gebhart/patrepeval huggingface dataset:
Determination of Enantiomeric Excess in Samples of Chiral Molecules Using Fourier Transform Vibrational Circular Dichroism Spectroscopy:  Simulation of Real-Time Reaction Monitoring (2004)

The first use of Fourier transform vibrational circular dichroism (FT-VCD) to follow changes in the percent enantiomeric excess (% EE) of chiral molecules in time using a flow cell sampling apparatus is reported. FT-VCD, as opposed to dispersive scanning VCD, eliminates the need to scan the VCD spectrum in time to monitor the % EE at more than one spectral location. The first use of partial least-squares chemometric analysis to determine % EE values from kinetic sets of VCD spectral data is also reported. These two advances have been used to monitor simultaneously changes in the fractional composition and the % EE of a mixture of two different chiral molecules. This simulates the progress of the chemical reaction from a chiral reactant to a chiral product where the % EE of both molecules can change with time. For the molecules studied, alpha-pinene, camphor, and borneol, the accuracy of following % EE changes for one species alone is approximately 1%, while for simultaneously following % EE changes in two species is approximately 2% for 10-20-min sampling periods at 4 cm(-)(1) spectral resolution. This accuracy can be increased for the same collection times or maintained for shorter periods of collection by lowering the spectral resolution. These findings demonstrate the potential for VCD to be used for real-time monitoring of the composition and % EE of chemical reactions involving the synthesis chiral molecules.
Abstract 5574: ZNF516 and FKBP6 promoter hypermethylation as a potential companion diagnostic panel for HPV-positive and inconclusive-Pap women (2012)

Abstract New biomarkers are needed to improve cervical cancer screening technologies, which are mostly based on cytological examination since the 1940's. HPV testing has been adopted for the triage of patients after a cervical cytology-screening test. HPV testing is now also increasingly used for screening in conjunction with cervical cytology. However, a percentage of HPV-positive and inconclusive-Pap women have negative biopsies when refered to colposcopy clinics. The aim of this study was to use a genome-wide discovery approach to identify novel epigenetic biomarkers for cervical cancer, which could be used as companion diagnostic panels to HPV and PAP. DNA from twelve normal and seven cervical cancer samples was enriched with Methylated DNA Immunoprecipitation (MeDIP), hybridized to Nimblegen 385K CpG Islands plus Promoter arrays and validated by quantitative Methylation Specific PCR in discovery (n=49) and prevalence cohorts (n=108). After correction and normalization performed using Nimblegen algorithms genes methylated in tumor and not in normal samples were ranked by methylation peak values and sequence homology. The most significant loci were verified against a report by Ongenaert et al. (BMC Med Genomics, 2008) that uses a relaxation ranking algorithm to identify re-expressed genes in cervical cancer cell lines after treatment with demethyalting agents. Two genes, ZNF516 and FKBP6, were identified as candidate epigenomic biomarkers after rigourous bioinformatics and in-silico analyses. These genes were also found to be re-expressed by Ongenaert et al. Using the most optimal cut-off as determined by ROC, ZNF516 promoter methylation had 90% sensitivity and 95% specificity (AUC=0.95) in the discovery cohort. FKBP6 promoter methylation had a sensitivity of 73% and a specificity of 79% in the same cohort. Promoter methylation of FKBP6 (OR=4.51, 95%C.I.=2.04-9.97, P&lt;0.001) and ZNF516 (OR=11.84, 95%C.I.=4.59-30.57, P&lt;0.001) was associated to HPV infection in the prevalence cohort. FKBP6 (OR=7.15, 95%C.I.=1.45-35.34, P=0.01) and ZNF516 (OR=26.72, 95%C.I.=2.61-273.05, P &lt;0.01) promoter methylation was associated with histological diagnosis of cervical cancer in the overall cohort, after controlling for age and HPV infection. Promoter methylation of ZNF516 and FKBP6 performed better than HPV at identifying normal from tumor tissue in the overall cohort. Our results suggest that a genome-wide approach using MeDIP-Chip and qMSP is useful for identifying novel screening and diagnostic markers. ZNF516 and FKBP6 were identified as a potential companion diagnostic panel for HPV-positive and inconclusive-Pap women. Examination of these biomarkers in a larger, independent cohort is warranted. Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 103rd Annual Meeting of the American Association for Cancer Research; 2012 Mar 31-Apr 4; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2012;72(8 Suppl):Abstract nr 5574. doi:1538-7445.AM2012-5574
Robot-Assisted and Wearable Sensor-Mediated Autonomous Gait Analysis<sup>§</sup> (2020)

In this paper, we propose an autonomous gait analysis system consisting of a mobile robot and custom-engineered instrumented insoles. The robot is equipped with an on-board RGB-D sensor, the insoles feature inertial sensors and force sensitive resistors. This system is motivated by the need for a robot companion to engage older adults in walking exercises. Support vector regression (SVR) models were developed to extract accurate estimates of fundamental kinematic gait parameters (i.e., stride length, velocity, foot clearance, and step length), from data collected with the robot's on-board RGB-D sensor and with the instrumented insoles during straight walking and turning tasks. The accuracy of each model was validated against ground-truth data measured by an optical motion capture system with N=10 subjects. Results suggest that the combined use of wearable and robot's sensors yields more accurate gait estimates than either sub-system used independently. Additionally, SVR models are robust to inter-subject variability and type of walking task (i.e., straight walking vs. turning), thereby making it unnecessary to collect subject-specific or task-specific training data for the models. These findings indicate the potential of the synergistic use of autonomous mobile robots and wearable sensors for accurate out-of-the-lab gait analysis.
Intelligent sampling decision scheme based on the AVM system (2014)

Wafer inspection plays a significant role in monitoring the quality of wafers production for continuous improvement. However, it requires measuring tools and additional cycle time to do real metrology, which is costly and time-consuming. Therefore, reducing sampling rate to as low as possible is a high priority to reduce production cost. Several sampling methods in the literature were proposed to achieve this goal. They utilised real sampling inspections as the representatives for the other related wafers to monitor the whole production process. Under the condition of stable manufacturing process, virtual metrology (VM) may be applied to monitor the quality of wafers, while real metrology is unavailable. Therefore, the sampling rate may further be reduced with a sampling decision scheme being designed according to reliable VM. Nevertheless, once a new production variation occurs between planned samplings and no real metrology is available during this period for updating the VM models, un-reliable VM predictions may be produced. The authors have developed the automatic virtual metrology (AVM) system for various VM applications. Therefore, this paper focuses on applying various indices of the AVM system to develop an intelligent sampling decision scheme for reducing sampling rate, while VM accuracy is still sustained.
Boundary mode lubrication of articular cartilage with a biomimetic diblock copolymer (2019)

We report the design of a diblock copolymer with architecture and function inspired by the lubricating glycoprotein lubricin. This diblock copolymer, synthesized by sequential reversible addition-fragmentation chain-transfer polymerization, consists of a cationic cartilage-binding domain and a brush-lubricating domain. It reduces the coefficient of friction of articular cartilage under boundary mode conditions (0.088 ± 0.039) to a level equivalent to that provided by lubricin (0.093 ± 0.011). Additionally, both the EC<sub>50</sub> (0.404 mg/mL) and cartilage-binding time constant (7.19 min) of the polymer are comparable to purified human and recombinant lubricin. Like lubricin, the tribological properties of this polymer are dependent on molecular architecture. When the same monomer composition was evaluated either as an AB diblock copolymer or as a random copolymer, the diblock effectively lubricated cartilage under boundary mode conditions whereas the random copolymer did not. Additionally, the individual polymer blocks did not lubricate independently, and lubrication could be competitively inhibited with an excess of binding domain. This diblock copolymer is an example of a synthetic polymer with lubrication properties equal to lubricin under boundary mode conditions, suggesting its potential utility as a therapy for joint pathologies like osteoarthritis.
Evidence for gene silencing by endogenous DNA methylation (1998)

Transformed cells can spontaneously silence genes by de novo methylation, and it is generally assumed that this is due to DNA methyltransferase activity. We have tested the alternative hypothesis that gene silencing could be due to the uptake of 5-methyl-dCMP into DNA, via the di- and triphosphonucleotides. 5-Methyl-dCMP would be present in cells from the ongoing repair of DNA. We have isolated a strain of Chinese hamster ovary (CHO) cells, designated HAM-, which spontaneously silences two tested genes at a very high frequency. We have shown that this strain incorporates 5-[3H]methyldeoxycytidine into 5-methylcytosine and thymine in DNA. It also has low 5-methyl-dCMP deaminase activity. Another HAM+ strain has high deaminase activity and a very low frequency of gene silencing. The starting strain, CHO K1, has a phenotype intermediate between HAM- and HAM+.
Genetic relatedness of hepatitis A virus strains recovered from different geographical regions (1992)

A pairwise comparison of the nucleic acid sequence of 168 bases from 152 wild-type or unique cell culture-adapted strains of hepatitis A virus (HAV) revealed that HAV strains can be differentiated genetically into seven unique genotypes (I to VII). In general, the nucleotide sequence of viruses in different genotypes differs at 15 to 25% of positions within this segment of the genome. Viruses from four of the genotypes (I, II, III and VII) were recovered from cases of hepatitis A in humans, whereas viruses from the other three genotypes (IV, V and VI) were isolated only from simian species developing a hepatitis A-like illness during captivity. Among non-epidemiologically related human HAV strains, 81 were characterized as genotype I, and 19 as genotype III. Within each of these major genotypes, there were two distinct groups (subgenotypes), which differed in sequence at approximately 7.5% of base positions. Each genotype and subgenotype has a characteristic amino acid sequence in this region of the polyprotein, with the most divergent genotypes differing at 10 of 56 residues. Strains recovered from some geographical regions belonged to a common (endemic) genotype, whereas strains from other regions belonged to several, probably imported, genotypes. Thus, HAV strains recovered in North America were for the most part closely related at the nucleotide sequence level, whereas in other regions, such as Japan and Western Europe, HAV strains were derived from multiple genotypes or sub-genotypes. These data indicate that patterns of endemic transmission can be differentiated from situations in which infections are imported due to travel.
Effect of alloying Ni inner electrodes on the leakage current degradation of BaTiO3-based multilayer ceramic capacitors (2020)

High-capacitance multilayer ceramic capacitors (MLCCs) are mostly electronic ceramic components in which Ni inner electrodes and BaTiO3-based dielectrics are laminated alternately. Owing to their usefulness in portable electronic devices such as smartphones, there is an ongoing demand to attain an MLCC with smaller dimensions and improved capacity. We investigated the effect of alloying Ni inner electrodes with various elements on the leakage current degradation of MLCCs. Fe, Cu, Zn, and Sn were chosen and added to Ni and co-fired with BaTiO3, from which Cu and Sn were alloyed with Ni. The leakage current degradation time of MLCCs using the Ni–Cu and Ni–Sn inner electrodes was longer than that of MLCCs using the Ni internal electrodes. In particular, the leakage current degradation of the MLCCs using Ni–Sn inner electrodes was significantly suppressed. This suppression effect increased as the thickness of the BaTiO3-based dielectrics decreased. This method of optimization of the Ni inner-electrode composition could lead to further miniaturization and increased capacity of MLCCs.
Beamforming in Plates Using Embedded Acoustic Metamaterial Lenses (2013)

In this paper we present a novel technique to design a single ultrasonic transducer system for selective damage interrogation. The design is based on the concept of acoustic metamaterials. The structural area around the transducer is dynamically tailored by using a periodic distribution of resonant inclusions acting as an acoustic lens. The inclusions are arranged in order to form a circular anisotropic lens having an ultrasonic transducer located at its centre. The properties of the lens can be locally tailored in the azimuthal direction allowing controlling the direction of excitation by simply tuning the frequencies of excitation. Numerical results show that the proposed lens design is able to create highly directional and collimated ultrasonic beams by using a single transducer, therefore, overcoming some of the major limitations due to phased array technology.
Aramid nanofiber-reinforced transparent nanocomposites (2015)

Nanoscale polymeric fibers are expected to bring about exceptional mechanical and optical properties in composite materials related to the better integration of different properties between fibers and polymers. The discovery of the first aramid nanofiber dispersion from commercial para-aramid macrofibers similar to Kevlar® developed by DuPont allowed the emergence of an innovative nanoscale building block with great potential for engineering novel high-performance polymer nanocomposites. Here we report the fabrication of aramid nanofiber-reinforced polyacrylic-acid thin films using vacuum-assisted flocculation. We show that the resulting composite has high transparency owing to the nanoscale size of the fibers. The multiple hydrogen bonds available at the interface between the polyacrylic acid and nanofibers result in significant improvement of mechanical properties, with Young's modulus outperforming single-walled carbon nanotube composites. The successful use of ANFs in producing transparent, strong and flexible polymer nanocomposites indicates their great potential as an effective reinforcing agent in optical applications.
<i>pnp</i> Si resonant interband tunnel diodewith symmetrical NDR (2001)

A Si-based resonant interband tunnel diode (RITD) is presented with a pnp configuration so that an integrated RITD can be easily used to form a latch. The I-V characteristics of this pnp RITD show symmetrical negative differential resistance (NDR) regions in both forward and reverse bias. The top diode shows a peak-to-valley current ratio (PVCR) of 1.63 with peak current density (Jp) of 1.5 kA/cm2, while the bottom diode shows a PVCR of 1.51 with Jp of 2.0 kA/cm2.
Gigantic tunneling magnetoresistance in magnetic Weyl semimetal tunnel junctions (2021)

We investigate the tunneling magnetoresistance in magnetic tunnel junctions (MTJs) comprised of Weyl semimetal contacts. We show that chirality-magnetization locking leads to a gigantic tunneling magnetoresistance ratio, an effect that does not rely on spin filtering by the tunnel barrier. Our results indicate that the conductance in the anti-parallel configuration is more sensitive to magnetization fluctations than in MTJs with normal ferromagnets, and predicts a TMR as large as 10<sup>4</sup> % when realistic magnetization fluctuations are accounted for. In addition, we show that the Fermi arc states give rise to a non-monotonic dependence of conductance on the misalignment angle between the magnetizations of the two contacts.
Human vitamin B <sub>12</sub> absorption measurement by accelerator mass spectrometry using specifically labeled <sup>14</sup> C-cobalamin (2006)

There is a need for an improved test of human ability to assimilate dietary vitamin B(12). Assaying and understanding absorption and uptake of B(12) is important because defects can lead to hematological and neurological complications. Accelerator mass spectrometry is uniquely suited for assessing absorption and kinetics of carbon-14 ((14)C)-labeled substances after oral ingestion because it is more sensitive than decay counting and can measure levels of (14)C in microliter volumes of biological samples with negligible exposure of subjects to radioactivity. The test we describe employs amounts of B(12) in the range of normal dietary intake. The B(12) used was quantitatively labeled with (14)C at one particular atom of the dimethylbenzimidazole (DMB) moiety by exploiting idiosyncrasies of Salmonella metabolism. To grow aerobically on ethanolamine, Salmonella enterica must be provided with either preformed B(12) or two of its precursors, cobinamide and DMB. When provided with (14)C-DMB specifically labeled in the C2 position, cells produced (14)C-B(12) of high specific activity (2.1 GBq/mmol, 58 mCi/mmol) (1 Ci = 37 GBq) and no detectable dilution of label from endogenous DMB synthesis. In a human kinetic study, a physiological dose (1.5 microg, 2.2 kBq/59 nCi) of purified (14)C-B(12) was administered and showed plasma appearance and clearance curves consistent with the predicted behavior of the pure vitamin. This method opens new avenues for study of B(12) assimilation.
Phase Detector for Power-Factor Controller (1984)

Positive feedback assures reliable switching. Three Phase Power Factor Controller includes three phase detectors, each produces rectangular waves of duration approximately equal to lag time between line voltage and motor current.
An Efficient Binary Integer Programming Model for Residency Time-Constrained Cluster Tools With Chamber Cleaning Requirements (2021)

Cluster tools play a significant role in the entire process of wafer fabrication. As the width of circuits in semiconductor chips shrinks down to less than 10nm, strict operational constraints are imposed on the operations of cluster tools in order to ensure the quality of processed wafers. Particularly, wafer residency time constraints and chamber cleaning requirements are commonly seen in etching, chemical vapor deposition, coating processes, etc. They make the scheduling problem of cluster tools more challenging. This work aims to provide a solution for dual-arm cluster tools with wafer residency time constraints and chamber cleaning requirements. To do so, it proposes a novel virtual wafer-based scheduling method. By this method, under a steady state, a PM processes either a real or virtual wafer at a time. When a PM processes a virtual one, its chamber can perform a cleaning operation. In this way, we can meet not only the strict residency time constraints for real wafers, but also innovatively meet chamber cleaning requirements. Based on such a novel scheduling method, an efficient binary integer programming model is established to optimize the throughput of cluster tools. Finally, experiments are performed to show the efficiency and effectiveness of the proposed method. <italic xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">Note to Practitioners</i> —To ensure wafer quality in semiconductor manufacturing, engineers have to impose wafer residency time constraints and chamber cleaning requirements on the operations of cluster tools. In order to tackle their scheduling problem with these constraints, this work proposes a novel method based on the use of virtual wafers. Under a one-cyclic schedule obtained for time-constrained cluster tools without chamber cleaning requirements, virtual wafers are loaded into the tool such that when a PM processes a virtual wafer, a chamber cleaning operation can be performed in practice. The key to solve this scheduling problem is to find a wafer loading sequence with the highest performance in terms of cycle time. To do so, this work establishes an efficient binary integer programming model to search for such a solution. Since the obtained solution is a periodical wafer loading sequence based on a one-wafer cyclic schedule, it can be easily implemented. Therefore, this work has a high practical value to numerous semiconductor manufacturers.
Tomographic image via background subtraction using an x‐ray projection image and <i>a priori</i> computed tomography (2009)

Kilovoltage x-ray projection images (kV images for brevity) are increasingly available in image guided radiotherapy (IGRT) for patient positioning. These images are two-dimensional (2D) projections of a three-dimensional (3D) object along the x-ray beam direction. Projecting a 3D object onto a plane may lead to ambiguities in the identification of anatomical structures and to poor contrast in kV images. Therefore, the use of kV images in IGRT is mainly limited to bony landmark alignments. This work proposes a novel subtraction technique that isolates a slice of interest (SOI) from a kV image with the assistance of a priori information from a previous CT scan. The method separates structural information within a preselected SOI by suppressing contributions to the unprocessed projection from out-of-SOI-plane structures. Up to a five-fold increase in the contrast-to-noise ratios (CNRs) was observed in selected regions of the isolated SOI, when compared to the original unprocessed kV image. The tomographic image via background subtraction (TIBS) technique aims to provide a quick snapshot of the slice of interest with greatly enhanced image contrast over conventional kV x-ray projections for fast and accurate image guidance of radiation therapy. With further refinements, TIBS could, in principle, provide real-time tumor localization using gantry-mounted x-ray imaging systems without the need for implanted markers.
Integrated photonic tunable basic units using dual-drive directional couplers (2019)

Photonic integrated circuits based on waveguide meshes and multibeam interferometers call for large-scale integration of Tunable Basic Units (TBUs) that feature beam splitters and waveguides. This units are loaded with phase actuators to provide complex linear processing functionalities based on optical interference and can be reconfigured dynamically. Here, we propose and experimentally demonstrate, to the best of our knowledge, for the first time, a thermally actuated Dual-Drive Directional Coupler (DD-DC) design integrated on a silicon nitride platform. It operates both as a standalone optical component providing arbitrary optical beam splitting and common phase as well as a low loss and potentially low footprint TBU. Finally, we report the experimental demonstration of the first integrated triangular waveguide mesh arrangement using DD-DC based TBUs and provide an extended analysis of its performance and scalability.