefulness in improving the classification correctness of LSTM-AD, a state-of-the-art anomaly detection model.
Rapidity gap cross sections measured with the ATLAS detector in pp collisions at $\sqrt{s} = 7 \mbox{~TeV}$ (2012)

Pseudorapidity gap distributions in proton-proton collisions at s = 7 TeV are studied using a minimum bias data sample with an integrated luminosity of 7.1 b -1 . Cross sections are measured differentially in terms of F , the larger of the pseudorapidity regions extending to the limits of the ATLAS sensitivity, at = 4.9, in which no final state particles are produced above a transverse momentum threshold p cut T . The measurements span the region 0 < F < 8 for 200 MeV < p cut T < 800 MeV. At small F , the data test the reliability of hadronisation models in describing rapidity and transverse momentum fluctuations in final state particle production. The measurements at larger gap sizes are dominated by contributions from the single diffractive dissociation process (pp Xp), enhanced by double dissociation (pp XY ) where the invariant mass of the lighter of the two dissociation systems satisfies M Y 7 GeV. The resulting cross section is d/d F 1 mb for F 3. The large rapidity gap data are used to constrain the value of the Pomeron intercept appropriate to triple Regge models of soft diffraction. The cross section integrated over all gap sizes is compared with other LHC inelastic cross section measurements.
Shuffling of amino acid sequence: an important control in synthetic peptide studies of nucleic acid-binding domains. Binding properties of fragments of a conserved eukaryotic RNA binding motif. (1992)

We have used synthetic peptides to study a conserved RNA binding motif in yeast poly(A)-binding protein. Two peptides, 45 and 44 amino acids in length, corresponding to amino and carboxyl halves of a 90-amino acid RNA-binding domain in the protein were synthesized. While the amino-terminal peptide had no significant affinity for nucleic acids, the carboxyl-terminal peptide-bound nucleic acids with similar characteristics to that for the entire 577 residue yeast poly(A)-binding protein. In 100 mM NaCl, the latter peptide retained over 50% of the intrinsic binding free energy of the protein, as well as, similar RNA versus DNA binding specificity. However, shuffling of the sequence of this 44 residue peptide had surprisingly little effect on its nucleic acid binding properties suggesting the overriding importance of amino acid composition as opposed to primary sequence. Deletion studies on the 44 residue peptide with the "correct" sequence succeeded in identifying amino acids important for conferring RNA specificity and for increasing our understanding of the molecular basis for nucleic acid binding by synthetic peptides. The shuffled peptide study, however, clearly indicates that considerable caution must be exercised before extrapolating results of structure/function studies on synthetic peptide analogues to the parent protein.
The first example of enamine–Lewis acid cooperative bifunctional catalysis: application to the asymmetric Aldol reaction (2008)

(-)-Sparteine directed lithiation of N-Boc-pyrrolidine, alkylation with chloromethylboronate pinacol ester and acid-based deprotection provides homoboroproline HX salt in 94% ee, which is then an efficient enamine-type pyrrolidine catalyst in an asymmetric aldol reaction when neutralised and especially when esterified in situ with a tartrate ester, for example, providing 90% ee of the aldol adduct derived from acetone and p-nitrobenzaldehyde.
Synthesis and complete NMR spectral assignment of thiophene‐substituted sulfinyl monomers (2004)

This paper describes the synthesis of thiophene-substituted sulfinyl monomers. It comprises a four-step reaction by which the thiophene unit is built in via Suzuki coupling. These monomers could be used as building blocks for the preparation of conducting polymers via a new concept: the sulfinyl precursor route i.e. via thiophene substituted poly(p-phenylenevinylene) precursors. Furthermore, the complete 1H and 13C NMR signal assignment is presented. In addition to being essential for the characterization of the polymers concerned, it offers useful input information for further improvement of chemical shift prediction software. Furthermore, the T1C relaxation decay times are demonstrated to have the potential of being a fast and robust criterion for the spectral assignment of analogous monomers.
Evaluating the Effects of Surface Tension and Viscosity on Two-Phase Flow in Horizontal Pipes (2018)

Abstract Two-phase gas/liquid flow in pipes is a common occurrence in the petroleum, chemical, nuclear and geothermal industry. In the petroleum industry, it is encountered in the production, transportation, and processing of hydrocarbon from oil and gas field. In designing these systems, accurate prediction of pressure drop is imperative which is determined from flow regime map. Unfortunately, most of the flow regime maps were developed for the air-water system and widely used for the gas/oil system. In spite of the practical importance the general applicability of these maps is not addressed. In order to improve the generality of flow regime maps it is necessary to evaluate the effect of fluid properties such as surface tension which differ by great magnitude (air/water = 72 dyne/cm and gas/oil = 35 dyne/cm) and viscosity (viscosity of water 1 centipoise and for oil 10 centipoises at standard condition) on the flow regimes. Thus, this study aims to evaluate the effects of surface tension and viscosity on the flow regimes in horizontal pipes. The most flow regime maps are generated using the air-water system and widely applied to the oil-gas system. In addition, the empirical equations based on flow regime maps are not accurate with relatively high error (20-30%). So that the applicability of these maps is limited due to the lacking knowledge of fluid properties effect. Evaluation of these properties will address the applicability of these maps for other systems. The objective of this study is to evaluate the effects of surface tension and viscosity on flow regimes in horizontal pipes and investigate its effects on boundary transition. The experiments were conducted on horizontal pipe flow-loop (length 30' and diameter 1") with two-phase air/ water. The range of superficial gas velocity is 0-60ft/s and superficial liquid velocity is 0-10ft/s. The effect of surface tension has been introduced by reducing the surface tension with the aid of a surfactant, and the effect of viscosity has been introduced by increasing the viscosity with aid of glycerin. Four different surfactant concentrations (0.02, 0.05 0.1, 0.5%) and four different glycerin concentrations (5,10,20,30%) have been selected to evaluate the effects of the surface tension and viscosity. The experimental data were utilized to generate flow pattern map and the effect of surface tension and viscosity were evaluated based on the variation in the boundaries of different flow patterns.