gebhart/patrepeval huggingface dataset:
Hyaluronidase Expression by an Oncolytic Adenovirus Enhances Its Intratumoral Spread and Suppresses Tumor Growth (2010)

Successful virotherapy requires efficient virus spread within tumors. We tested whether the expression of hyaluronidase, an enzyme which dissociates the extracellular matrix (ECM), could enhance the intratumoral distribution of an oncolytic adenovirus and improve its therapeutic activity. As a proof of concept, we demonstrated that intratumoral coadministration of hyaluronidase in mice-bearing tumor xenografts improves the antitumor activity of an oncolytic adenovirus. Next, we constructed a replication-competent adenovirus expressing a soluble form of the human sperm hyaluronidase (PH20) under the control of the major late promoter (MLP) (AdwtRGD-PH20). Intratumoral treatment of human melanoma xenografts with AdwtRGD-PH20 resulted in degradation of hyaluronan (HA), enhanced viral distribution, and induced tumor regression in all treated tumors. Finally, the PH20 cDNA was inserted in an oncolytic adenovirus that selectively kills pRb pathway-defective tumor cells. The antitumoral activity of the novel oncolytic adenovirus expressing PH20 (ICOVIR17) was compared to that of the parental virus ICOVIR15. ICOVIR17 showed more antitumor efficacy following intratumoral and systemic administration in mice with prestablished tumors, along with an improved spread of the virus within the tumor. Importantly, a single intravenous dose of ICOVIR17 induced tumor regression in 60% of treated tumors. These results indicate that ICOVIR17 is a promising candidate for clinical testing.
Anchoring of Surface Proteins to the Cell Wall of Staphylococcus aureus (2000)

Staphylococcus aureus sortase anchors surface proteins to the cell wall envelope by cleaving polypeptides at the LPXTG motif. Surface proteins are linked to the peptidoglycan by an amide bond between the C-terminal carboxyl and the amino group of the pentaglycine cross-bridge. We find that purified recombinant sortase hydrolyzed peptides bearing an LPXTG motif at the peptide bond between threonine and glycine. In the presence of NH(2)-Gly(3), sortase catalyzed exclusively a transpeptidation reaction, linking the carboxyl group of threonine to the amino group of NH(2)-Gly(3). In the presence of amino group donors the rate of sortase mediated cleavage at the LPXTG motif was increased. Hydrolysis and transpeptidation required the sulfhydryl of cysteine 184, suggesting that sortase catalyzed the transpeptidation reaction of surface protein anchoring via the formation of a thioester acyl-enzyme intermediate.
Molecular dissection of Fcγ receptor-mediated phagocytosis (1995)

Using an experimental model in COS-1 cells, we have examined the structural requirements for phagocytosis of IgG-sensitized cells by Fc gamma receptors. We have established that isoforms of each of the 3 classes of the Fc gamma receptors, Fc gamma RI, Fc gamma RII and Fc gamma RIII, are able to transmit a phagocytic signal in the absence of the other receptor class. Fc gamma I and Rc gamma RIIIA require a gamma-subunit for this signaling event, but Fc gamma RIIA does not. Fc gamma RIIA and the gamma-subunit associated with Fc gamma RI and Fc gamma RIIIA contain 2 copies of a conserved tyrosine-containing cytoplasmic sequence, YXXL. This sequence is important for phagocytosis and is phosphorylated on tyrosine after receptor ligation. The Fc gamma receptors Fc gamma RIIB1 and Fc gamma RIIB2 which contain only 1 copy of the YXXL cytoplasmic sequence do not include the phagocytosis of IgG-coated cells. Thus, the Fc gamma receptor isoforms differ in their ability to transmit a phagocytic signal. Structure/function studies also indicate that the Fc gamma receptors which induce phagocytosis differ in their requirements for phagocytic signaling.
Abstract PR02: Small molecules that specifically inhibit the D-loop activity of RAD51 (2017)

Abstract RAD51 plays a central role in homologous recombination (HR), which maintains genome integrity. RAD51 is commonly overexpressed in cancer cells relative to normal tissue and is considered a therapeutic target in oncology. One potential challenge for targeting RAD51 pharmacologically is that it mediates functions in both double-strand DNA break (DSB) repair and stabilization of stalled replication forks. In order to distinguish compound-mediated effects on these RAD51 functions, we developed a novel class of RAD51 inhibitors. In contrast to many previously reported RAD51 inhibitors, we sought to develop compounds that do not inhibit RAD51's ability to bind single-stranded DNA (ssDNA). Instead, these compounds prevent RAD51-ssDNA nucleoprotein filaments from invading into homologous double-stranded DNA templates and forming D-loops. Our initial lead compound RI(dl)-1 (an abbreviation for RAD51 inhibitor of D-loop formation #1) is capable of blocking RAD51-mediated D-loop formation in biochemical assays, using concentrations that do not prevent RAD51 binding to ssDNA. An analog of this compound, termed RI(dl)-2, provides even better inhibition of RAD51's D-loop activity in biochemical systems (IC50 15.8 µM). RI(dl)-2 reduces HR activity in cells in dose ranges that do not stimulate single strand annealing (SSA) activity, which distinguishes it more generalized RAD51 inhibitors. RI(dl)-2 also sensitizes several cancer cell lines to radiation-induced death. We now present the results of more extensive structure activity relationship (SAR) optimizations aimed at further improving the potency and selectivity of this class of compounds. Several of these compounds are capable of delaying the timely resolution of radiation-induced RAD51 foci, even though initial RAD51 foci are apparently normal at earlier time points. Similar focus kinetics are observed for gamma-H2AX in identically treated cells, supporting the interpretation that these compounds permit RAD51 assembly at DSBs but prevent the completion of DSB repair. Unlike RI(dl)-2, some these newer compounds sensitize cancer cells to mitomycin C. These specialized RAD51 inhibitory compounds are attractive candidates for potential use as radiation or chemotherapy sensitizers, since they may exert fewer toxic risks compared to more generalized inhibitors of the HR repair machinery. They may also serve to help distinguish the functions of RAD51 DSB repair and replication stress tolerance, which may enable better understanding of RAD51's roles in maintaining genome stability. This abstract is also being presented as Poster A02. Citation Format: Brian Budke, Wei Lv, Werner Tueckmantel, Alan Kozikowski, Philip Connell. Small molecules that specifically inhibit the D-loop activity of RAD51 [abstract]. In: Proceedings of the AACR Special Conference on DNA Repair: Tumor Development and Therapeutic Response; 2016 Nov 2-5; Montreal, QC, Canada. Philadelphia (PA): AACR; Mol Cancer Res 2017;15(4_Suppl):Abstract nr PR02.
Effects of a non-steroidal aromatase inhibitor on ovarian function in cattle (2011)

Effects of the non-steroidal aromatase inhibitor letrozole on ovarian function in cattle were determined. The hypothesis that letrozole would arrest growth of the dominant follicle, resulting in emergence of a new follicular wave at a predictable post-treatment interval, was tested. Heifers were assigned randomly to four groups 4 days after follicular ablation (~2½ days after wave emergence) and given intravenous doses of 500 (n = 9), 250 (n = 10), or 125 µg kg⁻¹ (n = 10) letrozole or phosphate-buffered saline (controls; n = 10). Blood was collected and ovarian structures were monitored daily by transrectal ultrasonography. Plasma concentrations of LH and FSH were measured by radioimmunoassay; plasma concentrations of letrozole were determined by high-performance liquid chromatography tandem mass spectrometry. A single intravenous dose of letrozole did not induce regression of the dominant follicle present at the time of treatment, nor did it directly affect FSH release. Conversely, treatment with letrozole increased endogenous concentrations of LH and extended the lifespan of the dominant follicle, which delayed the next FSH surge and subsequent follicular wave emergence. Letrozole continues to have potential as a non-steroidal treatment for controlling ovarian function in cattle.
Elimination of Borrelia burgdorferi from vector ticks feeding on OspA-immunized mice. (1992)

Although recombinant outer surface protein A (OspA) of Borrelia burgdorferi protects mice against injected Lyme disease spirochetes, the mode of protection has not yet been explored. Indeed, the efficacy of vaccine-induced immunity against a realistic vector-mediated challenge remains unexplored. Accordingly, we determined whether this immunogen protects mice against spirochetes delivered by nymphal Ixodes dammini ticks. Following challenge by tick bite, no spirochetes could be cultured from immunized mice, and no characteristic histopathology was found. The spirochete was not detected in ticks that fed on immunized animals and was present in virtually all ticks that fed on nonimmunized mice. We conclude that OspA-immunized mice are protected from spirochetal infection, at least in part, because the spirochete is destroyed in the infecting tick.
Exploring Metabolic Profile Differences between Colorectal Polyp Patients and Controls Using Seemingly Unrelated Regression (2015)

Despite the fact that colorectal cancer (CRC) is one of the most prevalent and deadly cancers in the world, the development of improved and robust biomarkers to enable screening, surveillance, and therapy monitoring of CRC continues to be evasive. In particular, patients with colon polyps are at higher risk of developing colon cancer; however, noninvasive methods to identify these patients suffer from poor performance. In consideration of the challenges involved in identifying metabolite biomarkers in individuals with high risk for colon cancer, we have investigated NMR-based metabolite profiling in combination with numerous demographic parameters to investigate the ability of serum metabolites to differentiate polyp patients from healthy subjects. We also investigated the effect of disease risk on different groups of biologically related metabolites. A powerful statistical approach, seemingly unrelated regression (SUR), was used to model the correlated levels of metabolites in the same biological group. The metabolites were found to be significantly affected by demographic covariates such as gender, BMI, BMI(2), and smoking status. After accounting for the effects of the confounding factors, we then investigated potential of metabolites from serum to differentiate patients with polyps and age matched healthy controls. Our results showed that while only valine was slightly associated, individually, with polyp patients, a number of biologically related groups of metabolites were significantly associated with polyps. These results may explain some of the challenges and promise a novel avenue for future metabolite profiling methodologies.
Hybrid HIV/MSCV LTR Enhances Transgene Expression of Lentiviral Vectors in Human CD34<sup>+</sup>Hematopoietic Cells (2001)

HIV-based lentiviral vectors can transduce nondividing cells, an important advantage over murine leukemia virus (MLV)-based vectors when transducing slowly dividing hematopoietic stem cells. However, we find that in human CD34(+) hematopoietic cells, the HIV-based vectors with an internal cytomegalovirus (CMV) promoter express transgenes 100- to 1,000-fold less than the MLV-based retroviral vector murine stem cell virus (MSCV). To increase the expression of the integrated lentivirus, we replaced CMV promoter with that of the Rous sarcoma virus or MSCV and obtained a modest augmentation in expression. A more dramatic effect was seen when the CMV enhancer/promoter was removed and the HIV long-terminal repeat (LTR) was replaced by a novel HIV/MSCV hybrid LTR. This vector retains the ability to transduce nondividing cells but now expresses its transgene (enhanced green fluorescent protein) 10- to 100-fold greater than the original HIV-based vector. When compared under identical conditions, the HIV vector with the hybrid LTR transduced a higher percentage of CD34(+) cells than the MSCV-based retroviral vector (19.4% versus 2.4%). The number of transduced cells and level of transgene expression remain constant over 5-8 weeks as determined by long-term culture-initiating cells, fluoresence-activated cell sorting, and nonobese diabetic/severe combined immunodeficiency repopulation assay.
Digital signal processor supporting two types of instruction sets (1995)

Abstract An architecture for a general purpose digital signal processor has been developed that enables the specification of peripherals and the core part to be easily changed for specific applications. an evaluation chip LSI providing 24‐bit fixed‐point arithmetic was created in order to verify the performance. This digital signal processor (DSP) basically uses RISC‐type architecture in order to simplify the hardware structure and provides two types of instruction sets, called RISC‐type and DSP‐type instructions, to maintain the benefit of the original DSP. the RISC‐type instruction set consists of several types of single‐task operating commands: arithmetic, logical, data transfer, branch, etc. It provides wide operand flexibility. On the other hand, the DSP‐type instruction set consists of parallel operating commands as provided for conventional DSP which execute several data processing and data transfer operations. However, operand flexibility is restricted by providing these two types of instruction sets in one LSI and a higher performance can be achieved than with conventional DSPs which have the same bit length and only one instruction set.
Data-dependent jitter and crosstalk-induced bounded uncorrelated jitter in copper interconnects (2004)

This paper resolves the jitter impairment of non-return-to-zero data in transmission lines. The limited bandwidth of the transmission line introduces data-dependent jitter. Crosstalk between neighbouring lines results in bounded uncorrelated jitter in the data eye. An analytical approach to representing data-dependent jitter and crosstalk-induced bounded uncorrelated jitter is presented. Comparison with jitter measurements of microstrip lines on FR4 board demonstrated accuracy to within 15% of the predictions for deterministic jitter.
Synthesis of Zeolites via Interzeolite Transformations without Organic Structure-Directing Agents (2015)

We report synthetic protocols and guiding principles inspired by mechanistic considerations for the synthesis of crystalline microporous solids via interzeolite transformations that avoid direct intervention by organic structure-directing agents. These protocols are specifically implemented to synthesize high-silica MFI (ZSM-5), CHA (chabazite), STF (SSZ-35), and MTW (ZSM-12) zeolites from FAU (faujasite) or BEA (beta) parent materials. These transformations succeed when they lead to daughter structures with higher framework densities, and their nucleation and growth become possible by the presence of seeds or of structural building units common to the parent and target structures, leading, in the latter case, to spontaneous transformations by choosing appropriate synthesis conditions. These protocols allow the synthesis of high-silica frameworks without the use of organic templates otherwise required. The NaOH/SiO2 ratio and Al content in reagents are used to enforce synchronization between the swelling and local restructuring within parent zeolite domains with the spalling of fragments or building units from seeds of the target structure. Seed-mediated interconversions preserve the habit and volume of the parent crystals because of the incipient nucleation of the target structure at the outer regions of the parent domains. The pseudomorphic nature of these transformations requires the concurrent nucleation of mesopores within daughter zeolite crystals because their framework density is larger than that for the parent zeolites. The approach and evidence described shows, for the first time, that a broad range of zeolites rich in silica, and thus more useful as catalysts, can be made without the organic templates originally used to discover them.
Novel fabric pressure sensors: design, fabrication, and characterization (2011)

Soft and pliable pressure sensors are essential elements in wearable electronics which have wide applications in modern daily lives. This paper presents a family of fabric pressure sensors made by sandwiching a piece of resistive fabric strain sensing element between two tooth-structured layers of soft elastomers. The pressure sensors are capable of measuring pressure from 0 to 2000kPa, covering the whole range of human-machine interactions. Apressure sensitivity of up to 2.98 × 10 - 3kPa - 1 was obtained. Theoretical modeling was conducted based on an energy method to predict the load-displacement relationship for various sensor configurations. By adjusting the Young's modulus of the two conversion layers, as well as the geometrical dimensions, the measurement ranges, and sensitivities of the sensors can be quantitatively determined. The sensors are being used for pressure measurements between the human body and garments, shoes, beds, and chairs.
<title>Biomedical diagnostic with diffusely backscattered linearly and circularly polarized light</title> (1997)

We report on the development of a method that records spatially dependent intensity patterns of polarized light that is diffusely backscattered from turbid materials. It is demonstrated that these intensity patterns can be used to differentiate between suspensions of cancerous and non- cancerous cells and to observe different metabolic cell processes.Our technique employs polarized light from a He-Ne laser, which is focused onto the surface of the scattering medium. A surface area of approximately 4 X 4 cm around the light input point is imaged through polarization- analysis optics onto a CCD camera. One can observe a manifold of intensity patterns by varying the polarization state of the incident laser light and changing the analyzer configuration to detect different polarization components of the backscattered light. Introducing the Mueller-matrix concept for diffusely backscattered light, a framework is provided to select a subset of measurements which comprehensively describe the optical properties of backscattering media.
Shorted Microstrip Patch Antenna Using Inductively Coupled Feed for UHF RFID Tag (2008)

A very small patch-type RFID tag antenna (UHF band) using ceramic material mountable on metallic surfaces is presented. The size of the proposed tag is 25 mm×25 mm×3 mm. The impedance of the antenna can be easily matched to the tag chip impedance by adjusting the size of the shorting plate of the patch and the size of the feeding loop. The measured maximum reading distance of the tag at 910 MHz was 5 m when it was mounted on a 400 mm × 400 mm metallic surface. The proposed design is verified by simulation and measurements which show good agreement.
Ultrasonic marker for physiologic diagnosis and method of using same (1984)

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SSA: simple scheduling algorithm for resilient packet ring networks (2006)

The resilient packet ring (RPR), defined under IEEE 802.17, has been proposed as a high-speed backbone technology for metropolitan area networks. RPR is introduced to mitigate the underutilisation and unfairness problems associated with the current technologies SONET and Ethernet, respectively. The key performance objectives of RPR are to achieve high bandwidth utilisation, optimum spatial reuse on the dual rings, and fairness. The RPR standard implements three traffic classes: Class A, Class B, and Class C. The RPR MAC has one queue for each traffic class. A potential performance limitation is associated with the head-of-line blocking. When the MAC uses a single FIFO to buffer frames awaiting access, a packet that is traversing through a congestion point may block transmission of other packets destined to a point before the congestion. The use of virtual destination queues (VDQs) to avoid the head-of-line blocking is introduced. Different bandwidth allocation policies are discussed to assign rates to VDQs. Finally, a bandwidth allocation policy is proposed, which would achieve the maximum utilisation at a very low complexity.
Unified End-to-End Speech Recognition and Endpointing for Fast and Efficient Speech Systems (2023)

Automatic speech recognition (ASR) systems typically rely on an external endpointer (EP) model to identify speech boundaries. In this work, we propose a method to jointly train the ASR and EP tasks in a single end-to-end (E2E) multitask model, improving EP quality by optionally leveraging information from the ASR audio encoder. We introduce a “switch” connection, which trains the EP to consume either the audio frames directly or low-level latent representations from the ASR model. This results in a single E2E model that can be used during inference to perform frame filtering at low cost, and also make high quality end-of-query (EOQ) predictions based on ongoing ASR computation. We present results on a voice search test set showing that, compared to separate single-task models, this approach reduces median endpoint latency by 120 ms (30.8% reduction), and 90th percentile latency by 170 ms (23.0% reduction), without regressing word error rate. For continuous recognition, WER improves by 10.6% (relative).
A robust meta-classification strategy for cancer diagnosis from gene expression data (2005)

One of the major challenges in cancer diagnosis from microarray data is to develop robust classification models which are independent of the analysis techniques used and can combine data from different laboratories. We propose a meta-classification scheme which uses a robust multivariate gene selection procedure and integrates the results of several machine learning tools trained on raw and pattern data. We validate our method by applying it to distinguish diffuse large B-cell lymphoma (DLBCL) from follicular lymphoma (FL) on two independent datasets: the HuGeneFL Affmetrixy dataset of Shipp et al. (www. genome.wi.mit.du/MPR /lymphoma) and the Hu95Av2 Affymetrix dataset (DallaFavera's laboratory, Columbia University). Our meta-classification technique achieves higher predictive accuracies than each of the individual classifiers trained on the same dataset and is robust against various data perturbations. We also find that combinations of p53 responsive genes (e.g., p53, PLK1 and CDK2) are highly predictive of the phenotype.