gebhart/patrepeval huggingface dataset:
Inhibition of Apoptosis of Activated Hepatic Stellate Cells by Tissue Inhibitor of Metalloproteinase-1 Is Mediated via Effects on Matrix Metalloproteinase Inhibition (2002)

The activated hepatic stellate cell (HSC) is central to liver fibrosis as the major source of collagens I and III and the tissue inhibitors of metalloproteinase-1 (TIMP-1). During spontaneous recovery from liver fibrosis, there is a decrease of TIMP expression, an increase in collagenase activity, and increased apoptosis of HSC, highlighting a potential role for TIMP-1 in HSC survival. In this report, we use tissue culture and in vivo models to demonstrate that TIMP-1 directly inhibits HSC apoptosis. TIMP-1 demonstrated a consistent, significant, and dose-dependent antiapoptotic effect for HSC activated in tissue culture and stimulated to undergo apoptosis by serum deprivation, cycloheximide exposure, and nerve growth factor stimulation. A nonfunctional mutated TIMP-1 (T2G mutant) in which all other domains are conserved did not inhibit apoptosis, indicating that inhibition of apoptosis was mediated through MMP inhibition. Synthetic MMP inhibitors also inhibited HSC apoptosis. Studies of experimental liver cirrhosis demonstrated that persistent expression of TIMP-1 mRNA determined by PCR correlated with persistence of activated HSC quantified by alpha smooth muscle actin staining, while in fibrosis, loss of activated HSC correlated with a reduction in TIMP-1 mRNA. We conclude that TIMP-1 inhibits apoptosis of activated HSC via MMP inhibition.
Free Leptin, Bound Leptin, and Soluble Leptin Receptor in Normal and Diabetic Pregnancies (1999)

We measured serum levels of free leptin, bound leptin, and soluble leptin receptor by specific RIA methods in 20 normal and 19 insulin-dependent diabetes mellitus subjects at 20 and 30 weeks gestation and postpartum, and analyzed the data using hierarchical statistical models. Total leptin levels rise from 20-30 weeks gestation (688 +/- 58 to 785 +/- 62 pmol/L, mean +/- SEM; P = 0.009). There is a significant postpartum fall to 445 +/- 47 pmol/L (P < 0.001). This rise is caused by the rise in the bound leptin levels, as there is no significant change in free leptin levels between 20 and 30 weeks (P = 0.17). There is a significant postpartum fall in free leptin levels (P < 0.001). Insulin requirements rise in the third trimester, but despite this there was no significant difference in free or bound leptin levels between the normal and diabetic subjects at any stage [free leptin, 223 +/- 35 and 266 +/- 24, 237 +/- 45 and 223 +/- 27, and 109 +/- 16 and 104 +/- 24 (P = 0.34); bound leptin, 410 +/- 73 and 428 +/- 54, 501 +/- 78 and 562 +/- 71, and 330 +/- 47 and 271 +/- 46 (P = 0.84); for normals and diabetics at 20 and 30 weeks gestation and postpartum, respectively]. Diabetic subjects, however, had significantly higher soluble leptin receptor levels at all stages (P << 0.001), which rose further in the third trimester from 3742 +/- 268 (mean +/- SEM) to 4134 +/- 239 pmol/L, whereas in the normal group there was a fall from 3149 +/- 169 to 2712 +/- 123 (P = 0.05). There is a linear relationship between the soluble leptin receptor levels and the body mass index in the diabetic group only. We conclude that there is no significant difference in free or bound leptin levels between the normal and insulin-dependent diabetic subjects either during pregnancy or postpartum, but female insulin-dependent diabetic subjects have significantly higher soluble leptin receptor levels. We speculate that high soluble leptin receptor levels might be implicated in the development of the leptin resistance in this group.
Evaluation of the Antioxidant Potential of Natural Products (1998)

Since reactive oxygen radicals play an important role in carcinogenesis and other human disease states, antioxidants present in consumable fruits, vegetables, and beverages have received considerable attention as cancer chemopreventive agents. Thus, in order to identify antioxidants in plant extracts, test materials were assessed for potential to scavenge stable 1,2-diphenyl-2-picrylhydrazyl (DPPH) free radicals, reduce TPA-induced free radical formation in cultured HL-60 human leukemia cells, and inhibit responses observed with a xanthine/xanthine oxidase assay system. Approximately 700 plant extracts were evaluated, and 28 were found to be active in the DPPH free radical scavenging assay. Based on secondary analyses performed to assess inhibition of 7,12-dimethylbenz(a)anthracene-induced preneoplastic lesion formation with a mouse mammary organ culture model, Chorizanthe diffusa Benth. (Polygonaceae), Mezoneuron cucullatum Roxb. (Leguminosae), Cerbera manghas L. (Apocynaceae) and Daphniphyllum calycinum Benth. (Daphniphyllaceae) were selected and subjected to bioassay-guided fractionation. 5,7,3',5'-Tetrahydroxy-8,4'-dimethoxyflavonol, 5,8,4'-trihydroxy-7,3'-dimethoxyflavonol, 5,3',4'-trihydroxy-7-methoxyflavonol, and 6,3',4'-trihydroxy-7-methoxyflavonol were identified as active principles from C. diffusa. Piceatannol, trans-resveratrol, apigenin and scirpusin A were found as the active principles of M. cucullatum, olivil, (-)-carinol, and (+)-cycloolivil were active principles from C. manghas, and 5,6,7,4'-tetrahydroxyflavone 3-O-rutinoside and kaempferol 3-O-neohesperidoside were active principles from D. calycinum. Of these substances, the hydroxystilbenes piceatannol and transresveratrol have thus far been shown to inhibit carcinogen-induced preneoplastic lesion formation in the mouse mammary gland organ culture model.
Comparison of acute lethal toxicity of commonly abused psychoactive substances (2004)

Despite residual uncertainties, the substantial difference in safety ratios suggests that abused substances can be rank-ordered on the basis of their potential acute lethality.
Multi-modal Attention Network Learning for Semantic Source Code Retrieval (2019)

Code retrieval techniques and tools have been playing a key role in facilitating software developers to retrieve existing code fragments from available open-source repositories given a user query (e.g., a short natural language text describing the functionality for retrieving a particular code snippet). Despite the existing efforts in improving the effectiveness of code retrieval, there are still two main issues hindering them from being used to accurately retrieve satisfiable code fragments from large-scale repositories when answering complicated queries. First, the existing approaches only consider shallow features of source code such as method names and code tokens, but ignoring structured features such as abstract syntax trees (ASTs) and control-flow graphs (CFGs) of source code, which contains rich and well-defined semantics of source code. Second, although the deep learning-based approach performs well on the representation of source code, it lacks the explainability, making it hard to interpret the retrieval results and almost impossible to understand which features of source code contribute more to the final results. To tackle the two aforementioned issues, this paper proposes MMAN, a novel Multi-Modal Attention Network for semantic source code retrieval. A comprehensive multi-modal representation is developed for representing unstructured and structured features of source code, with one LSTM for the sequential tokens of code, a Tree-LSTM for the AST of code and a GGNN (Gated Graph Neural Network) for the CFG of code. Furthermore, a multi-modal attention fusion layer is applied to assign weights to different parts of each modality of source code and then integrate them into a single hybrid representation. Comprehensive experiments and analysis on a large-scale real-world dataset show that our proposed model can accurately retrieve code snippets and outperforms the state-of-the-art methods.
Penalized logistic regression for detecting gene interactions (2007)

We propose using a variant of logistic regression (LR) with (L)_(2)-regularization to fit gene-gene and gene-environment interaction models. Studies have shown that many common diseases are influenced by interaction of certain genes. LR models with quadratic penalization not only correctly characterizes the influential genes along with their interaction structures but also yields additional benefits in handling high-dimensional, discrete factors with a binary response. We illustrate the advantages of using an (L)_(2)-regularization scheme and compare its performance with that of "multifactor dimensionality reduction" and "FlexTree," 2 recent tools for identifying gene-gene interactions. Through simulated and real data sets, we demonstrate that our method outperforms other methods in the identification of the interaction structures as well as prediction accuracy. In addition, we validate the significance of the factors selected through bootstrap analyses.
Central Nervous System Toxicity after Liver Transplantation (1987)

We describe severe central nervous system (CNS) toxicity, manifested by confusion, cortical blindness, quadriplegia, seizures, and coma, associated with cyclosporine treatment in three patients undergoing liver transplantation. CT and magnetic resonance studies disclosed a severe, diffuse disorder of the white matter. All side effects and radiographic findings were reversed with discontinuation or a reduction in the dose of cyclosporine. We also observed an inverse association between CNS side effects and total serum cholesterol levels after transplantation. A retrospective analysis of 54 liver transplantations performed in 48 patients revealed that 13 patients had symptoms of CNS toxicity associated with the use of cyclosporine. These patients' total serum cholesterol levels in the first week after transplantation were reduced as compared with those in patients without symptoms (mean +/- SE, 94 +/- 4 mg per deciliter vs. 132 +/- 6, or 2.44 +/- 0.10 mmol per liter vs. 3.43 +/- 0.16). We conclude that cyclosporine therapy for immunosuppression in liver transplantation may cause a syndrome of encephalopathy, seizures, and white-matter changes and that this is most likely to occur in patients with low total serum cholesterol levels after transplantation.
How to handle global transactions in heterogeneous database systems (2003)

One of the most important problems in the field of integrated heterogeneous database systems is transaction management. It is not sufficient to integrate only data models and query languages. In order to provide equivalent access to integrated heterogeneous databases as to homogeneous databases, a global transaction management is required. The authors discuss several aspects of transaction management for heterogeneous database systems. Even though different existing database systems are involved in the execution of most transactions, global serializability and recoverability is required. The authors propose a three-level transaction model. At the top- and middle-level, the semantics of operations are used in order to achieve a high degree of concurrency. For bottom-level transactions, their model allows the use of transaction managers of existing systems without changes. If no autonomous local transactions are allowed, the model provides global transactions with full serializability and recoverability.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Isolation of Primary and Immortalized CD34<sup>−</sup>Hematopoietic and Mesenchymal Stem Cells from Various Sources (2000)

Based on historical radiation experiments in rodents, the hematopoietic stem cell was defined by its biological properties and later by the expression of certain surface antigens (e.g., CD34), as well as the absence of lineage-specific markers (e.g., DR). Quite recently it was shown that hematopoietic reconstitution can also be achieved by CD34- stem cells, which can be isolated from the bone marrow, peripheral blood and cord blood cells. CD34-stem cells are considered to be predominately part of the quiescent stem cell pool of hematopoietic and mesenchymal stem cells. Due to novel techniques, CD34-stem cells can be expanded on the level of a true stem cell but also directed towards their differentiation into specified tissues or organ systems. This requires the establishment of primary fibroblast-like CD34- stem cells in vitro and their possible reversible and transient immortalization with optimized vector systems.
Systematic detection of putative tumor suppressor genes through the combined use of exome and transcriptome sequencing (2010)

Our results demonstrate that the combined application of high throughput sequencing to exome and allele-specific transcriptome analysis can reveal genes with known tumor suppressor characteristics, and a shortlist of novel candidates for the study of tumor suppressor activities.
Changes in Type II Kerogen Density as a Function of Maturity:  Evidence from the Kimmeridge Clay Formation (2005)

Kerogens were purified from 26 samples of the Kimmeridge Clay Formation over the full range of maturities pertinent to petroleum generation. Most samples comprised >90% amorphous organic matter (AOM). Prior to and during the early phase of petroleum generation, kerogen densities range between 1.18 and 1.25 g cm-3. During peak and late stage petroleum generation, densities increase to ∼1.35 g cm-3 as hydrogen indices decrease from ∼350 to 50 mg HC/g C. The data are qualitatively consistent with the loss of alkyl carbon from kerogen to petroleum and the increased aromatization of remaining carbon. The density increase observed for AOM contrasts with the data for vitrinite, which exhibits a decrease in density at maturity levels relevant to petroleum generation. The contrasting behavior of AOM and vitrinite is thought to reflect the differing structural composition of the two kerogen types, most obviously the greater initial aromaticity of vitrinite.
Agrin-Induced Acetylcholine Receptor Clustering Is Mediated by the Small Guanosine Triphosphatases Rac and Cdc42 (2000)

During neuromuscular junction formation, agrin secreted from motor neurons causes muscle cell surface acetylcholine receptors (AChRs) to cluster at synaptic sites by mechanisms that are insufficiently understood. The Rho family of small guanosine triphosphatases (GTPases), including Rac and Cdc42, can mediate focal reorganization of the cell periphery in response to extracellular signals. Here, we investigated the role of Rac and Cdc42 in coupling agrin signaling to AChR clustering. We found that agrin causes marked muscle-specific activation of Rac and Cdc42 in differentiated myotubes, as detected by biochemical measurements. Moreover, this activation is crucial for AChR clustering, since the expression of dominant interfering mutants of either Rac or Cdc42 in myotubes blocks agrin-induced AChR clustering. In contrast, constitutively active Rac and Cdc42 mutants cause AChR to aggregate in the absence of agrin. By indicating that agrin-dependent activation of Rac and Cdc42 constitutes a critical step in the signaling pathway leading to AChR clustering, these findings suggest a novel role for these Rho-GTPases: the coupling of neuronal signaling to a key step in neuromuscular synaptogenesis.
Antimicrobial, Antioxidant, and Anti-Inflammatory Activities of Essential Oils from Five Selected Herbs (2011)

Eucalyptus bridgesiana, Cymbopogon martinii, Thymus vulgaris, Lindernia anagallis, and Pelargonium fragrans are five species of herbs used in Asia. Their essential oils were analyzed by GC-MS, and a total of 36 components were detected. The results of our study indicated that, except for the essential oil of P. fragrans, all of the essential oils demonstrated obvious antimicrobial activity against a broad range of microorganisms. The C. martinii essential oil, which is rich in geraniol, was the most effective antimicrobial additive. All of the essential oils demonstrated antioxidant activities on 2,2-diphenyl-1-picrylhydrazyl radical scavenging assay, β-carotene/linoleic acid assay, and nitric oxide radical scavenging assay. Furthermore, the T. vulgaris essential oil, which possesses plentiful thymol, exhibited the highest antioxidant activity. For P. acnes-induced secretion of pro-inflammatory cytokines, the essential oils of P. aeruginosa, C. martinii, and T. vulgaris reduced the TNF-α, IL-1β, and IL-8 secretion levels of THP-1 cells.
The Long Signal Peptide Isoform and Its Alternative Processing Direct the Intracellular Trafficking of Interleukin-15 (2000)

Two isoforms of interleukin (IL)-15 exist: one with a short and another with a long signal peptide (LSP). Experiments using combinations of the LSP and mature proteins IL-2, IL-15, and green fluorescent protein revealed complex pathways of intracellular trafficking. In one pathway, the LSP was unprocessed, and IL-15 was not glycosylated, remained in the cytoplasm, and was degraded. The second trafficking pathway involved endoplasmic reticulum entry, N-linked glycosylation, and alternative partial LSP processing. The third pathway involved endoplasmic reticulum entry, followed by glycosylation, complete processing, and ultimately secretion. The complex intracellular trafficking patterns of LSP-IL-15 with its impediments to secretion as well as impediments to translation may be required due to the potency of IL-15 as an inflammatory cytokine. In terms of a more positive role, we propose that intracellular infection may relieve the burdens on translation and intracellular trafficking to yield effective IL-15 expression.
Glatiramer acetate in the treatment of multiple sclerosis (2001)

This review article summarises the initial preclinical studies as well as the different stages of clinical trials in multiple sclerosis (MS) with Copolymer 1 (Cop 1), recently denoted glatiramer acetate. Experimental studies on autoimmune encephalomyelitis (EAE), the animal model of MS, as well as studies on the mechanism of action in both animals and humans are discussed. The review describes the early clinical trials which were followed by Phase II and III trials, culminating in FDA approval in 1996 for the treatment of relapsing-remitting MS. The accumulated experience with glatiramer acetate indicates that its efficacy is apparently increased as a function of usage time while the favourable side effect profile is sustained. MRI studies revealed that treatment with glatiramer acetate resulted in a significant reduction of gadolinium (Gd)-enhancing lesions. Ongoing clinical trials which might extend its usage or change its mode of delivery are also described. Glatiramer acetate appears to be a treatment of choice for the relapsing-remitting type of MS.
Microfluidic platform for real-time signaling analysis of multiple single T cells in parallel (2008)

Deciphering the signaling pathways that govern stimulation of naïve CD4+ T helper cells by antigen-presenting cells via formation of the immunological synapse is key to a fundamental understanding of the progression of successful adaptive immune response. The study of T cell-APC interactions in vitro is challenging, however, due to the difficulty of tracking individual, non-adherent cell pairs over time. Studying single cell dynamics over time reveals rare, but critical, signaling events that might be averaged out in bulk experiments, but these less common events are undoubtedly important for an integrated understanding of a cellular response to its microenvironment. We describe a novel application of microfluidic technology that overcomes many limitations of conventional cell culture and enables the study of hundreds of passively sequestered hematopoietic cells for extended periods of time. This microfluidic cell trap device consists of 440 18 micromx18 micromx10 microm PDMS, bucket-like structures opposing the direction of flow which serve as corrals for cells as they pass through the cell trap region. Cell viability analysis revealed that more than 70% of naïve CD4+ T cells (TN), held in place using only hydrodynamic forces, subsequently remain viable for 24 hours. Cytosolic calcium transients were successfully induced in TN cells following introduction of chemical, antibody, or cellular forms of stimulation. Statistical analysis of TN cells from a single stimulation experiment reveals the power of this platform to distinguish different calcium response patterns, an ability that might be utilized to characterize T cell signaling states in a given population. Finally, we investigate in real time contact- and non-contact-based interactions between primary T cells and dendritic cells, two main participants in the formation of the immunological synapse. Utilizing the microfluidic traps in a daisy-chain configuration allowed us to observe calcium transients in TN cells exposed only to media conditioned by secretions of lipopolysaccharide-matured dendritic cells, an event which is easily missed in conventional cell culture where large media-to-cell ratios dilute cellular products. Further investigation into this intercellular signaling event indicated that LPS-matured dendritic cells, in the absence of antigenic stimulation, secrete chemical signals that induce calcium transients in T(N) cells. While the stimulating factor(s) produced by the mature dendritic cells remains to be identified, this report illustrates the utility of these microfluidic cell traps for analyzing arrays of individual suspension cells over time and probing both contact-based and intercellular signaling events between one or more cell populations.
Muscle twitch responses for shaping the multi-pad electrode for functional electrical stimulation (2010)

In this paper we present a method for optimization of multi-pad electrode spatial selectivity during transcutaneous Functional Electrical Stimulation (FES) of hand. The presented method is based on measurement of individual muscle twitch responses during low frequency electrical stimulation via pads within multi-pad electrode. Twitch responses are recorded by Micro-Electro-Mechanical Systems (MEMS) accelerometers. The aim of this methodology is to substitute bulky sensors, torque sensors and goniometers, in multi-pad electrode optimization algorithm with smaller and lighter sensors; therefore making multi-pad stimulation suitable for daily use. Additionally we present method for minimizing number of MEMS accelerometers, which relies on characteristic waveforms of joint acceleration during wrist or fingers flexion/extension. These signals can be used to train Artificial Neural Network (ANN) to distinguish between different waveform classes and define correlation of each pad and activated muscle beneath. Results presented in this paper show high agreement of goniometers based classification and accelerometers based classification. As for classification with minimized number of sensors (one accelerometer) our ANN backed algorithm achieved high degree of accurate classification in intra-subject testing, but lower performance in inter-subject testing.
Improving Odometric Accuracy for an Autonomous Electric Cart (2018)

In this paper, a study of the odometric system for the autonomous cart Verdino, which is an electric vehicle based on a golf cart, is presented. A mathematical model of the odometric system is derived from cart movement equations, and is used to compute the vehicle position and orientation. The inputs of the system are the odometry encoders, and the model uses the wheels diameter and distance between wheels as parameters. With this model, a least square minimization is made in order to get the nominal best parameters. This model is updated, including a real time wheel diameter measurement improving the accuracy of the results. A neural network model is used in order to learn the odometric model from data. Tests are made using this neural network in several configurations and the results are compared to the mathematical model, showing that the neural network can outperform the first proposed model.