gebhart/patrepeval huggingface dataset:
Development of a T7 Phage Display Library to Detect Sarcoidosis and Tuberculosis by a Panel of Novel Antigens (2015)

Sarcoidosis is a granulomatous inflammatory disease, diagnosed through tissue biopsy of involved organs in the absence of other causes such as tuberculosis (TB). No specific serologic test is available to diagnose and differentiate sarcoidosis from TB. Using a high throughput method, we developed a T7 phage display cDNA library derived from mRNA isolated from bronchoalveolar lavage (BAL) cells and leukocytes of sarcoidosis patients. This complex cDNA library was biopanned to obtain 1152 potential sarcoidosis antigens and a microarray was constructed to immunoscreen two different sets of sera from healthy controls and sarcoidosis. Meta-analysis identified 259 discriminating sarcoidosis antigens, and multivariate analysis identified 32 antigens with a sensitivity of 89% and a specificity of 83% to classify sarcoidosis from healthy controls. Additionally, interrogating the same microarray platform with sera from subjects with TB, we identified 50 clones that distinguish between TB, sarcoidosis and healthy controls. The top 10 sarcoidosis and TB specific clones were sequenced and homologies were searched in the public database revealing unique epitopes and mimotopes in each group. Here, we show for the first time that immunoscreenings of a library derived from sarcoidosis tissue differentiates between sarcoidosis and tuberculosis antigens. These novel biomarkers can improve diagnosis of sarcoidosis and TB, and may aid to develop or evaluate a TB vaccine.
SHORT CHAIN PEPTIDE INHIBITORS OF HUMAN RENIN (1985)

Abstract The phenylalanine residue in the C-terminal sequence of angiotensin II was found to be important for the design of renin inhibitors. 1-Naphthyl-alanine(Nal(1))-containing tripeptide analogues such as benzyloxycarbonyl-Nal (1)-His-Leucinal (ES-188) and benzyloxycarbonyl-Nal(1)-His-(3S,4S)-4-amino-3-hydroxy-6-methylheptanoic acid (Statine) 2(S)-methylbuthylamid (ES-254) showed high potency and specificity to human renin.
Operational Benefits of Real-Time Monitoring and Visualization in Data Centers (2009)

The 2007 US EPA report to Congress (US EPA, 2007) on the state of energy consumption in data centers brought to light the true energy inefficiencies built into today’s data centers. Marquez et al. (2008) conducted an initial analysis on the productivity of a Pacific Northwest National Lab computer using The Green Grid’s Data Center Energy Productivity metric (The Green Grid, 2008). Their study highlights how the Top500 ranking of computers disguises the serious energy inefficiency of today’s High Performance Computing data centers. In the rapidly expanding Cloud Computing space, the race will be won by the providers that deliver the lowest cost of computing — such cost is heavily influenced by the operational costs incurred by data centers. As a means to address the urgent need to lower the cost of computing, solution providers have been intensely focusing on real-time monitoring, visualization, and control/management of data centers. The monitoring aspect involves the widespread use of networks of sensors that are used to monitor key data center environmental variables such as temperature, relative humidity, air flow rate, pressure, and energy consumption. Such data is then used to visualize and analyze data center problem areas (e.g., hotspots), which is then followed by control/management actions designed to alleviate such problem areas. The authors have been researching the operational benefits of a network of sensors tied in to a software package that uses the data to visualize, analyze, and control/manage the data center cooling system and IT Equipment for maximum operational efficiency. The research is being conducted in a corporate production data center that is networked in to the authors’ company’s global network of data centers. Results will be presented that highlight the operational benefits that are realizable through real-time monitoring and visualization.
Oral beta-glucan adjuvant therapy converts nonprotective Th2 response to protective Th1 cell-mediated immune response in mammary tumor-bearing mice. (2007)

Beta (1-3)-D-glucans were identified almost 40 years ago as biological response modifiers that stimulated tumor rejection. In vitro studies have shown that beta-glucans bind to a lectin domain within complement receptor type 3 (CR3), or to, more recently described dectin-1 a beta-glucan specific receptor, acting mainly on phagocytic cells. In this study, we assessed the intracellular cytokine profiles of peripheral blood lymphocytes from mice bearing mammary tumors receiving i.v. anti-tumor mAbs combined or not with whole glucan particle suspension given orally (WGP, 400 microg every 24 hours). The proportions of T cells producing IL-4 and IFNgamma were determined by flow cytometry. The proportion of T cells producing IL-4 was significantly higher in tumor-bearing mice not receiving beta-glucan-enhanced therapy. Conversely, T cells from mice undergoing beta-glucan-enhanced therapy showed increased production of the Th1 cytokine IFNgamma. The switch from a Th2 to a Th1 response after WGP therapy was possibly mediated by intestinal mucosal macrophages releasing IL-12.
Adaptive optimizations of recursive queries in teradata (2012)

Recursive queries were introduced as part of ANSI SQL 99 to support processing of hierarchical data typical of air flight schedules, bill-of-materials, data cube dimension hierarchies, and ancestor-descendant information (e.g. XML data stored in relations). Recently, recursive queries have also found extensive use in web data analysis such as social network and click stream data. Teradata implemented recursive queries in V2R6 using static plans whereby a query is executed in multiple iterations, each iteration corresponding to one level of the recursion. Such a static planning strategy may not be optimal since the demographics of intermediate results from recursive iterations often vary to a great extent. Gathering feedback at each iteration could address this problem by providing size estimates to the optimizer which, in turn, can produce an execution plan for the next iteration. However, such a full feedback scheme suffers from lack of pipelining and the inability to exploit global optimizations across the different recursion iterations. In this paper, we propose adaptive optimization techniques that avoid the issues with static as well as full feedback optimization approaches. Our approach employs a mix of multi-iteration pre-planning and dynamic feedback techniques which are generally applicable to any recursive query implementation in an RDBMS. We also validated the effectiveness of our proposed techniques by conducting experiments on a prototype implementation using a real-life social network data from the FriendFeed online blogging service.
Partial-Power Converter Topology of Type II for Efficient Electric Vehicle Fast Charging (2021)

The increasing power levels handled by electric vehicle (EV) dc fast chargers will impose additional challenges to the switching devices in order to cope with the efficiency requirements. A cost-effective alternative to achieve highly efficient power conversion is through the partial-power conversion concept. This article validates the advantages of a step-down Type II partial-power converter (PPC), based on the phase-shifted full-bridge converter, for EV fast chargers. By exploiting the reduced voltage range of an EV battery pack along with the reduced power ratio for a Type II PPC, an extremely efficient charging process can be achieved. The concept is validated with the development of a 7-kW demonstrator, and hence, realistic efficiency measurements are obtained. Results indicate the effectiveness of charging a battery by merely handling 13.32% of the power provided to it, with a peak efficiency of 99.11%.
A Pd-Catalyzed in situ domino process for mild and quantitative production of 2,5-dimethylfuran directly from carbohydrates (2017)

A sustainable catalytic system is developed to be efficient for producing the biofuel 2,5-dimethylfuran directly from carbohydrate biomass <italic>via</italic> an <italic>in situ</italic> domino process under mild conditions.
Abstract 1640: A novel small molecule inhibitor of lysophosphatidic acid acyltransferase-beta inhibits pancreatic cancer cell proliferation and mTOR signaling (2014)

Abstract Lysophosphatidic acid acyltransferase (LPAAT-β), a phosphatidic acid (PA)-generating enzyme, plays an essential role in triglyceride synthesis. A less familiar role for LPAAT-β is that of a regulator of cell growth and differentiation by means of the function of its product, PA, which plays a vital role in the activation of key signal transduction proteins including Raf, PKC-ζ and mTOR. It is in this role that LPAAT-β presents as a potential therapeutic target in cancer. Accordingly, we developed a library of small molecule inhibitors of LPAAT-β with nanomolar activity against LPAAT-β enzyme activity in vitro (2012 Annual Meeting, Abstract #2470). We have now performed additional SAR and lead optimization to produce a potent small molecule that inhibits proliferation, mTOR signaling pathways, and total cellular PA levels at low micromolar concentrations. The lead compound also inhibits anchorage-independent growth of pancreatic cancer cell lines at nanomolar concentrations. This compound demonstrates effects on cellular signaling that are similar to the effects of LPAAT-β siRNA. Citation Format: Michelle A. Blaskovich, Yunting Luo, Yiyu Ge, Saïd M. Sebti, Harshani R. Lawrence, Nicholas J. Lawrence, Gregory M. Springett. A novel small molecule inhibitor of lysophosphatidic acid acyltransferase-beta inhibits pancreatic cancer cell proliferation and mTOR signaling. [abstract]. In: Proceedings of the 105th Annual Meeting of the American Association for Cancer Research; 2014 Apr 5-9; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2014;74(19 Suppl):Abstract nr 1640. doi:10.1158/1538-7445.AM2014-1640
Piezoelectrically actuated flextensional micromachined ultrasound transducers. II. Fabrication and experiments (2002)

This paper presents novel micromachined two-dimensional array piezoelectrically actuated flextensional transducers that can be used to generate sound in air or water. Micromachining techniques to fabricate these devices are also presented. Individual unimorph array elements consist of a thin piezoelectric annular disk and a thin, fully clamped, circular plate. We manufacture the transducer in two-dimensional arrays using planar silicon micromachining and demonstrate ultrasound transmission in air at 2.85 MHz with 0.15 microm/V peak displacement. The devices have a range of operating resonance frequencies starting from 450 kHz to 4.5 MHz. Such an array could be combined with on-board driving and addressing circuitry for different applications.
Optimizing injected dose in clinical PET by accurately modeling the counting-rate response functions specific to individual patient scans. (2005)

The methodology developed here allows one to directly estimate the optimal dose to inject for specific clinical scans and permits a detailed analysis of the sources of noise in PET data and of their variation with parameters such as patient weight.
METHOD OF MAKING ELECTRODES FOR ELECTROCHEMICAL CELL (1981)

multiplicity of (0,4) were investigated. The spatial distribution of lithium ions in an electrochemical cell containing this novel disordered carbon material was investigated in situ by Li-7 NMR using an electrochemical cell that was incorporated into a toroid cavity nuclear magnetic resonance (NMR) imager. The concentration of solvated Li{sup +} ions in the carbon anode appears to be larger than in the bulk electrolyte, is substantially lower near the copper/carbon interface, and does not change with cell charging.
Synthetic PPG generation from haemodynamic model with baroreflex autoregulation: a Digital twin of cardiovascular system (2019)

Synthetic data generation has recently emerged as a substitution technique for handling the problem of bulk data needed in training machine learning algorithms. Healthcare, primarily cardiovascular domain is a major area where synthetic physiological data like Photoplethysmogram (PPG), Electrocardiogram (ECG), Phonocardiogram (PCG), etc. are being used to improve accuracy of machine learning algorithm. Conventional synthetic data generation approach using mathematical formulations lack interpretability. Hence, aim of this paper is to generate synthetic PPG signal from a Digital twin platform replicating cardiovascular system. Such system can serve the dual purpose of replicating the physical system, so as to simulate specific `what if' scenarios as well as to generate large scale synthetic data with patho-physiological interpretability. Cardio-vascular Digital twin is modeled with a two chambered heart, haemodynamic equations and a baroreflex based pressure control mechanism to generate blood pressure and flow variations. Synthetic PPG signal is generated from the model for healthy and Atherosclerosis condition. Initial validation of the platform has been made on the basis of efficiency of the platform in clustering Coronary Artery Disease (CAD) and non CAD PPG data by extracting features from the synthetically generated PPG and comparing that with PPG obtained from Physionet data.
Hydrophobic displacement chromatography of proteins (2000)

Displacement chromatography of proteins was successfully carried out in both hydrophobic interaction and reversed-phase chromatographic systems using low-molecular weight displacers. The displacers employed for hydrophobic displacement chromatography were water soluble, charged molecules containing several short alkyl and/or aryl groups. Spectroscopy was employed to verify the absence of structural changes to the proteins displaced on these hydrophobic supports. Displacement chromatography on a reversed-phase material was employed to purify a growth factor protein from its closely related variants, demonstrating the high resolutions that can be achieved by hydrophobic displacement chromatography. This process combines the high-resolution/high-throughput characteristics of displacement chromatography with the unique selectivity of these hydrophobic supports and offers the chromatographic engineer a powerful tool for the preparative purification of proteins.
1310- to 1320-nm emission in Nd<sup>3+</sup>-ion-doped fluoroaluminate glasses (1998)

Nd3+-doped 1.3micrometers fiber amplifier has many inherent advantages, but two major problems must be overcome to achieve a device: signal excited-state absorption (ESA), and amplified spontaneous emission (ASE). Signal ESA around 1300 nm prevents gain in that region, and so red-shifts and gain out of the second telecom window. The ASE at 1050 nm has a branching ratio 5 time larger than the 1.3 micrometers transition; as a result it clamps signal gain at low values. Moreover, in many Nd3+-doped glass hosts the peak of emission lies at wavelengths above 1320 nm. In this paper we present new highly ionic fluoroaluminate glasses developed as hosts for the 1.3 micrometers -doped fiber amplifier and discuss aspects of glass design. (Formula available in paper) emission peaks between 1310 and 1317 nm were demonstrated in bulk glasses, and gain in the 1310-1320 nm region was measured in fiber. The gain and emission spectra show evidence of significantly reduced ESA. ASE filtering is discussed, focusing on Bragg grating filters and on absorbing co-dopants, such as (formula available in paper) The paper also assesses thermal and viscous properties of the core and cladding glasses for fiber drawing.
A Fast and Stable Photochromic Switch Based on the Opening and Closing of an Oxazine Ring (2005)

[reaction: see text] We have designed a molecular switch based on the photoinduced opening and thermal closing of an oxazine ring. Ultraviolet excitation of this molecule induces the cleavage of a [C-O] bond to form a p-nitrophenolate chromophore in less than 10 ns with a quantum yield of ca. 0.1. The photogenerated isomer reverts thermally to the original oxazine within 50 ns. Our photochromic switch survives more than 3000 excitation cycles without decomposing, even in air-saturated solutions.
On the feasibility of centrally-coordinated Peer-to-Peer live streaming (2011)

In this paper we present an exploration of central coordination as a way of managing P2P live streaming overlays. The main point is to show the elements needed to construct a system with that approach. A key element in the feasibility of this approach is a near real-time optimization engine for peer selection. Peer organization in a way that enables high bandwidth utilization plus optimized peer selection based on multiple utility factors make it possible to achieve large source bandwidth savings and provide high quality of user experience. The benefits of our approach are also seen most when NAT constraints come into play.
Designed protein- and peptide-based hydrogels for biomedical sciences (2021)

Proteins are fundamentally the most important macromolecules for biochemical, mechanical, and structural functions in living organisms. Therefore, they provide us with diverse structural building blocks for constructing various types of biomaterials, including an important class of such materials, hydrogels. Since natural peptides and proteins are biocompatible and biodegradable, they have features advantageous for their use as the building blocks of hydrogels for biomedical applications. They display constitutional and mechanical similarities with the native extracellular matrix (ECM), and can be easily bio-functionalized via genetic and chemical engineering with features such as bio-recognition, specific stimulus-reactivity, and controlled degradation. This review aims to give an overview of hydrogels made up of recombinant proteins or synthetic peptides as the structural elements building the polymer network. A wide variety of hydrogels composed of protein or peptide building blocks with different origins and compositions - including β-hairpin peptides, α-helical coiled coil peptides, elastin-like peptides, silk fibroin, and resilin - have been designed to date. In this review, the structures and characteristics of these natural proteins and peptides, with each of their gelation mechanisms, and the physical, chemical, and mechanical properties as well as biocompatibility of the resulting hydrogels are described. In addition, this review discusses the potential of using protein- or peptide-based hydrogels in the field of biomedical sciences, especially tissue engineering.
Abstract 3914: ZW49, a HER2-targeted biparatopic antibody-drug conjugate for the treatment of HER2-expressing cancers (2018)

Abstract Therapies targeting HER2 have transformed the treatment of patients with HER2-expressing breast and gastric cancers. Unfortunately, many patients recur following HER2-targeted treatments and new therapies are needed. Multiple antibody-drug conjugate (ADC) technologies are being explored in this setting, some of which utilize the anti-HER2 antibody trastuzumab. Here we present the preclinical characterization of a new anti-HER2 biparatopic ADC, ZW49, which is generated from the conjugation of a novel N-acyl sulfonamide auristatin payload to the inter-chain disulfide bond cysteines of the bispecific anti-HER2 IgG1 antibody ZW25, via a protease cleavable linker. A series of in vitro and in vivo experiments were performed to characterize ZW49 as a potential therapeutic candidate. In cellular binding assays, it was confirmed that the payload conjugation to ZW25 did not affect the antibody's binding to HER2-expressing cells. ZW49 displayed potent in vitro cytotoxicity in multiple cancer cell lines expressing HER2 and was efficacious in multiple patient-derived xenograft (PDX) models. In mice bearing the HBCx-13b HER2 3+ PDX, two doses of ZW49 administered two weeks apart generated tumor regressions. Furthermore, preliminary results from PDX models with lower levels of HER2 expression treated with ZW49 also generated regressions. In nonhuman primates ZW49 administered intravenously every two weeks for three doses was well tolerated. Based on these findings, we are proceeding with further development of ZW49 as a therapeutic candidate in HER2-expressing cancers. Citation Format: Kevin J. Hamblett, Phil W. Hammond, Stuart D. Barnscher, Vincent K. Fung, Rupert H. Davies, Grant R. Wickman, Andrea Hernandez, Tong Ding, Adam S. Galey, Geoffrey C. Winters, Jamie R. Rich, John S. Babcook. ZW49, a HER2-targeted biparatopic antibody-drug conjugate for the treatment of HER2-expressing cancers [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 3914.
Human Epithelial Basal Cells Are Cells of Origin of Prostate Cancer, Independent of CD133 Status (2012)

Normal prostatic epithelium is composed of basal and luminal cells. Prostate cancer can be initiated in both benign basal and luminal stem cells, but because basal cell markers are not expressed in patient tumors, the former result was unexpected. Since the cells of origin of prostate cancer are important therapeutic targets, we sought to provide further proof that basal stem cells have tumorigenic potential. Prostatic basal cells were enriched based on α2β1integrin(hi) expression and further enriched for stem cells using CD133 in nontumorigenic BPH-1 cells. Human embryonic stem cells (hESCs) were also used as a source of normal stem cells. To test their tumorigenicity, we used two alternate stromal-based approaches; (a) recombination with human cancer-associated fibroblasts (CAFs) or (b) recombination with embryonic stroma (urogenital mesenchyme) and treated host mice with testosterone and 17β-estradiol. Enriched α2β1integrin(hi) basal cells from BPH-1 cells resulted in malignant tumor formation using both assays of tumorigenicity. Surprisingly, the tumorigenic potential did not reside in the CD133(+) stem cells but was consistently observed in the CD133(-) population. CAFs also failed to induce prostatic tumors from hESCs. These data confirmed that benign human basal cells include cells of origin of prostate cancer and reinforced their importance as therapeutic targets. In addition, our data suggested that the more proliferative CD133(-) basal cells are more susceptible to tumorigenesis compared to the CD133(+)-enriched stem cells. These findings challenge the current dogma that normal stem cells and cells of origin of cancer are the same cell type(s).
Wireless Channel Charting: Theory, Practice, and Applications (2023)

Channel charting is a recently proposed framework that applies dimensionality reduction to channel state information (CSI) in wireless systems with the goal of associating a pseudo-position to each mobile user in a low-dimensional space: the channel chart. Channel charting summarizes the entire CSI dataset in a self-supervised manner, which opens up a range of applications that are tied to user location. In this article, we introduce the theoretical underpinnings of channel charting and present an overview of recent algorithmic developments and experimental results obtained in the field. We furthermore discuss concrete application examples of channel charting to network- and user-related applications, and we provide a perspective on future developments and challenges as well as the role of channel charting in next-generation wireless networks.
Tomographic microscopy of biological tissues by digital interference holography (2004)

The performance of digital interference holographic system is improved for microscopic imaging of biological tissues. Tomographic imaging of subsurface tissue structure is demonstrated for microscopic plant and animal tissues. The imaging process consists of holographic recording at a multitude of wavelengths followed by numerical superposition of 3D diffraction fields.