gebhart/patrepeval huggingface dataset:
New mechanism for methicillin resistance in Staphylococcus aureus: clinical isolates that lack the PBP 2a gene and contain normal penicillin-binding proteins with modified penicillin-binding capacity (1989)

Seventeen clinical isolates of Staphylococcus aureus (from the United States and Europe) selected for low (borderline)-level methicillin resistance (MIC of methicillin, 2 to 4 micrograms/ml; MIC of oxacillin, 0.5 to 8 micrograms/ml) were examined for their mechanisms of resistance. Five strains were typical of heterogeneous S. aureus: they gave positive reactions with a DNA probe specific for mec and contained a small fraction (10(-6] of highly resistant cells (MIC, greater than 100 micrograms/ml). The rest of the 12 strains were homogeneous with respect to their methicillin resistance: the MIC of methicillin for all cells was 2 to 4 micrograms/ml, and no cells for which MICs were 50 micrograms/ml or higher were detectable (less than 10(-9]. None of these strains reacted with the mec-specific DNA probe. One representative strain of each group was characterized in more detail. Strain CDC-1, prototype of heterogeneous methicillin-resistant S. aureus, contained penicillin-binding protein (PBP) 2a; its DNA could transform a methicillin-susceptible and novobiocin-resistant recipient to methicillin resistance with ca. 35% linkage to Novr. Introduction of the "factor X" determinant (K. Murakami and A. Tomasz, J. Bacteriol. 171:874-879, 1989) converted strain CDC-1 to high, homogeneous resistance. Strain CDC-6, prototype of the second group of isolates, showed completely homogeneous MICs of methicillin, oxacillin, and cefotaxime. The strain contained modified "normal" PBPs: PBPs 1 and 2 showed low drug reactivity (and/or cellular amounts), and PBP 4 was present in elevated amounts. No PBP 2a could be detected. DNA isolated from strain CDC-6 could transform the methicillin-susceptible and novobiocin-resistant strain to methicillin resistance in a multistep fashion, but this resistance showed no genetic linkage to the Nov marker. We suggest that staphylococci with borderline resistance may contain at least three different classes of mechanism: heterogeneous, methicillin-resistant S. aureus, PBPs of modified drug reactivities, and the previously reported hyperproduction of beta-lactamase (L.K. McDougal and C. Thornsberry, J. Clin Microbiol. 23:832-839, 1986).
A Two-Dimensional Analytical Model for Tunnel Field Effect Transistor and Its Applications (2013)

In this paper, a two-dimensional analytical model for the tunnel field effect transistor (TFET) on the silicon-on-insulator substrate is proposed. The accurate electrostatic potential and electric field of the device are obtained by solving the Poisson equation with appropriate boundary conditions. The accuracy of the proposed analytical model is verified by comparing with numerical simulation. It is shown that the electrical behavior of the TFET is more properly described by defining the zero vertical electric field at the channel/buried oxide interface. Furthermore, this analytical model is extended to implement in the hetero-material-gate (HMG) TFET. The physical principle of the HMG TFET can also be depicted, and electrical properties are characterized using this model.
Strategy for Rapid Detection of Carbapenemase-Producing Enterobacteriaceae (2014)

A prospective survey was conducted on 862 Enterobacteriaceae isolates with reduced susceptibility to carbapenems. The Carba NP test, UV spectrophotometry, and a DNA microarray were used to detect carbapenemase producers, and the results were compared to those from PCR and sequencing. The 172 carbapenemase producers were detected using the Carba NP test and UV spectrophotometry, whereas the DNA microarray failed to detect IMI producers. The use of the Carba NP test as a first screening, followed by the use of molecular techniques, has been determined to be an efficient strategy for identifying carbapenemase-producing Enterobacteriaceae.
Covalent Organic Frameworks: Chemistry beyond the Structure (2018)

Covalent organic frameworks (COFs) represent a new field of rapidly growing chemical research that takes direct inspiration from diverse covalent bonds existing between atoms. The success of linking atoms in two and three dimensions to construct extended framework structures moved the chemistry of COFs beyond the structures to methodologies, highlighting the possibility of prospective applications. Although structure to property relation in COFs has led to fascinating properties, chemical stability, processability and scalability were some of the important challenges that needed to be overcome for their successful implementation. In this Perspective, we take a closer look at the growth of COFs from mere supramolecular structures to potential industrializable materials.
<title>Breast tumor characterization using near-infrared spectroscopy</title> (1993)

NIR time resolved spectroscopy (TRS) is one of the most feasible methods which can be used for the characterization of biological systems, due to its non-invasive nature and safety features in measurement. Breast cancer is the leading cause of death in women ages 40 - 44 and accounts for 32% of all cancer diagnosis in women. The occurrence rate is as high as one out of nine women in the USA. Breast cancer is the most common form of cancer and the second leading cause of cancer death in North America. Therefore, it is natural for researchers in the field of NIR spectroscopy to have strong interest in optical properties of normal and abnormal breast tissue. One of the main interests of NIR spectroscopy in breast cancer is the localization of the tumor. Another important feature is to characterize an anomaly non- invasively since more than 75% of mammographical anomalies are found to be benign. This could reduce the anxiety that the patients would have, as well as lower the clinical expense for the biopsy and operation (approximately $4,000 per a case).
Experimental Studies on SAT-Based Test Pattern Generation for Industrial Circuits (2006)

Due to the ever increasing size of integrated circuits classical methods for automatic test pattern generation (ATPG) reach their limits. On the other hand recent advances in algorithms to solve the Boolean satisfiability (SAT) problem allow the application to large instances. This suggests to exploit modern SAT techniques for ATPG. Here, we present a SAT-based ATPG tool that is applicable to large industrial circuits. The performances of different SAT-solvers are experimentally evaluated and the potential for problem specific heuristics is shown. Further experiments show that most of the faults can be classified very efficiently independently of the circuit size.
Development of Water Recovery Demonstration System for Further Manned Space Exploration (2013)

For further manned space exploration, one critical issue is source recycling, especially water recovery. JAXA is approaching to prepare for an on-orbit demonstration with the development of the water recovery system by 2015. Based on the current situation in ISS, the processing objects are urine and condensate water generated by crew. Specific and technical examinations of the water recovery system demonstration have been conducted. Comparison and examination of various methods, such as reverse osmosis membrane, photocatalytic oxidation, electrolysis and electrodialysis were conducted. Consequently, electrolysis and electrodialysis took the leading role in this water recovery demonstration system.
Materials and methods for higher performance screen-printed flexible MRI receive coils (2016)

Using the proposed methods and materials, the SNR of printed coils approached that of commercial coils while using a new fabrication technique that provided more flexibility and close contact with the patient's body. Magn Reson Med 78:775-783, 2017. © 2016 International Society for Magnetic Resonance in Medicine.
Detecting subscribers using NAT devices in wireless data networks (2009)

A network address translation (NAT) device can aggregate/disaggregate traffic from/to multiple computers connected to the box appearing as one computer to the rest of the network. A wireless data service subscription may be shared by using a NAT device where multiple computers can then use the wireless service at the same time. This is transparent to the service provider since all traffic comes from and goes to the same address. However, it potentially can lead to lost revenue since the current prevalence of flat rate pricing schemes means that one paid subscription can be shared by many users. Therefore, it is important for service providers to be able to detect such subscribers and take proper action, e.g., put them on a different pricing scheme or add explicit terms to their contract to disallow this practice. In this paper, we propose a novel method to identify subscribers using NAT devices in real time. The key observation is that each device generates an independent number sequence (usually increasing) to fill the identification field of IP packet headers (IPID). Our basic technique involves detecting overlapping increasing IPID subsequences as an indication of multiple devices behind a single Internet Protocol (IP) address. Our complete solution takes into account various practical issues affecting the properties of IPID sequences.
Coulombic Effects in Ion Mobility Spectrometry (2009)

Ion mobility spectrometry (IMS) has been increasingly employed in a number of applications. When coupled to mass spectrometry (MS), IMS becomes a powerful analytical tool for separating complex samples and investigating molecular structure. Therefore, improvements in IMS-MS instrumentation, e.g., IMS resolving power and sensitivity, are highly desirable. Implementation of an ion trap for accumulation and pulsed ion injection to IMS based on the ion funnel has provided considerably increased ion currents and thus a basis for improved sensitivity and measurement throughput. However, large ion populations may manifest Coulombic effects contributing to the spatial dispersion of ions traveling in the IMS drift tube and reduction in the IMS resolving power. In this study, we present an analysis of Coulombic effects on IMS resolution. Basic relationships have been obtained for the spatial evolution of ion packets due to Coulombic repulsion. The analytical relationships were compared with results of a computer model that simulates IMS operation based on a first principles approach. Initial experimental results reported here are consistent with the computer modeling. A noticeable decrease in the IMS resolving power was observed for ion populations of >10,000 elementary charges. The optimum IMS operation conditions which would minimize the Coulombic effects are discussed.
Multi-resolution Compressive Sensing Reconstruction (2016)

We consider the problem of reconstructing an image from compressive measurements using a multi-resolution grid. In this context, the reconstructed image is divided into multiple regions, each one with a different resolution. This problem arises in situations where the image to reconstruct contains a certain region of interest (RoI) that is more important than the rest. Through a theoretical analysis and simulation experiments we show that the multi-resolution reconstruction provides a higher quality of the RoI compared to the traditional single-resolution approach.
EVALUATION OF 5’NUCLEASE BASED DETECTION ASSAYS TO DETECT<i>ESCHERICHIA COLI</i>O157:H7 FROM FOOD PRODUCTS (2001)

Two 5’nuclease‐based PCR methods (PCR‐LS‐50B and PCR‐7200) were evaluated to determine their sensitivity for detecting Escherichia coli O157:H7 from pure cultures and in food samples enriched in different media and after different incubation periods. The PCR‐7200 method was able to detect E. coli O157:H7 at ± 10 2 CFU/mL in pure culture in both mECB and EEB. In spiked meat samples, the PCR‐7200 procedure was capable of detecting the eaeA gene at lower concentrations than the PCR‐LS‐50B procedure, regardless of the meat type or enrichment medium. Escherichia coli O157:H7 spiked at 0.3 CFU/mL was detectable after 9 h in EEB, but it was not detected in mECB within 24 h. An enrichment time of 4 h in mECB was needed to detect E. coli O157:H7 when spiked at higher levels (41 CFU/mL). The detection levels reported in this study are similar with other reported PCR‐based detection techniques for E. coli O157:H7, however, the 5’nuclease‐based assays are less labor intensive and capable of higher sample throughput because of their automated detection and analysis steps.
Speaker recognition with polynomial classifiers (2002)

Modern speaker recognition applications require high accuracy at low complexity. We propose the use of a polynomial-based classifier to achieve these objectives. This approach has several advantages. First, polynomial classifier scoring yields a system which is highly computationally scalable with the number of speakers. Second, a new training algorithm is proposed which is discriminative, handles large data sets, and has low memory usage. Third, the output of the polynomial classifier is easily incorporated into a statistical framework allowing it to be combined with other techniques such as hidden Markov models. Results are given for the application of the new methods to the YOHO speaker recognition database.
From devices to people (2014)

Online services rely on unique identifiers of machines to tailor offerings to their users. An implicit assumption is made that each machine identifier maps to an individual. However, shared ma-chines are common, leading to interwoven search histories and noisy signals for applications such as personalized search and ad-vertising. We present methods for attributing search activity to individual searchers. Using ground truth data for a sample of almost four million U.S. Web searchers-containing both machine identifiers and person identifiers-we show that over half of the machine identifiers comprise the queries of multiple people. We characterize variations in features of topic, time, and other aspects such as the complexity of the information sought per the number of searchers on a machine, and show significant differences in all measures. Based on these insights, we develop models to accurately estimate when multiple people contribute to the logs ascribed to a single machine identifier. We also develop models to cluster search behavior on a machine, allowing us to attribute historical data accurately and automatically assign new search activity to the correct searcher. The findings have implications for the design of applications such as personalized search and advertising that rely heavily on machine identifiers to custom-tailor their services.
Multi-Potent Adult Progenitor Cells from Swine Bone Marrow. (2005)

Abstract Here, we show that Multi-potent Adult Progenitor Cells (MAPCs) can be derived from adult and fetal swine bone marrow. Swine MAPC (swMAPC) contain initially multiple different progenitors and mature cells; however, cultures are homogenous by 50 population doublings and can grow past 150 population doublings. SwMAPCs are CD44, CD45, and MHC-I, II negative, express Oct3a/4 at levels close to those seen in embryonic stem cells, and have telomerase activity leading to no telomere shortening with expansion. We also have very solid evidence that swMAPCs differentiate into most mesoderm, neuroectoderm, and endoderm lineages as demonstrated by a significant up-regulation of transcription factors and other lineage specific proteins in a time dependent fashion similar to development, measured by Q-RT-PCR as well as immunohistology. In addition, swMAPCs induced to the endothelial lineage form vascular tubes, to the hepatic lineage produce albumin and urea, and to the smooth muscle lineage display significant calcium flux in response to smooth muscle agonists. In addition, we are investigating the swMAPC differentiation into cardiomyocytes. Preliminary data indicates swMAPCs express TBX5, Nkx2.5, and GATA6 by day 7 at significant levels. As we have seen for rodent MAPCs, when swMAPCs are allowed to grow at high density, Oct3a/4 levels drop to undetectable ranges, the cells take on a mesenchymal stem cell (MSC) phenotype, and the differentiation potential is lost. When replated under low density conditions, oct3a/4 expression or differentiation capacity can not be re-induced, and cells remain MSC like. Therefore, we suggest that Oct3a/4 is not an in vitro culture phenomena but is already present in swMAPCs and cannot be recovered once lost with standard culturing techniques.
A scanning tunneling microscopy based potentiometry technique and its application to the local sensing of the spin Hall effect (2017)

A scanning tunneling microscopy based potentiometry technique for the measurements of the local surface electric potential is presented and illustrated by experiments performed on current-carrying thin tungsten films. The obtained results demonstrate a sub-millivolt resolution in the measured surface potential. The application of this potentiometry technique to the local sensing of the spin Hall effect is outlined and some experimental results are reported.
Stokes shift emission spectroscopy of key biomolecules in human tissues (2004)

The Stokes-shifted emission spectra were measured for various photoactive biomolecules such as tryptophan, collagen, NADH and flavin in aqueous solution and tissue. Information is obtained on the molecular activity in the tissue. This new approach allows for the extraction of information not obtained from excitation and/or fluorescence spectroscopy for a single spectral scan.
Novel Approach for Welding Stainless Steel Using Cr-Free Welding Consumables (2004)

This project was a SERDP seed grant that was extended from the normal one year duration to a total of two years. The goal of the project was to demonstrate the feasibility of a new approach for welding stainless steel using Cr-free consumables. Stainless steels are usually selected as a material of construction for their corrosion resistance. When they are fabricated into structures, stainless steel components are often joined by welding. In order to ensure that the welds exhibit sufficient corrosion resistance, filler metals matching or exceeding the chromium (Cr) content of the base metal must be used. The Cr content of Types 304 and 308 stainless steels, the most commonly used stainless steel and the filler metal used to weld, respectively, it is 18-20 wt%. Evaporation and oxidation of Cr from the molten weld pool results in emission of carcinogenic hexavalent Cr (Cr+6 or chromate) in the fumes. This is a significant health hazard for the welders and necessitates considerable expense for ventilation systems. In some conditions relevant to DOD interests, such as cramped ship interiors, it is extremely difficult to ventilate effectively. Furthermore, any future reduction in the Permissible Exposure Limit (PEL) for chromate in welding fume, which is under consideration by OSHA, will exacerbate the situation. It is the objective of this proposal to develop a Cr-free consumable for welding austenitic stainless steel that provides mechanical properties and corrosion resistance comparable to the Cr-bearing consumable that are currently used. The approach to solving this problem considers that, if stainless steel (SS) is to be welded with a filler metal that is different in composition than the base metal, then the corrosion of the welded structure will be controlled by the phenomenon of galvanic corrosion. Furthermore, passive metals such as stainless steels usually corrode in a localized nature.
Detection and clinical features of hepatitis C virus type 6 infections in blood donors from Hong Kong (1996)

The genotype distribution of hepatitis C virus (HCV) was investigated in 212 viraemic blood donors from Hong Kong. A subset of the samples was investigated using three different genotyping assays to establish the accuracy of each in this population. These assays were restriction fragment length polymorphism (RFLP) of amplified 5' noncoding region (5'NCR) sequences, RFLP of the core region, and a serotyping assay using peptides from two antigenic regions of NS4. Genotypes detected in Hong Kong blood donors were 1a (6.2%), 1b (58.8%), 2a (1.4%), 2b (1.4%), 3a (1.9%), and 6a (27.0%). All genotyping assays produced concordant results. No evidence was obtained for the presence of type 6 group variants recently identified in Southeast Asia, other than type 6a. A serotyping assay based upon the detection of type-specific antibody to epitopes in NS4 produced similar results to the genotyping assays (98% concordance), but a reduced sensitivity (75%) compared with genotyping methods. Sequence variation in NS4 was not the cause of the reduced rate of detection of type 6 antibody in this population. Eighty-four percent donors infected with type 6a were male, compared to 75% donors infected with type 1b. The median alanine transaminase (ALT) level in type 6 infected donors was lower than in type 1b, (43.8 and 51.1 U/l, respectively) although these values were not statistically significant (P = 0.094). There was no significant difference between the ages of donors infected with types 1b and 6a. Risk factors for HCV infection in the blood donors included blood transfusion, intravenous drug abuse, and tattooing. A significantly greater number of donors infected with HCV-6a reported a history of drug abuse (66%) than donors infected with HCV-1b (7%).
Deadline-aware datacenter tcp (D2TCP) (2012)

An important class of datacenter applications, called Online Data-Intensive (OLDI) applications, includes Web search, online retail, and advertisement. To achieve good user experience, OLDI applications operate under soft-real-time constraints (e.g., 300 ms latency) which imply deadlines for network communication within the applications. Further, OLDI applications typically employ tree-based algorithms which, in the common case, result in bursts of children-to-parent traffic with tight deadlines. Recent work on datacenter network protocols is either deadline-agnostic (DCTCP) or is deadline-aware (D3) but suffers under bursts due to race conditions. Further, D3 has the practical drawbacks of requiring changes to the switch hardware and not being able to coexist with legacy TCP. We propose Deadline-Aware Datacenter TCP (D2TCP), a novel transport protocol, which handles bursts, is deadline-aware, and is readily deployable. In designing D2TCP, we make two contributions: (1) D2TCP uses a distributed and reactive approach for bandwidth allocation which fundamentally enables D2TCP's properties. (2) D2TCP employs a novel congestion avoidance algorithm, which uses ECN feedback and deadlines to modulate the congestion window via a gamma-correction function. Using a small-scale implementation and at-scale simulations, we show that D2TCP reduces the fraction of missed deadlines compared to DCTCP and D3 by 75% and 50%, respectively.
60 GHz patch antenna in LTCC with an integrated EBG structure for antenna pattern improvements (2014)

We present a 60 GHz LTCC aperture-coupled patch antenna with an integrated Sievenpiper EBG structure used for suppression of TM mode surface waves. This is believed to be the first demonstration of a Sievenpiper EBG structure used inside a millimeterwave LTCC antenna. The merit of this EBG structure is to yield a predicted 6 dB improvement in broadside directivity. Without the EBG structure, edge diffraction of surface waves degrades the pattern into two main beams. The combination of a new LTCC material system (DuPont 9K7 GreenTape™) along with laser ablation processing for fine line and fine slot definition allowed the integration of a successful EBG structure with an aperture coupled patch antenna.