gebhart/patrepeval huggingface dataset:
Runge-Kutta type methods for differential-algebraic equations in mechanics (2011)

Differential-algebraic equations (DAEs) consist of mixed systems of ordinary differential equations (ODEs) coupled with linear or nonlinear equations. Such systems may be viewed as ODEs with integral curves lying in a manifold. DAEs appear frequently in applications such as classical mechanics and electrical circuits. This thesis concentrates on systems of index 2, originally index 3, and mixed index 2 and 3. Fast and efficient numerical solvers for DAEs are highly desirable for finding solutions. We focus primarily on the class of Gauss-Lobatto SPARK methods. However, we also introduce an extension to methods proposed by Murua for solving index 2 systems to systems of mixed index 2 and 3. An analysis of these methods is also presented in this thesis. We examine the existence and uniqueness of the proposed numerical solutions, the influence of perturbations, and the local error and global convergence of the methods. When applied to index 2 DAEs, SPARKmethods are shown to be equivalent to a class of collocation type methods. When applied to originally index 3 and mixed index 2 and 3 DAEs, they are equivalent to a class of discontinuous collocation methods. Using these equivalences, (s, s)–Gauss-Lobatto SPARK methods can be shown to be superconvergent of order 2s. Symplectic SPARK methods applied to Hamiltonian systems with holonomic constraints preserve well the total energy of the system. This follows from a backward error analysis approach. SPARK methods and our proposed EMPRK methods are shown to be Lagrange-d’Alembert integrators. This thesis also presents some numerical results for Gauss-Lobatto SPARK and EMPRK methods. A few problems from mechanics are considered. 2 Abstract Approved: Thesis Supervisor Title and Department
Sensor Node Localization with Uncontrolled Events (2012)

Event-driven localization has been proposed as a low-cost solution for node positioning in wireless sensor networks. In order to eliminate the costly requirement for accurate event control in existing methods, we present a practical design using uncontrolled events. The main idea is to estimate both event generation parameters and the location of sensor nodes simultaneously, by processing node sequences that can be easily obtained from event detections. Besides the basic design, we proposed two enhancements to further extract information embedded in node orderings for two scenarios: (i) node density is high; and (ii) abundant events are available. To demonstrate the generality of our design, both straight-line scan and circular wave propagation events are addressed in the article, and we evaluated the design with extensive simulation as well as a testbed implementation with 41 MICAz motes. Results show that with only randomly generated events, our design can effectively localize nodes with great flexibility while adding little extra cost at the resource constrained sensor node side. In addition, localization via uncontrolled events provides a potential option of achieving node positioning through long-term ambient events.
Gene Profiling Mechanisms of Cell Density-Dependent Growth in Myeloid and Lymphoid Leukemia Cell Lines. (2009)

Abstract Abstract 4420 Normal hematopoietic stem cells have been shown to be maintained through interaction with their environmental niches, such as osteoblastic and endothelial ones. The growth of leukemic cells has been shown to be stimulated by environmental niches (paracrine growth) or by cell-to-cell interaction or excreted factors of leukemic cells (autocrine growth). The growth of myeloid (MO7-E and HL-60) and lymphoid (Raji, U-266, Daudi and RPMI-1788) leukemia cell lines cultured at various cell densities in serum free medium (Sigma H 4281) with 1% BSA was evaluated. The cells cultured at higher cell densities (cultured cell densities ≥a 105/ml) showed logarithmic linear increases in cell number, whereas those at lower cell densities (cultured cell densities □… 104/ml) ceased increasing cell number. Supernatants of myeloid leukemia cells stimulated the growth of autologous clonogenic cells, but not those of lymphoid leukemia cells. Neutralizing antibodies (Abs) against various hematopoietic growth factors failed to inhibit cell growth except for anti-VEGF, which significantly decreased HL-60 leukemia cell growth. To clarify the nature of the cultured cell density on the growth of leukemia cells, leukemia cells were cultured at higher cell density (group H, cultured cell densities of 106/ml) or at lower cell density (group L, cultured cell densities 104/ml). After culture of 3-, 6-, 10-, and 24-hr, cells were serially harvested and total cellular RNA was extracted. Gene transcript levels were determined by using Real-Time PCR. Gene transcripts examined in the present study were as follows: polycomb (Bmi1), Hox (HOXA7, HOXA9, HOXB2, HOXB4, Meis 1), Caudal-related (CDX2, 4), Mef2c, c-Myb, Wnt (Wnt 3a, Wnt 5a, β-Catenin, β-Catenin, N-Cadherin), Notch (Notch-1, -2, -3 and Jagged-1, -2), CKI (p14, p15, p16, p18, p21, p27, p57), growth factor (VEGF, IGF-1, -2, Ang-1, -2, SDF-1), growth factor receptor (Flt-1, KDR, neurophilin-1, IGF-1R, Tie-1, -2, CXCR4), and growth related (c-Myc, CyclinD1, Foxo3a) genes. p18 and p21 gene expression was higher in group L compared with group H in two and all five groups, respectively. In contrast, p14 gene expression was higher in group H compared with group L. Any of the p15, p16, p27 and p57 genes was deleted. VEGF gene expression levels at 1-3- hr culture were higher in group H compared with group L. HOX, Meis 1 and Mef2c gene expression levels at 1- to 10- hr culture were higher in group H compared with group L. At 24-hr cultures, transcripts of myeloid and lymphoid cell lines for Bmi-1, Wnt-3a, and β-Catenin were higher, and those of lymphoid cell lines for Notch 1, 2, and 3 were higher in group H compared with group L. Taken together, our present results favor the conclusions that genes related to growth factors and transcription factors are sequentially and differentially expressed through cell-to-cell interaction and excreted autocrine growth factors of leukemia cells. Disclosures: No relevant conflicts of interest to declare.
Comparison of Chemotherapy Combined With Chidamide Versus Chemotherapy in the Frontline Treatment for Peripheral T-Cell Lymphoma (2022)

In summary, the combination of ChT and chidamide may provide a promising prospect for patients with newly diagnosed PTCL.
Real-Time Adaptive Motion Planning (RAMP) of Mobile Manipulators in Dynamic Environments With Unforeseen Changes (2008)

This paper introduces a novel and general real-time adaptive motion planning (RAMP) approach suitable for planning trajectories of high-DOF or redundant robots, such as mobile manipulators, in dynamic environments with moving obstacles of unknown trajectories. The RAMP approach enables simultaneous path and trajectory planning and simultaneous planning and execution of motion in real time. It facilitates real-time optimization of trajectories under various optimization criteria, such as minimizing energy and time and maximizing manipulability. It also accommodates partially specified task goals of robots easily. The approach exploits redundancy in redundant robots (such as locomotion versus manipulation in a mobile manipulator) through loose coupling of robot configuration variables to best achieve obstacle avoidance and optimization objectives. The RAMP approach has been implemented and tested in simulation over a diverse set of task environments, including environments with multiple mobile manipulators. The results (and also the accompanying video) show that the RAMP planner, with its high efficiency and flexibility, not only handles a single mobile manipulator well in dynamic environments with various obstacles of unknown motions in addition to static obstacles, but can also readily and effectively plan motions for each mobile manipulator in an environment shared by multiple mobile manipulators and other moving obstacles.
Fluids get tough (1989)

When a sufficiently large electric field is applied to certain fluids, they undergo marked changes in their rheological properties. These electrorheological (ER) fluids can, in a matter of milliseconds, make a transition from the liquid state to a 'weak solid' state with solid-like properties. Although the mechanism responsible for this phenomenon is still far from understood, the implications for hydraulic systems and common mechanical devices are significant.
Negative Regulation of Lymphocyte Activation by the Adaptor Protein LAX (2005)

The membrane-associated adaptor protein LAX is a linker for activation of T cells (LAT)-like molecule that is expressed in lymphoid tissues. Upon stimulation of T or B cells, it is phosphorylated and interacts with Grb2 and the p85 subunit of PI3K. LAX, however, is not capable of replacing LAT in the TCR signaling pathway. In this study we report that upon T or B cell activation, the LAX protein was up-regulated dramatically. Although disruption of the LAX gene by homologous recombination had no major impact on lymphocyte development, it caused a significant reduction in CD23 expression on mature B cells. Interestingly, naive LAX(-/-) mice had spontaneous germinal center formation. Compared with normal T and B cells, LAX(-/-) T and B cells were hyperresponsive and had enhanced calcium flux, protein tyrosine phosphorylation, MAPK and Akt activation, and cell survival upon engagement of the T or B AgRs. Our data demonstrate that LAX functions as a negative regulator in lymphocyte signaling.
Delivery of rapamycin‐loaded nanoparticle down regulates ICAM‐1 expression and maintains an immunosuppressive profile in human CD34<sup>+</sup> progenitor‐derived dendritic cells (2007)

Immune responses of dendritic cells (DCs) can be modulated by delivery of adjuvants to alter their maturation profile. The purpose of this study was to generate DCs from CD34(+) cells of human cord blood and characterize the effects of poly(D,L-lactic-co-glycolic acid) (PLGA)-nanoparticle encapsulated rapamycin in generating an immunosuppressive DC. Expression of ICAM-1 (intercellular adhesion molecule), a key molecule in DC-T cell interaction was increased in mature DCs in response to lipopolysaccharide (LPS). When rapamycin was encapsulated in the nanoparticle to maintain DCs in the immature state, ICAM-1 expression was down regulated. When delivered in the free form, rapamycin did not alter the expression of ICAM-1. Cytokine arrays exhibited an immunosuppressive profile of various cytokines in response to the nanoparticulate delivery of rapamycin. In addition, RT-PCR data demonstrated the presence of toll like receptor (TLR) 9 transcripts, although our DCs are myeloid in nature. In summary, our study demonstrates that DCs may be rendered immunosuppressive upon delivery of rapamycin-containing nanoparticles.
[AAV vector-mediated gene transfer and its application to the nervous system]. (2003)

AAV vectors are considered to be promising gene-delivery vehicles for gene therapy, because they are derived from non-pathogenic virus, efficiently transduce non-dividing cells, and cause long-term gene expression. Appropriate AAV serotypes are utilized depending on the type of target cells; e.g., neurons are efficiently transduced with AAV2 and AAV5 vectors, and an AAV1 vector is most suitable for muscles. Among various neurological disorders, Parkinson's disease (PD) is one of the most appropriate candidates of gene therapy. PD is a progressive neurodegenerative disorder that predominantly affects dopaminergic neurons in the substantia nigra. There are two major approaches to gene therapy of PD; i.e., 1) intrastriatal expression of dopamine (DA)-synthesizing enzyme genes, and 2) neuroprotection using the glial cell line-derived neurotrophic factor (GDNF) gene to prevent the disease progression. As for the initial step of clinical application, AADC (aromatic L-amino acid decarboxylase; the enzyme converting L-DOPA to DA) gene transfer in combination with oral administration of L-DOPA would be appropriate, since DA production can be regulated by the dose of L-DOPA. Preclinical studies are being conducted in MPTP-parkinsonian monkeys. AAV vector-mediated gene therapy would be feasible as a novel treatment of PD in the near future.
Chemical oxidation and DNA damage catalysed by inorganic sunscreen ingredients (1997)

Titanium dioxide (TiO2) has been noted (US Federal Register, 43FR38206, 25 August 1978) to be a safe physical sunscreen because it reflects and scatters UVB and UVA in sunlight. However, TiO2 absorbs about 70% of incident UV, and in aqueous environments this leads to the generation of hydroxyl radicals which can initiate oxidations. Using chemical methods, we show that all sunscreen TiO2 samples tested catalyse the photo-oxidation of a representative organic substrate (phenol). We also show that sunlight-illuminated TiO2 catalyses DNA damage both in vitro and in human cells. These results may be relevant to the overall effects of sunscreens.
Bias in Webster and Bias in Administrative Law--The Recent Jurispudence (1995)

Some courts," wrote the Supreme Court of Georgia over a century ago, "live by correcting the errors of others and adhering to their own....
Oxide-confined vertical-cavity semiconductor optical amplifier for 980-nm wavelength (1998)

Summary form only given. We have demonstrated an oxide-confined VCSOA with distinctly improved performance. Dynamic operation at 1 Gbit/s data rate shows the potential for applications in, for example, highly parallel switching networks. The wavelength-selective amplification behavior makes this device especially attractive for wavelength division multiplexing environments.
Bottom-Up Elucidation of Glycosidic Bond Stereochemistry (2017)

The lack of robust, high-throughput, and sensitive analytical strategies that can conclusively map the structure of glycans has significantly hampered progress in fundamental and applied aspects of glycoscience. Resolution of the anomeric α/β glycan linkage within oligosaccharides remains a particular challenge. Here, we show that "memory" of anomeric configuration is retained following gas-phase glycosidic bond fragmentation during tandem mass spectrometry (MS<sup>2</sup>). These findings allow for integration of MS<sup>2</sup> with ion mobility spectrometry (IM-MS<sup>2</sup>) and lead to a strategy to distinguish α- and β-linkages within natural underivatized carbohydrates. We have applied this fragment-based hyphenated MS technology to oligosaccharide standards and to de novo sequencing of purified plant metabolite glycoconjugates, showing that the anomeric signature is also observable in fragments derived from larger glycans. The discovery of the unexpected anomeric memory effect is further supported by IR-MS action spectroscopy and ab initio calculations. Quantum mechanical calculations provide candidate geometries for the distinct anomeric fragment ions, in turn shedding light on gas-phase dissociation mechanisms of glycosidic linkages.
Parosmia and Dysgeusia after Intravenous Propofol-Based General Anesthesia (2022)

Various drugs, including anesthetic agents, can cause parosmia in the perioperative period. There are reported cases of patients with alterations of smell and taste due to local anesthetics, nerve damage, or as a side effect of general anesthesia. We present a case of a 58-year-old male who developed parosmia and dysgeusia in the postoperative period after radical nephrectomy and inferior vena cava thrombectomy. The anesthetics used were fentanyl and propofol for general anesthesia and ropivacaine for epidural analgesia. Clinical examination did not reveal any pathology.
Security for Ambient Assisted Living: Multi-factor Authentication in the Internet of Things (2015)

This paper describes mechanisms for achieving strong, multi-factor authentication in Ambient Assisted Living environments. These mechanisms rely on biometric-based technologies to provide information security and privacy in the Internet of Things. The importance of user choice and ease of use of authentication methods in achieving universal access to services in assistive environments is described. Cryptographic algorithm and protocol solutions that depend on a Public Key Infrastructure for the protection of sensitive information are discussed. Lighter weight alternatives are then proposed that use authenticated key exchange to combat phishing and other attacks and provide mutual authentication and data confidentiality.
Familial pain syndromes from mutations of the Na<sub>v</sub>1.7 sodium channel (2009)

The literature currently suggests that voltage-gated sodium channels play a major role in the pathogenesis of neuropathic pain. Alterations in the expression and targeting of specific sodium channels within injured dorsal root ganglia neurons appear to predispose the neurons to abnormal firing properties, allowing for the development of neuropathic pain. Mutations of one particular sodium channel (Na(v)1.7) have been shown to cause inherited neuropathic pain in humans, specifically in erythromelalgia and paroxysmal extreme pain disorder. Inherited erythromelalgia is the first human pain syndrome to be understood at a molecular level, having been linked to gain-of-function mutations of Na(v)1.7. Conversely, a loss-of-function of the Na(v)1.7 channel can produce channelopathy-associated insensitivity to pain. Therefore, the Na(v)1.7 channel may provide a unique target for the pharmacotherapy of pain in humans. In this review article we summarize current knowledge regarding several different disease manifestations arising from changes within the Na(v)1.7 channel.
A Plaque Assay for Nuclear Polyhedrosis Viruses using a Solid Overlay (1977)

SUMMARY The nuclear polyhedrosis viruses of Trichoplusia ni and Autographa californica produce plaques in monolayers of Spodoptera frugiperda cells under a solid overlay containing agarose as the solidifying agent. Plaques are visible macroscopically after staining the cells with neutral red or with the tetrazolium salt, INT, and a linear dose response is observed. The sensitivity of the assay is less than that obtained using an end-point dilution technique; however, plaque formation does provide a simple means of cloning virus.
The identification of important concepts in highly structured technical papers (1993)

Automatic abstracting, typically based on extraction of important sentences from a text, has been treated as a largely separate task from automatic indexing. This paper describes an approach in which the indexing and abstracting tasks are effectively combined. It is applicable to highly structured empirical research papers, whose content can be organised using a semantic frame. During a scan of a source text, stylistic clues and constructs are used for extracting candidate fillers for the various slots in the frame. Subsequently, an actual concept name is chosen for each slot by comparing the various candidates and their weights.
Inositol trisphosphates in carbachol-stimulated rat parotid glands (1984)

Carbachol stimulation of rat parotid gland fragments prelabelled with myo-[3H]-inositol results in a large accumulation after 15 min of [3H]inositol trisphosphate. Only some of this is the D-1,4,5 isomer which would be expected to be derived from the known phosphatidylinositol bisphosphate. The predominant inositol trisphosphate is not susceptible to hydrolysis by human erythrocyte membranes. It yields altritol after periodate treatment followed by reduction and dephosphorylation, and, from partial dephosphorylation experiments, does not have a phosphate in the 2 position; the most likely structure of this inositol trisphosphate is therefore (D/L)-myo-inositol 1,3,4-trisphosphate. The possible origin and significance of this compound are discussed.
The role of DNA methylation in ageing and cancer (2018)

The aim of the present review paper is to survey the literature related to DNA methylation, and its association with cancer and ageing. The review will outline the key factors, including diet, which modulate DNA methylation. Our rationale for conducting this review is that ageing and diseases, including cancer, are often accompanied by aberrant DNA methylation, a key epigenetic process, which is crucial to the regulation of gene expression. Significantly, it has been observed that with age and certain disease states, DNA methylation status can become disrupted. For instance, a broad array of cancers are associated with promoter-specific hypermethylation and concomitant gene silencing. This review highlights that hypermethylation, and gene silencing, of the EN1 gene promoter, a crucial homeobox gene, has been detected in various forms of cancer. This has led to this region being proposed as a potential biomarker for diseases such as cancer. We conclude the review by describing a recently developed novel electrochemical method that can be used to quantify the level of methylation within the EN1 promoter and emphasise the growing trend in the use of electrochemical techniques for the detection of aberrant DNA methylation.
Immunological Effects and Membrane Interactions of Chitosan Nanoparticles (2009)

The objective of this study was to investigate the in vitro and in vivo effects of blank chitosan nanoparticles on various molecular markers such as nitric oxide (NO) production, IL-6 gene expression, and lymphocyte proliferation involved in the wound healing process. In addition, the membrane effects of chitosan nanoparticles were evaluated using phospholipid vesicles as a model membrane. Peripheral blood mononuclear cells (PBMC) were treated with blank chitosan nanoparticles, and the effect on NO production, IL-6 gene expression, and lymphocyte proliferation was evaluated. It was observed that IL-6 gene expression was not induced at any of the doses used; however, a statistically significant dose-dependent increase in NO production was observed at doses above 68.18 microg/mL equivalent to chitosan. Furthermore, chitosan nanoparticles showed a statistically significant and dose-dependent lymphocyte proliferation as compared to the control (P < 0.05). It was observed that blank chitosan nanoparticles resulted in strong membrane perturbation when evaluated by differential scanning calorimetry studies. The in vivo effects of the blank chitosan nanoparticles were evaluated using a wound healing model. Blank chitosan nanoparticles showed significantly higher NO production in vivo as compared to the control. Overall, the study clearly indicates the immunoactivating nature of chitosan nanoparticles and their strong membrane interactive potential.
Using Honeynets and the Diamond Model for ICS Threat Analysis (2022)

This report presents an approach to analyzing approximately 16 gigabytes of full packet capture data collected from an industrial control system honeynet - a network of seemingly vulnerable machines designed to lure attackers.