gebhart/patrepeval huggingface dataset:
MicroRNA signatures in tissues and plasma predict development and prognosis of computed tomography detected lung cancer (2011)

The efficacy of computed tomography (CT) screening for early lung cancer detection in heavy smokers is currently being tested by a number of randomized trials. Critical issues remain the frequency of unnecessary treatments and impact on mortality, indicating the need for biomarkers of aggressive disease. We explored microRNA (miRNA) expression profiles of lung tumors, normal lung tissues and plasma samples from cases with variable prognosis identified in a completed spiral-CT screening trial with extensive follow-up. miRNA expression patterns significantly distinguished: (i) tumors from normal lung tissues, (ii) tumor histology and growth rate, (iii) clinical outcome, and (iv) year of lung cancer CT detection. Interestingly, miRNA profiles in normal lung tissues also displayed remarkable associations with clinical features, suggesting the influence of a permissive microenvironment for tumor development. miRNA expression analyses in plasma samples collected 1-2 y before the onset of disease, at the time of CT detection and in disease-free smokers enrolled in the screening trial, resulted in the generation of miRNA signatures with strong predictive, diagnostic, and prognostic potential (area under the ROC curve ≥ 0.85). These signatures were validated in an independent cohort from a second randomized spiral-CT trial. These results indicate a role for miRNAs in lung tissues and plasma as molecular predictors of lung cancer development and aggressiveness and have theoretical and clinical implication for lung cancer management.
Enhancement of Cytotoxic Activity of Natural Killer Cells by Interleukin 2, and Antagonism between Interleukin 2 and Adenosine Cyclic Monophosphate (1985)

Two cytokines, interferon (IFN) and interleukin 2 (IL-2), activate murine natural killer (NK) cells in vitro. Together both factors synergize considerably. Antibody against IFN eliminates the response of NK cells to IFN as well as to IL-2, whereas antibody against IL-2 blocks the effect of IL-2 but not of IFN. These findings as well as previous observations imply that both factors act on the same cell but have different roles. We suggest that IFN induces NK cell activation and IL-2 enhances this effect. Further studies revealed that besides inducing cytotoxicity in NK cells IFN induces the production of prostaglandin E (PGE) which inhibits NK cell activation. We propose therefore that IFN has a dual effect on NK cells: it induces NK cells to become cytotoxic and initiates a negative feedback by increasing the production of PGE. IL-2, which synergizes with IFN in the activation of NK cells, ceases to do so when the negative feedback (PGE-mediated) is blocked with indomethacin. We infer that IL-2 enhances NK cell activity by interfering with the negative feedback rather than by aiding NK cell activation.
Bootstrapping non-parallel voice conversion from speaker-adaptive text-to-speech (2019)

Voice conversion (VC) and text-to-speech (TTS) are two tasks that share a similar objective, generating speech with a target voice. However, they are usually developed independently under vastly different frameworks. In this paper, we propose a methodology to bootstrap a VC system from a pretrained speaker-adaptive TTS model and unify the techniques as well as the interpretations of these two tasks. Moreover by offloading the heavy data demand to the training stage of the TTS model, our VC system can be built using a small amount of target speaker speech data. It also opens up the possibility of using speech in a foreign unseen language to build the system. Our subjective evaluations show that the proposed framework is able to not only achieve competitive performance in the standard intra-language scenario but also adapt and convert using speech utterances in an unseen language.
Fructan biosynthesis in transgenic plants (2002)

Data from plants transformed to accumulate fructan are assessed in the context of natural concentrations of reserve carbohydrates and natural fluxes of carbon in primary metabolism: Transgenic fructan accumulation is universally reported as an instantaneous endpoint concentration. In exceptional cases, concentrations of 60-160 mg g(-1) fresh mass were reported and compare favourably with naturally occurring maximal starch and fructan content in leaves and storage organs. Generally, values were less than 20 mg g(-1) for plants transformed with bacterial genes and <9 mg g(-1) for plant-plant transformants. Superficially, the results indicate a marked modification of carbon partitioning. However, transgenic fructan accumulation was generally constitutive and involved accumulation over time-scales of weeks or months. When calculated as a function of accumulation period, fluxes into the transgenic product were low, in the range 0.00002-0.03 nkat g(-1). By comparison with an estimated minimum daily carbohydrate flux in leaves for a natural fructan-accumulating plant in field conditions (37 nkat g(-1)), transgenic fructan accumulation was only 0.00005-0.08% of primary carbohydrate flux and does not indicate radical modification of carbon partitioning, but rather, a quantitatively minor leakage into transgenic fructan. Possible mechanisms for this low fructan accumulation in the transformants are considered and include: (i) rare codon usage in bacterial genes compared with eukaryotes, (ii) low transgene mRNA concentrations caused by low expression and/or high turnover, (iii) resultant low expression of enzyme protein, (iv) resultant low total enzyme activity, (v) inappropriate kinetic properties of the gene products with respect to substrate concentrations in the host, (vi) in situ product hydrolysis, and (vii) levan toxicity. Transformants expressing bacterial fructan synthesis exhibited a number of aberrant phenotypes such as stunting, leaf bleaching, necrosis, reduced tuber number and mass, tuber cortex discoloration, reduction in starch accumulation, and chloroplast agglutination. In severe cases of developmental aberration, potato tubers were replaced by florets. Possible mechanisms to explain these aberrations are discussed. In most instances, the attempted subcellular targeting of the transgene product was not demonstrated. Where localization was attempted, the transgene product generally mis-localized, for example, to the cell perimeter or to the endomembrane system, instead of the intended target, the vacuole. Fructosyltransferases exhibited different product specificities in planta than in vitro, expression in planta generally favouring the formation of larger fructan oligomers and polymers. This implies a direct influence of the intracellular environment on the capacity for polymerization of fructosyltransferases and may have implications for the mechanism of natural fructan polymerization in vivo.
Exploring NVIDIA-CUDA for video coding (2010)

Today, world is rapidly turning to high definition multimedia. From engineering and programming point of view, this usually means more computation is needed and more memory space is required to achieve these higher qualities. In this paper we explore the use of parallelization opportunities in graphics processors to accelerate video encoding. We evaluate the NVIDIA CUDA[1] toolkit and evaluate the performance of motion estimation in video encoding. The main goal of this paper is to evaluate the capabilities of NVIDIA/CUDA and develop a process for implementing video/multimedia applications. We have discovered that the difference in performance when CUDA is not used properly can be over 100x. We show how we were able to use CUDA capabilities to reduce the motion estimation time from 7000 milli seconds to 70 milli seconds.
A methodology for intelligent sensor validation and fusion used in tracking and avoidance of objects for automated vehicles (2005)

For longitudinal control the automated vehicles in intelligent vehicle highway system (IVHS) require sensors to estimate the relative distance and velocity between vehicles. High data fidelity of these sensors is required to maintain the reliability and safety of the IVHS. In this paper, the authors develop a methodology for validation and fusion of sensory readings obtained from multiple sensors used for tracking automated vehicles and for avoiding objects in its path. The authors introduce tracking models for the various operating states of the automated vehicle, namely vehicle following, maneuvering, i.e. split, merge, lane change, emergencies, and for the lead vehicle in a platoon. The Kalman filtering approach is proposed for the formation of real time validation gates. This along with the algorithmic sensor validation filter is used for sensory data validation. The validated data are then fused by using a Bayesian method called the probabilistic data association filter. The procedure is demonstrated by two examples using simulated data, data obtained from a platooning test set-up.
Intracranial Oligodendrogliomas: Image Findings in 26 Cases (1993)

We collected 26 cases of oligodendroglioma proved pathologically from 1979 to 1991, including 16 males and 10 females. The age ranged from 6 to 65 years (average 33). All of them occurred in the supratentorial compartment, and most cases involved the frontal lobe (77%). Radiologic studies included skull x-ray in 14 cases, angiography in 8 cases and computed tomography in all cases. Calcification (43%), erosion of the sella (6%) or enlargement of the sella (6%) were noted in skull x-ray. Angiogram showed mass effect with vascular displacement or stretch (100%), or tumor vessels and stain (38%). CT findings included: (1) mass with irregular margin (100%); (2) hypodense (50%); isodense (19%); hyperdense (4%); or mixed tumor density (27%); (3) calcification (81%); (4) tumor enhancement (65%); (5) cystic component (58%); (6) perifocal edema (23%); (7) hydrocephalus (31%); and (8) tumor hemorrhage (2%).
[Serum VEGF (vascular endothelial growth factor) concentration in patients with endometriosis]. (2000)

The theory of Sampson that endometrial cells and fragments desquamated during the menstrual period are transported through fallopian tubes into the peritoneal cavity where they implant, proliferate and develop into endometriotic lesions is generally accepted. Accumulating data suggest that deficient immunity against retrograde endometrium during menstruation may be involved in the pathophysiology of endometriosis. Recent studies in women with endometriosis demonstrated functional changes in several immunologic components in the peritoneal fluid as well as in sera of those patients. Among others it was shown that a wild pattern of cytokines take part in events occurring during endometrial cells implantation, proliferation and forming of endometriotic lesions. One of them VEGF seems to play a very important role in neovascularisation and implantation of ectopic endometrial lesions. In present study we evaluated the concentrations of VEGF in serum of patients with endometriosis and showed negative correlation between AFS score and VEGF concentration in peritoneal endometriosis. Above results do not confirm former observations indicating the role of VEGF in endometriosis pathogenesis.
Manipulating Fatty Acid Biosynthesis in Microalgae for Biofuel through Protein-Protein Interactions (2012)

Microalgae are a promising feedstock for renewable fuels, and algal metabolic engineering can lead to crop improvement, thus accelerating the development of commercially viable biodiesel production from algae biomass. We demonstrate that protein-protein interactions between the fatty acid acyl carrier protein (ACP) and thioesterase (TE) govern fatty acid hydrolysis within the algal chloroplast. Using green microalga Chlamydomonas reinhardtii (Cr) as a model, a structural simulation of docking CrACP to CrTE identifies a protein-protein recognition surface between the two domains. A virtual screen reveals plant TEs with similar in silico binding to CrACP. Employing an activity-based crosslinking probe designed to selectively trap transient protein-protein interactions between the TE and ACP, we demonstrate in vitro that CrTE must functionally interact with CrACP to release fatty acids, while TEs of vascular plants show no mechanistic crosslinking to CrACP. This is recapitulated in vivo, where overproduction of the endogenous CrTE increased levels of short-chain fatty acids and engineering plant TEs into the C. reinhardtii chloroplast did not alter the fatty acid profile. These findings highlight the critical role of protein-protein interactions in manipulating fatty acid biosynthesis for algae biofuel engineering as illuminated by activity-based probes.
N-Nitrosodimethylamine in Nonfat Dry Milk (1994)

In 1980, using a detection limit of 0.3 ppb, N-nitrosodimethylamine (NDMA) was found in 51 of 71 commercial nonfat dry milk samples. The range for the positive samples was from 0.3 to 6.5 ppb with a mean for all samples of 0.72 ppb. In 1992, the mean MDMA value for 56 samples of instantized nonfat dry milk samples was 1.05 ppb, the range was 0.1 to 5.3 ppb. A comparison of the NDMA content of regular nonfat dry milk powder and instantized powder showed no additional NDMA formation from instantizing. Several researchers have suggested that NDMA in nonfat dry milk forms during the direct-fire drying process while others have contended that the source was fluid milk. Eight tracking experiments in commercial processing plants detected no NDMA until the drying process began. Furthermore, most of the 62 samples of nonfat dry milk prepared by direct-fire drying contained NDMA while eight of nine samples dried by indirect-fire processes did not contain NDMA. Our results indicate that the main source of NDMA in nonfat dry milk is the direct-fire process used in its manufacture.
Triterpenoid Biosynthesis and Engineering in Plants (2011)

Triterpenoid saponins are a diverse group of natural products in plants and are considered defensive compounds against pathogenic microbes and herbivores. Because of their various beneficial properties for humans, saponins are used in wide-ranging applications in addition to medicinally. Saponin biosynthesis involves three key enzymes: oxidosqualene cyclases, which construct the basic triterpenoid skeletons; cytochrome P450 monooxygenases, which mediate oxidations; and uridine diphosphate-dependent glycosyltransferases, which catalyze glycosylations. The discovery of genes committed to saponin biosynthesis is important for the stable supply and biotechnological application of these compounds. Here, we review the identified genes involved in triterpenoid biosynthesis, summarize the recent advances in the biotechnological production of useful plant terpenoids, and discuss the bioengineering of plant triterpenoids.
Market Microstructure: A Practitioner's Guide (2002)

Knowledge of market microstructure—how investors' latent or hidden demands are ultimately translated into prices and volumes—has grown explosively in recent years. This literature is of special interest to practitioners because of the rapid transformation of the market environment by technology, regulation, and globalization. Yet, for the most part, the major theoretical insights and empirical results from academic research have not been readily accessible to practitioners. I discuss the practical implications of the literature, with a focus on price formation, market structure, transparency, and applications to other areas of finance.
Codon bias and gene expression (1991)

The frequencies with which individual synonymous codons are used to code their cognate amino acids is quite variable from genome to genome and within genomes, from gene to gene. One particularly well documented codon bias is that associated with highly expressed genes in bacteria as well as in yeast; this is the so-called major codon bias. Here, it is suggested that the major codon bias is not an arrangement for regulating individual gene expression. Instead, the data suggest that this codon bias, which is correlated with a corresponding bias of tRNA abundance, is a global arrangement for optimizing the growth efficiency of cells. On the practical side, it is suggested that heterologous gene expression is not as sensitive to codon bias as previously thought, but that it is quite sensitive to other characteristics of the heterologous gene.
Characterization and Analysis of the Proximal Janus Kinase 3 Promoter (2003)

Janus kinase 3 (Jak3) is a nonreceptor tyrosine kinase essential for signaling via cytokine receptors that comprise the common gamma-chain (gammac), i.e., the receptors for IL-2, IL-4, IL-7, IL-9, IL-15, and IL-21. Jak3 is preferentially expressed in hemopoietic cells and is up-regulated upon cell differentiation and activation. Despite the importance of Jak3 in lymphoid development and immune function, the mechanisms that govern its expression have not been defined. To gain insight into this issue, we set out to characterize the Jak3 promoter. The 5'-untranslated region of the Jak3 gene is interrupted by a 3515-bp intron. Upstream of this intron and the transcription initiation site, we identified an approximately 1-kb segment that exhibited lymphoid-specific promoter activity and was responsive to TCR signals. Truncation of this fragment revealed that core promoter activity resided in a 267-bp fragment that contains putative Sp-1, AP-1, Ets, Stat, and other binding sites. Mutation of the AP-1 sites significantly diminished, whereas mutation of the Ets sites abolished, the inducibility of the promoter construct. Chromatin immunoprecipitation assays showed that histone acetylation correlates with mRNA expression and that Ets-1/2 binds this region. Thus, transcription factors that bind these sites, especially Ets family members, are likely to be important regulators of Jak3 expression.
Reprogramming of human postmitotic neutrophils into macrophages by growth factors (2004)

It is generally recognized that postmitotic neutrophils give rise to polymorphonuclear neutrophils alone. We obtained evidence for a lineage switch of human postmitotic neutrophils into macrophages in culture. When the CD15+CD14- cell population, which predominantly consists of band neutrophils, was cultured with granulocyte macrophage-colony-stimulating factor, tumor necrosis factor-alpha, interferon-gamma, and interleukin-4, and subsequently with macrophage colony-stimulating factor alone, the resultant cells had morphologic, cytochemical, and phenotypic features of macrophages. In contrast to the starting population, they were negative for myeloperoxidase, specific esterase, and lactoferrin, and they up-regulated nonspecific esterase activity and the expression of macrophage colony-stimulating factor receptor, mannose receptor, and HLA-DR. CD15+CD14- cells proceeded to macrophages through the CD15-CD14- cell population. Microarray analysis of gene expression also disclosed the lineage conversion from neutrophils to macrophages. Macrophages derived from CD15+CD14- neutrophils had phagocytic function. Data obtained using 3 different techniques, including Ki-67 staining, bromodeoxyuridine incorporation, and cytoplasmic dye labeling, together with the yield of cells, indicated that the generation of macrophages from CD15+CD14- neutrophils did not result from a contamination of progenitors for macrophages. Our data show that in response to cytokines, postmitotic neutrophils can become macrophages. This may represent another differentiation pathway toward macrophages in human postnatal hematopoiesis.
TRIM32 Protein Modulates Type I Interferon Induction and Cellular Antiviral Response by Targeting MITA/STING Protein for K63-linked Ubiquitination (2012)

Viral infection activates several transcription factors including NF-κB and IRF3, which collaborate to induce type I interferons (IFNs) and innate antiviral response. MITA (also called STING) is a critical adaptor protein that links virus-sensing receptors to IRF3 activation upon infection by both RNA and DNA pathogens. Here we show that the E3 ubiquitin ligase tripartite motif protein 32 (TRIM32) ubiquitinated MITA and dramatically enhanced MITA-mediated induction of IFN-β. Overexpression of TRIM32 potentiated virus-triggered IFNB1 expression and cellular antiviral response. Consistently, knockdown of TRIM32 had opposite effects. TRIM32 interacted with MITA, and was located at the mitochondria and endoplasmic reticulum. TRIM32 targeted MITA for K63-linked ubiquitination at K20/150/224/236 through its E3 ubiquitin ligase activity, which promoted the interaction of MITA with TBK1. These findings suggest that TRIM32 is an important regulatory protein for innate immunity against both RNA and DNA viruses by targeting MITA for K63-linked ubiquitination and downstream activation.
Artificial Antigen-Presenting Cells Transduced with Telomerase Efficiently Expand Epitope-Specific, Human Leukocyte Antigen–Restricted Cytotoxic T Cells (2005)

Human telomerase reverse transcriptase (hTERT) is overexpressed in most human tumors, making it a potential target for cancer immunotherapy. hTERT-derived CTL epitopes have been identified previously, including p865 (RLVDDFLLV) and p540 (ILAKFLHWL), which are restricted by the human leukocyte antigen (HLA) class I A*0201 allele. However, it remains a major challenge to efficiently and consistently expand hTERT-specific CTLs from donor peripheral blood T lymphocytes. To bypass the need for generating conventional antigen-presenting cells (APC) on an autologous basis, we investigated the potential ability of fibroblast-derived artificial APCs (AAPC) to activate and expand HLA-A*0201-restricted CTLs. We show here that AAPCs stably expressing HLA-A*0201, human beta(2)-microglobulin, B7.1, intercellular adhesion molecule-1, and LFA-3, together with either p540 and p865 minigenes or the full-length hTERT, effectively stimulate tumoricidal, hTERT-specific CTLs. hTERT-expressing AAPCs stimulated both p540 and p865 CTLs as shown by peptide-specific cytolysis and tetramer staining, indicating that hTERT is processed by the AAPCs and that the two peptides are presented as codominant epitopes. The level of cytotoxic activity against a panel of tumors comprising hematologic and epithelial malignancies varied, correlating overall with the level of HLA-A2 and hTERT expression by the target cell. Starting from 100 mL blood, approximately 100 million hTERT-specific CTLs could be generated over the course of five sequential stimulations, representing an expansion of approximately 1 x 10(5). Our data show that AAPCs process hTERT antigen and efficiently stimulate hTERT-specific CTLs from human peripheral blood T lymphocytes and suggest that sufficient expansion could be achieved to be clinically useful for adoptive cell therapy.
Effectiveness of distance-decreasing attacks against impulse radio ranging (2010)

We expose the vulnerability of an emerging wireless ranging technology, impulse radio ultra-wide band (IR-UWB), to distance-decreasing attacks on the physical communication layer (PHY). These attacks violate the security of secure ranging protocols that allow two wireless devices to securely estimate the distance between them, with the guarantee that the estimate is an upper-bound on the actual distance. Such protocols serve as crucial building blocks in security-sensitive applications such as location tracking, physical access control, or localization.