gebhart/patrepeval huggingface dataset:
Adversarial classification (2004)

Essentially all data mining algorithms assume that the data-generating process is independent of the data miner's activities. However, in many domains, including spam detection, intrusion detection, fraud detection, surveillance and counter-terrorism, this is far from the case: the data is actively manipulated by an adversary seeking to make the classifier produce false negatives. In these domains, the performance of a classifier can degrade rapidly after it is deployed, as the adversary learns to defeat it. Currently the only solution to this is repeated, manual, ad hoc reconstruction of the classifier. In this paper we develop a formal framework and algorithms for this problem. We view classification as a game between the classifier and the adversary, and produce a classifier that is optimal given the adversary's optimal strategy. Experiments in a spam detection domain show that this approach can greatly outperform a classifier learned in the standard way, and (within the parameters of the problem) automatically adapt the classifier to the adversary's evolving manipulations.
Analysis of Tie receptor tyrosine kinase in haemopoietic progenitor and leukaemia cells (1997)

We generated a panel of monoclonal antibodies against the extracellular domain of the Tie receptor tyrosine kinase and studied its expression in human haemopoietic and tumour cell lines and in samples from leukaemia patients. Most of the erythroblastic/megakaryoblastic (6/8), 2/7 myeloid and 3/6 B-lymphoblastic leukaemia cell lines were Tie-positive. The erythroblastic/megakaryoblastic leukaemia cell lines also expressed the related Tie-2/Tek gene and, surprisingly, its recently cloned ligand gene angiopoietin-1, which was located in chromosome 8q23.1. In addition, 16% of freshly isolated leukaemia samples were Tie positive. Peripheral blood mononuclear cells were Tie negative, but a few Tie positive cells were found in immunoperoxidase staining of mobilized peripheral blood stem cells. Long-term culture of isolated umbilical cord blood CD34+ Tie+ and CD34+ Tie- cells indicated that the Tie+ fraction contained a slightly higher frequency of cobblestone area forming cells (CAFC). Thus, Tie is expressed on haemopoietic progenitor cells and some leukaemic blasts. The coexpression of Tie-2 and angiopoietin-1 in megakaryoblastic leukaemia cell lines suggests the existence of an autocrine ligand/receptor signalling loop in these cells.
GSI-I has a better effect in inhibiting hepatocellular carcinoma cell growth than GSI-IX, GSI-X, or GSI-XXI (2012)

Current studies are ongoing to find new drugs for the treatment of hepatocellular carcinoma (HCC). The discovery of drugs depends on the identification of molecules that can play essential roles in the development of liver cancer, for example, Notch pathway molecules. γ-Secretase inhibitors (GSIs) can inhibit the cleavage of intramembranous substrates of all Notch receptors and subsequently suppress Notch signaling. However, whether the inhibition of the Notch pathway can suppress or promote HCC growth is still under debate. In this study, we examined the expression of Notch pathway molecules in 20 pairs of HCC tissue with their normal counterparts and a panel of eight HCC cell lines. We also determined the effects of different types of GSI treatments on the cell growth of those HCC cell lines. Our results showed that the molecules of the Notch pathway were expressed in six of the eight HCC cell lines. Those six HCC cell lines were more sensitive to GSI-I treatment than the nonexpression ones. Among the four inhibitors, GSI-X and GSI-XXI exerted no effect on HCC cells growth at all. GSI-IX inhibited the growth of four HCC cell lines at 40 μmol/l. In contrast, most of these HCC cell lines were susceptible to a low concentration of GSI-I (1.2 μmol/l) treatment. The suppressive effect of GSI-I on cell growth was because of the inhibition of C-Myc, a Notch target gene. In addition, 80% (16/20) of the specimens showed either an increased expression of at least one Notch receptor or an augmented expression of Jagged1 compared with their normal counterparts. Our study reports for the first time that different kinds of GSIs can block the growth of several HCC cell lines. Our finding suggests that GSI-I is a potential chemical reagent and warrants additional testing in liver cancer therapeutics.
Computer-Assisted, Robot-Enhanced Open Microsurgery in an Animal Model (2005)

Background: Computer-assisted, robot-enhanced surgery improves laparoscopic and thoracoscopic surgery through tremor filtration, motion scaling, articulation, and improved ergonomics. Surgeons perform many open cases under magnification that magnifies the tremor present in all surgeons' hands, so the tremor filtration and motion scaling of robotic surgery may improve microsurgery. Our goal was to compare microvascular anastomoses performed with a robot-enhanced technique with a standard technique. Methods: We performed end-to-end anastomoses in 1-mm rat femoral arteries with interrupted 10-0 suture. We compared the anastomotic time, patency, and leak rates between traditional microsurgery techniques (by hand) and a robot-enhanced technique using the Zeus® robotic surgery system (Computer Motion, Goleta, California). The surgeon used an operative microscope for visualization in both techniques. Results: We performed 30 anastomoses by hand and 31 with Zeus. We observed a remarkable degree of tremor filtration in the robot-enhanced cases. Anastomotic times for both techniques demonstrated a learning curve. Anastomoses done by hand (mean time, 17.2 minutes) were significantly faster than those done with Zeus (mean time, 27.6 minutes) (P = 0.0006). All anastomoses from both groups were patent, and none leaked after 3 minutes. Conclusion: The Zeus system is effective at performing complex, open, microsurgery tasks in vivo. There was no measurable benefit from the remarkable tremor filtration and motion scaling offered by robot-enhanced surgery.
Cognitive deficits in major depression (2002)

Major depression is a mood disorder that is often accompanied by the impairment of cognitive functions. Although suggestive, the large range of existing neuropsychological, neuropsychiatric, and, lately, neuroimaging investigations have not yet given a consistent picture of the psychological and biological disturbances involved in this psychiatric disorder. The present study of the cognitive functions in depression was part of an extensive investigation, including neuropsychological testing, psychiatric examination, and neuroimaging. A representative sample of 40 severely depressed hospitalized patients and a group of 49 closely matched control subjects were tested with an extensive neuropsychological test battery. Results, corrected for various confounding factors, confirmed the current notion that depressed patients suffer from wide-spread cognitive impairments. The group analysis did not allow any hypothesis on a possible pattern to the dysfunctions, but heterogeneity in the test performances calls for further analysis of the data in patient subgroups in relation to neuroimaging results.
Stereotactic placement of depth electrodes in medically intractable epilepsy (2014)

The authors report on a safe, simplified, and less time-consuming method of SEEG depth electrode implantation, using standard and widely available surgical tools, making the technique a reasonable option for extraoperative monitoring of patients with medically intractable epilepsy in centers lacking the Talairach stereotactic armamentarium.
The formylpeptide chemoattractant receptor copurifies with a GTP-binding protein containing a distinct 40-kDa pertussis toxin substrate. (1988)

Detergent extraction of plasma membranes from differentiated HL60 cells, specifically labeled with the chemoattractant, formyl-Nle-Leu-Phe-Nle-[125I-Tyr] Lys, resulted in the solubilization of a receptor-radioligand complex. GTP-binding activity coeluted with the radioligand when the sodium cholate extract was purified by chromatography on wheat germ agglutinin-Sepharose 6MB. A molecular size of approximately 59 A was estimated for the lectin-Sepharose-purified receptor complex by gel filtration chromatography on Ultrogel AcA 34. The isolated complex eluted from the gel filtration column exhibited an enhanced rate of ligand dissociation in response to GTP gamma S. Approximately 0.65 mol of pertussis toxin substrate/mol of receptor was estimated following partial purification of the receptor-ligand complex by sequential chromatography on wheat germ agglutinin-Sepharose, DEAE-Fractogel, and Ultrogel AcA 34. The pertussis toxin substrate which copurified with the receptor was compared with two distinct G proteins, containing alpha-subunits of 40 and 41 kDa, previously purified from HL60 cell plasma membranes. Approximately 86% of the pertussis toxin substrate identified in the receptor preparation consisted of the 40-kDa polypeptide. Differences in the peptide maps indicate that the predominant G protein which coelutes with the receptor is distinct from the purified G protein with an alpha-subunit of 41 kDa but homologous to the purified G protein with an alpha-subunit of 40 kDa.
Photoactivated Fluorescence from Individual Silver Nanoclusters (2001)

Fluorescence microscopy of nanoscale silver oxide (Ag2O) reveals strong photoactivated emission for excitation wavelengths shorter than 520 nanometers. Although blinking and characteristic emission patterns demonstrate single-nanoparticle observation, large-scale dynamic color changes were also observed, even from the same nanoparticle. Identical behavior was observed in oxidized thin silver films that enable Ag2O particles to grow at high density from silver islands. Data were readily written to these films with blue excitation; stored data could be nondestructively read with the strong red fluorescence resulting from green (wavelengths longer than 520 nanometers) excitation. The individual luminescent species are thought to be silver nanoclusters that are photochemically generated from the oxide.
Thermo-optical Effect in Phase-Change Nanophotonics (2016)

Phase-change materials (PCMs) integrated with nanophotonic components enable tunable integrated optical devices and hold promise for emerging applications in long-term photonic data storage by exploiting the large contrast in optical properties when switched between amorphous and crystalline phase states. The phase transitions rely on short heat pulses, which can be conveniently supplied by optical means. Therefore, a proper understanding of the temperature-induced refractive index fluctuations, the thermo-optical effect, is essential for controlled and optimized device operation. Here we analyze the thermo-optical effect of Ge2Sb2Te5 nanojunctions integrated atop nanophotonic waveguides at telecommunication wavelengths. We extract the thermo-optical coefficients for the crystalline and amorphous phase state, both the real and imaginary part. We observe sign reversal of the thermo-optical coefficient upon phase change, which we trace back to different chromatic dispersion of the two phase states within the studied spectral regime. Our findings will allow for designing PCM-based modulators, nonvolatile memory systems, and reconfigurable photonic devices.
Myocardial gene transfer and long‐term expression following intracoronary delivery of adeno‐associated virus (2004)

Adeno-associated viral vectors (AAV) can direct long-term gene expression in post-mitotic cells. Previous studies have established that long-term cardiac gene transfer results from intramuscular injection into the heart. Cardiac gene transfer after direct intracoronary delivery of AAV in vivo, however, has been minimal in degree, and indirect intracoronary delivery, an approach used in an increasing number of studies, appears to be receiving more attention. To determine the utility of indirect intracoronary gene transfer of AAV, we used aortic and pulmonary artery cross clamping followed by proximal aortic injection of AAV encoding enhanced green fluorescent protein (AAV.EGFP) at 10(11) DNase resistant particles (drp; high-performance liquid chromatography (HPLC)-purified) per rat. Gene expression was quantified by fluorescent microscopy at four time points up to 1 year after vector delivery, revealing 20-32% transmural gene expression in the left ventricle at each time point. Histological analysis revealed little or no inflammatory response and levels of transgene expression were low in liver and undetectable in lung. In subsequent studies in pigs, direct intracoronary delivery into the left circumflex coronary artery of AAV.EGFP (2.64-5.28 x 10(13) drp; HPLC-purified) resulted in gene expression in 3 of 4 pigs 8 weeks following injection with no inflammatory response in the heart. PCR analysis confirmed AAV vector presence in the left circumflex perfusion bed. These data indicate that intracoronary delivery of AAV vector is associated with transgene expression in the heart, providing a means to obtain long-term expression of therapeutic genes.
Laser speckle contrast imaging in biomedical optics (2010)

First introduced in the 1980s, laser speckle contrast imaging is a powerful tool for full-field imaging of blood flow. Recently laser speckle contrast imaging has gained increased attention, in part due to its rapid adoption for blood flow studies in the brain. We review the underlying physics of speckle contrast imaging and discuss recent developments to improve the quantitative accuracy of blood flow measures. We also review applications of laser speckle contrast imaging in neuroscience, dermatology and ophthalmology.
A Fluoride-Derived Electrophilic Late-Stage Fluorination Reagent for PET Imaging (2011)

The unnatural isotope fluorine-18 ((18)F) is used as a positron emitter in molecular imaging. Currently, many potentially useful (18)F-labeled probe molecules are inaccessible for imaging because no fluorination chemistry is available to make them. The 110-minute half-life of (18)F requires rapid syntheses for which [(18)F]fluoride is the preferred source of fluorine because of its practical access and suitable isotope enrichment. However, conventional [(18)F]fluoride chemistry has been limited to nucleophilic fluorination reactions. We report the development of a palladium-based electrophilic fluorination reagent derived from fluoride and its application to the synthesis of aromatic (18)F-labeled molecules via late-stage fluorination. Late-stage fluorination enables the synthesis of conventionally unavailable positron emission tomography (PET) tracers for anticipated applications in pharmaceutical development as well as preclinical and clinical PET imaging.
Neural Cell Adhesion Molecule (NCAM) Expression in Nerves and Muscle of Developing Human Large Bowel (1996)

Most studies of neural cell adhesion molecule (NCAM) in human musculature are devoted to either developing or adult skeletal and cardiac muscle. The aim of this study was to determine the pattern of NCAM expression in the intestinal musculature of the developing human large bowel. In specimens of large bowel from foetuses (gestational age 8-20 weeks), we examined the immunohistochemical localisation of NCAM in parallel to those of alpha-smooth muscle actin and desmin. Within the developing neural complex, NCAM was expressed at all stages investigated. In intestinal muscle at 8 weeks, immunoreactivity for all antisera was restricted to the muscularis propria. The differentiating muscularis mucosae was demonstrated first at 15 weeks by immunostaining for alpha-smooth muscle actin, and this expression was followed by that of NCAM and desmin at 17 and 19 weeks, respectively. At 20 weeks, NCAM immunoreactivity in the external muscle was intense at the inner border of the circular muscle, with its concentration decreasing towards the outer margin of the muscular wall, whereas alpha-smooth muscle actin and desmin were uniformly distributed in all muscle layers. NCAM is expressed by nerves and muscle of developing human large intestine. Its appearance follows a predetermined pattern, which implies its relevance to the differentiation of intestinal muscle layers.
JAVA 1.1 developer's guide (1996)

From the Publisher:
Written by a highly technical and experienced Web programmer, this detailed guide uses many illustrations and examples to show users how to exploit Java to develop real-world applications. It's a must-have resource for experienced Web developers.
Explore the Java interface, Java in client/server environments, debugging, VRML extensions, network programming, protocol handlers, Java and the World Wide Web, and more
CD-ROM contains Sun's JDK v1.1, Visual Caf Lite from Symantec, a variety of third-party applets, and source code
Transformation of Human Leukocytes by Cocultivation with an Adult T Cell Leukemia Virus Producer Cell Line (1982)

The transmission of adult T cell leukemia virus, a human retrovirus, into fresh leukocytes from normal humans was examined. One of three virus-carrying cell lines, tested after being subjected to lethal x-irradiation, consistently transformed leukocytes from adult peripheral blood and umbilical cord blood. All the transformed cell lines expressed adult T cell leukemia virus-associated antigen, but transformed lines originating from adult and umbilical cord blood exhibited T cell and non-T, non-B cell surface natures, respectively. Efforts to transform human leukocytes with cell-free virus were unsuccessful.
A review of methods for the assessment of prediction errors in conservation presence/absence models (1997)

Predicting the distribution of endangered species from habitat data is frequently perceived to be a useful technique. Models that predict the presence or absence of a species are normally judged by the number of prediction errors. These may be of two types: false positives and false negatives. Many of the prediction errors can be traced to ecological processes such as unsaturated habitat and species interactions. Consequently, if prediction errors are not placed in an ecological context the results of the model may be misleading. The simplest, and most widely used, measure of prediction accuracy is the number of correctly classified cases. There are other measures of prediction success that may be more appropriate. Strategies for assessing the causes and costs of these errors are discussed. A range of techniques for measuring error in presence/absence models, including some that are seldom used by ecologists (e.g. ROC plots and cost matrices), are described. A new approach to estimating prediction error, which is based on the spatial characteristics of the errors, is proposed. Thirteen recommendations are made to enable the objective selection of an error assessment technique for ecological presence/absence models.
The role of prohibitin in cell signaling (2010)

Prohibitin-1 (PHB, also known as PHB1), a member of the Band-7 family of proteins, is highly conserved evolutionarily, widely expressed, and present in different cellular compartments. Genetic studies with different organism models have provided strong evidence for an important biological role of PHB in mitochondrial function, cell proliferation, and development. Recent discoveries regarding the involvement of PHB in phophatidylinositol-3-kinase (PI3K)/protein kinase B (Akt) and transforming growth factor-β (TGF-β)/signal transducers and activators of transcription signaling pathways, and earlier reports on the interaction of PHB with Raf and its critical role in Ras/mitogen-activated protein kinase (MAPK)/extracellular signal-regulated kinase (ERK) signaling opened up the possibility that PHB has functions outside of the mitochondria (extramitochondrial) and may be a multifunctional protein. The PI3K/Akt and Ras/MAPK/ERK signaling cascades are versatile signaling processes that diverge from the same receptor tyrosine kinase root, and are involved in cell metabolism, proliferation, and development. Here, we review the emerging role of PHB and its post-translational modifications in signal transduction pathways, especially in PI3K/Akt and Ras/MAPK/ERK signaling. A recent discovery of opposing effects of PHB on longevity under different metabolic states and its potential connection with insulin/insulin-like growth factor-I signaling is also discussed.
Implantation of Collagen IV/Poly(2-hydroxyethyl methacrylate) Hydrogels Containing Schwann Cells Into the Lesioned Rat Optic Tract (1998)

Poly (2-hydroxyethylmethacrylate) (PolyHEMA) hydrogels, when combined with extracellular matrix molecules and infiltrated with cultured Schwann cells, have the capability to induce CNS axonal regrowth after injury. We have further investigated these PolyHEMA hydrogels and their potential to bridge CNS injury sites. Collagen IV-impregnated hydrogels containing Schwann cells were implanted into the lesioned optic tract in 14 rats. On examination 2-4 months later, there was good adherence between the implants and CNS tissue, and large numbers of viable Schwann cells (S100+, GFAP+, Laminin+, and LNGFR+) were seen within the hydrogel matrices. Immunohistochemical analysis showed that the collagen IV-impregnated PolyHEMA hydrogels preferentially supported the transplanted Schwann cells and not host glial cells such as astrocytes (GFAP+) or oligodendroglia (CAII+). Macrophages (ED1+) were also seen within the sponge structure. Eighty-three percent of the implanted hydrogels contained RT97+ axons within their trabecular networks. Regrowing axons were associated with the transplanted Schwann cells and not with the small number of infiltrating astrocytes. RT97+ axons were traced up to 510 microm from the nearest host neuropil. These axons were sometimes myelinated by the transplanted Schwann cells and expressed the peripheral myelin marker Po+. WGA/HRP-labeled retinal axons were seen within transplanted hydrogel sponges, with 40% of the cases growing for distances up to 350-450 microm within the polymer network. The data indicate that impregnating PolyHEMA sponges with collagen IV can modify the host glial reaction and support the survival of transplanted Schwann cells. This study thus provides new information on how biomaterials could be used to modify and bridge CNS injury sites.
Graph drawing by force‐directed placement (1991)

Abstract We present a modification of the spring‐embedder model of Eades [Congressus Numerantium, 42, 149–160, (1984)] for drawing undirected graphs with straight edges. Our heuristic strives for uniform edge lengths, and we develop it in analogy to forces in natural systems, for a simple, elegant, conceptually‐intuitive, and efficient algorithm.
Dynamic plan generation for parameterized queries (2009)

Query processing in a DBMS typically involves two distinct phases: compilation, which generates the best plan and its corresponding execution steps, and execution, which evaluates these steps against database objects. For some queries, considerable resource savings can be achieved by skipping the compilation phase when the same query was previously submitted and its plan was already cached. In a number of important applications the same query, called a Parameterized Query (PQ), is repeatedly submitted in the same basic form but with different parameter values. PQ's are extensively used in both data update (e.g. batch update programs) and data access queries. There are tradeoffs associated with caching and re-using query plans such as space utilization and maintenance cost. Besides, pre-compiled plans may be suboptimal for a particular execution due to various reasons including data skew and inability to exploit value-based query transformation like materialized view rewrite and unsatisfiable predicate elimination. We address these tradeoffs by distinguishing two types of plans for PQ's: generic and specific plans. Generic plans are pre-compiled plans that are independent of the actual parameter values. Prior to execution, parameter values are plugged in to generic plans. In specific plans, parameter values are plugged prior to the compilation phase. This paper provides a practical framework for dynamically deciding between specific and generic plans for PQ's based on a mix of rule and cost based heuristics which are implemented in the Teradata 12.0 DBMS.