gebhart/patrepeval huggingface dataset:
Observations on the Systemic Administration of Autologous Lymphokine-Activated Killer Cells and Recombinant Interleukin-2 to Patients with Metastatic Cancer (1985)

We describe here the preliminary results of the systemic administration of autologous lymphokine-activated killer (LAK) cells and the recombinant-derived lymphokine interleukin-2 to patients with advanced cancer. This regimen was based on animal models in which the systemic administration of LAK cells plus interleukin-2 mediated the regression of established pulmonary and hepatic metastases from a variety of murine tumors in several strains of mice. We treated 25 patients with metastatic cancer in whom standard therapy had failed. Patients received both 1.8 to 18.4 X 10(10) autologous LAK cells, generated from lymphocytes obtained through multiple leukaphereses, and up to 90 doses of interleukin-2. Objective regression of cancer (more than 50 per cent of volume) was observed in 11 of the 25 patients: complete tumor regression occurred in one patient with metastatic melanoma and has been sustained for up to 10 months after therapy, and partial responses occurred in nine patients with pulmonary or hepatic metastases from melanoma, colon cancer, or renal-cell cancer and in one patient with a primary unresectable lung adenocarcinoma. Severe fluid retention was the major side effect of therapy, although all side effects resolved after interleukin-2 administration was stopped. Further development of this approach and additional patient follow-up are required before conclusions about its therapeutic value can be drawn.
RFID Tag and RF Structures on a Paper Substrate Using Inkjet-Printing Technology (2007)

In this paper, inkjet-printed UHF and microwave circuits fabricated on paper substrates are investigated for the first time as an approach that aims for a system-level solution for fast and ultra-low-cost mass production. First, the RF characteristics of the paper substrate are studied by using the microstrip ring resonator in order to characterize the relative permittivity (epsiv <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">r</sub> ) and loss tangent (tan delta) of the substrate at the UHF band for the first time reported. A UHF RFID tag module is then developed with the inkjet-printing technology, proving this approach could function as an enabling technology for much simpler and faster fabrication on/in paper. Simulation and well-agreed measurement results, which show very good agreement, verify a good performance of the tag module. In addition, the possibility of multilayer RF structures on a paper substrate is explored, and a multilayer patch resonator bandpass filter demonstrates the feasibility of ultra-low-cost 3-D paper-on-paper RF/wireless structures.
Prediction of locally stable RNA secondary structures for genome-wide surveys (2004)

The software described in this contribution will be available for download at http://www.tbi.univie.ac.at/~ivo/RNA/ as part of the Vienna RNA Package.
Comprehensive evaluation of transcriptome-based cell-type quantification methods for immuno-oncology (2019)

Supplementary data are available at Bioinformatics online.
Correcting sample selection bias in maximum entropy density estimation (2005)

We study the problem of maximum entropy density estimation in the presence of known sample selection bias. We propose three bias correction approaches. The first one takes advantage of unbiased sufficient statistics which can be obtained from biased samples. The second one estimates the biased distribution and then factors the bias out. The third one approximates the second by only using samples from the sampling distribution. We provide guarantees for the first two approaches and evaluate the performance of all three approaches in synthetic experiments and on real data from species habitat modeling, where maxent has been successfully applied and where sample selection bias is a significant problem. 1
In vitro effects of natural killer cells against Paracoccidioides brasiliensis yeast phase (1984)

Recently, data have been reported suggesting natural killer (NK) cells may function in natural resistance against a fungus, Cryptococcus neoformans. The primary objective of this study was to examine the reactivity of murine splenic cells against another fungus, Paracoccidioides brasiliensis. Levels of NK activity in effector cell pools were varied by: (i) removing nylon wool-adherent cells, (ii) fractionating splenic cells on Percoll discontinuous gradients, (iii) using old and young effector cell donor mice, (iv) using donors from different strains, and (v) pretreating donors with NK-augmenting and -depressing agents. The various effector cell pools were simultaneously used in the 4-h 51Cr release assay with YAC-1 targets to determine the NK reactivity and in the in vitro growth inhibition assay against P. brasiliensis yeast phase targets. In each case, the level of NK reactivity correlated with the ability of the effector cells to inhibit the in vitro growth of P. brasiliensis. NK activity and P. brasiliensis growth-inhibiting ability could be augmented by fractionation of splenic cells through nylon wool or Percoll gradients. The effector cells responsible for the NK activity and P. brasiliensis growth inhibition were characterized as being nylon wool nonadherent, being found in the low-density fractions from Percoll discontinuous gradients, and having no detectable Thy-1 antigen or immunoglobulin but having asialo GM1 on their surface. These data support the contention that NK or NK-like cells are responsible for limiting the in vitro growth of P. brasiliensis.
Bovine Interferon-τ Stimulates the Janus Kinase-Signal Transducer and Activator of Transcription Pathway in Bovine Endometrial Epithelial Cells1 (2001)

Trophoblastic bovine interferon-tau (bIFN-tau) suppresses luteolytic pulses of endometrial prostaglandin F(2alpha) (PGF(2alpha)) at the time of maternal recognition of pregnancy. This results in maintenance of the corpus luteum in cattle. The hypothesis that effects of bIFN-tau in the endometrium were through activation of the Janus kinase (JAK)-signal transducer and activator of transcription (STAT) pathway of signal transduction was tested. Whole cell, cytosolic, and nuclear extracts from bovine endometrial cells treated with bIFN-tau were analyzed by immunoprecipitation, immunoblotting, and electrophoretic mobility shift assays in a series of dose- and time-dependency experiments. Bovine IFN-tau stimulated tyrosine phosphorylation, homo- and heterodimer formation, nuclear translocation, and DNA binding of STAT proteins 1, 2, and 3. Moreover, bIFN-tau induced synthesis of interferon-regulatory factor. In conclusion, bIFN-tau stimulates the JAK-STAT pathway in the bovine endometrium. It is proposed that activation of the JAK-STAT pathway is involved in regulating the antiluteolytic effects of bIFN-tau.
Enhanced anti-influenza activity of a surfactant protein D and serum conglutinin fusion protein (2000)

We previously demonstrated that bovine serum conglutinin has markedly greater ability to inhibit influenza A virus (IAV) infectivity than other collectins. We now show that recombinant conglutinin and a chimeric protein containing the NH(2) terminus and collagen domain of rat pulmonary surfactant protein D (rSP-D) fused to the neck region and carbohydrate recognition domain (CRD) of conglutinin (termed SP-D/Cong(neck+CRD)) have markedly greater ability to inhibit infectivity of IAV than wild-type recombinant rSP-D, confirming that the potent IAV-neutralizing activity of conglutinin resides in its neck region and CRD. Furthermore, by virtue of incorporation of the NH(2) terminus and collagen domain of SP-D, SP-D/Cong(neck+CRD) caused substantially greater aggregation of IAV particles and enhancement of neutrophil binding of, and H(2)O(2) responses to, IAV than recombinant conglutinin or recombinant rSP-D. Hence, SP-D/Cong(neck+CRD) combined favorable antiviral and opsonic properties of conglutinin and SP-D. This study demonstrates an association of specific structural domains of SP-D and conglutinin with specific functional properties and illustrates that antimicrobial activities of wild-type collectins can be enhanced through recombinant strategies.
The Unfolded Protein Response: From Stress Pathway to Homeostatic Regulation (2011)

The vast majority of proteins that a cell secretes or displays on its surface first enter the endoplasmic reticulum (ER), where they fold and assemble. Only properly assembled proteins advance from the ER to the cell surface. To ascertain fidelity in protein folding, cells regulate the protein-folding capacity in the ER according to need. The ER responds to the burden of unfolded proteins in its lumen (ER stress) by activating intracellular signal transduction pathways, collectively termed the unfolded protein response (UPR). Together, at least three mechanistically distinct branches of the UPR regulate the expression of numerous genes that maintain homeostasis in the ER or induce apoptosis if ER stress remains unmitigated. Recent advances shed light on mechanistic complexities and on the role of the UPR in numerous diseases.
New Derivatives of 5-Aminolevulinic Acid for Photodynamic Therapy: Chemical Synthesis and Porphyrin Production in In Vitro and In Vivo Biological Systems (2006)

Photodynamic therapy (PDT) has become a new treatment for several oncological and nononcological disorders. This procedure involves systemic or topical administration of a lesion-localizing photosensitizer or prodrug, followed by irradiation with visible light to cause singlet oxygen-induced damage to the target tissue. 5-aminolevulinic acid (ALA) is an endogenous precursor for several photosensitizing porphyrins formed by heme biosynthesis, and has been studied for PDT with promising results for some superficial diseases of the skin and hollow internal organs. Hydrophilic ALA has a limited ability to penetrate certain biological barriers and has a relatively low selectivity for lesions. In addition, its ability to induce intracellular porphyrins has been shown to be low compared to most esters of ALA. This stimulated a search for lipophilic derivatives of ALA to overcome the shortcomings of ALA. Thirty-two new esters of ALA were prepared and their ability to induce porphyrin formation was assessed in the WiDr human carcinoma cell line in vitro and in the normal skin of Balb/c nude mice in vivo. Branched-chain alkyl esters and substituted benzyl esters were found to be the most efficient porphyrin precursors of the compounds studied.
Considerations for Ultimate CMOS Scaling (2012)

This review paper explores considerations for ultimate CMOS transistor scaling. Transistor architectures such as extremely thin silicon-on-insulator and FinFET (and related architectures such as TriGate, Omega-FET, Pi-Gate), as well as nanowire device architectures, are compared and contrasted. Key technology challenges (such as advanced gate stacks, mobility, resistance, and capacitance) shared by all of the architectures will be discussed in relation to recent research results.
An efficient MR phosphorous spectroscopic localization technique for studying ischemic heart (1999)

To obtain the spatially resolved (31)P spectroscopic image from myocardium during an acute myocardium ischemia at a high signal-to-noise ratio (SNR) in a very limited time window, we have exploited the spatial variation of the radiofrequency (RF) field produced by a single loop transmit/receive (TR) RF coil along its axis for spatial discrimination. By incrementally lengthening the duration of a square RF excitation pulse, the positional information can be systematically encoded as harmonics of various orders in MR signal. In the in vivo open-chest animal experiment, this RF coil was surgically sutured onto the epicardial surface of the left ventricular (LV) wall over the region perfused by the left anterior descending coronary artery. Using only 17 encoding steps, we have obtained one-dimensional (31)P spectroscopic images from both a multiple-layer phosphor phantom and an in vivo LV myocardium. In the animal study, the cardiac gating is used with respiratory synchronization. The MR data were only collected during the end diastole phase of the cardiac cycle (cardiac and respiratory synchronized) with an effective sequence repetition time (TR) of 6 seconds (to ensure the complete relaxation of the phosphorous magnetization). The total acquisition time for a complete experiment is about 10 minutes. Prior to the CSI reconstruction process, the raw data matrix was zero-filled in the spatial dimension. The spatially resolved metabolite map exhibited all the metabolite peaks including creatine phosphate and adenosine triphosphate. At the layer of endocardium, two peaks corresponding to 2, 3-diphosphoglycerate, which is contained in the erythrocytes, were clearly seen in the LV wall. Also, the method allows compensation in both volume and coil sensitivity variations for the resulting spectra. All results have demonstrated that it is an efficient nuclear magnetic resonance method capable of obtaining high-quality (31)P spectroscopic images with both excellent spatial localization and SNR in the research of cardiac ischemia. J. Magn. Reson. Imaging 1999;10:892-898.
Protein-Protein Interfaces: Architectures and Interactions in Protein-Protein Interfaces and in Protein Cores. Their Similarities and Differences (1996)

Protein structures generally consist of favorable folding motifs formed by specific arrangements of secondary structure elements. Similar architectures can be adopted by different amino acids sequences, although the details of the structures vary. It has long been known that despite the sequence variability, there is a striking preferential conservation of the hydrophobic character of the amino acids at the buried positions of these folding motifs. Differences in the sizes of the side-chains are accommodated by movements of the secondary structure elements with respect to each other, leading to compact packing. Scanning protein-protein interfaces reveals that similar architectures are also observed at and around their interacting surfaces, with preservation of the hydrophobic character, although not to the same extent. The general forces that determine the origin of the native structures of proteins have been investigated intensively. The major non-bonded forces operating on a protein chain as it folds into a three-dimensional structure are likely to be packing, the hydrophobic effect, and electrostatic interactions. While the substantial hydrophobic forces lead to a compact conformation, they are also nonspecific and cannot serve as a guide to a conformationally unique structure. For the general folding problem, it thus appears that packing is a prime candidate for determining a particular fold. Specific hydrogen-bonding patterns and salt-bridges have also been proposed to play a role. Inspection of protein-protein interfaces reveals that the hallmarks governing single chain protein structures also determine their interactions, suggesting that similar principles underlie protein folding and protein-protein associations. This review focuses on some aspects of protein-protein interfaces, particularly on the architectures and their interactions. These are compared with those present in protein monomers. This task is facilitated by the recently compiled, non-redundant structural dataset of protein-protein interfaces derived from the crystallographic database. In particular, although current view holds that protein-protein interfaces and interactions are similar to those found in the conformations of single-chain proteins, this review brings forth the differences as well. Not only is it logical that such differences would exist, it is these differences that further illuminate protein folding on the one hand and protein-protein recognition on the other. These are also particularly important in considering inhibitor (ligand) design.
Biochemical and Functional Characterization of the Ebola Virus VP24 Protein: Implications for a Role in Virus Assembly and Budding (2003)

The VP24 protein of Ebola virus is believed to be a secondary matrix protein and minor component of virions. In contrast, the VP40 protein of Ebola virus is the primary matrix protein and the most abundant virion component. The structure and function of VP40 have been well characterized; however, virtually nothing is known regarding the structure and function of VP24. Wild-type and mutant forms of VP24 were expressed in mammalian cells to gain a better understanding of the biochemical and functional nature of this viral protein. Results from these experiments demonstrated that (i) VP24 localizes to the plasma membrane and perinuclear region in both transfected and Ebola virus-infected cells, (ii) VP24 associates strongly with lipid membranes, (iii) VP24 does not contain N-linked sugars when expressed alone in mammalian cells, (iv) VP24 can oligomerize when expressed alone in mammalian cells, (v) progressive deletions at the N terminus of VP24 resulted in a decrease in oligomer formation and a concomitant increase in the formation of high-molecular-weight aggregates, and (vi) VP24 was present in trypsin-resistant virus like particles released into the media covering VP24-transfected cells. These data indicate that VP24 possesses structural features commonly associated with viral matrix proteins and that VP24 may have a role in virus assembly and budding.
Distinct Roles of Phosphoinositide-3 Kinase and Phospholipase Cγ2 in B-Cell Receptor-Mediated Signal Transduction (2005)

During B-cell receptor (BCR) signaling, phosphoinositide-3 kinase (PI3K) is thought to function upstream of phospholipase Cgamma2 (PLCgamma2). PLCgamma2 deficiency specifically impedes transitional type 2 (T2) to follicular (FO) mature B-cell transition. Here, we demonstrate that PI3K deficiency specifically impaired T2-to-FO mature B-cell transition and marginal zone B-cell development. Furthermore, we investigated the functional relationship between PI3K and PLCgamma2 using PI3K-/-, PLCgamma2-/-, and PI3K-/- PLCgamma2-/- B cells. Interestingly, PLCgamma2 deficiency had no effect on BCR-mediated PI3K activation, whereas PI3K deficiency only partially blocked activation of PLCgamma2. Moreover, whereas PI3K-/- PLCgamma2-/- double deficiency did not affect hematopoiesis, it resulted in embryonic lethality. PI3K-/- PLCgamma2-/- fetal liver cells transplanted into B-cell null JAK3-/- mice failed to restore development of peripheral B cells and failed to progress through early B-cell development at the pro-B- to pre-B-cell transition, a more severe phenotype than was observed with either PI3K or PLCgamma2 single-deficiency B cells. Consistent with this finding, BCR signaling was more severely impaired in the absence of both PI3K and PLCgamma2 genes than in the absence of either one alone. Taken together, these results demonstrate that whereas PI3K functions upstream of PLCgamma2, activation of PLCgamma2 can occur independently of PI3K and that PI3K and PLCgamma2 also have distinct functions in BCR signal transduction.
Opportunities for renewable bioenergy using microorganisms (2008)

Global warming can be slowed, and perhaps reversed, only when society replaces fossil fuels with renewable, carbon-neutral alternatives. The best option is bioenergy: the sun's energy is captured in biomass and converted to energy forms useful to modern society. To make a dent in global warming, bioenergy must be generated at a very high rate, since the world today uses approximately 10 TW of fossil-fuel energy. And, it must do so without inflicting serious damage on the environment or disrupting our food supply. While most bioenergy options fail on both counts, several microorganism-based options have the potential to produce large amounts of renewable energy without disruptions. In one approach, microbial communities convert the energy value of various biomass residuals to socially useful energy. Biomass residuals come from agricultural, animal, and a variety of industrial operations, as well as from human wastes. Microorganisms can convert almost all of the energy in these wastes to methane, hydrogen, and electricity. In a second approach, photosynthetic microorganisms convert sunlight into biodiesel. Certain algae (eukaryotes) or cyanobacteria (prokaryotes) have high lipid contents. Under proper conditions, these photosynthetic microorganisms can produce lipids for biodiesel with yields per unit area 100 times or more than possible with any plant system. In addition, the non-lipid biomass can be converted to methane, hydrogen, or electricity. Photosynthetic microorganisms do not require arable land, an advantage because our arable land must be used to produce food. Algae or cyanobacteria may be the best option to produce bioenergy at rates high enough to replace a substantial fraction of our society's use of fossil fuels.
A new implementation of the Ziv-Lempel incremental parsing algorithm (1991)

Combining a note by J. Rissanen (1983) and an idea of enumerative coding, the authors obtain a new implementation of the Ziv-Lempel incremental parsing algorithm for coding and decoding discrete data sequences. The space and the time complexities are linear for both the encoder and the decoder. The authors describe the algorithm.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Analysis of Blockage Effects on Urban Cellular Networks (2014)

Large-scale blockages such as buildings affect the performance of urban cellular networks, especially at higher frequencies. Unfortunately, such blockage effects are either neglected or characterized by oversimplified models in the analysis of cellular networks. Leveraging concepts from random shape theory, this paper proposes a mathematical framework to model random blockages and analyze their impact on cellular network performance. Random buildings are modeled as a process of rectangles with random sizes and orientations whose centers form a Poisson point process on the plane. The distribution of the number of blockages in a link is proven to be a Poisson random variable with parameter dependent on the length of the link. Our analysis shows that the probability that a link is not intersected by any blockages decays exponentially with the link length. A path loss model that incorporates the blockage effects is also proposed, which matches experimental trends observed in prior work. The model is applied to analyze the performance of cellular networks in urban areas with the presence of buildings, in terms of connectivity, coverage probability, and average rate. Our results show that the base station density should scale superlinearly with the blockage density to maintain the network connectivity. Our analyses also show that while buildings may block the desired signal, they may still have a positive impact on the SIR coverage probability and achievable rate since they can block significantly more interference.
Perspectives and challenges in performance assessment of model predictive control (2016)

Abstract The longevity of each MPC application is strongly related to its performance maintenance. This work provides an overview of the methodologies available to fulfill this task, including a discussion about some special requirements of performance assessment methodologies for typical industrial MPC applications. The available methodologies were compared using these requirements. The best approaches were selected and compared to a new method proposed by the authors. These techniques have been applied in two case studies: the Shell benchmark process and the quadruple‐tank process. The results show that the control policy (setpoint, soft constraints, targets) followed in the MPC application should be the determining factor in selecting the methodology for performance assessment.