gebhart/patrepeval huggingface dataset:
In vitro chemosensitivity to gemcitabine, oxaliplatin and zoledronic acid predicts treatment response in metastatic gastric cancer (2004)

Individual response of disseminated cancer to chemotherapy is unpredictable. In vitro chemotherapy-induced apoptosis can be measured and might be a method to evaluate in vivo activity of tested drugs. In this report, tumor cells of a patient with signet cell carcinoma of the stomach and diffuse bone marrow infiltration were cultured and tested for in vitro chemosensitivity. The drugs gemcitabine, oxaliplatin and zoledronic acid were found to induce in vitro tumor cell apoptosis synergistically, and subsequently were used as combination chemotherapy regimen. An initially existing disseminated intravascular coagulopathy quickly resolved and after 6 months of treatment on ongoing complete response was induced, thus confirming the results of in vitro chemosensitivity testing.
Facial Key Points Detection using Deep Convolutional Neural Network - NaimishNet (2017)

Facial Key Points (FKPs) Detection is an important and challenging problem in the fields of computer vision and machine learning. It involves predicting the co-ordinates of the FKPs, e.g. nose tip, center of eyes, etc, for a given face. In this paper, we propose a LeNet adapted Deep CNN model - NaimishNet, to operate on facial key points data and compare our model's performance against existing state of the art approaches.
Treatment evaluation of experimental staphylococcal infections: comparison of beta-lactam, lipopeptide, and glycopeptide antimicrobial therapy. (1990)

LY 146032, teicoplanin, vancomycin, oxacillin, cephalothin, cefamandole, ampicillin plus sulbactam, and cefoperazone plus sulbactam were studied against six isolates of staphylococci (including both Staphylococcus aureus and coagulase negative staphylococci) using in vivo and in vitro methods. In vitro susceptibility measurements demonstrated that all six isolates were sensitive to LY 146032 and vancomycin and that five of six isolates were sensitive to tiecoplanin, cefamandole, ampicillin plus sulbactam, and cefoperazone plus sulbactam. Comparison of antimicrobial therapy in an in vivo rabbit model demonstrated that cefoperazone plus sulbactam was active against the greatest number of isolates (five of six) based on a reduction of greater than or equal to 5.0 log10 colony forming units per milliliter (CFU/ml) from growth control at the end of the animal treatment study. Vancomycin and oxacillin were equal in achieving reductions of greater than or equal to 5.0 log10 CFU/ml in four of the six isolates. Comparing each isolate's in vivo outcome to in vitro data shows that in vitro susceptibility tests overpredict the sensitivity of these six isolates to LY 146032 and vancomycin, are variable for teicoplanin, cefamandole, ampicillin plus sulbactam, and cefoperazone plus sulbactam, and underpredict for oxacillin.
Initiation of GalNAc-type O-glycosylation in the endoplasmic reticulum promotes cancer cell invasiveness (2013)

Invasiveness underlies cancer aggressiveness and is a hallmark of malignancy. Most malignant tumors have elevated levels of Tn, an O-GalNAc glycan. Mechanisms underlying Tn up-regulation and its effects remain unclear. Here we show that Golgi-to-endoplasmic reticulum relocation of polypeptide N-acetylgalactosamine-transferases (GalNAc-Ts) drives high Tn levels in cancer cell lines and in 70% of malignant breast tumors. This process stimulates cell adhesion to the extracellular matrix, as well as migration and invasiveness. The GalNAc-Ts lectin domain, mediating high-density glycosylation, is critical for these effects. Interfering with the lectin domain function inhibited carcinoma cell migration in vitro and metastatic potential in mice. We also show that stimulation of cell migration is dependent on Tn-bearing proteins present in lamellipodia of migrating cells. Our findings suggest that relocation of GalNAc-Ts to the endoplasmic reticulum frequently occurs upon cancerous transformation to enhance tumor cell migration and invasiveness through modification of cell surface proteins.
Electrically Evoked Compound Action Potential Recording in Peripheral Nerves (2017)

Applications for bioelectric medicine can be found in all parts of the nervous system. The CNS – brain and spinal cord – contain targets for commercial neuromodulation therapies. Peripheral nerves are also modulated with commercially available systems during treatment for chronic pain and epilepsy, and developments are in progress for treating many other diseases. The electrically evoked compound action potential is a measure of the electrical response from the tissue to stimulation. It provides a direct insight into the electrophysiology of the stimulation, and despite its incorporation into cochlear implants it is a technology that is yet to find its way into commercial peripheral nerve stimulation applications. This review outlines the status of evoked compound action potential measurements on peripheral nerves and highlights the challenges which need to be overcome.
BGT: efficient and flexible genotype query across many samples (2015)

https://github.com/lh3/bgt.
Handbook of cognition and emotion (1999)

Partial table of contents: GENERAL ASPECTS. The Philosophy of Cognition and Emotion (W. Lyons). Basic Emotions (P. Ekman). Research Methods in Cognition and Emotion (W. Parrott & P. Hertel). COGNITIVE PROCESSES. Selective Attention and Anxiety: A Cognitive-Motivational Perspective (K. Mogg & B. Bradley). The Cognitive Science of Attention and Emotion (G. Matthews & A. Wells). Mood and Memory (H. Ellis & B. Moore). Autobiographical Memory (H. Healy & J. Williams). Inhibition Processes in Cognition and Emotion: A Special Case (T. Dalgleish, et al.). EMOTIONS. Anger (L. Berkowitz). Disgust: The Body and Soul Emotion (P. Rozin, et al.). Panic and Phobias (R. McNally). Sadness and its Disorders (M. Power). Jealousy and Envy (M. East & F. Watts). THEORIES IN COGNITION AND EMOTION. Network Theories and Beyond (J. Forgas). Appraisal Theory (K. Scherer). Multi-Level Theories of Cognition-Emotion Relations (J. Teasdale). APPLIED ISSUES. Creativity in the Domain of Emotion (J. Averill). Forensic Applications of Theories of Cognition and Emotion (D. Bekerian & S. Goodrich). Cognition and Emotion: Future Directions (T. Dalgleish & M. Power). Indexes.
Handbook of Cell-Penetrating Peptides (2006)

Since the first Handbook of Cell-Penetrating Peptides was prepared in 2001, the wealth of new information on the use of these peptides as transport systems has in fact served to confound the field. The constant internal change in the field of cell-penetrating peptides (CPPs) is due to recent research uncovering apparent ambiguities in cellular upta
A CACGTG motif of the Antirrhinum majus chalcone synthase promoter is recognized by an evolutionarily conserved nuclear protein. (1989)

In the chalcone synthase gene of Antirrhinum majus (snapdragon), 150 base pairs of the 5' flanking region contain cis-acting signals for UV light-induced expression. A nuclear factor, designated CG-1, specifically recognizes a hexameric motif with internal dyad symmetry, CACGTG, located within this light-responsive sequence. Binding of CG-1 is influenced by C-methylation of the CpG dinucleotide in the recognition sequence. CG-1 is a factor found in a variety of dicotyledonous plant species including Nicotiana tabacum, A. majus, Petunia hybrida, Arabidopsis thaliana, and Glycine max. CACGTG motifs contained within trans-acting factor recognition sites in various other plant promoters can interact with CG-1. In addition, the binding site of the human adenovirus major late transcription factor USF can compete for CG-1 binding to the chalcone synthase promoter. This suggests an evolutionary conservation of trans-acting factor recognition sites involved in divergent mechanisms of gene control.
Development of an attenuated mumps virus vaccine. II. Immune response of animals to vaccination with inactivated and live attenuated mumps viruses. (1969)

The immunogenicity and virulence of mumps viruses for mammals decreases during adaptation to growth of the virus in avian cells. However, mumps viruses grown for more than 30 passages in embryonated hen's eggs and/or CEF cell cultures can still infect mammalian cells in culture and alter the immune status of guinea pigs by infecting them. The immune responses of guinea pigs to even the most attenuated mumps viruses are qualitatively different from the responses to inactivated mumps viruses.
The Two Faces of Interferon-γ in Cancer (2011)

Interferon-γ is a cytokine whose biological activity is conventionally associated with cytostatic/cytotoxic and antitumor mechanisms during cell-mediated adaptive immune response. It has been used clinically to treat a variety of malignancies, albeit with mixed results and side effects that can be severe. Despite ample evidence implicating a role for IFN-γ in tumor immune surveillance, a steady flow of reports has suggested that it may also have protumorigenic effects under certain circumstances. We propose that, in fact, IFN-γ treatment is a double-edged sword whose anti- and protumorigenic activities are dependent on the cellular, microenvironmental, and/or molecular context. As such, inhibition of the IFN-γ/IFN-γ receptor pathway may prove to be a viable new therapeutic target for a subset of malignancies.
Molecular cloning and expression of collagenase-3, a novel human matrix metalloproteinase produced by breast carcinomas (1994)

A cDNA coding for a new human matrix metalloproteinase (MMP) has been cloned from a cDNA library derived from a breast tumor. The isolated cDNA contains an open reading frame coding for a polypeptide of 471 amino acids. The predicted protein sequence displays extensive similarity to the previously known MMPs and presents all the structural features characteristic of the members of this protein family, including the well conserved PRCGXPD motif, involved in the latency of the enzyme and the zinc-binding domain (HEXGHXXXXXHS). In addition, this novel human MMP contains in its amino acid sequence several residues specific to the collagenase subfamily (Tyr-214, Asp-235, and Gly-237) and lacks the 9-residue insertion present in the stromelysins. According to these structural characteristics, the MMP described herein has been tentatively called collagenase-3, since it represents the third member of this subfamily, composed at present of fibroblast and neutrophil collagenases. The collagenase-3 cDNA was expressed in a vaccinia virus system, and the recombinant protein was able to degrade fibrillar collagens, providing support to the hypothesis that the isolated cDNA codes for an authentic collagenase. Northern blot analysis of RNA from normal and pathological tissues demonstrated the existence in breast tumors of three different mRNA species, which seem to be the result of the utilization of different polyadenylation sites present in the 3'-noncoding region of the gene. By contrast, no collagenase-3 mRNA was detected either by Northern blot or RNA polymerase chain reaction analysis with RNA from other human tissues, including normal breast, mammary fibroadenomas, liver, placenta, ovary, uterus, prostate, and parotid gland. On the basis of the increased expression of collagenase-3 in breast carcinomas and the absence of detectable expression in normal tissues, a possible role for this metalloproteinase in the tumoral process is proposed.
A toolkit for computational molecular biology. III. MICRYFON – a (fairly) general program for input of protein coordinate files (1987)

The large number and variety of formats in use for storing protein coordinate data sets make it difficult to integrate the operation of programs from different laboratories. To ameliorate this situation a general input program, called MICRYFON , has been designed and written. MICRYFON will analyze and interpret many common protein coordinate formats without the specification of any `option' indicating which format the program is to expect.
Production of lymphokine mRNA by CD45R+ and CD45R− helper T cells from human peripheral blood and by human CD4+ T cell clones. (1989)

The expression of lymphokine mRNA by human CD4+CD45R+ and CD4+CD45R- Th cells was assessed after mitogen stimulation. These Ag have previously been shown to relate closely to virgin and primed T cells, respectively. CD4+CD45R+ (virgin) and CD4+CD45R- (primed) cell fractions were isolated by sorting double-labeled cells with a fluorescence-activated cell sorter. CD4+CD45R+ cells produced high levels of IL-2 mRNA when stimulated with either PMA together with calcium ionophore, or with PHA, but they expressed only trace quantities of mRNA for IL-4 or IFN-gamma. In contrast, CD4+CD45R- cells produced high levels of mRNA for IL-2, IL-4, and IFN-gamma. After 14 days of continuous culture, CD4+CD45R+ Th cells lost expression of the CD45R Ag, but gained high level expression of CDw29, such that they were indistinguishable from the cell population which originally expressed this Ag. At the same time, they acquired the ability to synthesize IL-4 mRNA. It seemed likely that the broad lymphokine profile of primed Th cells might mask clonal heterogeneity. Analysis of 122 CD4+ T cell clones showed that all of them synthesized IL-2 mRNA. One clone failed to express IL-4 mRNA, but did produce those for IL-2 and IFN-gamma. A total of 34 of the clones was investigated to determine expression of IFN-gamma mRNA; two of these clones were negative for IFN-gamma mRNA, and both expressed IL-2 and IL-4 message. These data suggest that while fresh virgin and primed peripheral blood T cells show a clear resolution of lymphokine production, a simple subdivision of human CD4+ T cell clones on the basis of their lymphokine production (such as that reported for mouse Th cell clones) is not possible.
Turbo multiuser detection for turbo-coded CDMA (2003)

An iterative receiver structure is proposed for decoding multiuser information data in a turbo-coded DS-CDMA system. The receiver performs two successive soft-output decisions, achieved by a soft-input soft-output (SISO) multiuser detector and a bank of single-user SISO channel decoders, through an iterative process. At each iteration, extrinsic information is extracted from detection and decoding stages and is then used as a priori information in the next iteration, just as in turbo decoding. A low-complexity SISO multiuser detector is developed based on a novel nonlinear interference suppression technique, which makes use of both soft-interference cancellation and instantaneous linear MMSE filtering. Turbo multiuser detectors for both the simple synchronous CDMA channels and the more complex asynchronous multipath CDMA channels are developed.
A breach in the blood-brain barrier (2005)

Proceedings of the National Academy of Sciences (PNAS), a peer reviewed journal of the National Academy of Sciences (NAS) - an authoritative source of high-impact, original research that broadly spans the biological, physical, and social sciences.
Data Preparation Process for Construction Knowledge Generation through Knowledge Discovery in Databases (2002)

As the construction industry is adapting to new computer technologies in terms of hardware and software, computerized construction data are becoming increasingly available. The explosive growth of many business, government, and scientific databases has begun to far outpace our ability to interpret and digest the data. Such volumes of data clearly overwhelm the traditional methods of data analysis such as spreadsheets and ad-hoc queries. The traditional methods can create informative reports from data, but cannot analyze the contents of those reports. A significant need exists for a new generation of techniques and tools with the ability to automatically assist humans in analyzing the mountains of data for useful knowledge. Knowledge discovery in databases (KDD) and data mining (DM) are tools that allow identification of valid, useful, and previously unknown patterns so that the construction manager may analyze the large amount of construction project data. These technologies combine techniques from machine learning, artificial intelligence, pattern recognition, statistics, databases, and visualization to automatically extract concepts, interrelationships, and patterns of interest from large databases. This paper presents the necessary steps such as (1) identification of problems, (2) data preparation, (3) data mining, (4) data analysis, and (5) refinement process required for the implementation of KDD. In order to test the feasibility of the proposed approach, a prototype of the KDD system was developed and tested with a construction management database, RMS (Resident Management System), provided by the U. S. Corps of Engineers. In this paper, the KDD process was applied to identify the cause(s) of construction activity delays. However, its possible applications can be extended to identify cause(s) of cost overrun and quality control/assurance among other construction problems. Predictable patterns may be revealed in construction data that were previously thought to be chaotic.
CD163 expression in leukemia cutis (2010)

Our results suggest that CD163 has utility as a specific marker for myeloid LC in conjunction with currently used immunohistochemical stains, but should not be used alone for diagnosis.
Measuring the Agreement between Sequences (1995)

The present article proposes a new method to assess distances between sequences of states, belonging to, for instance, event histories. It is based on the number of moves needed to turn one sequence into another sequence. This number of moves is standardized by relating it to the number of moves needed to turn the sequence into its reverse. Weighting it in different manners by the number of common elements in both sequences yields three different agreement measures, suited for different kinds of research questions. Life history data from 494 young adults show that applying our agreement measure to these data can yield insight in interesting relationships, otherwise not readily obtained.
An Analysis of OFDM Peak Power Reduction Techniques for WiMAX Systems (2006)

The main drawback of Orthogonal Frequency Division Multiplexing (OFDM) systems is the high peak-to-average power ratio (PAPR), which significantly reduces the efficiency of the transmit high power amplifier (H PA). Several methods have been proposed in the literature to reduce the peak power of OFDM signals and substantial gains were reported. In this paper, the effectiveness of some recently proposed methods is evaluated for WiMAX systems. Using typical HPA models and spectral masks, these PAPR reduction methods are evaluated in terms of the total system degradation.
Antibody-Linked Spherical Nucleic Acids for Cellular Targeting (2012)

Spherical nucleic acid (SNA) constructs are promising new single entity gene regulation materials capable of both cellular transfection and gene knockdown, but thus far are promiscuous structures, exhibiting excellent genetic but little cellular selectivity. In this communication, we describe a strategy to impart targeting capabilities to these constructs through noncovalent functionalization with a complementary antibody-DNA conjugate. As a proof-of-concept, we designed HER2-targeting SNAs and demonstrated that such structures exhibit cell type selectivity in terms of their uptake, and significantly greater gene knockdown in cells overexpressing the target antigen as compared to the analogous antibody-free and off-target materials.
A2B adenosine receptor dampens hypoxia-induced vascular leak (2007)

Extracellular adenosine has been implicated in adaptation to hypoxia and previous studies demonstrated a central role in vascular responses. Here, we examined the contribution of individual adenosine receptors (ARs: A1AR/A2AAR/A2BAR/A3AR) to vascular leak induced by hypoxia. Initial profiling studies revealed that siRNA-mediated repression of the A2BAR selectively increased endothelial leak in response to hypoxia in vitro. In parallel, vascular permeability was significantly increased in vascular organs of A2BAR(-/-)-mice subjected to ambient hypoxia (8% oxygen, 4 hours; eg, lung: 2.1 +/- 0.12-fold increase). By contrast, hypoxia-induced vascular leak was not accentuated in A1AR(-/-)-, A2AAR(-/-)-, or A3AR(-/-)-deficient mice, suggesting a degree of specificity for the A2BAR. Further studies in wild type mice revealed that the selective A2BAR antagonist PSB1115 resulted in profound increases in hypoxia-associated vascular leakage while A2BAR agonist (BAY60-6583 [2-[6-amino-3,5-dicyano-4-[4-(cyclopropylmethoxy)-. phenyl]pyridin-2-ylsulfanyl]acetamide]) treatment was associated with almost complete reversal of hypoxia-induced vascular leakage (eg, lung: 2.0 +/- 0.21-fold reduction). Studies in bone marrow chimeric A2BAR mice suggested a predominant role of vascular A2BARs in this response, while hypoxia-associated increases in tissue neutrophils were, at least in part, mediated by A2BAR expressing hematopoietic cells. Taken together, these studies provide pharmacologic and genetic evidence for vascular A2BAR signaling as central control point of hypoxia-associated vascular leak.
Novel Heparan Sulfate-Binding Peptides for Blocking Herpesvirus Entry (2015)

Human cytomegalovirus (HCMV) infection can lead to congenital hearing loss and mental retardation. Upon immune suppression, reactivation of latent HCMV or primary infection increases morbidity in cancer, transplantation, and late stage AIDS patients. Current treatments include nucleoside analogues, which have significant toxicities limiting their usefulness. In this study we screened a panel of synthetic heparin-binding peptides for their ability to prevent CMV infection in vitro. A peptide designated, p5+14 exhibited ~ 90% reduction in murine CMV (MCMV) infection. Because negatively charged, cell-surface heparan sulfate proteoglycans (HSPGs), serve as the attachment receptor during the adsorption phase of the CMV infection cycle, we hypothesized that p5+14 effectively competes for CMV adsorption to the cell surface resulting in the reduction in infection. Positively charged Lys residues were required for peptide binding to cell-surface HSPGs and reducing viral infection. We show that this inhibition was not due to a direct neutralizing effect on the virus itself and that the peptide blocked adsorption of the virus. The peptide also inhibited infection of other herpesviruses: HCMV and herpes simplex virus 1 and 2 in vitro, demonstrating it has broad-spectrum antiviral activity. Therefore, this peptide may offer an adjunct therapy for the treatment of herpes viral infections and other viruses that use HSPGs for entry.