gebhart/patrepeval huggingface dataset:
Calcium-Binding Protein Protocols (2002)

Calcium-binding proteins play an important role in a variety of vital biological processes, ranging from blood clotting and signal transduction in cells, to attaching proteins to membranes and serving as an integral source of calcium. In Calcium-Binding Protocols- Volume 1: Reviews and Case Histories and Volume 2: Methods and Techniques-Hans Vogel and a panel of leading researchers review the protein chemistry and behavior of this significant class proteins, and provide a comprehensive collection of proven experimental techniques for studying it both in vitro and in vivo. This second volume focuses on cutting-edge experimental techniques for studying the solution structure, stability, dynamics, calcium-binding properties, and biological activity of calcium-binding protein in general. In addition to enzymatic assays and more routine spectroscopic and protein chemistry techniques, there are also NMR approaches, thermodynamic analyses, kinetic measurements such as surface plasmon resonance, strategies for amino acid sequence alignments, and fluorescence methods to study the distribution of calcium and calcium-binding proteins in cells. The first companion volume, Reviews and Case Histories sets the stage for this volume by introducing the various classes of intra- and extracellular calcium-binding proteins and their mode of action. Comprehensive and highly practical, the two volumes of Calcium-Binding Protocols provide experimental and clinical biologists with a host of advanced experimental methods that can be applied successfully to the study of both existing and newly discovered members of this critically important class of proteins
Bacteriology of Human Experimental Gingivitis: Effect of Plaque and Gingivitis Score (1978)

The plaque flora isolated from discrete dentogingival sites during a human gingivitis experiment was analyzed as a function of the plaque score and of the gingivitis score. When the gingivitis score was plotted as a function of the plaque score, a nonbleeding gingivitis was associated with a proportional increase in the Actinomyces sp. at the expense of the Streptococcus sp. In particular, the percentage of Actinomyces israelii increased significantly, while the percent Streptococcus sanguis decreased significantly. A. israelii also increased significantly when a bleeding gingivitis developed. When the plaque score was plotted as a function of the gingivitis score, A. israelii increased significantly as the nonbleeding gingivitis developed, but A. viscosus and Bacteroides melaninogenicus increased significantly when the bleeding gingivitis developed. The availability of a sufficient number of plaques with a plaque score of 2.0 permitted the examination of the interrelationship of gingivitis and flora minus the effect of plaque biomass. The bacteriological profile showed that when bleeding occurred, the levels and proportions of A. viscosus and B. melaninogenicus increased significantly. These findings raise the possibility that proportional changes in the gingival plaque flora may uniquely contribute to the development of gingival inflammation in this experimental model.
Liquid Biopsy to Identify Actionable Genomic Alterations (2018)

Liquid biopsy has been used extensively in solid malignancies to detect actionable driver mutations, to monitor treatment response, to detect recurrence, to identify resistance mechanisms, and to prognosticate outcome. Although many liquid biopsy sequencing platforms are being used, only five test kits have received government approval. We review representative literature on these government-approved liquid biopsy kits, which are primarily used to detect EGFR mutation in lung cancer and RAS ( KRAS, NRAS, BRAF) mutations in colorectal carcinoma. Another emerging use of single-gene liquid biopsy is to detect PIK3CA mutations and to understand resistance to hormonal blockade in breast and prostate cancers. The two most commonly used next-generation sequencing (NGS) liquid biopsy tests (Guardant 360, Guardant Health; FoundationACT, Foundation Medicine Inc.) are discussed. The ability and the applicability of NGS platform to detect tumor mutation burden are also addressed. Finally, the use of circulating tumor DNA (ctDNA) to detect minimal residual disease may be the most important use of ctDNA in the setting of tumor heterogeneity. The ability to identify "shedders" and "nonshedders" of ctDNA may provide important insight into the clinicopathologic characteristics of the tumor and portend important prognostic significance regarding survival.
Macropinocytosis Exploitation by Cancers and Cancer Therapeutics (2016)

Macropinocytosis has long been known as a primary method for cellular intake of fluid-phase and membrane-bound bulk cargo. This review seeks to re-examine the latest studies to emphasize how cancers exploit macropinocytosis to further their tumorigenesis, including details in how macropinocytosis can be adapted to serve diverse functions. Furthermore, this review will also cover the latest endeavors in targeting macropinocytosis as an avenue for novel therapeutics.
Trifluoroacetate, a contaminant in purified proteins, inhibits proliferation of osteoblasts and chondrocytes (1999)

Peptides purified by HPLC are often in the form of a trifluoroacetate (TFA) salt, because trifluoroacetic acid is used as a solvent in reversed-phase HPLC separation. However, the potential effects of this contaminant in culture systems have not been addressed previously. TFA (10(-8) to 10(-7) M) reduced cell numbers and thymidine incorporation into fetal rat osteoblast cultures after 24 h. Similar effects were found in cultures of articular chondrocytes and neonatal mouse calvariae, indicating that the effect is not specific to one cell type or to one species of origin. When the activities of the TFA and hydrochloride salts of amylin, amylin-(1-8), and calcitonin were compared in osteoblasts, cell proliferation was consistently less with the TFA salts of these peptides, resulting in failure to detect a proliferative effect or wrongly attributing an antiproliferative effect. This finding is likely to be relevant to all studies of purified peptides in concentrations above 10(-9) M in whatever cell or tissue type. Such peptides should be converted to a hydrochloride or biologically equivalent salt before assessment of their biological effects is undertaken.
Interleukin-6 is an independent predictor of mortality in patients starting dialysis treatment (2002)

The present study demonstrates that the strong predictive value of elevated IL-6 levels for poor outcome in ESRD patients is similar in both HD and PD patients starting treatment.
Metabolic effects of IGF-I and insulin in spontaneously diabetic BB/w rats (1991)

To examine the influence of insulin-dependent diabetes on the metabolic response to insulin-like growth factor I (IGF-I), awake chronically catheterized diabetic and nondiabetic BB/w rats received IGF-I (5 micrograms.kg-1.min-1) or insulin (2 mU.kg-1.min-1) for 2 h while maintaining euglycemia. In nondiabetic rats, IGF-I and insulin produced similar twofold increases in glucose uptake, but insulin was more effective in reducing hepatic glucose production (90 +/- 15 vs. 5 +/- 11%; P less than 0.001) and beta-hydroxybutyrate levels (94 +/- 1 vs. 19 +/- 6%; P less than 0.001). In diabetic rats, insulin-stimulated glucose uptake was impaired (8.5 +/- 0.9 vs. 11.5 +/- 0.9 mg.kg-1.min-1 in nondiabetics; P less than 0.05). In contrast, IGF-I-stimulated glucose uptake was identical in diabetic and nondiabetic rats. Furthermore, IGF-I suppressed glucose production by 73% (P less than 0.01) and caused a greater lowering of beta-hydroxybutyrate levels (from 2.9 +/- 0.8 to 0.8 +/- 0.3 mumol/l) in diabetic rats. We conclude that 1) the capacity of IGF-I infusion to stimulate glucose uptake is maintained in spontaneously diabetic BB rats that are insulin resistant, and 2) IGF-I infusion suppresses elevated glucose production rates and plasma ketone concentrations in diabetic rats but is relatively ineffective in nondiabetic rats. Thus the metabolic responses to infused IGF-I do not appear to be diminished in diabetic rats with impaired responses to insulin.
An Overview Of Cardiovascular Disease Burden In The United States (2007)

Cardiovascular disease (CVD) is the leading cause of death and a major cause of disability worldwide. In the United States, CVD accounted for 34.4 percent of the 2.4 million deaths in 2003 and remain a major cause of health disparities and rising health care costs. In 2006, health care spending and lost productivity from CVD exceeded 400 billion dollars. The aging population, obesity epidemic, underuse of prevention strategies, and suboptimal control of risk factors could exacerbate the future CVD burden. Increased adherence to clinical and community-level guidelines and renewed emphasis on policy, environmental, and lifestyle changes will be crucial for its effective prevention and control.
Neural Network Learning and Expert Systems (1993)

Neural Network Learning and Expert Systems is the first book to present a unified and in-depth development of neural network learning algorithms and neural network expert systems. Especially suitable for students and researchers in computer science, engineering, and psychology, this text and reference provides a systematic development of neural network learning algorithms from a computational perspective, coupled with an extensive exploration of neural network expert systems which shows how the power of neural network learning can be harnessed to generate expert systems automatically. Features include a comprehensive treatment of the standard learning algorithms (with many proofs), along with much original research on algorithms and expert systems. Additional chapters explore constructive algorithms, introduce computational learning theory, and focus on expert system applications to noisy and redundant problems. For students there is a large collection of exercises, as well as a series of programming projects that lead to an extensive neural network software package. All of the neural network models examined can be implemented using standard programming languages on a microcomputer. Bradford Books imprint
Pseudomembranous colitis in Clostridium difficile-monoassociated rats (1983)

Germfree rats were monoassociated with either a toxin-producing strain of Clostridium difficile (Tox+) or a variant of this strain (ToxR) which produced much less toxin (1/10,000) in vivo and in vitro. Monoassociation of germfree rats with C. difficile Tox+ resulted in mortality (17%) and in pathology to the small and large intestines, livers, and lungs. Cecal filtrates from the Tox+-monoassociated rats were cytotoxic for tissue culture cells. The cytotoxicity of cecal filtrates could be blocked by sera from Tox+-monoassociated rats. Monoassociation of rats with C. difficile ToxR resulted in no deaths or pathology, and much less toxin was detected in the cecal filtrates of these animals than in those of rats colonized with the Tox+ strain. This gnotobiotic model may be useful for investigating the etiology, prophylaxis, therapy, and exacerbation of C. difficile-induced pseudomembranous colitis.
Three-Dimensional Hydrodynamic Focusing in Polydimethylsiloxane (PDMS) Microchannels (2004)

This paper presents a generalization of the hydrodynamic focusing technique to three-dimensions. Three-dimensional (3-D) hydrodynamic focusing offers the advantages of precision positioning of molecules in both vertical and lateral dimensions and minimizing the interaction of the sample fluid with the surfaces of the channel walls. In an ideal approach, 3-D hydrodynamic focusing could be achieved by completely surrounding the sample flow by a cylindrical sheath flow that constrains the sample flow to the center of the channel in both the lateral and the vertical dimensions. We present here design and simulation, 3-D fabrication, and experimental results from a piecewise approximation to such a cylindrical flow. Two-dimensional (2-D) and 3-D hydrodynamic focusing chips were fabricated using micromolding methods with polydimethylsiloxane (PDMS). Three-dimensional hydrodynamic focusing chips were fabricated using the "membrane sandwich" method. Laser scanning confocal microscopy was used to study the hydrodynamic focusing experiments performed in the 2-D and 3-D chips with Rhodamine 6G solution as the sample fluid and water as the sheath fluid.
5-Fluorouracil/Leucovorin Combined with Irinotecan and Oxaliplatin (FOLFIRINOX) as Second-Line Chemotherapy in Patients with Metastatic Pancreatic Adenocarcinoma (2011)

These results confirmed the good safety profile and the efficacy of the FOLFIRINOX regimen as second-line treatment of MPA.
Molecular Determinants of Alphavirus Neurovirulence: Nucleotide and Deduced Protein Sequence Changes during Attenuation of Venezuelan Equine Encephalitis Virus (1986)

The nucleotide and deduced amino acid sequences of the structural proteins of the TC-83 vaccine strain of Venezuelan equine encephalitis (VEE) virus have been determined from a cDNA clone containing the 26S mRNA coding region. A cDNA clone encoding the equivalent region of the virulent parent VEE virus [Trinidad donkey strain (TRD)] has been sequenced previously. Comparison of the sequences of the TC-83 and TRD cDNA clones revealed 13 nucleotide differences. Neither the organization of the structural proteins (5'-capsid-E3-E2-6K-E1-3') nor the length (3762 nucleotides) of the open reading frame coding for the viral polyprotein precursor was altered during attenuation. Of the 13 nucleotide differences between the cDNA clones of TC-83 and TRD, nine occurred in the dominant population of the respective genomic RNAs from plaque-purified viruses. Six of the nine mutations were clustered in the E2 surface glycoprotein gene. All five of the nucleotide changes which produced non-conservative amino acid substitutions in the encoded proteins were located in the E2 gene. Two mutations occurred in the E1 glycoprotein gene; one was silent and the other did not alter the chemical character of the E1 protein. One nucleotide difference was found in the non-coding region immediately preceding the 5'-end of the 26S mRNA. The E2 and non-coding region mutations are candidates for the molecular determinants of VEE virus neurovirulence.
A hierarchy of cameras for 3D photography (2003)

We investigate the relationship between camera design and 3D photography, by examining the influence of camera design on the estimation of the motion and structure of a scene from video data. To compute the 3D structure of a scene accurately from a moving vision sensor we need to be able to estimate the motion of the sensor from the recorded image information, a problem that has been well-studied By relating the differential structure of the time varying plenoptic function to different known and new camera designs, we can establish a hierarchy of cameras based upon the stability and complexity of the computations necessary to estimate structure and motion. At the low end of this hierarchy is the standard planar pinhole camera for which the structure from motion problem is non-linear and ill-posed. At the high end is a camera, which we call the full field of view polydioptric camera, for which the problem is linear and stable. In between are multiple view cameras with a large field of view which we have built, as well as omni-directional sensors. We develop design suggestions for a polydioptric camera especially suited for 3D photography, and we propose a linear algorithm utilizing this camera design to recover the structure of the scene.
Nematicidal efficacy of MCW‐2, a new nematicide of the fluoroalkenyl group, against the root‐knot nematode Meloidogyne javanica (2009)

Abstract BACKGROUND: The small number of available nematicides and restrictions on the use of non‐fumigant nematicides owing to high toxicity to human and non‐target organisms hinder effective nematode control. The nematicidal efficacy of MCW‐2, a new nematicide of the fluoroalkenyl group, was evaluated against the root‐knot nematode Meloidogyne javanica (Treub.) Chitwood. RESULTS: MCW‐2 showed irreversible nematicidal activity against second‐stage juveniles of M. javanica in vitro , following exposure for 48 h at concentrations as low as 0.5 mg L −1 , in contrast to fenamiphos or cadusafos. When exposed to MCW‐2 for shorter periods, motile juveniles became immobile with time after rinsing in water. MCW‐2 at 8 mg L −1 inhibited nematode hatching, which, however, recovered after rinsing in water. In pot and plot experiments, 0.5 mg MCW‐2 L −1 soil and 2 kg MCW‐2 ha −1 , respectively, controlled M. javanica similarly to or better than fenamiphos or cadusafos at the same concentrations or at their recommended doses. In the soil, the nematicidal activity of MCW‐2 was less persistent than that of fenamiphos. CONCLUSION: MCW‐2 has potential to be used as a new non‐fumigant nematicide that probably has a novel mode of action. Copyright © 2009 Society of Chemical Industry
Mutual authenticated quantum no-key encryption scheme over private quantum channel (2015)

We realize shamir's no-key protocol via quantum computation of Boolean permutation and private quantum channel. The quantum no-key (QNK) protocol presented here is one with mutual authentications, and proved to be unconditionally secure. An important property of this protocol is that0 its authentication key can be reused permanently.
Unified Pharmacophoric Model for Cannabinoids and Aminoalkylindoles Derived from Molecular Superimposition of CB1 Cannabinoid Receptor Agonists CP55244 and WIN55212-2 (1999)

Novel superimposition models were developed based on 3-D pharmacophore mapping of the two highly potent CB1 cannabinoid receptor agonists: the cannabinoid CP55244 and the aminoalkylindole (AAI) WIN55212-2. The superimposition models so derived confirm earlier speculation about certain key pharmacophoric elements common to both the cannabinoids and AAIs. The present models also provide insight into the curious observation that the C1 hydroxyl group of certain cannabinoids may be unnecessary for the cannabinoid activity. To test the validity of our superimposition models, Comparative Molecular Field Analysis (CoMFA) was employed to construct a 3D-QSAR using a mixed training set composed of twelve cannabinoids and twelve AAIs.
Re‐entry into the cell cycle is required for bFGF‐induced oligodendroglial dedifferentiation and survival (1996)

Remyelination in the CNS following demyelinating disease may be accomplished by surviving mature oligodendrocytes that dedifferentiate, proliferate, migrate, and finally regenerate myelin. We previously reported that basic fibroblast growth factor (bFGF) induces oligodendrocytes in primary mixed glial cultures to dedifferentiate and synthesize DNA (Grinspan et al.: J Neurosci Res 36:672-680, 1993). We now show that this effect is direct and not mediated through the effects of bFGF on other cell types, because we were able to demonstrate similar changes in oligodendrocyte phenotype in enriched oligodendrocyte cultures prepared by immunopanning. The bFGF-induced reversion to the precursor stage of the oligodendroglial lineage can be blocked by agents that inhibit entry to the cell cycle; thus oligodendroglial dedifferentiation is dependent on proliferation. We also report that 2 days of bFGF treatment inhibits oligodendroglial apoptosis. However, when oligodendroglia are prevented from entering the cell cycle in the presence of bFGF, apoptotic cell death is increased. Thus, bFGF induces oligodendroglial dedifferentiation if oligodendroglial DNA synthesis can occur but causes oligodendoglial apoptosis when oligodendroglial DNA synthesis is prevented. © 1996 Wiley-Liss, Inc.
Molecular structure of eight human autoreactive monoclonal antibodies (2001)

The heavy (H) and light (L) chain V-region sequences of eight human autoreactive immunoglobulin M (IgM) monoclonal antibodies (mAbs: BY-4, BY-7, BY-12, IRM-3, IRM-7, IRM-8, IRM-10 and CDC-1) were determined at the cDNA level. All VH and VL families were identified. Four different VH families were represented, VH3 being the most common as five of the mAbs (BY-7, BY-12, IRM-3, IRM-8 and CDC-1) used genetic elements of this family, whereas VH1, VH2 and VH4 were only present in IRM-7, BY-4 and IRM-10, respectively. BY-4, BY-7, BY-12, IRM-7 and IRM-10 reacted with a variety of self as well as non-self antigens, thus exhibiting polyreactive behaviour. Comparison of the gene segments utilized by these mAbs with their germline counterparts revealed that the gene segments were close to germline configuration. The length of H-CDR3 was found to be relatively long (27-60 nucleotides) among the polyreactive mAbs and the presence of Tyr and Trp residues in this region seems to be of vital importance for polyreactivity. We have analysed the utilization of gene elements and the presence of amino acid residues in regions particularly important for antigen binding, such as CDR. Common molecular features relating to the function of the mAbs are discussed.
Anxiolytic- and antidepressant-like effects of the non-peptide vasopressin V 1b receptor antagonist, SSR149415, suggest an innovative approach for the treatment of stress-related disorders (2002)

The limbic localization of the arginine vasopressin V(1b) receptor has prompted speculation as to a potential role of this receptor in the control of emotional processes. To investigate this possibility, we have studied the behavioral effects of SSR149415, the first selective and orally active non-peptide antagonist of vasopressin V(1b) receptors, in a variety of classical (punished drinking, elevated plus-maze, and light/dark tests) and atypical (fear/anxiety defense test battery and social defeat-induced anxiety) rodent models of anxiety, and in two models of depression [forced swimming and chronic mild stress (CMS)]. When tested in classical tests of anxiety, SSR149415 produced anxiolytic-like activity at doses that ranged from 1 to 30 mg/kg (i.p. or p.o.), but the magnitude of these effects was overall less than that of the benzodiazepine anxiolytic diazepam, which was used as a positive control. In contrast, SSR149415 produced clear-cut anxiolytic-like activity in models involving traumatic stress exposure, such as the social defeat paradigm and the defense test battery (1-30 mg/kg, p.o.). In the forced swimming test, SSR149415 (10-30 mg/kg, p.o.) produced antidepressant-like effects in both normal and hypophysectomized rats. Moreover, in the CMS model in mice, repeated administration of SSR149415 (10 and 30 mg/kg, i.p.) for 39 days improved the degradation of the physical state, anxiety, despair, and the loss of coping behavior produced by stress. These findings point to a role for vasopressin in the modulation of emotional processes via the V(1b) receptor, and suggest that its blockade may represent a novel avenue for the treatment of affective disorders.
AUTOMATIC INITIALIZATION FOR BODY TRACKING - Using Appearance to Learn a Model for Tracking Human Upper Body Motions (2008)

Social robots require the ability to communicate and recognize the intention of a human interaction partner. Humans commonly make use of gestures for interactive purposes. For a social robot, recognition of gestures is therefore a necessary skill. As a common intermediate step, the pose of an individual is tracked over time making use of a body model. The acquisition of a suitable body model, i.e. self-starting the tracker, however, is a complex and challenging task. This paper presents an approach to facilitate the acquisition of the body model during interaction. Taking advantage of a robust face detection algorithm provides the opportunity for automatic and markerless acquisition of a 3D body model using a monocular color camera. For the given human robot interaction scenario, a prototype has been developed for a single user configuration. It provides automatic initialization and failure recovery of a 3D body tracker based on head and hand detection information, delivering promising results.