gebhart/patrepeval huggingface dataset:
Optimizing qubit resources for quantum chemistry simulations in second quantization on a quantum computer (2015)

Quantum chemistry simulations on a quantum computer suffer from the overhead needed for encoding the fermionic problem in a bosonic system of qubits. By exploiting the block diagonality of a fermionic Hamiltonian, we show that the number of required qubits can be reduced by a factor of two or more. There is no need to go into the basis of the Hilbert space for this reduction because all operations can be performed in the operator space. The scheme is conceived as a pre-computational step that would be performed on a classical computer prior to the actual quantum simulation. We apply this scheme to reduce the number of qubits necessary to simulate both the Hamiltonian of the two-site Fermi-Hubbard model and the hydrogen molecule. Both quantum systems can then be simulated with a two-qubit quantum computer.
Selective multiple analyte detection using multi-mode excitation of a MEMS resonator (2022)

This work reports highly selective multiple analyte detection by exploiting two different mechanisms; absorption and thermal conductivity using a single MEMS device. To illustrate the concept, we utilize a resonator composed of a clamped-guided arch beam connected to a flexural beam and a T-shaped moveable mass. A finite element model is used to study the mode shapes and mechanical behavior of the device with good agreement reported with the experimental data. The resonator displays two distinct out-of-plane modes of vibration. For humidity detection, we utilize physisorption by functionalizing the surface with graphene oxide (GO), which has strong affinity toward water vapors. The GO solution is prepared and drop-casted over the mass surface using an inkjet printer. On the other hand, cooling the heated flexural beams is used for helium (He) detection (thermal-conductivity-based sensor). The sensor characteristics are extensively studied when the modes are individually and simultaneously actuated. Results affirm the successful utilization of each mode for selective detection of relative humidity and He. This novel mode-dependent selective detection of multiple analytes can be a promising building block for the development of miniature, low-powered, and selective smart sensors for modern portable electronic devices.
Acute Ischemia Induced by High-Density Culture Increases Cytokine Expression and Diminishes the Function and Viability of Highly Purified Human Islets of Langerhans (2017)

In order for cell-based insulin replacement to be applied as a treatment for type 1 diabetes, oxygen and nutrient delivery to β cells will need to be maintained. We demonstrate that even brief ischemic exposure such as would be experienced in encapsulation devices damages islet viability and β cell function and leads to increased inflammatory signaling.
VTP-43742 is a potent and selective RORγt blocker that demonstrates oral efficacy in a mouse model of autoimmunity through suppression of IL-17A production (THER7P.945) (2015)

Abstract Increased production of the inflammatory cytokine IL-17A by Th17 cells is a driver of multiple autoimmune disorders, including psoriasis, ankylosing spondylitis (AS) and psoriatic arthritis (PsA). The nuclear receptor RORγt, IL-23 and TGFb are required for the differentiation of Th17 cells. RORγt stabilizes the Th17 phenotype by increasing the expression of IL-23R and inducing the synthesis of IL-17A in Th17 cells. Antibodies targeting IL-23 or IL-17A are highly effective in the treatment of psoriasis, AS and PsA, validating the RORγt /Th17 pathway in human disease. VTP-43742 is an orally active inhibitor of RORgt that is being pursued for the treatment of autoimmune disorders. VTP-43742 binds to RORγt with high affinity (Ki=3.5 nM) and exhibits &amp;gt;1000-fold selectivity versus the RORa and RORβ isotypes. VTP-43742 inhibits Th17 differentiation and IL-17A secretion from mouse splenocytes (IC50=57 nM) without affecting Th1, Th2, or Treg cell differentiation. In the MOG35-55/CFA immunized mouse EAE model, orally dosed VTP-43742 significantly suppressed clinical symptoms, demyelination and mRNA expression of multiple inflammatory markers in the spinal cord. Importantly, VTP-43742 inhibits the secretion of IL-17A from activated hPBMCs (IC50=18 nM) and human whole blood (IC50=192 nM) from healthy and psoriatic donors. Further, VTP-43742 is well absorbed after oral administration in multiple animal species and has pharmacokinetics consistent with once-a-day dosing in humans.
A Hypothesis-Directed Approach to the Targeted Development of a Multiplexed Proteomic Biomarker Assay for Cancer (2015)

In recent years, hundreds of candidate protein biomarkers have been identified using discovery-based proteomics. Despite the large number of candidate biomarkers, few proteins advance to clinical validation. We propose a hypothesis-driven approach to identify candidate biomarkers, previously characterized in the literature, with the highest probability of clinical applicability. A ranking method, called the "hypothesis-directed biomarker ranking" (HDBR) system, was developed to score candidate biomarkers based on seven criteria deemed important in the selection of clinically useful biomarkers. To demonstrate its application, we applied the HDBR system to identify candidate biomarkers for the development of a diagnostic test for the early detection of colorectal cancer. One-hundred and fifty-one candidate biomarkers were identified from the literature and ranked based on the specified criteria. The top-ranked candidates represent a group of biomarkers whose further study and validation would be justified in order to expedite the development of biomarkers that could be used in a clinical setting.
Evaluation of transplacental transfer of mRNA vaccine products and functional antibodies during pregnancy and early infancy (2021)

Studies are needed to evaluate the safety and effectiveness of mRNA SARS-CoV-2 vaccination during pregnancy, and the levels of protection provided to their newborns through placental transfer of antibodies. We evaluated the transplacental transfer of mRNA vaccine products and functional anti-SARS-CoV-2 antibodies during pregnancy and early infancy in a cohort of 20 individuals vaccinated during pregnancy. We found no evidence of mRNA vaccine products in maternal blood, placenta tissue, or cord blood at delivery. However, we found time-dependent efficient transfer of IgG and neutralizing antibodies to the neonate that persisted during early infancy. Additionally, using phage immunoprecipitation sequencing, we found a vaccine-specific signature of SARS-CoV-2 Spike protein epitope binding that is transplacentally transferred during pregnancy. In conclusion, products of mRNA vaccines are not transferred to the fetus during pregnancy, however timing of vaccination during pregnancy is critical to ensure transplacental transfer of protective antibodies during early infancy.
Aufbau zur flächigen reflektrometrischen Schichtdickenbestimmung von lateral bewegten Schichtsystemen (2016)

Zusammenfassung Zur flächigen Schichtdickenbestimmung von lateral bewegten Schichtsystemen wurde erstmals ein Messsystem basierend auf dem reflektometrischen Messprinzip in Kombination mit einem Hyperspektralimager entwickelt. Eine Vorsatzoptik mit integriertem Auflichtpfad formt eine Messlinie, deren Reflexion am Messobjekt auf den Eingangsspalt des Hyperspektralimagers abgebildet wird. Aus den spektralen Daten der Reflektanz wird die Schichthöhe jedes örtlich auflösbaren Pixels des zu untersuchenden Objekts rekonstruiert. Bewegt sich das Messobjekt lateral linear gleichförmig, ergeben zusammengesetzte Messlinien eine Messfläche.
Highly absorbing gadolinium test device to characterize the performance of neutron imaging detector systems (2007)

We report on the fabrication and application of a novel neutron imaging test device made of gadolinium. It is designed for a real time evaluation of the spatial resolution, resolution direction, and distortions of a neutron imaging detector system. Measurements of the spatial resolution of (6)LiF doped ZnS scintillator screens with different thicknesses and of imaging plates were performed. The obtained results are in good agreement with comparison measurements using the standard knife edge detection method.
Superimposition and Detection of Frequency Modulated Tone for Light Path Tracing Employing Digital Signal Processing and Optical Filter (2012)

We propose a novel method for light path tracing and demonstrate it in 112Gb/s DP-16QAM transmission. The S/N of the detected label exceeds 24dB after 20span transmission. No crosstalk was observed in neighboring DWDM channels.
Biofunctionalization of carbon nanotubes for reversible site-specific protein immobilization (2021)

Carbon nanotubes (CNTs) emerge as biosensors due to their extraordinary electrical transport properties. Such applications depend on interfacing proteins with CNTs in an oriented manner while maintaining their structural and functional integrity, opening versatile opportunities for one-dimensional alignment and high-sensitivity sensing of protein interactions and conformational dynamics. Here, we devised a novel surface architecture for reversible protein immobilization on CNTs via a short peptide tag for fabrication of reusable biosensors for multiple protein analysis. To this end, we conjugated pyrene-poly(ethylene glycol) with tris-nitrilotriacetic acid (Py-PEG-tris-NTA) for site-specific immobilization of oligohistidine(His)-tagged proteins. We demonstrate spontaneous self-assembly of Py-PEG-tris-NTA on CNTs and graphene, as well as specific capturing of His-tagged green fluorescent protein after loading the NTA chelators with Ni(II) ions. The protein binding capacity of tris-NTA-functionalized CNTs could be restored by an imidazole wash, allowing for repeated immobilization cycles. Reflectance interference spectroscopy and fluorescence lifetime analysis confirmed a specific and reversible binding of proteins on CNT-coated silica substrates as well as close interfacing to the CNT surface.
Channel Covariance Estimation in Multiuser Massive Mimo Systems with an Approach Based on Infinite Dimensional Hilbert Spaces (2020)

We propose a novel algorithm to estimate the channel covariance matrix of a desired user in multiuser massive MIMO systems. The algorithm uses only knowledge of the array response and rough knowledge of the angular support of the incoming signals, which are assumed to be separated in a well-defined sense. To derive the algorithm, we study interference patterns with realistic models that treat signals as continuous functions in infinite dimensional Hilbert spaces. By doing so, we can avoid common and unnatural simplifications such as the presence of discrete signals, ideal isotropic antennas, and infinitely large antenna arrays. An additional advantage of the proposed algorithm is its computational simplicity: it only requires a single matrix-vector multiplication. In some scenarios, simulations show that the estimates obtained with the proposed algorithm are close to those obtained with standard estimation techniques operating in interference-free and noiseless systems.
Experimental and Analytical Performance Evaluation of Short Circular Hydrodynamic Journal Bearings Used in Rotary Blood Pumps (2013)

Rotary blood pumps (RBPs) have demonstrated considerable promise while treating heart failure patients, such that they are being placed at an earlier stage of the disease. These devices may therefore be required to operate for prolonged durations which yields the need for RBPs exhibiting high durability, reliability, and blood compatibility. Noncontacting bearings, utilizing magnetic and/or hydrodynamic suspension techniques, appear to provide a suitable solution to these challenges. Hydrodynamic suspension has the advantage that it does not need feedback control systems. Among various hydrodynamic bearing types, the circular journal bearing has the particular benefit of easy manufacturing. This study presents methods to evaluate the performance of short (length to diameter ratio <1) circular hydrodynamic journal bearings (HJBs) for RBPs. Analytical calculations with specific boundary conditions are presented to predict the rotor's eccentricity under equilibrium states and thus the related performance parameters such as load capacity, power loss, and shear rates. These results and boundary conditions were confirmed experimentally in a specially designed test set-up. The bearing performance was found to correlate to analytical solutions using the full Sommerfeld boundary condition instead of the half Sommerfeld condition conventionally used for such applications. Geometrical and operational parameter variations showed that HJB designs with a short Sommerfeld Number SS >0.02 can provide sufficient fluid film thicknesses and low shear rates. The measurements were further used to evaluate the bearings' stability. The estimation of the stability threshold drawn in relation to a modified stability index and the equilibrium eccentricity of the rotor allows the prediction of stability for short circular HJB designs under full Sommerfeld condition.
A flow system for partial automation of plating efficiency tests (1981)

A flow system that sterilely deposits a known number of cells into a collection vessel has been constructed and evaluated. In this device, the cells from a single-cell suspension flow through a nozzle that constrains them to the center of the emerging jet. The cells in the jet are illuminated by a 0.5-mW helium-neon laser; they are detected, sized and counted on the basis of the light scattered as they pass through the laser beam. The device has been used for plating efficiency tests in a tissue culture laboratory. We found that it saved considerable labor by eliminating the dilution step from the standard plating efficiency procedure. The biologic effect of machine plating was determined by comparing plating efficiencies of KHT, CHO-T5, and CHO-AA8 cells established by hand plating with those established by machine plating. Results indicate that machine plating reduces the plating efficiency of the CHO-T5 cells while the plating efficiencies of the CHO-AA8 and KHT cells are unaffected.
Oxygen barrier materials from renewable sources: Material properties of softwood hemicellulose‐based films (2006)

Abstract The aim of this study was to investigate the film‐forming ability of the hemicellulose O ‐acetyl‐galactoglucomannan (AcGGM) and to evaluate its potential as a barrier material. The polymer film was evaluated by measurement of its oxygen permeability (Ox‐Tran® Mocon), thermal properties (differential scanning calorimetry), and dynamic mechanical properties under a humidity scan (humidity‐scan DMA). The AcGGM was isolated from industrial process water obtained from mechanical wood pulping. The self‐supporting films were formed by solution‐casting from water. As expected, a plasticizer was needed to avoid brittleness, and glycerol, sorbitol, and xylitol were compared. However, these additives resulted in higher sensitivity to moisture, which might be less beneficial for some applications. Interesting oxygen barrier and mechanical strength properties were achieved in a film obtained from a physical blend of AcGGM and either alginate or carboxymethylcellulose, both having a substantially higher molecular weight than AcGGM. No phase separation was observed, since all the components used were rich in hydroxyl functionalities. When a plasticizer was also added to the binary mixture, a compromise between (1) low O 2 permeability, (2) high mechanical toughness, and (3) flexibility of an AcGGM‐based film was obtained. © 2006 Wiley Periodicals, Inc. J Appl Polym Sci 100: 2985–2991, 2006
Brachyspiral colitis: An evolving problem (2014)

The name “Brachyspiral colitis” recently was introduced into the literature on swine diseases to describe the situation where colitis, diarrhea and/or dysentery occur in pigs infected with one or more pathogenic Brachyspira species (Hampson, 2012). The term was created to emphasise an increasing understanding of the diversity of anaerobic intestinal spirochetes in the genus Brachyspira and the fact that a number of different species may have a role in inducing inflammation in the large intestine. &#13;\n&#13;\nUntil only a few years ago most veterinarians would have felt comfortable with the concept of there being two pathogenic Brachyspira species capable of causing disease in pigs, each associated with a distinct named disease. The first was the strongly hemolytic Brachyspira hyodysenteriae causing swine dysentery, a severe mucohemorrhagic colitis seen mainly in grower and finisher pigs. The second was the weakly hemolytic Brachyspira pilosicoli causing porcine intestinal spirochetosis (porcine colonic spirochetosis), a milder form of colitis seen mainly in weaner and grower pigs. Other weakly hemolytic species colonising pigs generally were thought of as being commensals.&#13;\n&#13;\nNow it is known that there are at least three strongly hemolytic pathogenic Brachyspira species that may infect swine and cause a swine dysentery-like disease; furthermore, there is increasing evidence that one or more of the other weakly hemolytic species besides B. pilosicoli also have pathogenic potential in swine and other species. Specifically, the weakly hemolytic Brachyspira murdochii is increasingly being implicated as an occasional cause of mild colitis in pigs (Jensen et al., 2000; Weissenböck et al., 2005; Komarek et al., 2009; Osorio et al., 2013). It is also clear that individual pigs on different farms may be colonised with more than one Brachyspira species and/or strains that may contribute towards causing disease symptoms.&#13;\n&#13;\nIn and interesting parallel, the ceca and colon of adult chickens and other poultry species may be colonised by a number of Brachyspira species that can induce inflammation, wet feces and reduced egg production. This disease complex (most commonly is associated with B. intermedia and/or B. pilosicoli) currently is known as “Avian Intestinal “Spirochetosis” (Hampson, 2013), but for clarity and consistency with the revised disease nomenclature in pigs it might be better if it was to be called “Brachyspiral typhlitis”.
P1–250: Development and characterization of a validated multiplex panel for detection of beta‐amyloid peptides in human CSF (2013)

Considered along with neuropsychological and/or neuroimaging data, baseline AD biomarker profiles may be used to stratify and enrich particular patient populations, which may enhance the success of clinical trials and natural history studies. However, challenges with existing AD biomarker assays, including issues with repeatability and reproducibility within and across centers and across manufactured lots, limit their clinical utility. Herein, we report development and analytical validation of a human A b peptide multiplex panel for measurement of A b 38, A b 40, and A b 42 in human CSF using fit-for-purpose and Clinical and Laboratory Standards Institute principles. The panel was developed using MSD's MULTI-ARRAY® technology and was optimized to minimize CSF matrix effects and interferences. Analytical validation was performed across multiple panel lots to verify consistency in sensitivity, accuracy, and precision. The human A b peptide panel demonstrated excellent sensitivity, performance, and inter-lot reproducibility. Measured levels of the three A b peptides in human CSF fell within the quantitative ranges of the assays and were consistent with literature reports. Assay precision, accuracy, and total error were determined from human CSF control samples. Dilution linearity and spike recovery testing demonstrated minimal matrix effects and accurate quantitation of A b peptide over the range of the assays. The assays showed no significant cross-reactivity or interference from closely related A b peptides. The human A b peptide panel was developed and analytically validated to measure A b 38, A b 40, and A b 42 in human CSF. The panel had good analytical performance characteristics, inter-lot consistency, and the ability to measure A b peptide levels in human CSF samples. This panel will support ongoing efforts to standardize AD biomarker testing and opens the door to multiplexing with other key biomarker assays such as phosphorylated and total tau.
Integrated All-Optical Controlled Amplitude Modulator Using Laser Delivered Signals (2022)

We experimentally demonstrate integrated all-optical controlled amplitude modulation. Range of 0.25 mW control power is used to tune 15 dB of the output optical intensity. The design is fabricated in a commercial silicon photonics process.
Association of T P53 and CDKN2A Mutation Profile with Tumor Mutation Burden in Head and Neck Cancer (2022)

These data emphasize the role of tumor subsite in evaluation of mutational profiles in HNSCC, and link defects in TP53 and CDKN2A to elevated TMB levels in some tumor subgroups.
Estrogen’s and Progesterone’s Impact on Gene Expression in the Mouse Lacrimal Gland (2005)

The hypothesis tested in the study was that the effect of estrogen and progesterone on the lacrimal gland is mediated through specific receptors and that hormonal effects involve the regulation of gene expression and protein synthesis.Lacrimal glands were collected from young adult, ovariectomized mice, that were treated with 17beta-estradiol, progesterone, 17beta-estradiol plus progesterone or vehicle for 2 weeks. Glands were pooled according to treatment, processed for the isolation of RNA, and evaluated for differentially expressed mRNAs by using gene microarrays. Bioarray data were analyzed with sophisticated bioinformatics and statistical programs. The expression of selected genes was verified by using gene chips and quantitative real-time PCR methods.The results demonstrate that 17beta-estradiol, progesterone, or both hormones together significantly influences the expression of hundreds of genes in the mouse lacrimal gland. Sex steroid treatment led to numerous alterations in gene activities related to transcriptional control, cell growth and/or maintenance, cell communication, signal transduction, enzyme catalysis, immune expression, and the binding and metabolism of nucleic acids and proteins. A number of the 17beta-estradiol, progesterone or 17beta-estradiol plus progesterone effects on gene expression were similar, but most were unique to each treatment. Of particular interest was the finding that these hormones seem to contribute little to the known sex-related differences in gene expression of the lacrimal gland.These results support the hypothesis that estrogen's and progesterone's action on the lacrimal gland involves the regulation of numerous genes. However, these hormone effects do not appear to represent a major factor underlying the sexual dimorphism of gene expression in lacrimal tissue.
ROBOTİK UYGULAMALARIN FEN BİLGİSİ ÖĞRETMEN ADAYLARININ BAZI 21.YÜZYIL BECERİLERİ ÜZERİNDEKİ ETKİSİNİN İNCELENMESİ (2020)

Bu çalışmada Lego setleri ile yapılan uygulamalar ile fen bilgisi öğretmen adaylarının bazı 21.yüzyıl becerileri üzerinde etkisinin incelenmesi amaçlanmıştır. Çalışma Amasya Üniversitesinde Fen Bilgisi Eğitimi Anabilim dalı 3.sınıfta öğrenim gören 6 öğretmen adayı ile gerçekleştirilmiştir. Örneklem belirlemede kolay ulaşılabilir durum örneklemesi yöntemi kullanılmıştır. Araştırma verileri öğretmen adaylarının sürecin başında, ortasında ve sonunda kullandıkları zihin haritaları, günlükler ve yarı yapılandırılmış görüşmeden oluşmaktadır. Eğitsel robotik uygulamasında yeni bir ürün ortaya çıkarmak öğretmen adaylarının motivasyonlarını artırarak sürecin eğlenceli geçmesini sağlamıştır. Robot modellerini programlama aşamasında biraz zorlandıkları için motivasyonları düşmüştür. Bunun yanında yapılan robot etkinlikleri ile problem çözme, yaratıcılık, işbirliği, iletişim gibi 21.yüzyıl becerilerinden öğrenme ve yenilik becerileri alanlarına etki ettiği sonucuna ulaşılmıştır.