gebhart/patrepeval huggingface dataset:
Cell surface peptidase CD26/DPPIV mediates G-CSF mobilization of mouse progenitor cells (2003)

CXC ligand 12 (CXCL12; also known as stromal cell-derived factor 1alpha/SDF-1alpha) chemoattracts hematopoietic stem and progenitor cells (HSCs/HPCs) and is thought to play a crucial role in the mobilization of HSCs/HPCs from the bone marrow. CD26 (dipeptidylpeptidase IV [DPPIV]) is a membrane-bound extracellular peptidase that cleaves dipeptides from the N-terminus of polypeptide chains. CD26 has the ability to cleave CXCL12 at its position-2 proline. We found by flow cytometry that CD26 is expressed on a subpopulation of normal Sca-1+c-kit+lin- hematopoietic cells isolated from mouse bone marrow, as well as Sca-1+c-kit-lin- cells, and that these cells possess CD26 peptidase activity. To test the functional role of CD26 in CXCL12-mediated normal HSC/HPC migration, chemotaxis assays were performed. The CD26 truncated CXCL12(3-68) showed an inability to induce the migration of sorted Sca-1+c-kit+lin- or Sca-1+c-kit-lin- mouse marrow cells compared with the normal CXCL12. In addition, CXCL12(3-68) acts as an antagonist, resulting in the reduction of migratory response to normal CXCL12. Treatment of Sca-1+c-kit+lin- mouse marrow cells, and myeloid progenitors within this population, or Sca-1+c-kit-lin- cells with a specific CD26 inhibitor, enhanced the migratory response of these cells to CXCL12. Finally, to test for potential in vivo relevance of these in vitro observations, mice were treated with CD26 inhibitors during granulocyte colony-stimulating factor (G-CSF)-induced mobilization. This treatment resulted in a reduction in the number of progenitor cells in the periphery as compared with the G-CSF regimen alone. This suggests that a mechanism of action of G-CSF mobilization involves CD26.
Multidrug-Resistant Candida auris Misidentified as Candida haemulonii: Characterization by Matrix-Assisted Laser Desorption Ionization–Time of Flight Mass Spectrometry and DNA Sequencing and Its Antifungal Susceptibility Profile Variability by Vitek 2, CLSI Broth Microdilution, and Etest Method (2015)

Candida auris is a multidrug-resistant yeast that causes a wide spectrum of infections, especially in intensive care settings. We investigated C. auris prevalence among 102 clinical isolates previously identified as Candida haemulonii or Candida famata by the Vitek 2 system. Internal transcribed spacer region (ITS) sequencing confirmed 88.2% of the isolates as C. auris, and matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) easily separated all related species, viz., C. auris (n = 90), C. haemulonii (n = 6), C. haemulonii var. vulnera (n = 1), and Candida duobushaemulonii (n = 5). The in vitro antifungal susceptibility was determined using CLSI broth microdilution (CLSI-BMD), the Vitek 2 antifungal susceptibility test, and the Etest method. C. auris isolates revealed uniformly elevated fluconazole MICs (MIC50, 64 μg/ml), and an alarming percentage of isolates (37%) exhibited elevated caspofungin MICs by CLSI-BMD. Notably, 34% of C. auris isolates had coexisting elevated MICs (≥2 μg/ml) for both fluconazole and voriconazole, and 10% of the isolates had elevated coexisting MICs (≥2 μg/ml) to two additional azoles, i.e., posaconazole and isavuconazole. In contrast to reduced amphotericin B MICs by CLSI-BMD (MIC50, 1 μg/ml) for C. auris, elevated MICs were noted by Vitek 2 (MIC50, 8 μg/ml), which were statistically significant. Candida auris remains an unnoticed pathogen in routine microbiology laboratories, as 90% of the isolates characterized by commercial identification systems are misidentified as C. haemulonii. MALDI-TOF MS proved to be a more robust diagnostic technique for rapid identification of C. auris. Considering that misleading elevated MICs of amphotericin B by the Vitek AST-YS07 card may lead to the selection of inappropriate therapy, a cautionary approach is recommended for laboratories relying on commercial systems for identification and antifungal susceptibility testing of rare yeasts.
From Melanocyte to Metastatic Malignant Melanoma (2010)

Malignant melanoma is one of the most aggressive malignancies in human and is responsible for almost 60% of lethal skin tumors. Its incidence has been increasing in white population in the past two decades. There is a complex interaction of environmental (exogenous) and endogenous, including genetic, risk factors in developing malignant melanoma. 8-12% of familial melanomas occur in a familial setting related to mutation of the CDKN2A gene that encodes p16. The aim of this is to briefly review the microanatomy and physiology of the melanocytes, epidemiology, risk factors, clinical presentation, historical classification and histopathology and, more in details, the most recent discoveries in biology and genetics of malignant melanoma. At the end, the final version of 2009 AJCC malignant melanoma staging and classification is presented.
Diffusion coefficient of DNA molecules during free solution electrophoresis (2001)

The free-draining properties of DNA normally make it impossible to separate nucleic acids by free-flow electrophoresis. However, little is known, either theoretically or experimentally, about the diffusion coefficient of DNA molecules during free-flow electrophoresis. In fact, many authors simply assume that the Nernst-Einstein relation between the mobility and the diffusion coefficient still holds under such conditions. In this paper, we present an experimental study of the diffusion coefficient of both ssDNA and dsDNA molecules during free-flow electrophoresis. Our results unequivocally show that a simplistic use of Nernst-Einstein's relation fails, and that the electric field actually has no effect on the thermal diffusion process. Finally, we compare the dependence of the diffusion coefficient upon DNA molecular size to results obtained previously by other groups and to Zimm's theory.
A Marginal Benefit Approach for Vaccinating Influenza “Superspreaders” (2014)

Our approach offers a means of estimating willingness to pay for search costs associated with targeted vaccination of superspreaders, which can inform policies regarding whether a targeted intervention should be implemented and, if so, up to what levels.
Comparative Effects of Tissue Plasminogen Activator, Streptokinase, and Staphylokinase on Cerebral Ischemic Infarction and Pulmonary Clot Lysis in Hamster Models (1999)

Thrombolytic agents cause similar dose-related extension of FCI after MCA ligation and PCL, irrespective of the agent or systemic plasmin generation.
Quantitative Structure−Activity Relationships for γδ T Cell Activation by Bisphosphonates (2003)

gammadelta T cells are the first line of defense against many infectious organisms and are also involved in tumor cell surveillance and killing. They are stimulated by a broad range of small, phosphorus-containing antigens (phosphoantigens) as well as by the bisphosphonates commonly used in bone resorption therapy, such as pamidronate and risedronate. Here, we report the activation of gammadelta T cells by a broad range of bisphosphonates and develop a pharmacophore model for gammadelta T cell activation, in addition to using a comparative molecular similarity index analysis (CoMSIA) approach to make quantitative relationships between gammadelta T cell activation by bisphosphonates and their three-dimensional structures. The CoMSIA analyses yielded R(2) values of approximately 0.8-0.9 and q(2) values of approximately 0.5-0.6 for a training set of 45 compounds. Using an external test set, the activities (IC(50) values) of 16 compounds were predicted within a factor of 4.5, on average. The CoMSIA fields consisted of approximately 40% hydrophobic, approximately 40% electrostatic, and approximately 20% steric interactions. Since bisphosphonates are known to be potent, nanomolar inhibitors of the mevalonate/isoprene pathway enzyme farnesyl pyrophosphate synthase (FPPS), we also compared the pharmacophores for gammadelta T cell activation with those for FPPS inhibition, using the Catalyst program. The pharmacophores for gammadelta T cell activation and FPPS inhibition both consisted of two negative ionizable groups, a positive charge feature and an endocyclic carbon feature, all having very similar spatial dispositions. In addition, the CoMSIA fields were quite similar to those found for FPPS inhibition by bisphosphonates. The activities of the bisphosphonates in gammadelta T cell activation were highly correlated with their activities in FPPS inhibition: R = 0.88, p = 0.002, versus a human recombinant FPPS (N = 9 compounds); R = 0.82, p < 0.0001, for an expressed Leishmania major FPPS (N = 45 compounds). The bisphosphonate gammadelta T cell activation pharmacophore differs considerably, however, from that reported previously for gammadelta T cell activation by phosphoantigens (Gossman, W.; Oldfield, E. J. Med. Chem. 2002, 45, 4868-4874), suggesting different primary targets for the two classes of compounds. The ability to quite accurately predict the activity of bisphosphonates as gammadelta T cell activators by using 3D QSAR techniques can be expected to help facilitate the design of additional bisphosphonates for potential use in immunotherapy.
Splanchnic Perfusion Evaluation during Hemorrhage and Resuscitation with Gastric Near-Infrared Spectroscopy (2001)

Direct measurement of tissue oxygen saturation with a prototype side-illuminating near-infrared spectroscopy gastric probe appeared to rapidly reflect changes in splanchnic perfusion.
SiO2 film stress distribution during thermal oxidation of Si (1988)

A laser reflection technique is used to investigate the relaxation of SiO2 film stress which occurs during the dry thermal oxidation of Si between 700 and 1000 °C. Included is a determination of the stress distribution in the oxide by two independent methods: (1) measurement on oxides of various thicknesses from 100 to 800 Å, and (2) repeated stress measurements on chemically thinned SiO2 films, viz. etch-back analysis toward the interface. Agreement is found between these experiments. These thin film stress measurements are achieved by the use of ultrathin Si substrates (75 μm). Essentially, an increase in film stress with decreasing film thickness is observed. Rapid stress relaxation is observed for all temperatures studied and is attributed to a time-dependent oxide viscosity. The influence of these measured properties on the kinetics of Si oxidation is discussed.
Correlation between enzyme activity and hinge‐bending domain displacement in 3‐phosphoglycerate kinase (1989)

Diffuse X-ray-scattering data give evidence for large-scale structural change in pig muscle 3-phosphoglycerate kinase upon substrate binding. Simultaneous binding of 3-phosphoglycerate and MgATP either to the unmodified enzyme or to its active methylated derivative leads to about an 0.1-nm decrease in radius of gyration. These data coincide well with the previous data for yeast 3-phosphoglycerate kinase. When, instead of methylation, the two reactive thiol groups of pig muscle 3-phosphoglycerate kinase are carboxamidomethylated, the enzyme becomes inactive and the radii of gyration of its 'apo' and 'holo' forms do not differ within limits of experimental error. Thus, a correlation exists between the activity of 3-phosphoglycerate kinase and its substrate-induced large-scale conformational change. This correlation is a strong argument in favor of the functional importance of domain locking in the reaction catalyzed by 3-phosphoglycerate kinase.
Collective Behavior of Magnetic Nanoparticles in Polyelectrolyte Brushes (2008)

Polyelectrolyte brushes loaded with magnetic nanoparticles can be formed through the reaction of immobilized Fe2+/3+ ions in the brush. These particles show very unusual magnetic properties, not normally associated with such small nanoparticles. Upon application of an external magnetic field, the brushes showed reversible dimensional changes.
Folic acid and sulfasalazine for colorectal carcinoma chemoprevention in patients with ulcerative colitis: the old and new evidence. (2003)

Both sulfasalazine therapy and folate supplementation have a protective effect in colorectal cancer development in a population of patients with longstanding ulcerative colitis. Randomized controlled trials are needed to explore these hypotheses.
In vitro activity of Bay 09867, a new quinoline derivative, compared with those of other antimicrobial agents (1983)

The in vitro activity of Bay 09867, a new quinoline derivative, was compared with those of norfloxacin, nalidixic acid, ceftazidime, cefaclor, cefuroxime, gentamicin, and other antimicrobial agents, when appropriate, against 410 recent clinical isolates. The minimal inhibitory concentrations of Bay 09867 for 90% of Enterobacteriaceae, Pseudomonas aeruginosa, Haemophilus influenzae, Neisseria gonorrhoeae, streptococci, Staphylococcus aureus, and Bacteroides fragilis strains were between 0.008 and 2 micrograms/ml. Bay 09867 was considerably more active against the gram-negative bacteria tested than were other agents tested. Gentamicin-resistant Enterobacteriaceae, P. aeruginosa, and methicillin-resistant S. aureus were highly susceptible to Bay 09867. Strains less susceptible to nalidixic acid and norfloxacin tended to be less susceptible to Bay 09867. The protein binding of Bay 09867 was about 20%.
A Monocyte Conditioned Medium Is More Effective Than Defined Cytokines in Mediating the Terminal Maturation of Human Dendritic Cells (1997)

Mature human dendritic cells can be generated in substantial numbers from nonproliferating progenitors in human blood using a two-step protocol. T cell-depleted mononuclear cells are first cultured with granulocyte-macrophage colony-stimulating factor and interleukin-4 (IL-4) and then exposed to monocyte conditioned medium (MCM). The dendritic cells generated using this approach are rendered terminally mature and are the most potent antigen presenting cells identified to date in humans. We sought to characterize factors in MCM that induce the terminal differentiation of dendritic cells. MCM contained substantial, although varying, quantities of several factors including tumor necrosis factor-alpha, IL-1beta, IL-6, and interferon-alpha. However, none of the four factors, individually or in various combinations, could fully substitute for the MCM to generate irreversibly differentiated dendritic cells. The yields, percentage of cells expressing the mature phase marker CD83, and mixed leukocyte reaction-stimulatory function were lower when defined cytokines were used in the place of MCM. Therefore, the full maturation of dendritic cells, because it entails changes in many known cell and molecular properties, requires a number of different cytokines that are released in tandem from appropriately stimulated monocytes. We propose that MCM-matured dendritic cells will be the most effective adjuvants for immunotherapy in vivo.
Porous Single‐Crystalline Palladium Nanoparticles with High Catalytic Activities (2012)

Palladium's pore cousin: a facile approach is described for the size-controlled preparation of porous single-crystalline Pd nanoparticles. These porous Pd nanoparticles exhibit size-independent catalytic activities for the Suzuki coupling and are more active than commercial Pd/C catalysts.
Real-Time Ophthalmoscopic Findings of Superselective Intraophthalmic Artery Chemotherapy in a Nonhuman Primate Model (2011)

Real-time retinal imaging is feasible in a nonhuman primate model of SSIOAC. Application to SSIOAC in children may shed insight into reported vascular toxicities.
Analyzing geographic queries (2004)

The aim of this study was to analyze the 2001 Excite query log to&#13;\ninvestigate the extent and variation of Web queries containing&#13;\ngeographic terms. In particular, an investigation into what people&#13;\nsearch for when they use geographic terms, the ways in which&#13;\nthey describe a geographic location, the terminology used to find&#13;\ngeographically related information and the structure of users’&#13;\nqueries when looking for geographically related information on&#13;\nthe Web. This study also attempted to determine how&#13;\ngeographically related queries differ from other queries.&#13;\nGeographically related queries formed nearly one fifth of all&#13;\nqueries submitted to Excite, the terms occurring most frequently&#13;\nbeing place names. Geographic queries were also shown to be&#13;\nlonger than average and the association of two or more terms&#13;\nwithin geographic queries was found to be high.
Carbon nanotube transistors scaled to a 40-nanometer footprint (2017)

The International Technology Roadmap for Semiconductors challenges the device research community to reduce the transistor footprint containing all components to 40 nanometers within the next decade. We report on a p-channel transistor scaled to such an extremely small dimension. Built on one semiconducting carbon nanotube, it occupies less than half the space of leading silicon technologies, while delivering a significantly higher pitch-normalized current density-above 0.9 milliampere per micrometer at a low supply voltage of 0.5 volts with a subthreshold swing of 85 millivolts per decade. Furthermore, we show transistors with the same small footprint built on actual high-density arrays of such nanotubes that deliver higher current than that of the best-competing silicon devices under the same overdrive, without any normalization. We achieve this using low-resistance end-bonded contacts, a high-purity semiconducting carbon nanotube source, and self-assembly to pack nanotubes into full surface-coverage aligned arrays.
Radioprotective and Antitumor Activity of Some Novel Amino Acids and Imidazoles Containing Thieno[2,3-d]pyrimidine Moiety (2009)

A variety of novel thieno[2,3-d]pyrimidine derivatives, comprising amino acids 3a–l, imidazothieno-pyrimidines 4A, 4b–h, and 7, were obtained via the reaction of 4-chloro-5,6-dimethylthieno[2,3-d]pyrimidine 1 with a variety of reagents. The structures of these compounds were confirmed by microanalysis, IR, 1H NMR, and mass spectrometry. Some of the obtained compounds showed promising radioprotective and antitumor activities.
TLRs in the Gut. III. Immune responses to flagellin in Crohn's disease: good, bad, or irrelevant? (2006)

Recent observations suggest that bacterial flagellin may be a target of the seemingly aberrant innate and adaptive immune responses that are associated with Crohn's disease. This article discusses the evidence that supports a role for flagellin in Crohn's disease and considers the potential roles of these responses in the pathophysiology of this disorder.
Machine Learning for Cancer Immunotherapies Based on Epitope Recognition by T Cell Receptors (2019)

In the last years, immunotherapies have shown tremendous success as treatments for multiple types of cancer. However, there are still many obstacles to overcome in order to increase response rates and identify effective therapies for every individual patient. Since there are many possibilities to boost a patient's immune response against a tumor and not all can be covered, this review is focused on T cell receptor-mediated therapies. CD8<sup>+</sup> T cells can detect and destroy malignant cells by binding to peptides presented on cell surfaces by MHC (major histocompatibility complex) class I molecules. CD4<sup>+</sup> T cells can also mediate powerful immune responses but their peptide recognition by MHC class II molecules is more complex, which is why the attention has been focused on CD8<sup>+</sup> T cells. Therapies based on the power of T cells can, on the one hand, enhance T cell recognition by introducing TCRs that preferentially direct T cells to tumor sites (so called TCR-T therapy) or through vaccination to induce T cells <i>in vivo</i>. On the other hand, T cell activity can be improved by immune checkpoint inhibition or other means that help create a microenvironment favorable for cytotoxic T cell activity. The manifold ways in which the immune system and cancer interact with each other require not only the use of large omics datasets from gene, to transcript, to protein, and to peptide but also make the application of machine learning methods inevitable. Currently, discovering and selecting suitable TCRs is a very costly and work intensive <i>in vitro</i> process. To facilitate this process and to additionally allow for highly personalized therapies that can simultaneously target multiple patient-specific antigens, especially neoepitopes, breakthrough computational methods for predicting antigen presentation and TCR binding are urgently required. Particularly, potential cross-reactivity is a major consideration since off-target toxicity can pose a major threat to patient safety. The current speed at which not only datasets grow and are made available to the public, but also at which new machine learning methods evolve, is assuring that computational approaches will be able to help to solve problems that immunotherapies are still facing.
Successful treatment of malignant melanoma in situ with topical 5% imiquimod cream (2005)

Topical imiquimod can be used successfully for the treatment of malignant melanoma in situ on the face.
Dealing with missing values in large-scale studies: microarray data imputation and beyond (2009)

High-throughput biotechnologies, such as gene expression microarrays or mass-spectrometry-based proteomic assays, suffer from frequent missing values due to various experimental reasons. Since the missing data points can hinder downstream analyses, there exists a wide variety of ways in which to deal with missing values in large-scale data sets. Nowadays, it has become routine to estimate (or impute) the missing values prior to the actual data analysis. After nearly a decade since the publication of the first missing value imputation methods for gene expression microarray data, new imputation approaches are still being developed at an increasing rate. However, what is lagging behind is a systematic and objective evaluation of the strengths and weaknesses of the different approaches when faced with different types of data sets and experimental questions. In this review, the present strategies for missing value imputation and the measures for evaluating their performance are described. The imputation methods are first reviewed in the context of gene expression microarray data, since most of the methods have been developed for estimating gene expression levels; then, we turn to other large-scale data sets that also suffer from the problems posed by missing values, together with pointers to possible imputation approaches in these settings. Along with a description of the basic principles behind the different imputation approaches, the review tries to provide practical guidance for the users of high-throughput technologies on how to choose the imputation tool for their data and questions, and some additional research directions for the developers of imputation methodologies.
Iron Loading and Disease Surveillance (1999)

Iron is an oxidant as well as a nutrient for invading microbial and neoplastic cells. Excessive iron in specific tissues and cells (iron loading) promotes development of infection, neoplasia, cardiomyopathy, arthropathy, and various endocrine and possibly neurodegenerative disorders. To contain and detoxify the metal, hosts have evolved an iron withholding defense system, but the system can be compromised by numerous factors. An array of behavioral, medical, and immunologic methods are in place or in development to strengthen iron withholding. Routine screening for iron loading could provide valuable information in epidemiologic, diagnostic, prophylactic, and therapeutic studies of emerging infectious diseases.
2-(4-Alkylpiperazin-1-yl)quinolines as a New Class of Imidazole-Free Histamine H3Receptor Antagonists (2004)

With the aim of identifying structurally novel, centrally acting histamine H(3) antagonists, a series of 2-(4-alkylpiperazin-1-yl)quinolines was prepared. Systematic variation of the substituents led to highly potent histamine H(3) antagonists with low polar surface area and appropriate log P for blood-brain barrier penetration.