gebhart/patrepeval huggingface dataset:
Evidence for a field effect in early prostate cancer (PCa): Gene expression profiles in normal-appearing prostate tissue (NT) adjacent to tumor (T) as predictors of clinical outcome. (2013)

5029 Background: We previously identified genes whose expression predicts aggressive PCa (clinical recurrence (cR), prostate cancer death (PCD), adverse pathology) when assessed in histologically heterogeneous tumor foci and in biopsies (Klein ASCO 2012). These results enabled the definition of a multi-gene Genomic Prostate Score (GPS), which has been clinically validated (Cooperberg AUA 2013). There is interest regarding a possible field effect in PCa, i.e. molecular alterations throughout the gland that may influence PCa development. We conducted exploratory analyses to evaluate gene expression, including GPS, in adjacent normal-appearing tissue (NT) for prediction of cR and PCD. Methods: Cohort sampling was used to select 127 patients with and 374 without cR from 2,641 patients treated with RP for T1/T2 PCa. Expression of 732 genes was measured by qRT-PCR separately in T and NT (defined as > 3 mm from T) specimens. GPS (0-100 units) was determined using the genes and algorithm from the validation study. Analysis used Cox proportional hazards models and Storey’s false discovery rate (FDR) control. Results: 410 evaluable patients had paired T and NT. Of the 405 genes which were predictive of outcome in T (FDR < 20%), 289 (71%) showed similar but weaker effects in NT. 47 genes were associated with cR in NT (FDR < 20%), of which 34 also concordantly predicted cR in T (FDR < 20%). GPS assessed in NT significantly predicted time to cR (HR/20 units = 1.8; 95% CI: 1.3-2.4; p< 0.001) and PCD (HR/20 units = 1.9; 95% CI: 1.2-3.0; p = 0.005) but was less predictive than GPS in T (HR/20 units = 4.8 for cR; 95% CI: 3.7-6.2; p < 0.001 and HR/20 units = 6.9 for PCD; 95% CI: 4.4-10.7; p < 0.001). The strongest components of GPS in predicting cR and PCD in NT were stromal response and androgen signaling genes (p < 0.05); proliferation and cellular organization genes did not consistently provide a significant contribution in NT. Conclusions: These data indicate that gene expression profiles, including GPS, can predict outcome in NT, albeit more weakly than in tumor. These findings suggest that there is an underlying field effect associated with the development of aggressive PCa.
A new synthesis of 2,1‐benzisothiazoles (1975)

Abstract A novel synthesis of 2,1‐benzisothiazoles is described. When an o ‐toluidine or N ‐sulfinyl‐ o ‐toluidine is allowed to react with an N ‐sulfinylsulfonamide, a 2,1‐benzisothiazole is formed.
Ranking service units for providing and protecting highly available services with load balancing (2010)

In highly available systems, continuous load balancing in the presence of failure is essential to avoid performance degradation. The Availability Management Framework (AMF) is a middleware service that manages the availability of the applications' services by coordinating their provision among the application's redundant components. The application's components that collaborate to provide a service are logically grouped into a service unit (SU). For management purpose, the SU workload is abstracted as a service instance (SI). Redundant SUs that collaborate to protect a set of Sis are grouped into a service group (SG). The assignment of the Sis to the SUs is a runtime operation performed by AMF. For some redundancy models, NWay and NWayActive, this assignment is performed for each SI according to a predefined ranked list of the SUs in the SG. In this paper we discuss the challenges of defining this ranking at configuration time and propose an approach that automatically generates the ranked list of SUs at that time and guaranties continuous load balancing.
Early bone apposition to hydrophilic and hydrophobic titanium implant surfaces: a histologic and histomorphometric study in minipigs (2013)

Substantial bone apposition occurs between day 5 and day 10. The data suggest that the hydrophilic surface can provoke a slight tendency toward increased bone apposition in minipigs after 15 days. A direct comparison of two hydrophilic surfaces with varying geometries is of limited relevance.
Magneto-optical recording with optical mudulation and magnetic field modulation. (1991)

The magneto-optical recording characteristics of three types of DyFeCo films with a quadri-layers structure were measured using three recording methods: the optical modulation method, magnetic field modulation method and the laser off method. In the laser off method, the laser power was lowered only while the magnetic field was changing.As for carrier to noise ratio (C/N), the transitionmetal (TM) rich type medium was best with the optical modulation method. C/N with the magnetic field modulation was lower than that with optical modulation method. The three media were similar to the magnetic field modulation method.The laser off method improved the C/N and the magnetic field dependence of the C/N. Especially TM rich type medium exhibited the same C/N value as in the optical modulation.
Digital Signal Processing Chip Implementation for Detection and Analysis of Intracardiac Electrograms (1994)

The adoption of digital signal processing (DSP) microchips for detection and analysis of electrocardiographic signals offers a means for increased computational speed and the opportunity for design of customized architecture to address real-time requirements. A system using the Motorola 56001 DSP chip has been designed to realize cycle-by-cycle detection (triggering) and waveform analysis using a time-domain template matching technique, correlation waveform analysis (CWA). The system digitally samples an electrocardiographic signal at 1000 Hz, incorporates an adaptive trigger for detection of cardiac events, and classifies each waveform as normal or abnormal. Ten paired sets of single-chamber bipolar intracardiac electrograms (1-500 Hz) were processed with each pair containing a sinus rhythm (SR) passage and a corresponding arrhythmia segment from the same patient. Four of ten paired sets contained intraatrial electrograms that exhibited retrograde atrial conduction during ventricular pacing; the remaining six paired sets of intraventricular electrograms consisted of either ventricular tachycardia (4) or paced ventricular rhythm (2). Of 2,978 depolarizations in the test set, the adaptive trigger failed to detect 6 (99.8% detection sensitivity) and had 11 false triggers (99.6% specificity). Using patient dependent thresholds for CWA to classify waveforms, the program correctly identified 1,175 of 1,197 (98.2% specificity) sinus rhythm depolarizations and 1,771 of 1,781 (99.4% sensitivity) abnormal depolarizations. From the results, the algorithm appears to hold potential for applications such as real-time monitoring of electrophysiology studies or detection and classification of tachycardias in implantable antitachycardia devices.
An Industrial Process for Synthesizing Lodenosine (FddA) (2003)

Two industrial synthetic approaches to Lodenosine (1, FddA, 9-(2,3-dideoxy-2-fluoro-beta-D-threo-pentofuranosyl) adenine) via a purine riboside or a purine 3'-deoxyriboside are described. Several novel applications of deoxygenation and fluorination methods are compared considering reaction yields, economy, safety and environmental concerns.
Atmospheric turbulence effects on the performance of a free space optical link employing orbital angular momentum multiplexing (2013)

We experimentally investigate the performance of an orbital angular momentum (OAM) multiplexed free space optical (FSO) communication link through emulated atmospheric turbulence. The turbulence effects on the crosstalk and system power penalty of the FSO link are characterized. The experimental results show that the power of the transmitted OAM mode will tend to spread uniformly onto the neighboring mode in medium-to-strong turbulence, resulting in severe crosstalk at the receiver. The power penalty is found to exceed 10 dB in a weak-to-medium turbulence condition due to the turbulence-induced crosstalk and power fluctuation of the received signal.
The Optoelectronic Nose: Colorimetric and Fluorometric Sensor Arrays (2018)

A comprehensive review on the development and state of the art of colorimetric and fluorometric sensor arrays is presented. Chemical sensing aims to detect subtle changes in the chemical environment by transforming relevant chemical or physical properties of molecular or ionic species (i.e., analytes) into an analytically useful output. Optical arrays based on chemoresponsive colorants (dyes and nanoporous pigments) probe the chemical reactivity of analytes, rather than their physical properties (e.g., mass). The chemical specificity of the olfactory system does not come from specific receptors for specific analytes (e.g., the traditional lock-and-key model of substrate-enzyme interactions), but rather olfaction makes use of pattern recognition of the combined response of several hundred olfactory receptors. In a similar fashion, arrays of chemoresponsive colorants provide high-dimensional data from the color or fluorescence changes of the dyes in these arrays as they are exposed to analytes. This provides chemical sensing with high sensitivity (often down to parts per billion levels), impressive discrimination among very similar analytes, and exquisite fingerprinting of extremely similar mixtures over a wide range of analyte types, in both the gas and liquid phases. Design of both sensor arrays and instrumentation for their analysis are discussed. In addition, the various chemometric and statistical analyses of high-dimensional data (including hierarchical cluster analysis (HCA), principal component analysis (PCA), linear discriminant analysis (LDA), support vector machines (SVMs), and artificial neural networks (ANNs)) are presented and critiqued in reference to their use in chemical sensing. A variety of applications are also discussed, including personal dosimetry of toxic industrial chemical, detection of explosives or accelerants, quality control of foods and beverages, biosensing intracellularly, identification of bacteria and fungi, and detection of cancer and disease biomarkers.
<i>Thermoanaerobacter brockii</i> alcohol dehydrogenase: Characterization of the active site metal and its ligand amino acids (1997)

The active-site metal ion and the associated ligand amino acids in the NADP-linked, tetrameric enzyme Thermoanaerobacter brockii alcohol dehydrogenase (TBADH) were characterized by atomic absorption spectroscopy analysis and site-directed mutagenesis. Our preliminary results indicating the presence of a catalytic zinc and the absence of a structural metal ion in TBADH (Peretz & Burstein. 1989. Biochemistry 28:6549-6555) were verified. To determine the role of the putative active-site zinc, we investigated whether exchanging the zinc for other metal ions would affect the structural and/or the enzymatic properties of the enzyme. Substituting various metal ions for zinc either enhanced or diminished enzymatic activity, as follows: Mn2+ (240%); Co2+ (130%); Cd2+ (20%); Cu2+ or V3+ (< 5%). Site-directed mutagenesis to replace any one of the three putative zinc ligands of TBADH, Cys 37, His 59, or Asp 150, with the non-chelating residue, alanine, abolished not only the metal-binding capacity of the enzyme but also its catalytic activity, without affecting the overall secondary structure of the enzyme. Replacing the three putative catalytic zinc ligands of TBADH with the respective chelating residues serine, glutamine, or cysteine damaged the zinc-binding capacity of the mutated enzyme and resulted in a loss of catalytic activity that was partially restored by adding excess zinc to the reaction. The results imply that the zinc atom in TBADH is catalytic rather than structural and verify the involvement of Cys 37, His 59, and Asp 150 of TBADH in zinc coordination.
ChemInform Abstract: Preparation of (‐)‐Nutlin‐3 Using Enantioselective Organocatalysis at Decagram Scale. (2014)

Abstract The target compound is synthesized in 13 steps with a longest linear sequence of 8 steps.
Characterization of the Antibody Reactivity to Synthetic Peptides from Different Parts of the Hepatitis C Virus Genome (1996)

Infection by hepatitis C virus (HCV)*, the aetiologic agent responsible for the majority of non-A-non-B posttransfusion hepatitis, is detected by assaying for antibodies against structural and nonstructural recombinant proteins or synthetic peptides. The aim of this study was to characterize the antibody reactivity of selected sera against antigenic peptides spanning immunodominant regions of the core, NS4 and NS5 HCV proteins. Reactivity to synthetic peptides was determined by enzyme immunoassay (EIA) for 11 selected sera from blood donors (good responders), for 27 selected sera from hemodialysis patients (poor responders), all positive for HCV antibodies (tested by different second and third-generation assays), and for 7 negative sera. Some peptides from the core and the NS4 region were widely recognized by the tested sera. Sera not reactive with core, NS4, or NS5 region by some immunoblot assays exhibited reactivity against peptides from these proteins. Autoimmune reactivity associated with HCV infection was evaluated by using a synthetic peptide derived from the GOR peptide; 8/11 HCV-positive sera were found reactive against this peptide. No correlation was found between reactivity to any of the peptides tested and the presence of HCV RNA in the serum or with HCV genotype. The EIA reactivity of peptides from the core region suggested a multideterminant antigenic structure, where reactivity of each epitope may be differentially affected by neighboring amino acids depending on individual sera. This situation was particularly evidenced in selected sera from poor responder specimens where a more restricted antibody response to core peptides was observed. Reactivity of sera from HCV-infected patients with synthetic peptides from the core, NS4, and NS5 regions indicated the presence of multiple linear epitopes (particularly in the core region) that may be used in a mixture for immunodiagnosis; however, the length and exact position of the synthetic peptides must be chosen carefully.
A design model for pneumatic fracturing enhanced bioremediation (1995)

This paper presents the equations developed to describe contaminant transport in fractured porous soil beds, accounting for diffusion, adsorption and reaction. The model accounts for phase partitioning of the solute to the three different phases (solid, water and vapor) and the biodegradation of the solute in the porous bed. The resulting coupled partial differential equations were solved numerically using the finite-difference technique. Parametric sensitivity analyses to determine the factors influencing contaminant transport in fractured media was also conducted in this study.
Synthetic Competitive Antagonists of Corticotropin-Releasing Factor: Effect on ACTH Secretion in the Rat (1984)

Polypeptide analogs of the known members of the corticotropin-releasing factor (CRF) family were synthesized and tested in vitro and in vivo for enhanced potency or competitive antagonism. Predictive methods and physicochemical measurements had suggested an internal secondary alpha-helical conformation spanning about 25 residues for at least three members of the CRF family. Maximization of alpha-helix-forming potential by amino acid substitutions from the native known sequences (rat/human and ovine CRF, sauvagine, and carp and sucker urotensin 1) led to the synthesis of an analog that was found to be more than twice as potent as either of the parent peptides in vitro. In contrast, certain amino-terminally shortened fragments, such as alpha-helical CRF or ovine CRF residues 8 to 41, 9 to 41, and 10 to 41, were found to be competitive inhibitors in vitro. Selected antagonists were examined and also found to be active in vivo.
Stereo fundus photography: automatic evaluation of retinal topography (2000)

A set of fast algorithms for image adjustment and stereo matching directed to the improvement of image quality, quantitative measurements of retinal topography, and automatic detection of different pathologies is discussed. Usually automatic evaluations of the retina are performed with scanning laser systems, which use multiple laser scans to render 3 D volumes and extract depth information for the retinal features. Similar results can be achieved with regular fundus cameras. There are three steps to the proposed method. The most important step is the adjustment of color, brightness and contrast of the stereo images. The mean and the variance of each color component are calculated and equalized along the longitudes of the eyeball. The next step is the epipolar line adjustment in the two images. The algorithm is based on the fast estimation of the epipolar geometry in the left and right parts of the images and further nonlinear line-to-line adjustment of the stereo pair. During the third step occlusion errors are eliminated and a disparity map calculated. It is done by a combination of the classical correlation matching along the adjusted epipolar lines and by a new technique based on a double search in the occlusion areas.
N-substituted 11-(4-piperidylene)-5,6-dihydro-11H-benzo-[5,6]cyclohepta [1,2-b]pyridines. Antihistamines with no sedating liability. (1986)

Conversion of the basic tertiary amino function of the potent antihistamine, azatadine (Optimine), to neutral carbamate function results in compounds which retain significant antihistamine activity with little or no CNS effects. In guinea pigs the N-ethoxycarbonyl derivative 4 had the same antihistamine potency as terfenadine, a clinically used non-sedating antihistamine. In mice, 4 was a potent antihistamine while lacking CNS effects. The 8-chloro-N-ethoxycarbonyl 5 (loratadine, Sch 29851) was the most potent antihistamine in the series, had no CNS side effects, and was selected for clinical evaluation.
Detection and classification of eye state in IR camera for driver drowsiness identification (2009)

An eye detection and eye state (open/close) classification methodology for driver drowsiness identification using IR camera has been presented in this paper. In this proposed methodology, otsu thresholding is used to extract face region. Eye localization is done by locating facial landmarks such as eyebrow and possible face center. Morphological operation and K-means is used for accurate eye segmentation. A hierarchial noise removal procedure is applied on the segmented image to get proper eye shape. Then a set of shape features are calculated and trained using nonlinear SVM to get the status of the eye. Experiment shows that the proposed methodology gives excellent segmentation results for both open eyes (both bright and dark pupil) and closed eyes and also classifies correctly.
Traffic management and resource allocation in small wired/wireless networks (2009)

We consider the problem of traffic management in small networks with both wireless and wired devices, connected to the Internet through a single gateway. Examples of such networks are small office networks or residential networks, where typically traffic management is limited to flow prioritization through port-based filtering.
Delta-tocotrienol is the most bioactive natural tocotrienol in the prevention of pancreatic cancer transformation (2008)

3826 Background: Pancreatic cancer is one of the most lethal cancers in need of novel interventions. A role for dietary bioactive compounds in pancreatic cancer prevention is plausible because epidemiological studies indicate that consumption of fruits, vegetables, and cereal foods is associated with a lower risk of developing pancreatic cancer. Tocotrienols are bioactive components of cereal foods such as oats, barley, rice bran, and palm. These compounds have been demonstrated to have anticancer and chemopreventive activity in a wide variety of cancer types; however their activity in pancreatic cancer is unknown. In this study we investigated the comparative effects of the four natural tocotrienol compounds in order to determine the most bioactive tocotrienol against pancreatic cancer  Methods: We first determined the anti-proliferative (MTT assay) and pro-apoptotic activity of α, β, γ and δ-tocotrienol in immortalized normal human pancreatic ductal epithelial cells (HPDE C7), HPDE cells transformed with oncogenic Kras (C7-Kras), as well as human pancreatic cancer cell lines MiaPaCa-2 and AsPc-1. We then determined the effect of the tocotrienol compounds on malignant transformation (colony formation) in MiaPaca-2 cells and NF-κB/p65 activity in these cells. The activity of the tocotrienol was also compared to gemcitabine, α-tocopherol, and δ-tocopherol.  Results: Tocotrienols significantly inhibited the cell growth of transformed C7-Kras, and pancreatic cancer cells in a concentration and time-dependent manner but had no effect on ‘normal’ HPDE cells. The IC 50 of growth inhibition were 40, 45 and 60 μ M for δ, γ and β tocotrienol compounds, respectively. The IC 50 of growth inhibition for gemcitabine was 20 μ M. In contrast α-tocotrienol, α-tocopherol and δ-tocopherol had no growth inhibitory activity. Malignant transformation was inhibited by 70, 30, 19 and 6% with δ, γ, β and α tocotrienol compounds, respectively in MiaPaca-2 cells. Malignant transformation inhibition for gemcitabine was 89%.The apoptosis inducing activity of δ tocotrienol was far greater than γ and β-tocotrienols and gemcitabine. Furthermore nuclear DNA binding of NF-κB/p65 activity was inhibited by 36, 30, 15 and 5% with δ, γ, β and α tocotrienols, respectively.  Conclusion: (1) δ-tocotrienol is the most bioactive tocotrienol compound against pancreatic cancer; (2) δ-tocotrienol is not toxic to non-transformed pancreatic epithelial cells; (3) δ-tocotrienol has more apoptotic activity against pancreatic cancer cells compared to gemcitabine; (4) δ and γ-tocotrienols significantly inhibit nuclear DNA binding activity of NF-κB/p65. These data support further studies to determine the role of δ-tocotrienol in the prevention of pancreatic cancer progression.