gebhart/patrepeval huggingface dataset:
Small Intestinal Submucosa: A Tissue-Derived Extracellular Matrix That Promotes Tissue-Specific Growth and Differentiation of Cells in Vitro (1998)

The importance of understanding cell–extracellular matrix (ECM) interaction is now evident as scientists, engineers, and physicians search for novel scaffolds that support and maintain tissue-specific cellular growth and function both in vivo and in vitro. Small intestinal submucosa (SIS) represents an ECM that has been derived from porcine intestine while preserving its natural composition and architecture. More recently, an extract of this physiologic ECM, which forms a three-dimensional gel in vitro, has been developed. When compared to routinely used culture substrata (e.g., plastic, Vitrogen, and Matrigel), intact SIS and SIS-derived gel possess unique compositional and architectural features. Simple squamous epithelial (pulmonary artery), fibroblastic (Swiss 3T3), glandular epithelial (adenocarcinoma), and smooth muscle-like (urinary bladder) cells were seeded upon intact SIS and SIS-derived gel and their morphologic response evaluated. For each of the four cell types studied, intact SIS and SIS-derived gel were equivalent or superior in their ability to support and maintain expression of tissue-specific phenotype when compared to the routinely used substrata, plastic, Vitrogen, and Matrigel. Therefore, SIS may provide a novel biologically derived scaffold for the growth and study of a variety of cell types in vitro. Such information regarding the influence of substrate structure and function on cell behavior will be useful in the development of successful tissue engineering strategies.
Verification of Male Infertility Biomarkers in Seminal Plasma by Multiplex Selected Reaction Monitoring Assay (2011)

Seminal plasma is a promising biological fluid to use for noninvasive clinical diagnostics of male reproductive system disorders. To verify a list of prospective male infertility biomarkers, we developed a multiplex selected reaction monitoring assay and measured the relative abundance of 31 proteins in 30 seminal plasma samples from normal, nonobstructive azoospermia and post-vasectomy individuals. Median levels of some proteins were decreased by more than 100-fold in nonobstructive azoospermia or post-vasectomy samples, in comparison with normal samples. To follow up the most promising candidates and measure their concentrations in seminal plasma, heavy isotope-labeled internal standards were synthesized and used to reanalyze 20 proteins in the same set of samples. Concentrations of candidate proteins in normal seminal plasma were found in the range 0.1-1000 μg/ml but were significantly decreased in nonobstructive azoospermia and post-vasectomy. These data allowed us to select, for the first time, biomarkers to discriminate between normal, nonobstructive azoospermia, and post-vasectomy (simulated obstructive azoospermia) seminal plasma samples. Some testis-specific proteins (LDHC, TEX101, and SPAG11B) performed with absolute or nearly absolute specificities and sensitivities. Cell-specific classification of protein expression indicated that Sertoli or germ cell dysfunction, but not Leydig cell dysfunction, was observed in nonobstructive azoospermia seminal plasma. The proposed panel of biomarkers, pending further validation, could lead to a clinical assay that can eliminate the need for testicular biopsy to diagnose the category of male infertility, thus providing significant benefits to patients as well as decreased costs associated with the differential diagnosis of azoospermia.
Single cell analysis of phosphoinositide 3-kinase/Akt and ERK activation in acute myeloid leukemia by flow cytometry. (2006)

Our study shows that flow cytometry is a reliable method for detecting Akt and ERK phosphorylation in all patients' samples. Activation can also be detected in the most immature blast cells, which represent exquisite target cells for new therapeutics.
Typhlitis. An 18-year experience and postmortem review (1990)

A review of pediatric autopsy results at the Texas Children's Hospital, Baylor College of Medicine from 1970 through 1987 was conducted. Thirty-three cases of typhlitis were identified in patients with acute leukemia and two cases each in patients with lymphoblastic lymphoma and aplastic anemia. Patients ranged in age from 10 months to 17 years. Fifty-seven percent were male and 43% were female. All were myelosuppressed. A postmortem incidence rate of 24% was determined for patients with acute leukemia. Common symptoms included abdominal pain and distention in 78% of patients and acute lower gastrointestinal bleeding in 35%. Abdominal radiographs varied in spectrum from a nonspecific bowel gas pattern to frank right colonic pneumatosis intestinalis. Thirty-three patients received chemotherapy within 30 days before onset of abdominal symptoms. All patients were febrile (greater than 38.5 degrees C), and 33 received broad-spectrum antibiotics. Three patients received amphotericin B. Premortem, 84% of organisms cultured from blood were bacterial whereas 16% were fungal. Fungal pathogens accounted for 53% of new microorganisms seen at autopsy. Postmortem examination showed typhlitis in the following anatomic distributions: (1) confined to the cecum; (2) involving the cecum and ileum; (3) involving the cecum, ileum, and ascending colon; or (4) involving the cecum, with sporadic ulcers throughout the intestine. This review includes clinical and postmortem features of typhlitis and current strategies for diagnosis and management.
High-Sensitivity C-Reactive Protein: A Novel and Promising Marker of Coronary Heart Disease (2001)

hs-CRP has prognostic utility in patients with acute coronary syndromes and is a strong independent predictor of future coronary events in apparently healthy subjects.
Monocyte-derived alveolar macrophages drive lung fibrosis and persist in the lung over the life span (2017)

Little is known about the relative importance of monocyte and tissue-resident macrophages in the development of lung fibrosis. We show that specific genetic deletion of monocyte-derived alveolar macrophages after their recruitment to the lung ameliorated lung fibrosis, whereas tissue-resident alveolar macrophages did not contribute to fibrosis. Using transcriptomic profiling of flow-sorted cells, we found that monocyte to alveolar macrophage differentiation unfolds continuously over the course of fibrosis and its resolution. During the fibrotic phase, monocyte-derived alveolar macrophages differ significantly from tissue-resident alveolar macrophages in their expression of profibrotic genes. A population of monocyte-derived alveolar macrophages persisted in the lung for one year after the resolution of fibrosis, where they became increasingly similar to tissue-resident alveolar macrophages. Human homologues of profibrotic genes expressed by mouse monocyte-derived alveolar macrophages during fibrosis were up-regulated in human alveolar macrophages from fibrotic compared with normal lungs. Our findings suggest that selectively targeting alveolar macrophage differentiation within the lung may ameliorate fibrosis without the adverse consequences associated with global monocyte or tissue-resident alveolar macrophage depletion.
On the development of a confocal Rayleigh-Brillouin microscope (2007)

This Note illustrates how a confocal microscope may be modified to conduct Rayleigh-Brillouin mapping experiments that yield very useful information on the mechanical properties of interfacial materials in small volume elements. While the modifications to the microscope are quite straightforward, they do entail significant changes in the optical design. The instrument described herein consists of an argon ion laser equipped with an actively stabilized intercavity etalon that serves as the excitation source for a modified Zeiss LSM 310 confocal laser scan microscope. The optics of the microscope were reconfigured to enable interfacing of the microscope with a tandem triple-pass Fabry-Perot interferometer. This instrument enables three-dimensional Rayleigh-Brillouin spectral mapping of samples at micron spatial resolution. The performance of the instrument and its ability to perform both lateral and depth scans of the acoustic phonon velocity and, hence, the longitudinal modulus across bonded polymer/polymer and polymer/ceramic interfaces are illustrated and discussed.
Benefits of Influenza Vaccination for Low-, Intermediate-, and High-Risk Senior Citizens (1998)

This study confirms that healthy senior citizens as well as senior citizens with underlying medical conditions are at risk for the serious complications of influenza and benefit from vaccination. All individuals 65 years or older should be immunized with this vaccine.
CII-DC-AdTRAIL cell gene therapy inhibits infiltration of CII-reactive T cells and CII-induced arthritis (2003)

Previously, we described an APC-adenovirus (APC-Ad) FasL cell gene therapy method which could be used to deplete autoreactive T cells in vivo. FasL was toxic, however, and controlled regulation of FasL was not achieved. Here we describe an improved approach to delivering TNF-related apoptosis-inducing ligand (TRAIL) in vivo in which collagen II-induced (CII-induced) arthritis-susceptible (CIA-susceptible) DBA/1j mice were treated with CII-pulsed DCs that had been transfected with a novel Ad system. The Ad was engineered to exhibit inducible TRAIL under the control of the doxycycline-inducible (DOX-inducible) tetracycline response element (TRE). Four groups of mice were treated with CII-DC-AdTRAIL+DOX, CII-DC-AdTRAIL (no DOX), CII-DC-AdGFP+DOX, or DC-AdTRAIL+DOX (no CII), beginning 2 weeks after priming with CII in CFA. The incidence of arthritis and infiltration of T cells in the joint was significantly decreased in CII-DC-AdTRAIL+DOX-treated mice. The in vitro splenic T cell proliferative response and induction of IFN- to bovine CII stimulation were also significantly reduced in mice treated with CII-DC-AdTRAIL+DOX. AdTRAIL+DOX was not toxic to DCs or mice but could induce activated T cells to undergo apoptosis in the spleen. Our results suggest that CII-DC-AdTRAIL+DOX cell gene therapy is a safe and effective method for inhibiting the development of CIA.
Flow Cytometric Immunophenotyping and Minimal Residual Disease Analysis in Multiple Myeloma (2009)

Presence of normal plasma cells (PCs), hemodilution of bone marrow aspirate, and changes in the immunophenotype are important considerations in minimal residual disease (MRD) assessment in multiple myeloma (MM). We evaluated 124 subjects-107 with MM, 11 with Hodgkin lymphoma, and 6 allogeneic stem cell transplantation donors-for the immunophenotype of neoplastic, reactive, and normal PCs respectively. Of the patients with MM, 36 were evaluated for MRD and 23 for a change in immunophenotype after chemotherapy. The immunophenotype of normal and reactive PCs was similar and differed from that of neoplastic PCs with respect to CD19, CD45, CD56, CD52, CD20, and CD117. At least 2 antigens were aberrantly expressed in all cases and 3 in 90.7% of MM cases. A change in the immunoprofile of PCs was observed in 18 (78%) of 23 cases. By using flow cytometry, we detected MRD in all samples, and a neoplastic PC index (percentage of neoplastic PCs/total bone marrow PCs) of less than 30 could differentiate immunofixation (IFx)- from IFx+ samples (complete and partial responders, respectively).
N-Acylated .alpha.-Amino Acids as Novel Oral Delivery Agents for Proteins (1995)

A series of N-acylated alpha-amino acids were synthesized and shown to improve the oral delivery of two protein drugs, salmon calcitonin (sCT) and interferon-alpha. Forty-five compounds in this series were tested in vivo in rats and primates. A significant positive correlation was found between the log P of the acylated amino acids and the decrease in serum calcium following oral dosage of sCT in rats. Such a correlation was not found for interferon-alpha. These derivatized amino acids only weakly inhibited the activity of trypsin or leucine aminopeptidase. Histological examinations of rat intestinal tissue after oral dosing of acylated amino acid/protein combinations revealed no detectable pathology.
Iridium‐Catalyzed Regioselective Silylation of Aromatic and Benzylic CH Bonds Directed by a Secondary Amine (2014)

Reported herein is an iridium-catalyzed, regioselective silylation of the aromatic C-H bonds of benzylamines and the benzylic C-H bonds of 2,N-dialkylanilines. In this process, (hydrido)silyl amines, generated in situ by dehydrogenative coupling of benzylamine or aniline with diethylsilane, undergo selective silylation at the C-H bond γ to the amino group. The products of this silylation are suitable for subsequent oxidation, halogenation, and cross-coupling reactions to deliver benzylamine and arylamine derivatives.
Human Tissue Kallikreins: A Family of New Cancer Biomarkers (2002)

Kallikreins are a subgroup of the serine protease enzyme family. Until recently, it was thought that the human kallikrein gene family contained only three members. In the past 3 years, the entire human kallikrein gene locus was discovered and found to contain 15 kallikrein genes. Kallikreins are expressed in many tissues, including steroid hormone-producing or hormone-dependent tissues such as the prostate, breast, ovary, and testis. Most, if not all, kallikreins are regulated by steroid hormones in cancer cell lines. There is strong but circumstantial evidence linking kallikreins and cancer. Prostate-specific antigen (PSA; hK3) and, more recently, human glandular kallikrein (hK2) are widely used tumor markers for prostate cancer. Three other kallikreins, hK6, hK10, and hK11, are emerging new serum biomarkers for ovarian and prostate cancer diagnosis and prognosis. Several other kallikreins are differentially expressed at both the mRNA and protein levels in various endocrine-related malignancies, and they have prognostic value. The coexpression of many kallikreins in the same tissues (healthy and malignant) points to the possible involvement of kallikreins in cascade enzymatic pathways. In addition to their diagnostic/prognostic potential, kallikreins may also emerge as attractive targets for therapeutics.
HAYEK, SCHMITT Y EL ESTADO DE DERECHO (1991)

Adrenomedullin (ADM) is a hypotensive and vasodilator peptide belonging to the calcitonin gene-related peptide family. It is secreted <i>in vitro</i> by endothelial cells and vascular smooth muscle cells, and is significantly upregulated by a number of stimuli. Moreover, ADM participates in the regulation of hematopoietic compartment, solid tumors and leukemias, such as acute myeloid leukemia (AML). To better characterize ADM involvement in AML pathogenesis, we investigated its expression during human hematopoiesis and in leukemic subsets, based on a morphological, cytogenetic and molecular characterization and in T cells from AML patients. In hematopoietic stem/progenitor cells and T lymphocytes from healthy subjects, <i>ADM</i> transcript was barely detectable. It was expressed at low levels by megakaryocytes and erythroblasts, while higher levels were measured in neutrophils, monocytes and plasma cells. Moreover, cells populating the hematopoietic niche, including mesenchymal stem cells, showed to express <i>ADM</i>. <i>ADM</i> was overexpressed in AML cells <i>versus</i> normal CD34<sup>+</sup> cells and in the subset of leukemia compared with hematopoietic stem cells. In parallel, we detected a significant variation of <i>ADM</i> expression among cytogenetic subgroups, measuring the highest levels in inv(16)/t(16;16) or complex karyotype AML. According to the mutational status of AML-related genes, the analysis showed a lower expression of <i>ADM</i> in <i>FLT3</i>-ITD, <i>NPM1</i>-mutated AML and <i>FLT3</i>-ITD/<i>NPM1</i>-mutated cases compared with wild-type ones. Moreover, <i>ADM</i> expression had a negative impact on overall survival within the favorable risk class, while showing a potential positive impact within the subgroup receiving a not-intensive treatment. The expression of 135 genes involved in leukemogenesis, regulation of cell proliferation, ferroptosis, protection from apoptosis, HIF-1α signaling, JAK-STAT pathway, immune and inflammatory responses was correlated with <i>ADM</i> levels in the bone marrow cells of at least two AML cohorts. Moreover, <i>ADM</i> was upregulated in CD4<sup>+</sup> T and CD8<sup>+</sup> T cells from AML patients compared with healthy controls and some <i>ADM</i> co-expressed genes participate in a signature of immune tolerance that characterizes CD4<sup>+</sup> T cells from leukemic patients. Overall, our study shows that <i>ADM</i> expression in AML associates with a stem cell phenotype, inflammatory signatures and genes related to immunosuppression, all factors that contribute to therapy resistance and disease relapse.
Estimating simple functions on the union of data streams (2001)

Massive data sets often arise as physically distributed, parallel data streams. We present algorithms for estimating simple functions on the union of such data streams, while using only logarithmic space per stream. Each processor observes only its own stream, and communicates with the other processors only after observing its entire stream. This models the set-up in current network monitoring products. Our algorithms employ a novel coordinated sampling technique to extract a sample of the union; this sample can be used to estimate aggregate functions on the union. The technique can also be used to estimate aggregate functions over the distinct “labels” in one or more data streams, e.g., to determine the zeroth frequency moment (i.e., the number of distinct labels) in one or more data streams. Our space and time bounds are the best known for these problems, and our logarithmic space bounds for coordinated sampling contrast with polynomial lower bounds for independent sampling. We relate our distributed streams model to previously studied non-distributed (i.e., merged) streams models, presenting tight bounds on the gap between the distributed and merged models for deterministic algorithms.
Catalytic properties and inhibition of proline-specific dipeptidyl peptidases II, IV and VII (2003)

There is currently intense interest in the emerging group of proline-specific dipeptidases, and their roles in the regulation of biological processes. Dipeptidyl peptidase IV (DPP-IV) is involved in glucose metabolism by contributing to the regulation of glucagon family peptides and has emerged as a potential target for the treatment of metabolic diseases. Two other proline-specific dipeptidases, DPP-VII (also known as quiescent cell proline dipeptidase) and DPP-II, have unknown functions and have recently been suggested to be identical proteases based on a sequence comparison of human DPP-VII and rat DPP-II (78% identity) [Araki, Li, Yamamoto, Haneda, Nishi, Kikkawa and Ohkubo (2001) J. Biochem. 129, 279-288; Fukasawa, Fukasawa, Higaki, Shiina, Ohno, Ito, Otogoto and Ota (2001) Biochem. J. 353, 283-290]. To facilitate the identification of selective substrates and inhibitors for these enzymes, a complete biochemical profile of these enzymes was obtained. The pH profiles, substrate specificities as determined by positional scanning, Michaelis-Menten constants and inhibition profiles for DPP-VII and DPP-II were shown to be virtually identical, strongly supporting the hypothesis that they are the same protease. In addition, substrate specificities, catalytic constants and IC(50) values were shown to be markedly different from those of DPP-IV. Selective DPP-IV and DPP-VII substrates were identified and they can be used to design selective inhibitors and probe further into the biology of these enzymes.
Nasal Delivery of Vaccines (1996)

Only relatively recently the significance of inducing not only systemic immunity but also significant local immunity at susceptible mucosal surfaces has become appreciated. A new field of mucosal immunity has been established as information accumulates on mucosal-associated lymphoid tissue (MALT) and on its role in both local and systemic immune responses. This review describes the formation of vaccines to be delivered to one of MALT components, i.e. the nasal-associated lymphoid tissue (NALT), which bears some similarities with the Peyer's patches of the intestine. The association of antigens with adjuvants and particulate carriers such as microparticles, nanoparticles and liposomes is emphasised.
Isolation and characterization of tumorigenic extrahepatic cholangiocarcinoma cells with stem cell‐like properties (2010)

Recent studies suggest that the ability to form and grow tumors specifically resides in a small cell population called cancer stem cells (CSCs). These studies were conducted mainly on various human cancers; however, isolation and characterization of stem cells from cholangiocarcinoma have not been attempted. The molecular markers CD24, CD44, CD34, and epithelial cell adhesion molecule (EpCAM) are widely used, individually or in combination, to characterize some types of CSCs. In this study, we used these markers to identify a subpopulation of cells in extrahepatic cholangiocarcinoma (ECC) with cancer stem/progenitor cell-like properties. We found that CD24(+) CD44(+) EpCAM(high) cells (0.39-2.27%) were present in human ECC tissues. The expression of a CD24(+) CD44(+) EpCAM(high) subpopulation was consistent with primary cancers and could be duplicated during serial in vivo passaging in NOD/SCID mice. CD24(+) CD44(+) EpCAM(high) cells isolated from 3 cholangiocarcinoma xenografts showed high tumorigenic potential compared with CD24(-) CD44(-) EpCAM(low/-) cells. These tumorigenic ECC cells exhibited the stem cell properties of self-renewal and ability to produce heterogeneous progeny. We report the identification of a CSC population in ECC characterized by CD24, CD44 and EpCAM phenotypes. Our findings could provide new insight into the tumorigenesis of cholangiocarcinoma and offer a potential target for anti-cancer therapy.
A theoretical study of surface-to-borehole electromagnetic logging in cased holes (1989)

Abstract A new electromagnetic logging method, in which the source is a horizontal loop coaxial with a cased drill hole and the secondary axial fields are measured at depth within the casing, has been analyzed. The analysis, which is for an idealized model of an infinite pipe in a conductive whole space, has shown that the casing and formation are uncoupled at the low frequencies that would be used in field studies. The field inside the casing may be found by first finding the field in the formation and then using this field as an incident field for the pipe alone. This result permits the formation response to be recovered from the measured field in the borehole by applying a correction for the known properties of the casing. If the casing response cannot be accurately predicted, a separate logging tool employing a higher frequency transmitter could be used to determine the required casing parameters in the vicinity of the receiver.This logging technique shows excellent sensitivity to changes in formation conductivity, but it is not yet known how well horizontal stratification can be resolved. One of its most promising applications will be in monitoring, through repeated measurements, changes in formation conductivity during production or enhanced recovery operations.
Chemistry and Biology of Cyclic Depsipeptides of Medicinal and Biological Interest (2004)

Cyclodepsipeptides comprise a wide variety of cyclic peptides of natural origin and are characterized by the occurrence of at least one ester linkage. The great interest that this class of natural products has elicited in scientific community is explained by their wide range of biological activities, intriguing mechanisms of action and attractive molecular architecture. For example, they display a variety of biological effects, such as immunosuppressant, antibiotic, antifungi, antiinflammatory or antitumoral activities. In addition, many of these cyclic depsipeptides represent useful tools for the research of biological processes involved in cellular regulation. The present review deals with the most interesting aspects of the biology and the chemistry of some of these compounds.