gebhart/patrepeval huggingface dataset:
Overexpression of the Nocardia lactamduransα‐Aminoadipyl‐Cysteinyl‐Valine Synthetase in Streptomyces lividans (1996)

Formation of the tripeptide delta-(L-alpha-aminoadipyl)-L-cysteinyl-D-valine (Aad-Cys-Val) is catalyzed by a multienzyme peptide synthetase encoded by the pcbAB gene in producers of beta-lactam antibiotics. The pcbAB gene of Nocardia lactamdurans was overexpressed in Streptomyces lividans giving a high Aad-Cys-Val synthetase activity. The synthetase was purified 2785-fold to near homogeneity showing a molecular mass of 430 kDa by SDS/PAGE. The protein was identified in the gels with antibodies to Aad-Cys-Val synthetase and by the formation of aminoacyl-synthetase thioester complex with [14C]valine. The purified synthetase used alpha-aminoadipic acid or its lactam 6-oxopiperidine 2-carboxylic acid but was unable to use piperideine 6-carboxylic acid or pipecolic acid as substrates to form Aad-Cys-Val. L-Cystathionine, (2-amino-2-carboxyethyl)-L-homocysteine, was used as substrate and formed Aad-Cys-Val with the same efficiency as L-cysteine. The product of the reaction eluted with authentic Aad-Cys-Val. The synthetase preparation was able to hydrolyze L-cystathionine by a pyridoxal-phosphate-independent mechanism which is not inhibited by propargylglycine, to form Aad-Cys-Val.
Dense Optical Flow Field Estimation Using Recursive Lms Filtering (2006)

Publication in the conference proceedings of EUSIPCO, Florence, Italy, 2006
The Transfer of Energy from a Tornado into the Ground (2001)

Doppler radar is currently used with considerable success to detect tornadic storms in turbulent weather systems, but such radar cannot determine when the tornado is in actual contact with the ground. Recent research has shown that as a tornado makes contact with the ground surface a significant amount of kinetic energy is expended in overcoming the resistance of the wind flow at the fluid/solid interface (Tatom, 1993; Tatom et al. , 1995). This expended energy is transformed into a combination of heat, acoustic waves, and seismic vibrations, as shown in Figure 1. Although quantification of the total energy expended can be reasonably accomplished, no theoretical model exists for computing the distribution of energy among the three types noted. Furthermore, with regard to seismic energy the question arises as to the partitioning of the seismic energy into body waves and surface waves. If answers to these questions can be found, some idea of the amplitude and frequency response of the resulting seismic signal can be obtained. As part of a recent research project, considerable attention was directed to this issue, and some progress was made in obtaining answers to the questions raised.

Although turbulent weather systems that generate tornadoes are highly stochastic in nature, a quantitative approximation of the energy at the air-ground interface can be attempted based on a simplification of the tornado's geometry, as illustrated in Figure 1. In this simplification the contact area of the tornado AT is assumed to be the interface on which energy transfer takes place. For a turbulent flow over a flat surface (Reynold's number > 105) the pressure fluctuations \batchmode \documentclass[fleqn,10pt,legalpaper]{article} \usepackage{amssymb} \usepackage{amsfonts} \usepackage{amsmath} \pagestyle{empty} \begin{document} \(P_{w}^{{^\prime}}\) \end{document} develop as a result of the turbulent eddies that are generated normal to the flat surface. Although a viscous atmospheric sublayer exists above the ground surface where the turbulence …
Flexible Optik: aktuelle Entwicklungen bei molekularen Gelen (2012)

Eine einzigartige Kombination von Eigenschaften macht die Organogele auf der Basis von Zuckerketalen, deren Synthese kürzlich beschrieben wurde, für die Entwicklung von flexiblen optischen Bauteilen und als intelligente Materialien für potenzielle Anwendungen zur Herstellung mikrophotonischer Systeme geeignet. Hauptmerkmale bei der Selbstorganisation dieser Gelbildner waren konformative Einschränkungen und die Neigung zu Wechselwirkungen.
Gene clustering by Latent Semantic Indexing of MEDLINE abstracts (2004)

The 50-gene document collection used in this study can be interactively queried at http://shad.cs.utk.edu/sgo/sgo.html.
High resolution surface imaging arrays interrogated with microfluidically controlled metalized plates (2014)

Microfluidically controlled metalized plates are proposed for the first time as a low-cost interrogation mechanism for high resolution surface imaging arrays. The pixels of the envisioned imaging system are formed as a dense array of sub-wavelength size slot spiral resonators etched at the ground plane of a microwave substrate. The resonance frequencies of these resonators shift based on the dielectric properties of the material sample within their close proximity. Interrogation of the resonance frequency of each resonator is done by utilizing metalized plates as RF shorts between read-out microstrip lines and resonators. The metalized plates can be repositioned within the microfluidic channels by use of a single micropump unit to sequentially interrogate resonance frequencies of all pixels to extract an image. The concept is introduced through simulations and experiments carried over a 1D material sample. An example 2D imaging system is also presented (through computational simulations) for imaging of tumorous excised breast tissue. The proposed technique alleviates the needs for expensive/complex RF switch based interrogation circuitries or bulky/slow mechanical raster scans.
Enhancement and Neutralization of Feline Infectious Peritonitis Virus Infection in Feline Macrophages by Neutralizing Monoclonal Antibodies Recognizing Different Epitopes (1993)

The interaction between the enhancing and neutralizing activities of three monoclonal antibodies (MAbs) (5-6-2, 6-4-2 and 7-4-1) to the spike protein of feline infectious peritonitis virus (FIPV) strain 79-1146 was determined using feline macrophages. At a high MAb concentration, all of the three MAbs completely inhibited the FIPV infection at 37 C. However, two of them (6-4-2 and 7-4-1) enhanced FIPV infection when either the MAb concentration or reaction temperature was lowered. These MAbs also exerted an immediate infectivity-enhancing activity for up to 10 min of reaction and by 20 min, neutralizing activities were observed. Only MAb 5-6-2 consistently showed neutralizing activity regardless of the reaction conditions. Competition with sera from cats experimentally infected with FIPV strain 79-1146 or feline enteric coronavirus strain 79-1683 showed that the two epitopes recognized by MAb 5-6-2 and MAb 6-4-2, respectively, are also recognized by the natural host.
Effects of speculation on performance and issue queue design (2004)

Current trends in microprocessor designs indicate increasing pipeline depth in order to keep up with higher clock frequencies and increased architectural complexity. Speculatively issued instructions are particularly sensitive to increases in pipeline depth. In this brief, we use load hit speculation as an example, and evaluate its cost effectiveness as pipeline depth increases. Our results indicate that as pipeline depth increases, speculation is more essential for performance but can drastically alter the utilization of pipeline resources, particularly the issue queue. We propose an alternative, more cost-effective design that takes into consideration the different issue queue utilization demands without degrading overall processor performance.
Marker Panel Predictive of Lymph Node Metastasis in Young Patients with Breast Carcinoma (1998)

Breast cancer is being diagnosed more frequently in young women. It is important to identify tumors with greater metastatic potential since this information will provide a basis for noninvasive staging of the axilla. The studied population consisted of 66 patients with infiltrating breast carcinoma (56 ductal, 10 lobular) aged 20-34 (mean 29) years. Lymph node status was correlated with the following parameters: size, grade, p53 expression, MIB-1, CD44, c-Erb-2, estrogen, progesterone receptors, and a family history of breast cancer. Immunohistochemical studies utilizing avidinbiotin-peroxidase complex method were performed on formalin-fixed, paraffinembedded tissue. Thirty-nine patients (59%) had positive lymph nodes and 27 (41%) had negative lymph nodes. In multivariate logistic regression analysis, two models with size (p=.0002) and p53 (p=.0379) or size (p=.0002) and MIB-1 (p=.0462) were predictive of nodal involvement. For TI lesions, p53 positivity increased the probability of nodal involvement from 18% to 46% and, for T2 lesions, from 65% to 89%. In the second model, for TI lesions MIB-1 positivity increased the probability of nodal involvement from 10% to 36% and, for T2 lesions, from 48% to 82%. Size, p53, and MIB-1 were found to be valid independent predictors of lymph node metastasis in TI and T2 breast carcinomas in young women. The combination of size with p53 or MIB-1 increases dramatically the predictive impact of these parameters on nodal status. These data may prove useful in selecting patients with increased risk of dissemination and provide a basis for staging the axilla noninvasively.
Table S1 addendum from The MD Anderson Prostate Cancer Patient-derived Xenograft Series (MDA PCa PDX) Captures the Molecular Landscape of Prostate Cancer and Facilitates Marker-driven Therapy Development (2023)

&lt;p&gt;PDXs growth rate and list of publications in which MDA PCa PDX were used.&lt;/p&gt;
A Proximity Sensor Based No-Touch Mechanism for Mobile Applications on Smart Phones (2012)

Smart phones with touch screens have become very popular and have changed our behaviors of using handsets. However, using touch screens is not safe for mobile phone users especially when they are driving cars. Thus, many applications using smart phones cannot be initiated because users who are driving the cars cannot easily touch the small icons on the screens of smart phones. To overcome this issue, we propose a proximity sensors based "no-touch" mechanism for smart phones by applying proximity sensors to initiate mobile applications without the need of touching the screen. We will discuss how to implement the proximity-sensors driven "no-touch" mechanism in Android platform and investigate its performance issues regarding detection accuracy and power consumption. Speech-oriented applications using the proposed "no-touch" mechanism on Android is also demonstrated in this paper.
COMPARISON OF HISTIDINE-TRYPTOPHAN-KETOGLUTARATE SOLUTION AND UNIVERSITY OF WISCONSIN SOLUTION FOR ORGAN PRESERVATION IN CLINICAL PANCREAS TRANSPLANTATION (2004)

Within this range of cold ischemia time, UW and HTK demonstrate similar efficacy in pancreas preservation.
Super resolved optical system for objects with finite sizes using circular gratings (2015)

We present a real time all optical super resolution method for exceeding the diffraction limit of an imaging system which has a circular aperture. The resolution improvement is obtained using two fixed circular gratings which are placed in predetermined positions. The circular gratings generate synthetic circular duplications of the aperture, thus they are the proper choice for a circular aperture optical system. The method is applicable for both spatially coherent and incoherent illuminations, as well as for white light illumination. The resolution improvement is achieved by limiting the object field of view. The proposed method is presented analytically, demonstrated via numerical simulations, and validated by laboratory experiments.
Important role of CCR2 in a murine model of coronary vasculitis (2012)

Collectively, our findings provide novel insights into the role of CCR2 in the pathogenesis of vasculitis as seen in KD and highlight novel therapeutic targets, specifically for individuals resistant to first-line treatments.
Turing patterns in systems with high-order interactions (2022)

Turing theory of pattern formation is among the most popular theoretical means to account for the variety of spatio-temporal structures observed in Nature and, for this reason, finds applications in many different fields. While Turing patterns have been thoroughly investigated on continuous support and on networks, only a few attempts have been made towards their characterization in systems with higher-order interactions. In this paper, we propose a way to include group interactions in reaction-diffusion systems, and we study their effects on the formation of Turing patterns. To achieve this goal, we rewrite the problem originally studied by Turing in a general form that accounts for a microscropic description of interactions of any order in the form of a hypergraph, and we prove that the interplay between the different orders of interaction may either enhance or repress the emergence of Turing patterns. Our results shed light on the mechanisms of pattern-formation in systems with many-body interactions and pave the way for further extensions of Turing original framework.
Effective Disinfection of a Burn Unit after Two Cases of Sepsis Caused by Multi-Drug–Resistant Acinetobacter baumannii (2018)

Our results support the use of the hydrogen peroxide/silver cations dry-mist system as an adjunct to standard manual cleaning and disinfection protocols used in the healthcare environment because of its broad-spectrum and high antimicrobial activity. This system may be a valuable option to consider, particularly in the control of microbial outbreaks.
The Application of Artificial Intelligence Technology in the Diagnosis of Acute Pancreatitis (2019)

Present acute pancreatitis surgical treatment often uses percutaneous catheter drainage minimally invasive surgery. Physicians generally based on the understanding of the patient's two-dimensional CT images to puncture and guide the catheter into position within the abdominal cavity to perform drainage of the free effusion to develop a surgical plan before surgery. The successful key to the CT-guided puncture and drainage is the accurate positioning of the inflammatory region. It is hard to divide the edges of each region accurately because there are many organs in abdomen CT image and some of the acute pancreatitis CT have free effusion regions. The localization and segmentation of each part in clinical treatment are influenced by the personal experience and ability of the physician. Computed Tomography Severity Index (CTSI) score is a result gotten from the analysis of the image to determine whether the patient has to get the operation or not. We collected 125 cases of CT images with the marked pancreas and free effusion area. Building models through Faster R-CNN object detection, the region growing and Gaussian filter to determine the survival pancreas, normal pancreas or free effusion area in CT images accurately. Reconstruct the three-dimensional structure image and related structure positioning, calculate the percentage of pancreatic necrosis, the number of necrotic areas and the size of the area, and then calculate the CTSI score. The experimental results were evaluated through three indicators of Dice Score, the volume overlap error (VOE) and the relative volume error (RVD). The accuracy rate of the automatic segmentation area compared to the standard area is 92 %, which can provide the physicians with an objective analysis of the surgical plan before surgery to improve the accuracy and safety.
Comparative Study of Eight Equations of State for Predicting Hydrocarbon Volumetric Phase Behavior (1988)

Summary The objective of this study is to present a review of eight equations of state (EOS’s) and compare their ability to predict the volumetric and phase equilibria of gas-condensate systems. Included in the study are the Peng-Robinson (PR), the Soave-Redlich-Kwong (SRK), the Schmidt-Wenzel (SW), the Usdin-McAuliffe (UM), the Heyen, the Kubic, the Adachi-Lu (AL), and the Patel-Teja (PT) EOS’s. The SW equation exhibits a superior predictive capability for volumetric properties of condensate systems. The PR equation is found to represent the phase equilibrium behavior of condensate systems accurately. In terms of compressibility factors, the SW and PT equations give better predictions than other equations.
Real-time drug testing using patient-derived organoids from resected breast cancer brain metastases. (2021)

e14003 Background: Brain metastases (BrMet) remain a clinically challenge. There is an increase interest in evaluating the efficiacy of systemic therapy for BrMet. Patient-derived organoids (PDO) and xenografts (PDX) are thought to capture the tumor heterogeneity and molecular alterations of the source tumor, and may be used as ‘avatars’ for therapeutic response assessment of the source patient. PDO has an advantage over PDX with a shorter establishment time, and thus, may allow a real-time drug sensitivity testing. The objective of this study was to determine the feasibility of establishing PDO from resected breast cancer BrMet and to evaluate the drug sensitivities in a time period amenable to eventual implemention into clinical utiliity. Methods: Under an IRB-approved protocol, resected BrMet tissues were prospectively collected at the time of clinically indicated neurosurgical procedure as part of a banking program. Tumors were directly cultured as 3-D organoids. DNA and RNA were collected. Drug testing panels included standard clinical care drugs or drug combinations as well as those selected based on the molecular profiling. When clinically conducted next-generation sequencing testing reports were available, we also tested drugs (or class of drugs) that were suggested as a potential therapeutic consideration in these reports. When possible, Nanostring PanCancer Panel evaluation was conducted at the time of PDO establishment to guide the selection of drugs. Results: To date, 11 breast cancer BrMet samples have been collected. 8/11 were successfully established as ‘direct from operating room’ PDO and underwent drug panel testing. The reasons for 3 cases not drug tested include: no viable tumor (confirmed by clinical pathology report as necrosis only) and primary brain tumor (not metastasis). Of the 8 PDO, the clinical subtypes were 5HER2+, 2HR-HER2-, and 1HR+HER2- cases.The median time from collection to the drug testing results availability was 11 days (range: 7-19 days). The median number of drugs or drug combinations tested was 23 (range: 7-32). The drug testing revealed various patterns of sensitivities to chemotherapies and targeted therapies. Nanostring PanCancer testing of PDO identified potential targetable pathways for which PDO demonstrated sensitivity when the drugs were matched to the associated molecular pathway. Conclusions: While the expected number of cases has been much lower due to COVID-19 pandemic-related change in clinical practice patterns and research operations, we have successfully demonstrated that the real-time establishment of BrMet PDO is feasible and may be used as a platform for further investigations. Real-time PDO could be potentially employed to predict drug sensitives for prioritizing drug therapy options in a clinically meaningful time-frame. PDO platform may be used to investigating biomarkers and mechanisms of response and resistance to therapy.
Biomarkers for detection and surveillance of bladder cancer (2013)

We find that no currently available bladder cancer urinary marker is sensitive enough to eliminate the need for cystoscopy. In addition, cytology remains integral to the detection of occult cancer. However, owing to their relatively high sensitivities, these markers may be used to extend the period between cystoscopies in the surveillance of patients with transitional cell carcinoma. Further study is required to determine which markers, alone or in panel, would best accomplish this.
Three-Dimensional Electron Microscopic Imaging of Membrane Invaginations in Escherichia coli Overproducing the Chemotaxis Receptor Tsr (2004)

Electron tomography is a powerful method for determining the three-dimensional structures of large macromolecular assemblies, such as cells, organelles, and multiprotein complexes, when crystallographic averaging methods are not applicable. Here we used electron tomographic imaging to determine the molecular architecture of Escherichia coli cells engineered to overproduce the bacterial chemotaxis receptor Tsr. Tomograms constructed from fixed, cryosectioned cells revealed that overproduction of Tsr led to formation of an extended internal membrane network composed of stacks and extended tubular structures. We present an interpretation of the tomogram in terms of the packing arrangement of Tsr using constraints derived from previous X-ray and electron-crystallographic studies of receptor clusters. Our results imply that the interaction between the cytoplasmic ends of Tsr is likely to stabilize the presence of the membrane networks in cells overproducing Tsr. We propose that membrane invaginations that are potentially capable of supporting axial interactions between receptor clusters in apposing membranes could also be present in wild-type E. coli and that such receptor aggregates could play an important role in signal transduction during bacterial chemotaxis.
The relationship between laboratory‐based outcome measures and mortality in end‐stage renal disease: A systematic review (2009)

Despite data that traditional laboratory-based outcome measures in dialysis are improving over time, population-based data indicate that mortality rates are not improving in parallel. With increased focus on performance measures based on laboratory-based outcomes (e.g., hematocrit, albumin, and parathyroid hormone), less emphasis has been placed on other markers, some of which may be stronger predictors of mortality. We performed a systematic review to interpret the predictive value of laboratory-based outcome measures in dialysis. We identified studies with data regarding the predictive value of laboratory-based outcomes for mortality in dialysis. We calculated the sample size-weighted pooled relative risk of death with dichotomized "high" vs. "low" levels of each measure. We rank-ordered predictors by scaling the pooled relative risk of each measure by its pooled standard deviation. There were 5171 titles, of which 128 (representing 44 laboratory-based outcomes) were selected. Nine were significantly associated with mortality, in order of decreasing scaled effect size: (1) tumor necrosis factor-alpha, (2) hematocrit, (3) interleukin-6, (4) troponin T, (5) Kt/V(urea), (6) prealbumin, (7) urea reduction ratio, (8) serum albumin, and (9) C-reactive protein. Other oft-cited measures such as calcium phosphate product and parathyroid hormone were not significantly associated with mortality in pooled analysis. Quality improvement efforts to improve traditional laboratory-based outcomes in end-stage renal disease are necessary, but likely insufficient, to improve overall mortality in dialysis. Renewed consideration of cardiovascular, inflammatory, and nutritional markers that are especially strong predictors of mortality may have important implications for risk stratification and targeted therapeutic interventions.
Modeling and Characterization of Dielectrophoretic Assembly Process for Nanobelts (2005)

Robust manufacturing methods are needed for nanocomponent assembly, and one must understand the physics to optimize the processing and to develop control schemes to deal with the inherent uncertainty. We are studying field induced assembly of a new class of semiconducting metal oxides — nanobelts — that have been demonstrated for chemical sensing. We have demonstrated the integration of nanobelts with electrodes to make sensors by dielectrophoresis (DEP). The SnO2 nanobelts (width ~ 100–300 nm, thickness ~ 30–40 nm) were suspended in ethanol and introduced into a microchannel, and were assembled across the electrodes. Modeling suggests that attraction should occur at all frequencies over this range. Targeted experiments were performed to quantify surface and material properties for input to the modeling, and FEMLAB simulations were performed to validate the model. The goal of the modeling is to optimize the assembly of nanostructures in a manufacturing process at the wafer-scale.