gebhart/patrepeval huggingface dataset:
Salt-Induced Swelling and Electrochemical Property Change of Hyaluronic Acid/Myoglobin Multilayer Films (2007)

The ionic strength in supporting electrolyte solution had a significant influence on the electrochemical and electrocatalytic behaviors of myoglobin (Mb) in {HA/Mb}n films, which were assembled layer-by-layer on pyrolytic graphite (PG) electrodes with oppositely charged hyaluronic acid (HA) and Mb. The results of cyclic voltammetry (CV), quartz crystal microbalance (QCM), scanning electron microscopy (SEM), rotating disk voltammetry (RDV), and electrochemical impedance spectroscopy (EIS) showed that after incubation with testing solution at high concentration of salt (CKCl), the {HA/Mb}n films swelled and the film permeability was enhanced, suggesting that the external salt ions and accompanied water molecules in the exposure solution are incorporated into the films. Systematic investigation of the type and size effect of counterions in supporting electrolyte solution on the electrochemical responses for the {HA/Mb}n films and the positive shift of the formal potential (E degrees ') with CKCl suggest that it is cationic rather than anionic counterions that control the electrode process of {HA/Mb}n films at PG electrodes with electron hopping mechanism. The salt-induced swelling of {HA/Mb}n films facilitated the transportation of counterions, and then accelerated the electron transfer of Mb in the films with the underlying electrodes, making the film electrodes show better CV responses. The comparative study showed that only Mb layer-by-layer films assembled with "soft" and flexible polyions could demonstrate the salt-induced effect and that the {HA/Mb}n films showed better swelling capability than {PSS/Mb}n films (PSS = poly(styrenesulfonate)) due to the unique character of HA.
Damage to the Insula Disrupts Addiction to Cigarette Smoking (2007)

A number of brain systems have been implicated in addictive behavior, but none have yet been shown to be necessary for maintaining the addiction to cigarette smoking. We found that smokers with brain damage involving the insula, a region implicated in conscious urges, were more likely than smokers with brain damage not involving the insula to undergo a disruption of smoking addiction, characterized by the ability to quit smoking easily, immediately, without relapse, and without persistence of the urge to smoke. This result suggests that the insula is a critical neural substrate in the addiction to smoking.
Thin Film Assemblies of Molecularly-Linked Metal Nanoparticles and Multifunctional Properties (2009)

The use of metal nanoparticles as building blocks toward thin film assembly creates intriguing opportunities for exploring multifunctional properties. Such an exploration requires the ability to engineer the size, shape, composition, and especially interparticle properties in nanoparticle assemblies for harnessing the collective properties of the nanoscale building blocks. This article highlights some of the important findings of our investigations of thin film assemblies of molecularly linked nanoparticles for exploiting their multifunctional and collective properties in molecular recognition and chemical sensing. The thermally activated processing approach presents a viable pathway for nanoengineering metal, alloy, and core-shell nanoparticles as building blocks. The molecular mediator-templating approach offers an effective strategy to thin film assemblies of the nanoscale building blocks that impart multifunctional properties. In such thin film assemblies, the interparticle interactions and structures dictate the correlation between the nanostructural parameters and the optical and electrical properties. By highlighting selected examples involving ligand-framework binding of ionic species at the film/liquid interface and electrical responses to molecular sorption at the film/gas interface, the multifunctional properties of the thin film assemblies are further discussed in terms of interparticle covalent, hydrogen bonding, ionic, or van der Waals interactions in a framework-type architecture for the creation of molecular recognition and chemical sensing sites that can be tuned chemically or electrochemically. Implications of these insights to expanding the exploration of nanoparticle thin film assemblies for a wide range of technological applications are also discussed.
Evaluation of five glycoprotein tumour markers (CEA, CA-50, CA-19-9, CA-125, CA-15-3) for the prognosis of renal-cell carcinoma (1997)

Increased levels of glycoprotein tumour markers have been observed in sera of patients with renal-cell carcinoma. Five different glycoprotein markers [carcinoembryonic antigen (CEA), CA-50, CA-19-9, CA-125 and CA-15-3] were assessed in 154 consecutive patients with renal-cell carcinoma before initiation of therapy. To evaluate their prognostic information, the serum tumour markers were compared with tumour stage and grade. Actuarial survival was calculated using the Kaplan-Meier method, and univariate and multivariate analyses were performed to determine the prognostic significance of the markers. Elevated serum levels were found for all markers tested except for CEA. For CA-125 and for CA-15-3, elevated serum levels were correlated to clinical stage and tumour grade. For patients with elevated CA-125, survival time was significantly shorter than for patients with normal CA-125 levels. Using the Cox proportional-hazard model, we identified clinical stage, tumour grade and serum CA-125 as independent prognostic factors. Serum CA-125 and CA-15-3 may be useful as an adjunct in the staging of renal-cell carcinoma. CA-125 also gives prognostic information and might be of predictive value in renal-cell carcinoma.
Representation and Learning in Information Retrieval (1991)

This dissertation introduces a new theoretical model for text classification systems, including systems for document retrieval, automated indexing, electronic mail filtering, and similar tasks. The Concept Learning model emphasizes the role of manual and automated feature selection and classifier formation in text classification. It enables drawing on results from statistics and machine learning in explaining the effectiveness of alternate representations of text, and specifies desirable characteristics of text representations. The use of syntactic parsing to produce indexing phrases has been widely investigated as a possible route to better text representations. Experiments with syntactic phrase indexing, however, have never yielded significant improvements in text retrieval performance. The Concept Learning model suggests that the poor statistical characteristics of a syntactic indexing phrase representation negate its desirable semantic characteristics. The application of term clustering to this representation to improve its statistical properties while retaining its desirable meaning properties is proposed. Standard term clustering strategies from information retrieval (IR), based on cooccurrence of indexing terms in documents or groups of documents, were tested on a syntactic indexing phrase representation. In experiments using a standard text retrieval test collection, small effectiveness improvements were obtained. As a means of evaluating representation quality, a text retrieval test collection introduces a number of confounding factors. In contrast, the text categorization task allows much cleaner determination of text representation properties. In preparation for the use of text categorization to study text representation, a more effective and theoretically well-founded probabilistic text categorization algorithm was developed, building on work by Maron, Fuhr, and others. Text categorization experiments supported a number of predictions of the Concept Learning model about properties of phrasal representations, including dimensionality properties not previously measured for text representations. However, in carefully controlled experiments using syntactic phrases produced by Church's stochastic bracketer, in conjunction with reciprocal nearest neighbor clustering, term clustering was found to produce essentially no improvement in the properties of the phrasal representation. New cluster analysis approaches are proposed to remedy the problems found in traditional term clustering methods.
Bidirectional alterations of interhemispheric parietal balance by non-invasive cortical stimulation (2009)

Transcranial direct current stimulation is a painless, non-invasive brain stimulation technique that allows one to induce polarity-specific excitability changes in the human brain. Here, we investigated, for the first time in a 'proof of principle' study, the behavioural effect of transcranial direct current stimulation on visuospatial attention in both healthy controls and stroke patients suffering from left visuospatial neglect. We applied anodal, cathoP:dal or sham transcranial direct current stimulation (57 microA/cm(2), 10 min) to the left or right posterior parietal cortex. Using a visual detection task in a group of right-handed healthy individuals (n = 20), we observed that transcranial direct current stimulation enhanced or impaired performance depending on stimulation parameters (i.e. current polarity) and stimulated hemisphere. These results are in good accordance with classic models of reciprocal interhemispheric competition ('rivalry'). In a second experiment, we investigated the potential of transcranial direct current stimulation to ameliorate left visuospatial neglect (n = 10). Interestingly, both the inhibitory effect of cathodal transcranial direct current stimulation applied over the unlesioned posterior parietal cortex and the facilitatory effect of anodal transcranial direct current stimulation applied over the lesioned posterior parietal cortex reduced symptoms of visuospatial neglect. Taken together, our findings suggest that transcranial direct current stimulation applied over the posterior parietal cortex can be used to modulate visuospatial processing and that this effect is exerted by influencing interhemispheric reciprocal networks. These novel findings also suggest that a transcranial direct current stimulation-induced modulation of interhemispheric parietal balance may be used clinically to ameliorate visuospatial attention deficits in neglect patients.
What makes the bacteriophage Î» Red system useful for genetic engineering: molecular mechanism and biological function (2001)

Recent studies have generated interest in the use of the homologous recombination system of bacteriophage lambda for genetic engineering. The system, called Red, consists primarily of three proteins: lambda exonuclease, which processively digests the 5'-ended strand of a dsDNA end; beta protein, which binds to ssDNA and promotes strand annealing; and gamma protein, which binds to the bacterial RecBCD enzyme and inhibits its activities. These proteins induce a 'hyper-rec' state in Escherichia coli and other bacteria, in which recombination events between DNA species with as little as 40 bp of shared sequence occur at high frequency. Red-mediated recombination in the hyper-rec bacterium proceeds via a number of different pathways, and with the involvement of different sets of bacterial proteins, depending in part on the nature of the recombining DNA species. The role of high-frequency double-strand break repair/recombination in the life cycle of the lambdoid phages is discussed.
Evaluation of DNA from the Papanicolaou Test to Detect Ovarian and Endometrial Cancers (2013)

Papanicolaou (Pap) smears have revolutionized the management of patients with cervical cancers by permitting the detection of early, surgically curable tumors and their precursors. In recent years, the traditional Pap smear has been replaced by a liquid-based method, which allows not only cytologic evaluation but also collection of DNA for detection of human papillomavirus, the causative agent of cervical cancer. We reasoned that this routinely collected DNA could be exploited to detect somatic mutations present in rare tumor cells that accumulate in the cervix once shed from endometrial or ovarian cancers. A panel of genes that are commonly mutated in endometrial and ovarian cancers was assembled with new whole-exome sequencing data from 22 endometrial cancers and previously published data on other tumor types. We used this panel to search for mutations in 24 endometrial and 22 ovarian cancers and identified mutations in all 46 samples. With a sensitive massively parallel sequencing method, we were able to identify the same mutations in the DNA from liquid Pap smear specimens in 100% of endometrial cancers (24 of 24) and in 41% of ovarian cancers (9 of 22). Prompted by these findings, we developed a sequence-based method to query mutations in 12 genes in a single liquid Pap smear specimen without previous knowledge of the tumor's genotype. When applied to 14 samples selected from the positive cases described above, the expected tumor-specific mutations were identified. These results demonstrate that DNA from most endometrial and a fraction of ovarian cancers can be detected in a standard liquid-based Pap smear specimen obtained during routine pelvic examination. Although improvements need to be made before applying this test in a routine clinical manner, it represents a promising step toward a broadly applicable screening methodology for the early detection of gynecologic malignancies.
Regulation of Reactive Oxygen Species and Genomic Stability in Hematopoietic Stem Cells (2008)

Hematopoietic stem cells (HSCs) are defined by their ability both to self-renew and to give rise to fresh blood cells throughout the lifetime of an animal. The failure of HSCs to self-renew during aging is believed to depend on several intrinsic (cell-autonomous) and extrinsic (non-cell-autonomous) factors. In this review, we focus on how dysregulation of reactive oxygen species (ROS) and disruptions of genomic stability can impair HSC functions. Recently, it was shown that long-term self-renewing HSCs normally possess low levels of intracellular ROS. However, when intracellular ROS levels become excessive, they cause senescence or apoptosis, resulting in a failure of HSC self-renewal. Repression of intracellular ROS levels in HSCs by treatment with an antioxidant that scavenges ROS can rescue HSC functions, indicating that excess ROS levels are at the root of HSC failure. Products of numerous genes that are involved in either DNA-damage responses or longevity-related signaling contribute to the maintenance of the HSC self-renewal capacity. Further investigations on the molecular mechanisms of ROS regulation and on the manipulation of excess ROS levels could lead to the development of novel therapeutics for hematopoietic diseases, regenerative medicine, and the prevention of leukemia.
Purification of cachectin, a lipoprotein lipase-suppressing hormone secreted by endotoxin-induced RAW 264.7 cells. (1985)

Previous studies have indicated that endotoxin and other bacterial and protozoal products can stimulate macrophages to produce a factor that can suppress the activity of the enzyme lipoprotein lipase (LPL), in vivo and in vitro. In the present report we describe the purification of this factor, cachectin, to apparent homogeneity from the conditioned medium of endotoxin-stimulated RAW 264.7 cells. The isolated protein has an isoelectric point of 4.7 and a subunit molecular weight of 17,000. Although cachectin's isoelectric point and molecular weight are similar to those described for interleukin 1, pure cachectin has no leukocyte-activating factor (LAF) activity. Cachectin at a concentration of 10(-11) M has the ability to suppress the LPL activity of the 3T3-L1 adipocyte cell line by 80%. Binding studies using radio-labeled cachectin and 3T3-L1 adipocytes and C2 myotubules revealed approximately 10(4) high-affinity receptors per cell on both cell types (Ka, 3 X 10(9]. Cachectin receptors were also present on liver membranes but were absent on erythrocytes and lymphocytes. The isolation of cachectin and characterization of its receptor should facilitate further investigations into the role of cachectin and other macrophage mediators in the metabolic derangements that occur during infection and cachexia.
The development of multiple reaction monitoring assays for liver‐derived plasma proteins (2007)

There is wide interpatient variability in toxicity to chemotherapeutic drugs and a lack of routine clinical tests for prospectively identifying patients at risk of developing toxicity from chemotherapy. An empirically driven MS strategy has been developed to monitor liver-derived plasma proteins as potential biomarkers of early toxicity. Multiple reaction monitoring (MRM) has been used to assess 46 candidate peptides from 18 liver-derived proteins. Following an iterative process of assay design, optimisation and assessment we selected 29 MRM assays (median CV 4.6%, range 1.2-11.6%) and monitored changes in levels of plasma proteins from a small number of colorectal cancer (CRC) patients undergoing chemotherapy. We demonstrated MRM assay robustness, and show that patients undergo minor elevation in plasma proteins when profiled on Day 3 of the chemotherapeutic regime. The MRM assays were in general agreement with 2-D DIGE-based quantitation from the same patient samples. The data supports the application of MRM-based methods as facile, highly reproducible, medium-throughput techniques that warrant expanded investigation for clinical utility in identifying patients at risk of developing chemotoxicity.
Local feature analysis: a general statistical theory for object representation (1996)

Low-dimensional representations of sensory signals are key to solving many of the computational problems encountered in high-level vision. Principal component analysis (PCA) has been used in the past to derive practically useful compact representations for different classes of objects. One major objection to the applicability of PCA is that it invariably leads to global, non-topographic representations that are not amenable to further processing and are not biologically plausible. In this paper we present a new mathematical construction, local feature analysis (LFA), for deriving local topographic representations for any class of objects. The LFA representations are sparse-distributed and, hence, are effectively low-dimensional and retain all the advantages of the compact representations of the PCA. But, unlike the global eigenmodes, they give a description of objects in terms of statistically derived local features and their positions. We illustrate the theory by using it to extract local features for three ensembles: 2D images of faces without background, 3D surfaces of human heads, and finally 2D faces on a background. The resulting local representations have powerful applications in head segmentation and face recognition.
<title>Error-bounded reduction of triangle meshes with multivariate data</title> (1996)

Interactive visualization is complicated by the complexity of the objects being visualized. Sampled or computed scientific data is often dense, in order to capture high frequency components in measured data or to accurately model a physical process. Common visualization techniques such as isosurfacing on such large meshes generate more geometric primitives than can be rendered in an interactive environment. Geometric mesh reduction techniques have been developed in order to reduce the size of a mesh with little compromise in image quality. Similar techniques have been used for functional surfaces (terrain maps) which take advantage of the planar projection. We extend these methods to arbitrary surfaces in 3D and to any number of variables defined over the mesh by developing a algorithm for mapping from a surface mesh to a reduced representation and measuring the introduced error in both the geometry and the multivariate data. Furthermore, through error propagation, our algorithm ensures that the errors in both the geometric representation and multivariate data do not exceed a user-specified upper bound.
Molecular Complexes of Homologous Alkanedicarboxylic Acids with Isonicotinamide:  X-ray Crystal Structures, Hydrogen Bond Synthons, and Melting Point Alternation (2003)

Crystallization of α,ω-alkanedicarboxylic acids (HOOC−(CH2)n-2−COOH, n = 2−6) with isonicotinamide (IN) is carried out in 1:2 and 1:1 stoichiometry. Five cocrystals of (diacid)·(IN)2 composition (diacid = oxalic acid, malonic acid, succinic acid, glutaric acid, and adipic acid) are characterized by X-ray diffraction at 153(2) K. Tapes of acid−pyridine O−H···N and amide−amide N−H···O hydrogen bond synthons stabilize these five crystal structures as predicted by the hierarchic model: the best donor (COOH) and best acceptor group (pyridine N) hydrogen bond as acid−pyridine and the second best donor−acceptor group (CONH2) aggregates as an amide dimer. Glutaric acid and adipic acid cocrystallize in 1:1 stoichiometry also, (diacid)·(IN), with acid−pyridine and acid−amide hydrogen bonds. Synthon energy calculations (ΔEsynthon, RHF/6-31G**) explain the observed hydrogen bond preferences in 1:2 (five examples) and 1:1 (two examples) cocrystals. The acid−pyridine hydrogen bond is favored over the acid−amide dimer for strong carboxylic acids because the difference between ΔEacid-pyridine and ΔEacid-amide (−2.21 kcal mol-1) is greater than the difference for weak acids (−0.77 kcal mol-1), which cocrystallize with both of these hydrogen bond synthons. We suggest ΔEsynthon as a semiquantitative parameter to rank hydrogen bond preferences and better understand supramolecular organization in the multifunctional acid−IN system. Melting point alternation in five homologous (diacid)·(IN)2 cocrystals is correlated with changes in crystal density and packing fraction.
Optoelectronic properties of polymer-nanocrystal composites active at near-infrared wavelengths (2005)

We report a systematic study of the optoelectronic processes occurring in composites made of near-infrared (IR) emitting nanocrystals and conjugated polymers. We focus on PbSe and InAs∕ZnSe blended with polyphenylenevinylene-type polymers. We find that the process responsible for quenching the visible luminescence of the polymer by the nanocrystal varies depending on the nanocrystal composite. Moreover, the high (66%) energy-transfer efficiency from the polymer to the PbSe nanocrystal does result in significant emission at the near IR. Our measurements suggest that the host may be doping the PbSe nanocrystal, thus making the nonradiative Auger process favorable. For InAs we find the energy levels well aligned inside the polymer band gap, making it an efficient charge trap which acts as a luminescence center. Through two-dimensional numerical modeling of the charge transport in such composite films we highlight the importance of morphology (nanocrystal distribution) control.