gebhart/patrepeval huggingface dataset:
FIZZ2/RELM-β Induction and Role in Pulmonary Fibrosis (2011)

Found in inflammatory zone (FIZZ) 2, also known as resistin-like molecule (RELM)-β, belongs to a novel cysteine-rich secreted protein family named FIZZ/RELM. Its function is unclear, but a closely related family member, FIZZ1, has profibrotic activities. The human ortholog of rodent FIZZ1 has not been identified, but human FIZZ2 has significant sequence homology to both rodent FIZZ2 (59%) and FIZZ1 (50%). Given the greater homology to rodent FIZZ2, analyzing the role of FIZZ2 in a rodent model of bleomycin-induced pulmonary fibrosis would be of greater potential relevance to human fibrotic lung disease. The results showed that FIZZ2 was highly induced in lungs of rodents with bleomycin-induced pulmonary fibrosis and of human patients with idiopathic pulmonary fibrosis. FIZZ2 expression was induced in rodent and human lung epithelial cells by Th2 cytokines, which was mediated via STAT6 signaling. The FIZZ2 induction in murine lungs was found to be essential for pulmonary fibrosis, as FIZZ2 deficiency significantly suppressed pulmonary fibrosis and associated enhanced extracellular matrix and cytokine gene expression. In vitro analysis indicated that FIZZ2 could stimulate type I collagen and α-smooth muscle actin expression in lung fibroblasts. Furthermore, FIZZ2 was shown to have chemoattractant activity for bone marrow (BM) cells, especially BM-derived CD11c(+) dendritic cells. Notably, lung recruitment of BM-derived cells was impaired in FIZZ2 knockout mice. These findings suggest that FIZZ2 is a Th2-associated multifunctional mediator with potentially important roles in the pathogenesis of fibrotic lung diseases.
The effect of liquid phase on VOC removal in trickle-bed biofilters (1998)

The objective of this work was to analyze the effect of water content on the removal of volatile organic compounds (VOCs) in gas phase trickle-bed biofilters. Previous studies revealed that excessive accumulation of biomass in the reactor had a negative effect on contaminant removal efficiency. To solve this problem, periodic backwash was used to remove excess biomass and maintain an effective operation. Results showed that the ether removal efficiency dropped immediately after backwashing and gradually improved to reach the optimal value within about 24 hours. The initial drop in performance can be attributed to biological effects, such as loss of active biomass and the necessity for an adaptation period for the microbial culture. However, mass transfer limitations due to the water retained in the reactor may also be important. To investigate the effect of water content on the biofilter performance, an experiment evaluated the effect of draining after backwashing was conducted. Biofilters were allowed to drain for different periods of time before restarting the reactors. A longer lapse time in draining before the restart resulted in better ether removal efficiency. The improvement of biofilter performance after backwashing was explained with a combination of biological and physical effects. A mathematical model was then used to simulate the performance of the biofilter under these conditions and to support the conclusions obtained. The mathematical model considered a three-phase system (biofilm, water, and gas phase), dunamic processes, non-uniform bacterial population, and one limiting substrate.
[ARV-7: A biomarker for the treatment of metastatic castration-resistant prostate cancer]. (2019)

As more and more patients with metastatic prostate cancer develop resistance to androgen-deprivation therapy (ADT) and consequently castration-resistant prostate cancer (CRPC), reasonable selection of therapies is becoming increasingly important for the prediction of the therapeutic results. Many studies show that androgen receptor splice variant 7 (AR-V7) is involved in the development and progression of CRPC and that the expression of AR-V7, absolutely higher in CRPC than in hormone-nave prostate cancer, plays a significant role in the mechanisms of resistance to abiraterone, enzalutamide and taxane chemotherapies. Further more, some clinical trials have revealed that the AR-V7 level may indicate the prognosis of different therapeutic options: AR-V7 negative in circulating tumor cells suggesting the effectiveness of a new hormonal therapy and taxane chemotherapy while AR-V7 positive indicating the poor result of a new hormonal therapy. These findings show that AR-V7 could be a biomarker for therapeutic options and the prognostic evaluation of CRPC.
Interpolation Based Tracking for Fast Object Detection in Videos (2011)

Detecting objects in images and videos is very challenging due to i) large intra-class variety and ii) pose/scale variations. It is hard to build strong recognition engines for generic object categories, while applying them to large video collections is computationally infeasible (due to the explosion of frames to test). In this paper, we present a detection-by-interpolation framework, where object-tracking is achieved by interpolating between candidate object detections in a subset of the video frames. Given the location of an object in two frames of a video-shot, our algorithm tries to identify the locations of the object in the intermediate frames. We evaluate two tracking solutions based on greedy and dynamic programming approaches, and observe that a hybrid method gives significant performance boost as well as speedup in detection. On 6 hours of HD quality video, we were able to cut-down the detection time from 10000 hours to 1500 hours, while simultaneously improving the detection accuracy from 54% to 68%. As a result of this work, we build a dataset of 100,000 car images, spanning a wide range of viewpoints, scale and make, about 100 times larger than existing collections [2], [3].
The C-Type Lectin Receptor SIGNR3 Binds to Fungi Present in Commensal Microbiota and Influences Immune Regulation in Experimental Colitis (2013)

Inflammatory bowel disease is a condition of acute and chronic inflammation of the gut. An important factor contributing to pathogenesis is a dysregulated mucosal immunity against commensal bacteria and fungi. Host pattern-recognition receptors (PRRs) sense commensals in the gut and are involved in maintaining the balance between controlled responses to pathogens and overwhelming innate immune activation. C-type lectin receptors (CLRs) are PRRs recognizing glycan structures on pathogens and self-antigens. Here we examined the role of the murine CLR specific intracellular adhesion molecule-3 grabbing non-integrin homolog-related 3 (SIGNR3) in the recognition of commensals and its involvement in intestinal immunity. SIGNR3 is the closest murine homolog of the human dendritic cell-specific intercellular adhesion molecule-3-grabbing non-integrin (DC-SIGN) receptor recognizing similar carbohydrate ligands such as terminal fucose or high-mannose glycans. We discovered that SIGNR3 recognizes fungi present in the commensal microbiota. To analyze whether this interaction impacts the intestinal immunity against microbiota, the dextran sulfate sodium-induced colitis model was employed. SIGNR3(-/-) mice exhibited an increased weight loss associated with more severe colitis symptoms compared to wild-type control mice. The increased inflammation in SIGNR3(-/-) mice was accompanied by a higher level of TNF-α in colon. Our findings demonstrate for the first time that SIGNR3 recognizes intestinal fungi and has an immune regulatory role in colitis.
A hybrid protein between IFN‐γ and IL‐2 (1986)

The complementary DNAs encoding human interferon-gamma (IFN-gamma) and human interleukin-2 (IL-2), two different proteins involved in the same immune system, were fused to code a hybrid protein, which was expressed in E. coli to investigate the interactions of these two proteins at the molecular level. Through immunoprecipitation analysis, this protein was revealed to be of about 31 kDa, which was expected from nucleotide sequencing, and to have the antigenicities of both IFN-gamma and IL-2. The extract from bacteria expressing this hybrid protein showed at least two biological activities: an antiviral activity derived from IFN-gamma and the ability to support the growth of natural killer (NK) cells derived from IL-2. Comparing the enhancement of NK cell activity of this hybrid protein with IFN-gamma and IL-2, this hybrid protein appears to conserve each activity almost completely without diminishing the other.
Macromedia Coldfusion 5: Training from the Source with Cdrom (2001)

From the Publisher:
The lessons in this book take you step by step through a series of projects that will teach you how to take a Web site that's just another pretty face and turn it into an interactive, functional site capable of responding to any level of user request. If you've never done any programming before but have some experience with HTML, this introductory-level book will show you how to create a Web site that really means business. You'll learn how to integrate a product database into a site, build pages to show fresh information and respond to visitor requests, produce product lists, responses, and emails to output that information, and much more. The enclosed CD-ROM contains everything you'll need to complete the projects, plus completed files for you to compare with your own results.
<i>In Vivo</i>Effects of Recombinant Human Stem Cell Factor Treatment:<i>A Morphologic and Immunohistochemical Study of Bone Marrow Biopsies</i> (1995)

Bone marrow (BM) aspirate and biopsy specimens from seven female patients with advanced or metastatic breast cancer and preserved marrow function treated on a phase I trial of recombinant methionyl human stem cell factor (r-metHuSCF; SCF) were evaluated by immunohistochemical staining before and after treatment with SCF. Doses of SCF included 10 g/kg/day in 2 patients, 25 micrograms/kg/day in 2 patients, and 50 micrograms/kg/day in 3 patients administered as subcutaneous bolus injections for 14 days. Following treatment, bone marrow cellularity increased up to 1.6-fold (P = NS), with an increased frequency of promyelocytes (P < .002), but an unchanged relative frequency of other marrow hematopoietic cells. The mean relative frequency of BM CD34+ progenitor cells increased from 0.9% to 1.8% (P < .001). The mean proportion of BM cells stained by Ki-67/MIB 1 and PCNA/PC10, monoclonal antibodies (MoAb) recognizing proliferation-associated nuclear proteins, increased from 18.6% to 35.4% (P < .003) and from 32.4% to 49.4% (P < .01), respectively. Most of the Ki-67 and PCNA positive cells were represented by promyelocytes, proerythroblasts, and myeloblasts. SCF therapy was not associated with marrow fibrosis or increases in the number of macrophages. Peripheral white blood cell counts increased 1.3- to 3.6-fold following SCF. The mean absolute neutrophil counts increased from 3.9 x 10(9)/L (range 2.6-5.3) to 7.2 x 10(9)/L (range 4.7-12.3), and reticulocyte counts increased by a mean of 1.5 fold (range 1.2-fold to 2.0-fold). No consistent difference in platelet counts was seen. These results suggest that SCF given in vivo is effective in increasing the frequency of CD34+ BM progenitor cells, and has the capacity to increase the proliferation and differentiation rate of hematopoietic precursor cells. These effects indicate that SCF may represent a cytokine capable of affecting multiple hematopoietic lineages.
Reversal of acute renal failure by bortezomib-based chemotherapy in patients with multiple myeloma (2007)

Paraprotein induced renal failure is a frequent complication of multiple myeloma and is associated with poor survival. Previously, reversal of renal function has been hampered by the lack of fast acting and highly effective myeloma therapy and most patients remained or became dependent on hemodialysis. Here we show reversal of acute paraprotein-induced renal failure by bortezomib-based therapy in 5 out of 8 patients. Improvement of renal function was preceded by a significant reduction in paraprotein concentration in all patients, with improvement in renal function.
Strategies for characterization of ganglioside inner esters I—fast atom bombardment mass spectrometry (1990)

A comparison of old and new fast atom bombardment (FAB) mass spectrometric strategies for characterization of ganglioside inner esters (lactones) is presented. Data obtained for lactones of GD3 (NeuAc alpha 2----8NeuAc alpha 2----3Gal beta 1----4Glc beta 1----1Cer) using negative ion FAB mass spectrometry of underivatized materials, negative ion FAB mass spectrometry following ammonolysis, and positive ion FAB mass spectrometry following ammonolysis and permethylation are presented and discussed. The latter method uses well-known reactions to produce a novel type of ganglioside derivative, highly amenable to analysis by positive ion FAB mass spectrometry, which is introduced to simplify unambiguous location of NeuAc residues involved in ester linkages to other sugars.
Relevance of multidrug resistance to rheumatoid arthritis: development of a new therapeutic hypothesis. (1996)

Multidrug resistance in hematologic malignancies and some solid tumors is mediated by a cell membrane pump known as the P-glycoprotein (P-gp). P-gp rapidly transports a variety of heterocyclic agents (including many natural product antiproliferative drugs) out of tumor cells thus abrogating their anticancer effects. P-gp can be competitively inhibited by exposure to antirheumatic drugs including antimalarials and cyclosporin A. Such inhibitors are being used as chemosensitizers (CS) to enhance the effects of chemotherapy in drug resistant tumors. P-gp is also expressed by some normal cells including macrophages and cytotoxic lymphocytes. Recent studies of purified natural killer (NK) cells have shown that both the drug efflux and NK cytotoxic functions can be inhibited by CS agents, suggesting that both drug efflux and cytotoxicity may be mediated by P-gp's molecular transport function. NK cell cytotoxicity is mediated by secreted molecules such as granzymes and perforins. Both tumor necrosis factor alpha (TNF-alpha) producing macrophages and NK cells are present in the synovial tissues and fluid in early and advanced rheumatoid arthritis (RA). We hypothesize that antiarthritic effects of the antimalarials and cyclosporine and perhaps glucocorticoids are partially attributable to the inhibition of P-gp function thereby blocking TNF-alpha release by macrophages, TNF-alpha activation of NK cells, and NK cell secretion of cytotoxins in the rheumatoid joint. This hypothesis permits the mechanism of action of some antirheumatic drugs to be classified, and may aid in the development of combination therapy for RA and other autoimmune disorders.
An experimental study on induction motor drive with a single phase — Three phase matrix converter (2009)

This paper deals with a control method and a designing method of the capacitance of the compensation capacitor for a single phase to three phase matrix converters (MCs) with the variable speed drive capability of induction motors (IMs). Assuming the application of railway tractions, automobiles and elevators, motors drive inertial load. In such cases, both the load power and the load voltage increase in proportion to the rotor speed. The amplitude of the compensation capacitor voltage is controlled to absorb the single phase power fluctuation, along with the load power. We propose a method to decide the input side parameters such as the capacitance of the compensation capacitor, considering the input voltage and the power of the IM. We experimentally verify that a single phase to three phase MC can drive IMs with the proposed method.
SparkNN: A Distributed In-Memory Data Partitioning for KNN Queries on Big Spatial Data (2020)

The increase in GPS-enabled devices and proliferation of location-based applications have resulted in an abundance of geotagged (spatial) data. As a consequence, numerous applications have emerged that utilize the spatial data to provide different types of location-based services. However, the huge amount of available spatial data presents a challenge to the efficiency of these location-based services. Although the advent of big data frameworks like Apache Spark has enabled the processing of large amounts of data efficiently, they are designed for general (non-spatial) data. That is due to the build-in data partitioning mechanism that does not take into account the spatial proximity of the data. Therefore, these big data frameworks cannot be readily used for spatial analytics such as efficiently answering spatial queries. To fill this gap, this paper proposes SparkNN, an in-memory partitioning and indexing system for answering spatial queries, such as <em>K</em>-nearest neighbor, on big spatial data. SparkNN is implemented on top of Apache Spark and consists of three layers to facilitate efficient spatial queries. The first layer is a spatial-aware partitioning layer, which partitions the spatial data into several partitions ensuring that the load of the partitions is balanced and data objects with close proximity are placed in the same, or neighboring, partitions. The second layer is a local indexing layer, which provides a spatial index inside each partition to speed up the data search within the partition. The third layer is a global index, which is placed in the master node of Spark to route spatial queries to the relevant partitions. The efficiency of SparkNN was evaluated by extensive experiments with big spatial datasets. The results show SparkNN significantly outperforms the state-of-the-art Spark system when evaluated on the same set of queries.
Monte Carlo Hidden Markov Models: Learning Non-Parametric Models of Partially Observable Stochastic Processes (1999)

We present a learning algorithm for non-parametric hidden Markov models with continuous state and observation spaces. All necessary probability densities are approximated using samples, along with density trees generated from such samples. AMonte Carlo version of Baum-Welch (EM) is employed to learn models from data. Regularization during learning is achieved using an exponential shrinking technique. The shrinkage factor, which determines the effective capacity of the learning algorithm, is annealed down over multiple iterations of BaumWelch, and early stopping is applied to select the right model. Once trained, Monte Carlo HMMs can be run in an any-time fashion. We prove that under mild assumptions, Monte Carlo Hidden Markov Models converge to a local maximum in likelihood space, just like conventional HMMs. In addition, we provide empirical results obtained in a gesture recognition domain. 1 Introduction Hidden Markov models (HMMs) [27] have been applied successfully to a large rang...
Safe mutations for deep and recurrent neural networks through output gradients (2018)

While neuroevolution (evolving neural networks) has been successful across a variety of domains from reinforcement learning, to artificial life, to evolutionary robotics, it is rarely applied to large, deep neural networks. A central reason is that while random mutation generally works in low dimensions, a random perturbation of thousands or millions of weights will likely break existing functionality. This paper proposes a solution: a family of safe mutation (SM) operators that facilitate exploration without dramatically altering network behavior or requiring additional interaction with the environment. The most effective SM variant scales the degree of mutation of each individual weight according to the sensitivity of the network's outputs to that weight, which requires computing the gradient of outputs with respect to the weights (instead of the gradient of error, as in conventional deep learning). This safe mutation through gradients (SM-G) operator dramatically increases the ability of a simple genetic algorithm-based neuroevolution method to find solutions in high-dimensional domains that require deep and/or recurrent neural networks, including domains that require processing raw pixels. By improving our ability to evolve deep neural networks, this new safer approach to mutation expands the scope of domains amenable to neuroevolution.
Solid-Phase Synthesis of Diverse Peptide Tertiary Amides By Reductive Amination (2015)

The synthesis of libraries of conformationally constrained peptide-like oligomers is an important goal in combinatorial chemistry. In this regard an attractive building block is the N-alkylated peptide, also known as a peptide tertiary amide (PTA). PTAs are conformationally constrained because of allylic 1,3 strain interactions. We report here an improved synthesis of these species on solid supports through the use of reductive amination chemistry using amino acid-terminated, bead-displayed oligomers and diverse aldehydes. The utility of this chemistry is demonstrated by the synthesis of a library of 10,000 mixed peptoid-PTA oligomers.
Modulation and coding for throughput-efficient optical systems (1994)

Optical direct-detection systems are currently being considered for some high-speed intersatellite links, where data rates of a few hundred megabits per second are envisioned under power and pulsewidth constraints. The authors investigate the capacity, cutoff rate, and error-probability performance of uncoded and trellis-coded systems for various modulation schemes and under throughput and power constraints. Modulation schemes considered are on-off keying, pulse-position modulation (PPM), overlapping PPM, and multipulse (combinatorial) PPM.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
A novel mobility management mechanism based on an efficient Locator/ID separation scheme (2009)

The challenge to provide seamless mobility in the near future emerges as a key topic in various standardization bodies. In this paper, on the basis of an efficient and scalable Locator/ID separation (LIDS) architecture, a mobility management mechanism is designed. There are two contributions of our solution. Firstly, we separate the access network from the core network. Besides, to provide the seamless mobility support, locator/ID separation is used which can provide transparency to the upper layer applications. Then, the performance analysis is presented for both horizontal and vertical handover scenarios. The results show that our LIDS based architecture provides an outstanding network-based mobility management with route optimization support compared with the IP based approaches Mobile IPv6 and Proxy Mobile IPv6).
Customer Centric Cloud Service Model and a Case Study on Commerce as a Service (2009)

This paper proposes a cloud service model that centers around customer business requirements. The model covers the customers' subscribed services and the service providers' offered cloud services. It covers the relationship among offering versus subscription, cloud infrastructure service versus cloud application service, configuration versus customization of cloud services, etc. It then depicts a customer centric cloud service model which models the artifacts of enterprises owned by public serving cloud services. It's an extension of enterprise services to open service ecosystem leveraging the latest technical innovation of cloud computing. Later, this paper carries out a case study on an IBM software group ongoing project, commerce as a service, which aims to provide e-commerce functions as services over a cloud infrastructure.