gebhart/patrepeval huggingface dataset:
A re-examination of text categorization methods (1999)

This paper reports a controlled study with statistical signicance tests on ve text categorization methods: the Support Vector Machines (SVM), a k-Nearest Neighbor (kNN) classi er, a neural network (NNet) approach, the Linear Leastsquares Fit (LLSF) mapping and a Naive B a yes (NB) classier. We focus on the robustness of these methods in dealing with a skewed category distribution, and their performance as function of the training-set category frequency. Our results show that SVM, kNN and LLSF signi cantly outperform NNet and NB when the number of positive training instances per category are small (less than ten), and that all the methods perform comparably when the categories are su ciently common (over 300 instances).
Electrical Alternans and Vulnerability to Ventricular Arrhythmias (1994)

Electrical alternans affecting the ST segment and T wave is common among patients at increased risk for ventricular arrhythmias. Subtle electrical alternans on the electrocardiogram may serve as a noninvasive marker of vulnerability to ventricular arrhythmias.
Hypothermia-associated Protection from Ischemic Brain Injury (1996)

There is a large amount of experimental evidence that mild hypothermia in laboratory animals will protect the brain from ischemic injury. Conversely, mild hyperthermia will exacerbate injury. Supporting data in humans are limited. However, cerebral protection has consistently been demonstrated in humans subjected to complete circulatory arrest during profound hypothermia. Induced and passive mild hypothermia have become common in the management of patients at risk for ischemic neurological injury. Currently, brain temperature is managed largely by altering core temperature. Limitations of this approach are that gradients can develop between brain and core temperatures as a result of the surgical intervention, anesthetic interventions, or the patient's pathology. Further, large reductions in systemic temperature may place an undue burden on systemic physiology and, in extreme examples, systemic factors may adversely affect neurological well-being. Obviously, proper temperature management in humans at high risk for neurological injury will benefit from the following factors: First, greater evidence is needed that small changes in temperature modulate outcome in humans, commensurate with demonstrations of benefit in animals. Second, better methods are needed to monitor brain temperature during periods of risk for ischemic injury. And third, management techniques should be identified that will use brain-to-core temperature gradients to the patient's advantage, thus producing optimal alterations in brain temperature while minimally affecting systemic temperature and physiology. Before these goals can be accomplished, more research is needed, both in laboratory animals and in humans.
Facile synthesis of novel indolo[3,2-b]carbazole derivatives and a chromogenic-sensing 5,12-dihydroindolo[3,2-b]carbazole (2008)

Novel indolo[3,2-b]carbazole derivatives and a chromogenic-sensing 5,12-dihydroindolo[3,2-b]carbazole have been synthesized starting from tetra-tert-butylated 6,12-diaryl-5,11-dihydroindolo[3,2-b]carbazoles, which were prepared via an efficient tert-butylation of 6,12-diaryl-5,11-dihydroindolo[3,2-b]carbazoles.
Identification of conformational B-cell Epitopes in an antigen from its primary sequence (2010)

This study demonstrates that prediction of conformational B-cell epitope in an antigen is possible from is primary sequence. This study will be very useful in predicting conformational B-cell epitopes in antigens whose tertiary structures are not available. A web server CBTOPE has been developed for predicting B-cell epitope http://www.imtech.res.in/raghava/cbtope/.
Control-flow analysis of dynamic languages via pointer analysis (2015)

We demonstrate how to map a control-flow analysis for a higher-order language (dynamic languages are typically higher-order) into a pointer analysis for a first-order language, such as C. This allows us to use existing pointer analysis tools to perform a control-flow analysis, exploiting their technical advancements and the engineering effort that went into developing them. We compare the results of two recent parallel pointer analysis tools with a parallel control-flow analysis tool. While it has been known that a control-flow analysis of higher-order languages and a pointer analysis of first-order languages are very similar, we demonstrate that these two analyses are actually more similar than previously thought. We present the first mapping between a high-order control-flow analysis and a pointer analysis.
The Effects of SO<sub>2</sub> and SO<sub>3</sub> Poisoning on Cu/Zeolite SCR Catalysts (2009)

&lt;div class="htmlview paragraph"&gt;Copper/zeolite catalysts are the leading urea SCR catalysts for NOx emission treatment in diesel applications. Sulfur poisoning directly impacts the overall SCR performance and is still a durability issue for Cu/zeolite SCR catalysts. Most studies on sulfur poisoning of Cu/zeolite SCR catalysts have been based on SO&lt;sub&gt;2&lt;/sub&gt; as the poisoning agent. It is important to investigate the relative poisoning effects of SO&lt;sub&gt;3&lt;/sub&gt;, especially for systems with DOCs in front of Cu/zeolite SCR catalysts.&lt;/div&gt; &lt;div class="htmlview paragraph"&gt;It was observed that SCR activity was significantly reduced for samples poisoned by SO&lt;sub&gt;3&lt;/sub&gt; vs. those poisoned by SO&lt;sub&gt;2&lt;/sub&gt;. The sulfur was released mainly as SO&lt;sub&gt;2&lt;/sub&gt; for both samples poisoned by SO&lt;sub&gt;2&lt;/sub&gt; and SO&lt;sub&gt;3&lt;/sub&gt;. The temperatures and the magnitudes of released SO&lt;sub&gt;2&lt;/sub&gt; peaks however, were very different between the samples poisoned by SO&lt;sub&gt;2&lt;/sub&gt; vs. SO&lt;sub&gt;3&lt;/sub&gt;. The results indicate that sulfur poisoning by SO&lt;sub&gt;2&lt;/sub&gt; and SO&lt;sub&gt;3&lt;/sub&gt; are not equivalent, with different poisoning mechanisms and impacts. This study raises an important sulfur poisoning concern for the systems with DOCs in front of Cu/zeolite SCR catalysts in diesel engine applications.&lt;/div&gt;
Two Acyclic Kahalalides from the Sacoglossan Mollusk Elysia rufescens (1997)

The sacoglossan mollusk Elysia rufescens elaborates six cyclic depsipeptides, kahalalides A−F. Its green algal diet (Bryopsis sp.) contains kahalalide G, which is an acyclic analogue of kahalalide F. Further analysis of the molluskan extract revealed two new acyclic peptides, kahalalide H (1) and kahalalide J (2), which share only four amino acids (leucine, phenylalanine, serine, and valine) with kahalalide F. Both contain aspartic acid and 4-hydroxyproline residues, and kahalalide J (2) also contains lysine. They have in common a β-hydroxy fatty acid, 3-hydroxy-9-methyldecanoic, previously encountered in kahalalide E. For kahalalide H (1) we succeeded in determining the sequential positions of the antipodal d- and l-phenylalanine. In common with the acyclic constituent of the alga, kahalalide G, the new compounds lack significant cytotoxicity.
Optimization techniques in modern sampling theory (2009)

Sampling theory has benefited from a surge of research in recent years, due in part to intense research in wavelet theory and the connections made between the two fields. In this chapter we present several extensions of the Shannon theorem, which treat a wide class of input signals, as well as nonideal-sampling and constrained-recovery procedures. This framework is based on an optimization viewpoint, which takes into account both the goodness of fit of the reconstructed signal to the given samples, as well as relevant prior knowledge on the original signal. Our exposition is based on a Hilbert-space interpretation of sampling techniques, and relies on the concepts of bases (frames) and projections. The reconstruction algorithms developed in this chapter lead to improvement over standard interpolation approaches in signal- and image-processing applications.
Human Breast Cancer Tissues Contain Abundant Phosphatidylcholine(36∶1) with High Stearoyl-CoA Desaturase-1 Expression (2013)

Breast cancer is the leading cause of cancer and mortality in women worldwide. Recent studies have argued that there is a close relationship between lipid synthesis and cancer progression because some enzymes related to lipid synthesis are overexpressed in breast cancer tissues. However, lipid distribution in breast cancer tissues has not been investigated. We aimed to visualize phosphatidylcholines (PCs) and lysoPCs (LPCs) in human breast cancer tissues by performing matrix assisted laser desorption/ionization-imaging mass spectrometry (MALDI-IMS), which is a novel technique that enables the visualization of molecules comprehensively. Twenty-nine breast tissue samples were obtained during surgery and subjected to MALDI-IMS analysis. We evaluated the heterogeneity of the distribution of PCs and LPCs on the tissues. Three species [PC(32∶1), PC(34∶1), and PC(36∶1)] of PCs with 1 mono-unsaturated fatty acid chain and 1 saturated fatty acid chain (MUFA-PCs) and one [PC(34∶0)] of PCs with 2 saturated fatty acid chains (SFA-PC) were relatively localized in cancerous areas rather than the rest of the sections (named reference area). In addition, the LPCs did not show any biased distribution. The relative amounts of PC(36∶1) compared to PC(36∶0) and that of PC(36∶1) to LPC(18∶0) were significantly higher in the cancerous areas. The protein expression of stearoyl-CoA desaturase-1 (SCD1), which is a synthetic enzyme of MUFA, showed accumulation in the cancerous areas as observed by the results of immunohistochemical staining. The ratios were further analyzed considering the differences in expressions of the estrogen receptor (ER), human epidermal growth factor receptor 2 (HER2), and Ki67. The ratios of the signal intensity of PC(34:1) to that of PC(34:0) was higher in the lesions with positive ER expression [corrected]. The contribution of SCD1 and other enzymes to the formation of the observed phospholipid composition is discussed.
An architectural map of the anaphase-promoting complex (2006)

The anaphase-promoting complex or cyclosome (APC) is an unusually complicated ubiquitin ligase, composed of 13 core subunits and either of two loosely associated regulatory subunits, Cdc20 and Cdh1. We analyzed the architecture of the APC using a recently constructed budding yeast strain that is viable in the absence of normally essential APC subunits. We found that the largest subunit, Apc1, serves as a scaffold that associates independently with two separable subcomplexes, one that contains Apc2 (Cullin), Apc11 (RING), and Doc1/Apc10, and another that contains the three TPR subunits (Cdc27, Cdc16, and Cdc23). We found that the three TPR subunits display a sequential binding dependency, with Cdc27 the most peripheral, Cdc23 the most internal, and Cdc16 between. Apc4, Apc5, Cdc23, and Apc1 associate interdependently, such that loss of any one subunit greatly reduces binding between the remaining three. Intriguingly, the cullin and TPR subunits both contribute to the binding of Cdh1 to the APC. Enzymatic assays performed with APC purified from strains lacking each of the essential subunits revealed that only cdc27Delta complexes retain detectable activity in the presence of Cdh1. This residual activity depends on the C-box domain of Cdh1, but not on the C-terminal IR domain, suggesting that the C-box mediates a productive interaction with an APC subunit other than Cdc27. We have also found that the IR domain of Cdc20 is dispensable for viability, suggesting that Cdc20 can activate the APC through another domain. We have provided an updated model for the subunit architecture of the APC.
Exosome‐mediated inflammasome signaling after central nervous system injury (2015)

Abstract Neuroinflammation is a response against harmful effects of diverse stimuli and participates in the pathogenesis of brain and spinal cord injury ( SCI ). The innate immune response plays a role in neuroinflammation following CNS injury via activation of multiprotein complexes termed inflammasomes that regulate the activation of caspase 1 and the processing of the pro‐inflammatory cytokines IL ‐1β and IL ‐18. We report here that the expression of components of the nucleotide‐binding and oligomerization domain (NOD)‐like receptor protein‐1 ( NLRP ‐1) inflammasome, apoptosis speck‐like protein containing a caspase recruitment domain ( ASC ), and caspase 1 are significantly elevated in spinal cord motor neurons and cortical neurons after CNS trauma. Moreover, NLRP 1 inflammasome proteins are present in exosomes derived from CSF of SCI and traumatic brain‐injured patients following trauma. To investigate whether exosomes could be used to therapeutically block inflammasome activation in the CNS , exosomes were isolated from embryonic cortical neuronal cultures and loaded with short‐interfering RNA (si RNA ) against ASC and administered to spinal cord‐injured animals. Neuronal‐derived exosomes crossed the injured blood–spinal cord barrier, and delivered their cargo in vivo, resulting in knockdown of ASC protein levels by approximately 76% when compared to SCI rats treated with scrambled si RNA . Surprisingly, si RNA silencing of ASC also led to a significant decrease in caspase 1 activation and processing of IL ‐1β after SCI . These findings indicate that exosome‐mediated si RNA delivery may be a strong candidate to block inflammasome activation following CNS injury. image We propose the following signaling cascade for inflammasome activation in peripheral tissues after CNS injury: CNS trauma induces inflammasome activation in the nervous system and secretion of exosomes containing inflammasome protein cargo into cerebral spinal fluid. The inflammasome containing exosomes then fuse with target cells to activate the innate immune response in peripheral tissues. We suggest that these findings may be used to develop new therapeutics to treat the devastating inflammation and cell destruction evoked by CNS injuries. IL‐1β and IL‐18 = pro‐inflammatory cytokines.
Electric field effect on magnetization at the Fe/MgO(001) interface (2010)

Density-functional calculations are performed to explore magnetoelectric effects originating from the influence of an external electric field on magnetic properties of the Fe/MgO(001) interface. It is shown that the effect on the interface magnetization and magnetocrystalline anisotropy can be substantially enhanced if the electric field is applied across a dielectric material with a large dielectric constant. In particular, we predict an enhancement of the interface magnetoelectric susceptibility by a factor of the dielectric constant of MgO over that of the free standing Fe (001) surface. We also predict a significant effect of electric field on the interface magnetocrystalline anisotropy due to the change in the relative occupancy of the 3d-orbitals of Fe atoms at the Fe/MgO interface. These results may be interesting for technological applications such as electrically controlled magnetic data storage.
Central Role of Muc5ac Expression in Mucous Metaplasia and Its Regulation by Conserved 5′ Elements (2007)

Mucus hypersecretion contributes to morbidity and mortality in many obstructive lung diseases. Gel-forming mucins are the chief glycoprotein components of airway mucus, and elevated expression of these during mucous metaplasia precedes the hypersecretory phenotype. Five orthologous genes (MUC2, MUC5AC, MUC5B, MUC6, and MUC19) encode the mammalian gel-forming mucin family, and several have been implicated in asthma, cystic fibrosis, and chronic obstructive pulmonary disease pathologies. However, in the absence of a comprehensive analysis, their relative contributions remain unclear. Here, we assess the expression of the entire gel-forming mucin gene family in allergic mouse airways and show that Muc5ac is the predominant gel-forming mucin induced. We previously showed that the induction of mucous metaplasia in ovalbumin-sensitized and -challenged mouse lungs occurs within bronchial Clara cells. The temporal induction and localization of Muc5ac transcripts correlate with the induced expression and localization of mucin glycoproteins in bronchial airways. To better understand the tight regulation of Muc5ac expression, we analyzed all available 5'-flanking sequences of mammalian MUC5AC orthologs and identified evolutionarily conserved regions within domains proximal to the mRNA coding region. Analysis of luciferase reporter gene activity in a mouse transformed Clara cell line demonstrates that this region possesses strong promoter activity and harbors multiple conserved transcription factor-binding motifs. In particular, SMAD4 and HIF-1alpha bind to the promoter, and mutation of their recognition motifs abolishes promoter function. In conclusion, Muc5ac expression is the central event in antigen-induced mucous metaplasia, and phylogenetically conserved 5' noncoding domains control its regulation.
Expression of centrosome‐associated gene products is linked to tetraploidization in mantle cell lymphoma (2007)

In mantle cell lymphoma (MCL), a blastoid variant with a striking tendency to harbor chromosome numbers in the tetraploid range has been identified. Centrosome aberrations have recently been implicated in the induction of aneuploidy in many human malignancies including MCL by malsegregation of chromosomes during anaphase of mitosis. Recently, we showed that centrosome aberrations occur more frequently in tetraploid MCL as compared to their diploid counterparts. To test the hypothesis of an association between tetraploidization and expression of genes coding for centrosomal proteins in MCL, tumor RNA of 33 MCL samples was hybridized to custom-made cDNA microarrays, representing 4,628 distinct human gene-specific fragments, with particular enrichment for cancer-relevant (n = 2,440) and centrosome-associated genes (n = 359). Notably, 4 of the 6 most significant genes (CAMKK2, PCNT2, TUBGCP3, TUBGCP4) discriminating between diploid and near-tetraploid MCL code for centrosomal proteins. As confirmed by quantitative RT-PCR analysis, calcium/calmodulin-dependent protein kinase II (CAMKK2), pericentrin (PCNT2) and gamma-tubulin complex associated protein 3 (TUBGCP3) were all found to be significantly higher expressed in near-tetraploid than in diploid MCL samples. In conclusion, we describe a comprehensive expression signature of a set of genes associated with tetraploidization in MCL. The high expression level of centrosome-associated gene products in blastoid MCL matches the description of more frequent centrosome aberrations in this MCL variant.
Design of non-uniform capacity-approaching signaling for optical wireless intensity channels (2008)

Analysis and design of near capacity approaching non-uniform signaling for optical intensity pulse amplitude modulation (PAM) channels is presented. A discrete nonuniform source distribution with quantized-level probabilities is presented. The proposed source distribution approaches the channel capacity while remaining practical for implementation. A significant gap in the mutual information between the non-uniform quantized-level distributions and uniform M-ary PAM is obtained. For example, at low SNR, non-uniform binary signalling has over four times the rate of uniform constellations. Multilevel coding and multistage decoding are proposed to approach the rate gains due to non-uniform signaling.
Radioimmunotherapy of neoplastic meningitis in rats using an alpha-particle-emitting immunoconjugate. (1994)

Because of their short range and high linear energy transfer, alpha-particles may be particularly effective in the treatment of neoplastic meningitis. Monoclonal antibody 81C6 was labeled with alpha-particle-emitting 211At using N-succinimidyl3-[211At]astatobenzoate, and the efficacy and toxicity of this immunoconjugate were evaluated in an athymic rat model. Animals were given injections via a chronic indwelling catheter with 5 x 10(5) TE-671 human rhabdomyosarcoma cells and treated 8 days later with single intrathecal doses of either saline or 4-18 microCi of 211At-labeled specific 81C6 antibody or isotype-matched control 211At-labeled 45.6 antibody. In the first experiment, 4, 7, and 13 microCi 211At-labeled 81C6 produced statistically significant (P = 0.004-0.02) increases in median survival of 33, 29, and 51%, respectively, as compared with saline. Two of 10 animals receiving the 13-microCi dose lived for 6 months before being killed for histological analysis. In the second experiment, 12 microCi of 211At-labeled 45.6 did not increase median survival significantly relative to saline control, while 12 microCi of 211At-labeled 81C6 increased median survival by 113% (P < 0.005) and resulted in 33% apparent cures. Five of 10 animals receiving 18 microCi of 211At-labeled 81C6 survived until they were killed at 295 days. An additional study was performed in animals given intrathecal injections of 5 x 10(6) TE-671 cells and given a single dose of 18 microCi of 211At-labeled 81C6 or 211At-labeled 45.6. At this higher cell number, significantly prolonged survival was still seen for specific antibody as compared with saline (P < 0.001) and control antibody (P < 0.05). These results suggest that treatment with 211At-labeled monoclonal antibodies may be a valuable approach for neoplastic meningitis.
High aspect ratio silicon etch: A review (2010)

High aspect ratio (HAR) silicon etch is reviewed, including commonly used terms, history, main applications, different technological methods, critical challenges, and main theories of the technologies. Chronologically, HAR silicon etch has been conducted using wet etch in solution, reactive ion etch (RIE) in low density plasma, single-step etch at cryogenic conditions in inductively coupled plasma (ICP) combined with RIE, time-multiplexed deep silicon etch in ICP-RIE configuration reactor, and single-step etch in high density plasma at room or near room temperature. Key specifications are HAR, high etch rate, good trench sidewall profile with smooth surface, low aspect ratio dependent etch, and low etch loading effects. Till now, time-multiplexed etch process is a popular industrial practice but the intrinsic scalloped profile of a time-multiplexed etch process, resulting from alternating between passivation and etch, poses a challenge. Previously, HAR silicon etch was an application associated primarily with microelectromechanical systems. In recent years, through-silicon-via (TSV) etch applications for three-dimensional integrated circuit stacking technology has spurred research and development of this enabling technology. This potential large scale application requires HAR etch with high and stable throughput, controllable profile and surface properties, and low costs.