gebhart/patrepeval huggingface dataset:
PM01183, a new DNA minor groove covalent binder with potent <i>in vitro</i> and <i>in vivo</i> anti‐tumour activity (2010)

PM01183 is shown to bind to selected DNA sequences and promoted apoptosis by inducing double-strand breaks at nanomolar concentrations. The potent anti-tumour activity of PM01183 in several murine models of human cancer supports its development as a novel anti-neoplastic agent.
Reliability and validity of Endotower, a virtual reality trainer for angled endoscope navigation. (2002)

We hypothesized that a simulator designed to train surgical novices angled laparoscopic navigation would show an improvement in subjects' performance, a high test re-test reliability and high internal validity as measured by standardized coefficient alpha. It was also predicted that simulator performance would be strongly related to objectively assess perceptual and visuospatial ability. EndoTower has good face validity in that it mimics precisely the performance of an angled laparoscope and previous studies suggest construct validity. In this study, EndoTower is shown to be a trainer intended for laparoscopic skill than can test for inherent perceptual and visuospatial ability.
Germanium strip detector Compton telescope using three dimensional readout (2003)

Compton telescopes using two germanium strip detectors with depth resolution have been demonstrated at the Naval Research Lab. Depth resolution allows interactions to be located to less than 1 mm, down from 1 cm with no depth resolution, which improves the imaging resolution of the telescope substantially. Compton images and reconstructed energy spectra of events in which gamma rays interact three times in the two detectors but did not deposit their full energy (i.e. Three-Compton) are examined. Finally, the multiple modes of the system including a standard Compton telescope and a Three-Compton telescope are compared.
Nanocrystallization of zirconium subjected to surface mechanical attrition treatment (2008)

A nanostructured surface layer with thickness of about 20 µm was formed on commercially pure zirconium using surface mechanical attrition treatment (SMAT). The microstructural features of the surface layer were systematically investigated using optical microscopy (OM), x-ray diffraction (XRD), transmission electron microscopy (TEM) and high-resolution transmission electron microscopy (HRTEM), respectively. Based on the results obtained, a grain refinement mechanism induced by plastic deformation during SMAT of Zr is proposed. At the initial stage of SMAT, twinning dominates the plastic deformation of Zr and divides the coarse grains of Zr into finer twin plates. With increasing strain, intersection of twins occurs, and dislocation slips are activated, becoming the predominant deformation mode instead of twinning. As a result of the dislocation slips, high-density dislocation arrays are formed, which further subdivide the twin plates into subgrains of size about 200-400 nm. With a further increase of strain, the dislocations accumulate and rearrange to minimize the energy state of the high-strain-energy subgrains, the dense dislocation walls convert to grain boundaries, and the submicronic grains are subdivided, leading to the formation of nanosized grains at the top of the treated surface.
Androgen deprivation induces human prostate epithelial neuroendocrine differentiation of androgen-sensitive LNCaP cells (2006)

Neuroendocrine (NE) cells are the minor cell populations in normal prostate epithelial compartments. During prostate carcinogenesis, the number of NE cells in malignant lesions increases, correlating with its tumorigenicity and hormone-refractory growth. It is thus proposed that cancerous NE cells promote prostate cancer (PCa) cell progression and its androgen-independent proliferation, although the origin of the cancerous NE cells is not clear. To investigate the role of cancerous NE cells in prostate carcinogenesis, we characterized three NE subclone cell lines-NE-1.3, NE-1.8 and NE-1.9, which were transdifferentiated from androgen-sensitive human PCa LNCaP cells by culturing in an androgen-depleted environment, resembling clinical androgen-ablation therapy. These subclone cells acquire many features of NE cells seen in clinical prostate carcinomas, for example exhibiting a neuronal morphology and expressing multiple NE markers, including neuron-specific enolase, chromogranin B, neurotensin, parathyroid hormone-related peptide, and to a lesser degree for chromogranin A, while lacking androgen receptor (AR) or prostate specific antigen (PSA) expression. These cells represent terminally differentiated stable cells because after 3 months of re-culturing in a medium containing androgenic activity, they still retained the NE phenotype and expressed NE markers. Despite these NE cells having a slow growth rate, they readily developed xenograft tumors. Furthermore, media conditioned by these NE cells exhibited a stimulatory effect on proliferation and PSA secretion by LNCaP cells in androgen-deprived conditions. Additionally, we found that receptor protein tyrosine phosphatase alpha plays a role in upregulating multiple NE markers and acquiring the NE phenotype. These NE cells thus represent cancerous NE cells and could serve as a useful cell model system for investigating the role of cancerous NE cells in hormone-refractory proliferation of PCa cells.
Cytoprotective roles for autophagy (2010)

Macroautophagy (referred to as autophagy in this review) is a genetically regulated bulk degradation program conserved from yeast to humans, in which cytoplasmic substrates, such as damaged organelles and long-lived proteins, are delivered to lysosomes for degradation. In this review, we consider recent data that highlight possible mechanisms whereby autophagy mediates cytoprotective effects. These include the ability of autophagy to buffer against starvation, protect against apoptotic insults and clear mitochondria, aggregate-prone proteins and pathogens. These effects are pertinent to the roles of autophagy in normal human physiology, including the early neonatal period and ageing, as well as a variety of diseases, including cancer, neurodegenerative conditions and infectious diseases.
Reclaim the Streets (2009)

Merging the radical ecology of Britain's powerful anti‐road‐building movement and the carni‐valesque nature of the countercultural rave scene of the early 1990s, Reclaim the Streets (RTS) became a catalyst for the global anti‐capitalist movements that came to light during the Seattle World Trade Organization (WTO) protests of 1999. Combining a radical ecological and social critique with creative forms of direct action and a dedication to non‐hierarchical organization, the group's innovative tactics inspired a new generation of radical activists in the global North.
BPTF promotes tumor growth and predicts poor prognosis in lung adenocarcinomas (2015)

BPTF, a subunit of NURF, is well known to be involved in the development of eukaryotic cell, but little is known about its roles in cancers, especially in non-small-cell lung cancer (NSCLC). Here we showed that BPTF was specifically overexpressed in NSCLC cell lines and lung adenocarcinoma tissues. Knockdown of BPTF by siRNA significantly inhibited cell proliferation, induced cell apoptosis and arrested cell cycle progress from G1 to S phase. We also found that BPTF knockdown downregulated the expression of the phosphorylated Erk1/2, PI3K and Akt proteins and induced the cleavage of caspase-8, caspase-7 and PARP proteins, thereby inhibiting the MAPK and PI3K/AKT signaling and activating apoptotic pathway. BPTF knockdown by siRNA also upregulated the cell cycle inhibitors such as p21 and p18 but inhibited the expression of cyclin D, phospho-Rb and phospho-cdc2 in lung cancer cells. Moreover, BPTF knockdown by its specific shRNA inhibited lung cancer growth in vivo in the xenografts of A549 cells accompanied by the suppression of VEGF, p-Erk and p-Akt expression. Immunohistochemical assay for tumor tissue microarrays of lung tumor tissues showed that BPTF overexpression predicted a poor prognosis in the patients with lung adenocarcinomas. Therefore, our data indicate that BPTF plays an essential role in cell growth and survival by targeting multiply signaling pathways in human lung cancers.
Transforming growth factor-beta modulates the high-affinity receptors for epidermal growth factor and transforming growth factor-alpha. (1985)

The epidermal growth factor (EGF) receptor mediates the induction of a transformed phenotype in normal rat kidney (NRK) cells by transforming growth factors (TGFs). The ability of EGF and its analogue TGF-alpha to induce the transformed phenotype in NRK cells is greatly potentiated by TGF-beta, a polypeptide that does not interact directly with binding sites for EGF or TGF-alpha. Our evidence indicates that TGF-beta purified from retrovirally transformed rat embryo cells and human platelets induces a rapid (t 1/2 = 0.3 h) decrease in the binding of EGF and TGF-alpha to high-affinity cell surface receptors in NRK cells. No change due to TGF-beta was observed in the binding of EGF or TGF-alpha to lower affinity sites also present in NRK cells. The effect of TGF-beta on EGF/TGF-alpha receptors was observed at concentrations (0.5-20 pM) similar to those at which TGF-beta is active in promoting proliferation of NRK cells in monolayer culture and semisolid medium. Affinity labeling of NRK cells and membranes by cross-linking with receptor-bound 125I-TGF-alpha and 125I-EGF indicated that both factors interact with a common 170-kD receptor structure. Treatment of cells with TGF-beta decreased the intensity of affinity-labeling of this receptor structure. These data suggest that the 170 kD high-affinity receptors for EGF and TGF-alpha in NRK cells are a target for rapid modulation by TGF-beta.
Computer-Aided Design of Highly Linear, High-Power Varactor-Tuned Frequency Modulators (2005)

A systematic approach to the design of linear high-power varactor-tuned frequency modulators is presented. It is shown that a few simple measurements on the free-running oscillator together with a suitable use of modern general-purpose optimization programs allow the designer to predict and control all aspects of the design problem, including linearity of the frequency-voltage characteristic, the R.F. voltage swing across the varactor junction, and the optimum choice of the varactor diode itself.
Reducing Ground-Plane Effects on UWB Monopole Antennas (2011)

A common problem with planar ultrawideband (UWB) monopole antennas is that their performance is heavily affected by the ground plane. To resolve this problem, a novel approach is proposed in this letter. Slots along the top edge of the ground are introduced to minimize the ground-plane effects by changing the current distribution. An equivalent circuit model is developed to obtain an insight view of the behavior of the slots. Computer simulation and measured results are obtained, and they confirm the validity of the proposed method.
Increased nociceptive response in mice lacking the adenosine A1 receptor (2004)

The role of the adenosine A1 receptor in nociception was assessed using mice lacking the A1 receptor (A1R-/-) and in rats. Under normal conditions, the A1R-/- mice exhibited moderate heat hyperalgesia in comparison to the wild-type mice (A1R+/+). The mechanical and cold sensitivity were unchanged. The antinociceptive effect of morphine given intrathecally (i.t.), but not systemically, was reduced in A1R-/- mice and this reduction in the spinal effect of morphine was not associated with a decrease in binding of the mu-opioid ligand DAMGO in the spinal cord. A1R-/- mice also exhibited hypersensitivity to heat, but not mechanical stimuli, after localized inflammation induced by carrageenan. In mice with photochemically induced partial sciatic nerve injury, the neuropathic pain-like behavioral response to heat or cold stimulation were significantly increased in the A1R-/-mice. Peripheral nerve injury did not change the level of adenosine A1 receptor in the dorsal spinal cord in rats and i.t. administration of R-PIA effectively alleviated pain-like behaviors after partial nerve injury in rats and in C57/BL/6 mice. Taken together, these data suggest that the adenosine A1 receptor plays a physiological role in inhibiting nociceptive input at the spinal level in mice. The C-fiber input mediating noxious heat is inhibited more than other inputs. A1 receptors also contribute to the antinociceptive effect of spinal morphine. Selective A1 receptor agonists may be tested clinically as analgesics, particularly under conditions of neuropathic pain.
Prevention of Pain on Injection of Propofol (1996)

We undertook a randomized, placebo-controlled, double-blind study to compare the use of alfentanil 1 mg and lidocaine 40 mg for the reduction of pain during injection of propofol. Eighty-nine patients were randomly allocated to one of three groups: Group L, lidocaine 40 mg added to 180 mg propofol; Group A, alfentanil 1 mg 30 s prior to propofol; or Group P, placebo (normal saline). The incidence of pain in the placebo group was 67%. Both treatment groups had a significantly lower incidence of pain than the placebo group (P < 0.002). There was no significant difference in the incidence of pain between the groups receiving lidocaine or alfentanil (13% and 24%, respectively). There was no significant difference in the induction dose of propofol between the groups. Fifty-two percent of patients who experienced pain at induction had recall of that pain in the recovery room. Alfentanil 1 mg and lidocaine 40 mg are both effective in reducing pain during injection of propofol.
An Introduction to Mass Spectrometry Ionization: An Excerpt from <i>The Expanding Role of Mass Spectrometry in Biotechnology</i>, 2nd ed.; MCC Press: San Diego, 2005 (2004)

ril Mass spectrometry has been described as the smallest scale in the world, not because of the mass spectrometer’s size but because of the size of what it weighs—molecules. Over the past decade, mass spectrometry has undergone tremendous technological improvements, allowing for its application to proteins, peptides, carbohydrates, DNA, drugs, and many other biologically relevant molecules. Due to ionization sources such as electrospray ionization and matrix-assisted laser desorption/ionization (MALDI), mass spectrometry has become an irreplaceable tool in the biological sciences. This chapter provides an overview of mass spectrometry, focusing on ionization sources and their significance in the development of mass spectrometry in biomolecular analysis. A mass spectrometer determines the mass of a molecule by measuring its mass-to-charge ratio (m/z). Ions are generated by inducing either the loss or gain of a charge from a neutral species. Once formed, ions are electrostatically directed into amass
Effects of soil management systems on soil microbial activity, bulk density and chemical properties (2001)

The objective of this experiment was to study the effects of soil management systems on the bulk density, chemical soil properties, and on the soil microbial activity on a Latossolo Vermelho distrófico (Oxisol). Soil samples were collected from plots under the following management conditions: a) natural dense "cerrado" vegetation (savanna); b) degraded Brachiaria decumbens pasture, 20 years old; c) no-tillage treatment with annual crop sequence (bean, corn, soybean and dark-oat in continuous rotation), 8 years old; d) conventional tillage treatment with crop residues added to the soil, and annual crop sequence, 10 years old. The continuous use of no-tillage system resulted in an increase in microbial biomass and decrease in soil basal respiration, therefore displaying evident long-term effects on the increase of soil C content. The no-tillage system also provided an improvement in bulk density and chemical properties of the soil. Hence, the no-tillage management system could be an alternative for the conservation and maintenance of physical and chemical conditions and the productive potential of "cerrado" soils.
Microstructural manipulation and architecture design of carbon-based electrochemical systems (2013)

Thesis: Ph. D., Massachusetts Institute of Technology, Department of Chemical Engineering, February 2014.
Applications of Thread Prioritization in SMT Processors (1999)

Previous work in multithreading, and specifically in simultaneous multithreading (SMT), has focused primarily on increasing total instruction throughput. While this focus is sufficient in some application domains, widespread deployment of multithreaded processors will require robust behavior across a variety of platforms. For instance, interactive systems must be concerned with the execution latency of foreground userinterface threads. Multiuser systems must be concerned with fair allocation of throughput among competing users. A multithreaded processor that seeks solely to maximize throughput will favor efficient threads at the expense of any potential latency or fairness
Finding the optimal location for public charging stations – a GIS-based MILP approach (2019)

Electric Vehicles (EVs) have achieved a significant development because of the continuous technology revolution and policy supports in recent years, which leads to a larger demand of charging stations. Strategies about how to find the optimal location for charging facilities are urgently needed in order to further assist the development of EVs. This paper focus on the return of investments on EV charging stations and proposes a Mixed Integer Linear Programming (MILP) model based on Geographic Information System (GIS) to identify the optimal location of charging stations in cities. Traffic flow data and land-use classifications are used as important inputs, and six important constraints are included in the MILP model with the objective function of maximizing the total profits of new charging stations. The effectiveness of the proposed method is then demonstrated by implementing a case study in Västerås, Sweden.
Statistical mechanics of error-correcting codes (1999)

PACS. 89.90+n { Other areas of general interest to physicists. PACS. 89.70+c { Information science. PACS. 05.50+q { Lattice theory and statistics; Ising problems. Abstract. { We investigate the performance of error-correcting codes, where the code word comprises products of K bits selected from the original message and decoding is carried out utilizing a connectivity tensor with C connections per index. Shannon’s bound for the channel capacity is recovered for large K and zero temperature when the code rate K=C is nite. Close to optimal error-correcting capability is obtained for nite K and C. We examine the nite-temperature case to assess the use of simulated annealing for decoding and extend the analysis to accommodate other types of noisy channels. Error-correcting codes are of signicant practical importance as they provide mechanisms for retrieving the original message after possible corruption due to noise during transmission. They are being used extensively in most means of information transmission from satellite communication to the storage of information on hardware devices. The coding eciency, measured in the percentage of informative transmitted bits, plays a crucial role in determining
Thermodynamics of Aβ(1−40) Amyloid Fibril Elongation (2005)

We describe herein the characterization of the equilibrium point for A beta(1-40) amyloid fibril elongation in phosphate-buffered saline at 37 degrees C. Seeded fibril elongation progresses rapidly to a reproducible end point of 0.7-1.0 microM unpolymerized monomeric peptide. This remaining monomeric material is functional, since after concentration it supports fibril elongation. Incubation of fibrils in the same buffer results in dissociation to a final monomer concentration in the same range. This robust C(r) value is equivalent to the A beta(1-40) fibril dissociation constant, Kd. The fact that a similar value for Kd is obtained from a ratio of dissociation and elongation rate constants further supports the view that these values are associated with a position of dynamic equilibrium and therefore are related to free energies of amyloid fibril elongation. The C(r) value reported here for wild-type A beta(1-40) fibrils corresponds to a free energy of fibril elongation of about -9 kcal/mol, a value similar to free energies of folding for small globular proteins. Elongation and dissociation of amyloid fibrils from point mutants of A beta(1-40) also yield C(r) values, different for different mutants, that reflect stabilizing/destabilizing effects. Interestingly, assembly of A beta(1-40) fibrils in the presence of a saturating concentration of the amyloid dye thioflavin T does not measurably affect fibril stability, in contrast to the commonly observed stabilization of globular proteins by ligand binding. The ability to quantify and compare amyloid fibril thermodynamic stabilities makes it possible to include fibrils, and potentially other aggregates, in quantitative descriptions of protein folding landscapes.
Proteinase-Activated Receptor 1 (PAR1) Regulates Leukemic Stem Cell Functions (2014)

External signals that are mediated by specific receptors determine stem cell fate. The thrombin receptor PAR1 plays an important role in haemostasis, thrombosis and vascular biology, but also in tumor biology and angiogenesis. Its expression and function in hematopoietic stem cells is largely unknown. Here, we analyzed expression and function of PAR1 in primary hematopoietic cells and their leukemic counterparts. AML patients' blast cells expressed much lower levels of PAR1 mRNA and protein than CD34 + progenitor cells. Constitutive Par1-deficiency in adult mice did not affect engraftment or stem cell potential of hematopoietic cells. To model an AML with Par1-deficiency, we retrovirally introduced the oncogene MLL-AF9 in wild type and Par1 2/2 hematopoietic progenitor cells. Par1-deficiency did not alter initial leukemia development. However, the loss of Par1 enhanced leukemic stem cell function in vitro and in vivo. Re-expression of PAR1 in Par1 2/2 leukemic stem cells delayed leukemogenesis in vivo. These data indicate that Par1 contributes to leukemic stem cell maintenance.
Regulation of cortical and subcortical glutamate receptor subunit expression by antipsychotic drugs (1995)

Because glutamate is an important modulator of subcortical dopamine (DA) function, and abnormal glutamate/DA interactions may be involved in the pathophysiology of schizophrenia, we examined the effect of chronically administered antipsychotic drugs (APDs) on the levels of specific glutamate receptor subunits in the terminal fields of nigrostriatal and mesocorticolimbic DA systems. By immunoblotting procedures using antibodies specific for the NMDAR1, GluR1, and GluR2 subunits, we found that haloperidol (predominantly a D2-like antagonist) increased NMDAR1 subunit immunoreactivity (and mRNA levels) in the striatum, while the D1-like antagonist SCH 23390 had the opposite effect. No effect was seen on GluR1 or GluR2 levels. The result that D1-like and D2-like receptor antagonism can reciprocally regulate NMDAR1 expression is consistent with our observation that complete unilateral destruction of the nigrostriatal DA pathway with 6-hydroxy-dopamine had no effect on striatal NMDAR1 subunit levels. Further examination of these striatal effects revealed that chronic treatment with the D2-like receptor antagonist raclopride significantly increased NMDAR1 levels in the striatum, while the 5-HT2a/2c antagonist mianserin tended to produce an increase that did not achieve statistical significance. These findings indicate that the dopaminergic antagonist properties of haloperidol are likely most responsible for its regulation of this subunit. In contrast, the atypical APD clozapine had no effect on striatal NMDAR1 levels, consistent with the relatively weaker influence of this drug on nigrostriatal DA function. The second major finding of the present study was the ability of haloperidol and clozapine to increase GluR1 levels in the medial prefrontal cortex (PFC), whereas chronic SCH 23390 treatment decreased GluR1 levels.