gebhart/patrepeval huggingface dataset:
Predictive biomarker discovery and validation for the targeted chemotherapeutic ixabepilone (2006)

3011 Background: Ixabepilone is a microtubule stabilizing agent with significant therapeutic value in breast cancer (BC) patients. To identify predictive biomarkers capable of identifying patients likely to receive optimal benefit from ixabepilone treatment, preclinical and clinical studies were carried out. Several biomarkers discovered using preclinical models were validated in a neoadjuvant BC clinical study ( CA163080 ) and one, estrogen receptor 1 (ER), was shown to double the pathological complete response (pCR) rate in patients treated with ixabepilone. To identify candidate sets of biomarkers that could further increase the pCR rate we have performed post-hoc analyses of the preclinical and clinical data. Methods: Eighteen BC cell lines were classified as sensitive or resistant (S/R) based on the IC50 values for ixabepilone treatment. Gene expression profiling of the BC cell lines was conducted and genes correlated with the S/R classification were identified using a k-Nearest Neighbors algorithm. Patients in clinical study CA163080 underwent a pretreatment core needle biopsy from which RNA was isolated and gene expression profiles generated (data available on 134 patients). Analyses using the preclinical and clinical markers were conducted using various statistical tools. Results: Several markers used in combination with ER were found to be capable of tripling the pCR to ixabepilone in CA163080. In addition to ER other predictive markers were identified that were as predictive as ER, including several genes whose expression is anti-correlated with ER and are part of the ER pathway. Finally, various sub-group analyses were performed and manifested the importance of clinical sample variation that needs to be considered for the analysis. Conclusions: Several single biomarkers identified from preclinical studies were validated in the clinical study CA163080 , demonstrating the utility of this approach. Such markers can be used in combination to better identify patients likely to respond to ixabepilone in future clinical trials. Furthermore, molecular response markers that can be tied to the mechanism of drug resistance can be used for further developing chemotherapy in drug development. [Table: see text]
Upregulation of the 2-5A Synthetase/RNase L Antiviral Pathway Associated with Chronic Fatigue Syndrome (1994)

Levels of 2',5'-oligoadenylate (2-5A) synthetase, bioactive 2-5A, and RNase L were measured in extracts of peripheral blood mononuclear cells (PBMCs) from 15 individuals with chronic fatigue syndrome (CFS) before and during therapy with the biological response modifier poly(I).poly(C12U) and were compared with levels in healthy controls. Patients differed significantly from controls in having a lower mean basal level of latent 2-5A synthetase (P < .0001), a higher pretreatment level of bioactive 2-5A (P = .002), and a higher level of pretherapy RNase L activity (P < .0001). PBMC extracts from 10 persons with CFS had a mean basal level of activated 2-5A synthetase higher than the corresponding control value (P = .009). All seven pretherapy PBMC extracts tested were positive for the replication of human herpesvirus 6 (HHV-6). Therapy with poly(I).poly(C12U) resulted in a significant decrease in HHV-6 activity (P < .01) and in downregulation of the 2-5A synthetase/RNase L pathway in temporal association with clinical and neuropsychological improvement. The upregulated 2-5A pathway in CFS before therapy is consistent with an activated immune state and a role for persistent viral infection in the pathogenesis of CFS. The response to therapy suggests direct or indirect antiviral activity of poly(I).poly(C12U) in this situation.
Intrinsic luminance loss in phosphorescent small-molecule organic light emitting devices due to bimolecular annihilation reactions (2008)

Operational degradation of blue electrophosphorescent organic light emitting devices (OLEDs) is studied by examining the luminance loss, voltage rise, and emissive layer photoluminescence quenching that occur in electrically aged devices. Using a model where defect sites act as deep charge traps, nonradiative recombination centers, and luminescence quenchers, we show that the luminance loss and voltage rise dependence on time and current density are consistent with defect formation due primarily to exciton-polaron annihilation reactions. Defect densities ∼1018cm−3 result in &gt;50% luminance loss. Implications for the design of electrophosphorescent OLEDs with improved lifetime are discussed.
Metamaterials for omnidirectional reflectors and hollow-core waveguides (2006)

We show that metamaterials have omnidirectional reflecting properties in the frequency region between the magnetic plasma frequency and the electric plasma frequency. These properties are useful for reflectivity control, low loss mirrors, and hollow-core waveguides.
Improved GaN-based HEMT performance by nanocrystalline diamond capping (2012)

As a wide-bandgap semiconductor, gallium nitride (GaN) is an attractive material for next-generation power devices. To date, the capabilities of GaN-based high electron mobility transistors (HEMTs) have been limited by self-heating effects (drain current decreases due to phonon scattering-induced carrier velocity reductions at high drain fields). Despite awareness of this, attempts to mitigate thermal impairment have been limited due to the difficulties involved with placing high thermal conductivity materials close to heat sources in the device. Heat spreading schemes have involved growth of AIGaN/GaN on single crystal or CVD diamond, or capping of fullyprocessed HEMTs using nanocrystalline diamond (NCD). All approaches have suffered from reduced HEMT performance or limited substrate size. Recently, a "gate after diamond" approach has been successfully demonstrated to improve the thermal budget of the process by depositing NCD before the thermally sensitive Schottky gate and also to enable large-area diamond implementation.
Managing Overloaded Hosts for Dynamic Consolidation of Virtual Machines in Cloud Data Centers under Quality of Service Constraints (2012)

Dynamic consolidation of virtual machines (VMs) is an effective way to improve the utilization of resources and energy efficiency in cloud data centers. Determining when it is best to reallocate VMs from an overloaded host is an aspect of dynamic VM consolidation that directly influences the resource utilization and quality of service (QoS) delivered by the system. The influence on the QoS is explained by the fact that server overloads cause resource shortages and performance degradation of applications. Current solutions to the problem of host overload detection are generally heuristic based, or rely on statistical analysis of historical data. The limitations of these approaches are that they lead to suboptimal results and do not allow explicit specification of a QoS goal. We propose a novel approach that for any known stationary workload and a given state configuration optimally solves the problem of host overload detection by maximizing the mean intermigration time under the specified QoS goal based on a Markov chain model. We heuristically adapt the algorithm to handle unknown nonstationary workloads using the Multisize Sliding Window workload estimation technique. Through simulations with workload traces from more than a thousand PlanetLab VMs, we show that our approach outperforms the best benchmark algorithm and provides approximately 88 percent of the performance of the optimal offline algorithm.
The 5'-leader sequence of tobacco mosaic virus RNA enhances the expression of foreign gene transcripts<i>in vitro</i>and<i>in vivo</i> (1987)

A 67-nucleotide portion of the non-coding, 5'-leader sequence of tobacco mosaic virus RNA [defined as omega' (Gr. omega prime)] has been shown to enhance the translation of contiguous foreign gene transcripts both in vitro and in vivo. Chemically-synthesized omega', containing convenient linker sequences, was inserted into derivatives of an in vitro transcription plasmid (pSP64) between the bacteriophage-SP6 promoter and sequences coding for either chloramphenicol acetyltransferase (CAT) or neomycin phosphotransferase (NPTII). Run-off in vitro transcripts, with or without a 5'-cap structure (G(5')ppp(5')G) and/or the omega' sequence, were tested in mRNA-dependent cell-free translation systems derived from rabbit reticulocyte lysate, wheat germ extract or Escherichia coli (MRE 600). In all cases, the presence of omega' increased the translational expression of both reporter genes, typically between 2- to 10-fold. Electroporation of isolated mesophyll protoplasts from Nicotiana tabacum cv. Xanthi, or microinjection of oocytes from Xenopus laevis, with SP6-transcripts containing the CAT-coding region confirmed and extended the value of omega' as a potential translational enhancer of gene expression in vivo.
Electrophoretic Separation of Nanoparticles with a Discrete Number of Functional Groups (2006)

Abstract A concept is describe that facilitates the modification of colloidal nanoparticles of different materials with an exactly known number of variable functional groups. In particular, a procedure for the surface functionalization of nanoparticles with a controlled number of mono‐ or bifunctional poly(ethylene glycol) (PEG) molecules of suitable chain length is reported. Conjugates of nanoparticles with one, two, and three PEG molecules per nanoparticle could be separated using gel electrophoresis. Molecules with additional functionalities could be conjugated to the free ends of the bifunctional PEG molecules. In this way the PEG molecules act as convenient spacers that allow for the sorting of nanoparticles with a discrete number of functional groups.
Explicit MDS Codes for Optimal Repair Bandwidth (2014)

MDS codes are erasure-correcting codes that can correct the maximum number of erasures for a given number of redundancy or parity symbols. If an MDS code has $r$ parities and no more than $r$ erasures occur, then by transmitting all the remaining data in the code, the original information can be recovered. However, it was shown that in order to recover a single symbol erasure, only a fraction of $1/r$ of the information needs to be transmitted. This fraction is called the repair bandwidth (fraction). Explicit code constructions were given in previous works. If we view each symbol in the code as a vector or a column over some field, then the code forms a 2D array and such codes are especially widely used in storage systems. In this paper, we address the following question: given the length of the column $l$, number of parities $r$, can we construct high-rate MDS array codes with optimal repair bandwidth of $1/r$, whose code length is as long as possible? In this paper, we give code constructions such that the code length is $(r+1)\log_r l$.
Electrochemical SELEX Technique for the Selection of DNA Aptamers against the Small Molecule 11-Deoxycortisol (2019)

Aptamers have received considerable attention due to their numerous advantages as biorecognition receptors. However, the tediousness and high cost of the conventional selection process of aptamers remain major challenges that limit their widespread use. To overcome these limitations, here we designed a new electrochemical SELEX platform that enables a rapid, efficient, and cost-effective enrichment method for the identification of aptamers, particularly against small molecules. The selection platform is based on the immobilization of the target analyte on gold electrodes that leads to improved selection efficiency and enables in situ monitoring of the enriched DNA using square-wave voltammetry. Compared with the conventional SELEX method, this selection protocol avoids the use of beads as a solid matrix and fluorescently labeled DNA, which is usually required for small molecules, thus offering simplified aptamer/target incubation, washing, and elution steps. Moreover, the DNA recovery can be detected by simply measuring the current of the electrodes in a ferro/ferricyanide redox couple. This would eliminate the need for fluorescence labeling, which significantly reduces the cost of the procedure. The approach was successfully applied for the selection of high-affinity aptamers that bind specifically to the small molecule 11-deoxycortisol hormone using eight rounds. One of the selected aptamers that showed a dissociation constant at the subnanomolar level was used to construct a competitive voltammetric aptasensor exhibiting high sensitivity, selectivity against other steroid analogues, and possible applicability in serum samples. Thus this SELEX approach offers great promise for a faster, simpler, and more economic aptamer identification method for various targets including small molecules for a wide variety of applications.
Electrochemical Removal and Concentration of Hydrogen Sulfide from Coal Gas (1984)

An electrochemical membrane concentration cell was demonstrated as an effective means of removing and concentrating H/sub 2/S from a hot gas stream. The device consists of a high temperature molten sulfide electrolyte with porous carbon electrodes. The process-gas is passed through the cathode chamber, where H/sub 2/S is selectively removed. With passage of current, the anion migrates to the anode, where elemental sulfur is evolved. Removal rates and cell overpotentials are reported as functions of current densities, gas flow rates and composition, and temperature.
High temporal resolution cardiac cone-beam CT using a slowly rotating C-arm gantry (2009)

Purpose: To achieve three dimensional isotropic dynamic cardiac CT imaging with high temporal resolution for evaluation of cardiac function with a slowly rotating C-arm system. Method and Materials: A recently introduced extension to compressed sensing, viz. Prior Image Constrained Compressed Sensing (PICCS), in which a prior image is used as a constraint in the reconstruction has enabled this application. An in-vivo animal experiment (e.g. a beagle model) was conducted using an interventional C-arm system. The imaging protocol was as follows: contrast was injected, the contrast equilibrated, breathing was suspended for ~14 seconds during which time 420 equally spaced projections were acquired. This data set was used to reconstruct a fully sampled blurred image volume using the conventional FDK algorithm (e.g. the prior image). Then the data set was retrospectively gated into 19 phases according to the recorded ECG signal (heart rate ~ 95bpm) and images were reconstructed with the PICCS algorithm. Results: Cardiac MR was used as the gold standard due to its high temporal resolution. The same short-axis slice was selected from the PICCS-CT data set and the MR data set. Manual contouring on the peak systolic and peak diastolic frames was performed to assess the ejection fraction contribution from this single plane. The calculated ejection fractions with PICCS-CT agreed well with the MR results. Conclusion: We have demonstrated the ability to use a slowly rotating interventional C-arm system in order to make measurements of cardiac function. The new technique provides high isotropic spatial resolution (~0.5 mm) along with high temporal resolution (~ 33 ms). The evaluation of cardiac function demonstrated a great agreement with single slice cardiac MR.
An RNAi-enhanced Logic Circuit for Cancer Specific Detection and Destruction (2010)

Abstract : Modern breast cancer therapies utilize non-specific approaches to kill or remove cancerous cells, inflicting significant collateral damage to healthy cells. In response to the need for highly targeted detection and destruction of cancerous cells, we propose to implement multi-input genetic circuits that act as cell state classifiers based on mRNA or microRNA expression profiling. The mRNA sensing project is focused on the MCF-7 breast adenocarcinoma cell line. MCF-7 cells overexpress Gata3, NPY1R and TFF1 mRNA relative to healthy cells. Based on our bioinformatics analysis, taking into account the three biomarkers allows for dramatically improved specificity in comparison to targeting single genes. We therefore design a three-input AND gate that triggers a response only when all three biomarkers are expressed above a defined threshold. In second approach we implement transcriptional/post-transcriptional regulatory circuit that senses expression levels of a customizable set of endogenous microRNAs and computes whether to trigger a response if the expression levels match a pre-determined profile of interest. We have created a circuit that computes a complex abstract logic (miR1 AND miR2+3 AND NOT miR4 AND NOTmiR5 AND NOT miR6) and selectively triggers output response in HeLa but not in other cells.
A camera-based method for calibrating projection color displays (2006)

Almost all presentations today are given electronically using projection display technology. In such presentations, color images often do not reproduce correctly due to lack of projector calibration. In cases where the color imagery is intended to convey an important message, this problem can severely diminish the value of a presentation. Examples include technical, educational, and marketing presentations attempting to demonstrate color and image quality effects. Depending on the severity of the miscalibration, important information such as text and graphical elements can change color name or become difficult to discern. We propose a simple technique for calibrating projection displays using a digital camera as a color measurement device. The camera is first calibrated via visual luminance matching of projected colors. A target of known RGB values then is projected on the screen, and captured with the digital camera. The camera signals are processed through the camera calibration to produce luminance signals, and the latter are used to calibrate the tone response of the projector. The approach produces a tone response correction that is satisfactory for many applications, and most importantly, eliminates the need for costly and tedious measurement of colors projected on a screen.
Photochromic and Luminescence Switching Properties of a Versatile Diarylethene-Containing 1,10-Phenanthroline Ligand and Its Rhenium(I) Complex (2004)

A versatile bis(2,5-dimethyl-3-thienyl)-1,10-phenanthroline photochromic ligand has been successfully synthesized via a Suzuki cross-coupling reaction. The excitation wavelength for photochromic reaction of the dithienylphenanthroline could be extended from lambda </= 340 nm in the UV region to ca. 480 nm in the visible region, corresponding to the MLCT excitation, through the incorporation into the rhenium(I) tricarbonyl system. Reversible switching of the emissive state by the photochromic reaction has also been demonstrated.
Bacterial Cysteine-Inducible Cysteine Resistance Systems (2016)

Because of its toxicity, the bacterial intracellular cysteine level is stringently regulated at biosynthesis. This work describes the identification and characterization of two novel cysteine-inducible systems that regulate, through degradation and efflux, the cysteine resistance of Pantoea ananatis, a member of the family Enterobacteriaceae that shows great potential for producing substances useful for industrial purposes. We propose that this novel mechanism for sensing and regulating cysteine levels is a safety valve enabling adaptation to sudden changes in intra- or extracellular cysteine levels in bacteria. Our findings provide important insights into optimizing the production of cysteine and related biomaterials by P. ananatis and also a deep understanding of sulfur/cysteine metabolism and regulation in this plant pathogen and related bacteria.
A fractal-based region-oriented color image compression scheme for VLSI implementation (2002)

We propose a method for compressing color images using region-oriented coding techniques. After formulating both the image processing and the VLSI implementation demands, we compare different region-oriented approaches, thereby demonstrating the superiority of the Hilbert fractal-based approach.
Haptic Revolver (2018)

We present Haptic Revolver, a handheld virtual reality controller that renders fingertip haptics when interacting with virtual surfaces. Haptic Revolver's core haptic element is an actuated wheel that raises and lowers underneath the finger to render contact with a virtual surface. As the user's finger moves along the surface of an object, the controller spins the wheel to render shear forces and motion under the fingertip. The wheel is interchangeable and can contain physical textures, shapes, edges, or active elements to provide different sensations to the user. Because the controller is spatially tracked, these physical features can be spatially registered with the geometry of the virtual environment and rendered on-demand. We evaluated Haptic Revolver in two studies to understand how wheel speed and direction impact perceived realism. We also report qualitative feedback from users who explored three application scenarios with our controller.
Production of neuraminidase by<i>Micromonospora viridifaciens</i> (1987)

A range of microorganisms were screened for new and high producer strains of neuraminidase (EC 3.2.1.18). High neuraminidase activity was found in the culture filtrates of Actinomycetes of the genus Micromonospora, and Micromonospora viridifaciens showed the highest enzyme activity. Neuraminidase production by M. viridifaciens was highly induced by the presence of the substrate colominic acid and the product N-acetylneuraminic acid. The purified neuraminidase of M. viridifaciens could cleave α(2–3), α(2–6), and α(2–8) glycosidic linkages.
New 8-(trifluoromethyl)-substituted quinolones. The benefits of the 8-fluoro group with reduced phototoxic risk (1992)

A series of 8-(trifluoromethyl)-substituted quinolones has been prepared and evaluated for in vitro and in vivo antibacterial activity, and phototolerance in a mouse phototolerance assay. These analogues were compared to the corresponding series of 6,8-difluoro- and 6-fluoro-8H-quinolones (ciprofloxacin type). Although their in vitro antibacterial activities are less than the 6,8-difluoro analogues, the 8-(trifluoromethyl)quinolones are generally equivalent to their 8H analogues. In vivo, they are comparable to the 6,8-difluoro series and show up to 10-fold improvement in efficacy when compared to their ciprofloxacin counterparts vs Streptococcus pyogenes and Streptococcus pneumonia. In the phototolerance model, the 8-(trifluoromethyl)quinolones are comparable to the 8H-quinolones. Both of these series display much higher no effect doses (greater tolerance) than the corresponding 6,8-difluoroquinolones.
CT-based clinical phantom validation of Eigen's real time four degree of freedom mechanical tracker for 3-D transrectal ultrasound guided prostate biopsy (2008)

This study investigated the effect of chronic intracerebroventricular (IVT) infusion of a hypertonic NaCl (400 mmol/l) artificial cerebrospinal fluid (aCSF) on blood pressure and whole body pressor responsiveness, in control rats (CH) and in rats implanted with deoxycorticosterone acetate (DOCA; DH). An isotonic aCSF was infused into another group of control (Cl) and DOCA (Dl) rats. Indirect systolic blood pressure (SBP) was measured using a tail-cuff technique once a week prior to and during the infusion period. Following 2 weeks of infusion, SBP increased significantly only in the DH and CH groups. In urethane-anaesthetized rats, the pressor response to intravenous infusions of norepinephrine and angiotensin II (Ang II) increased significantly in DH rats. When compared with Cl and Dl rats, those from the CH group also exhibited an enhanced response to norepinephrine and Ang II. However, this increase was not as great as in the DH animal. These results show that whole body pressor responses to norepinephrine and Ang II, increase in rats receiving chronic IVT infusion of hypertonic NaCl. These responses coincide with moderate but significant increases in SBP. These data indicate that sodium chloride acts at a central site to increase norepinephrine and Ang II pressor responsiveness in mineralocorticoid hypertension.