gebhart/patrepeval huggingface dataset:
Characterization of Lymphocyte-Activating Factor (LAF) Produced by Human Mononuclear Cells: Biochemical Relationship of High and Low Molecular Weight Forms of LAF (1979)

Abstract Human mononuclear cells (MNL) stimulated with Salmonella typhosa endotoxin (LPS), Actinomyces viscosus cell wall extracts, phorbol myristic acetate (PMA), or phytohemagglutinin (PHA) produced a factor that was mitogenic for mouse thymocytes. These agents not only enhanced the production of this mitogenic factor(s) by cultures of MNL enriched for glass-adherent cells, but also by nonadherent cell cultures. However, when the monocyte contamination of the nonadherent cell population was decreased to less than 0.5%, the remaining nonadherent cells did not generate significant thymocyte mitogenic activity, suggesting that either the contaminating monocytes were the cell source of the factor in the nonadherent cell population or that the production of the factor by nonadherent cells was monocyte dependent. The results of biochemical studies support the former possibility as follows: 1). The mitogenic activity produced by both adherent and nonadherent MNL eluted from Bio-Gel P-100 columns with m.w. of 50,000 to 70,000 and 12,000 to 22,000, values that are characteristic of the two forms of lymphocyte activity factor (LAF) produced by human monocytes. 2). The lower m.w. form of “thymocyte mitogenic” activity produced by the adherent as well as nonadherent MNL when characterized further both exhibited the same behavior on Bio-Gel P-100, DEAE cellular and hydroxylapatite. 3). When the lower m.w. LAF was reconstituted with 2% human serum, concentrated and rechromatographed on Bio-Gel P-100, a significant portion of the LAF activity appeared in the 50,000 to 70,000 m.w. range, suggesting that the higher m.w. form of LAF may actually be a complex of the lower m.w. LAF with a human serum component(s). In conclusion, a small population of contaminating monocytes in a nonadherent MNL population is capable of producing significant amounts of LAF, and LAF may exist free or in association with a component(s) of human serum.
A Core Human Microbiome as Viewed through 16S rRNA Sequence Clusters (2012)

We explore the microbiota of 18 body sites in over 200 individuals using sequences amplified V1-V3 and the V3-V5 small subunit ribosomal RNA (16S) hypervariable regions as part of the NIH Common Fund Human Microbiome Project. The body sites with the greatest number of core OTUs, defined as OTUs shared amongst 95% or more of the individuals, were the oral sites (saliva, tongue, cheek, gums, and throat) followed by the nose, stool, and skin, while the vaginal sites had the fewest number of OTUs shared across subjects. We found that commonalities between samples based on taxonomy could sometimes belie variability at the sub-genus OTU level. This was particularly apparent in the mouth where a given genus can be present in many different oral sites, but the sub-genus OTUs show very distinct site selection, and in the vaginal sites, which are consistently dominated by the Lactobacillus genus but have distinctly different sub-genus V1-V3 OTU populations across subjects. Different body sites show approximately a ten-fold difference in estimated microbial richness, with stool samples having the highest estimated richness, followed by the mouth, throat and gums, then by the skin, nasal and vaginal sites. Richness as measured by the V1-V3 primers was consistently higher than richness measured by V3-V5. We also show that when such a large cohort is analyzed at the genus level, most subjects fit the stool "enterotype" profile, but other subjects are intermediate, blurring the distinction between the enterotypes. When analyzed at the finer-scale, OTU level, there was little or no segregation into stool enterotypes, but in the vagina distinct biotypes were apparent. Finally, we note that even OTUs present in nearly every subject, or that dominate in some samples, showed orders of magnitude variation in relative abundance emphasizing the highly variable nature across individuals.
Glia maturation factor‐β is produced by thymoma and may promote intratumoral T‐cell differentiation (2005)

The present study suggests that T-cell development in thymoma may be maintained partly by GMFB produced by the tumour cells.
Nicotinamide-substituted complexes as redox markers. 1. Synthesis and UV investigation of rhenium and technetium mixed-ligand systems (1998)

In order to develop a redox delivery system for Tc radiotracers the synthesis of new nicotinamide and pyridinium salt-substituted Re(V) mixed-ligand complexes of the ‘3+1’ type is described. The complexation of 99/99mTc with these ligands was studied by thin layer chromatography and UV-VIS spectroscopy. The reduction of the pyridinium salt with sodium dithionite to the 1,4-dihydropyridine was carried out on the free ligand and on the complex. The stability of the 1,4-dihydropyridines was observed by UV-VIS spectrometry. © 1998 John Wiley & Sons, Ltd.
Intentions (2009)

Knowing the intent of a search query allows for more intelligent ways of retrieving relevant search results. Most of the recent work on automatic detection of query intent uses supervised learning methods that require a substantial amount of labeled data; manually collecting such data is often time-consuming and costly. Human computation is an active research area that includes studies of how to build online games that people enjoy playing, while in the process providing the system with useful data. In this work, we present the design principles behind a new game called Intentions, which aims to collect data about the intent behind search queries.
Exciton Dissociation in CdSe Quantum Dots by Hole Transfer to Phenothiazine (2008)

Ultrafast charge transfer from quantum dots (QDs) is essential for their application in solar cells. Photoinduced hole transfer from CdSe QDs (with first exciton peak at 462 nm and estimated radius of 1.8 nm) to phenothiazine (PTZ) was investigated by time-resolved fluorescence and transient absorption spectroscopy. Fluorescence lifetime measurements showed that the presence of PTZ reduced the exciton lifetime of CdSe QDs, and the quenching rate increased with increasing PTZ concentration. Transient absorption spectra of CdSe−PTZ complexes directly revealed the formation of PTZ cation radical, suggesting that the excitons in CdSe dissociated by hole transfer to PTZ. A kinetic model based on a Poisson distribution of the number of adsorbates on each QD was found to adequately describe the adsorbate concentration-dependent fluorescence decay kinetics. According to this model, the hole transfer time was ∼2.5 ns in 1:1 CdSe−PTZ complexes and reached ∼300 ps in samples with an average of ∼6 PTZ per QD.
Isolation of Anti-Hapten Specific Antibody Fragments from Combinatorial Libraries (2003)

The generation of high-affinity antibodies (Abs) against hapten targets (molecular weight below 1000 Dalton) presents particular problems not encountered with larger antigens (Ags). By their nature, haptens are invisible to the host immune system unless presented as an epitope conjugated to a suitable immunogenic carrier protein, such as bovine thyroglobulin. The principal interest in anti-hapten Abs is as detection molecules for use in diagnostic assays. These typically use dipstick (qualitative) or, more commonly, enzymelinked immunosorbant assay (ELISA) formats, for the quantification and/or detection of targets such as environmental pollutants or for monitoring the presence of drugs in clinical samples. There are also applications related to biological functions, e.g., Abs directed against signal molecules enhance the study of cell signaling pathways and have potential as candidate therapeutic agents.
Improved GaAs solar cells with very thin junctions (1976)

Violet cells with 500-1000 A junction depths have been made in GaAs by narrow junction diffusion followed by anodization. The best AM0 efficiencies obtained by this technique have been 10.5% (14% at AM1). GaAlAs-GaAs structures with very thin GaAlAs layers are much more promising, and efficiencies of over 18% at AM0 have been measured (21.9% at AM1).
Strained-Layer Epitaxy of Germanium-Silicon Alloys (1985)

Despite the dominant position of silicon in semiconductor electronics, its use is ultimately limited by its incompatibility with other semiconducting materials. Strained-layer epitaxy overcomes problems of crystallographic compatibility and produces high-quality heterostructures of germanium-silicon layers on silicon. This opens the door to a range of electronic and photonic devices that are based on bandstructure physics.
Evidence for a multistep pathogenesis of a myelodysplastic syndrome (1984)

Somatic cell genetic approaches utilizing the cellular mosaicism present in women heterozygous for glucose-6-phosphate dehydrogenase (G6PD) have provided information relevant to the pathogenesis of some neoplastic disorders. With these techniques, we studied a 61-year-old woman with a myelodysplastic syndrome. GdB/GdA heterozygosity was demonstrated in skin and cultured T lymphocytes, which exhibited both A and B type G6PD. In contrast, erythrocytes, platelets, granulocytes, and marrow nucleated cells displayed almost exclusively G6PD type B. In addition, 21 of 24 Epstein-Barr virus-transformed B lymphoblastoid lines that expressed a single immunoglobulin light chain showed only type B G6PD, suggesting that the stem cells involved by this disease were clonal and could differentiate to B lymphocytes as well as to mature granulocytes, erythrocytes , and platelets. Cultured skin fibroblasts and phytohemagglutinin-stimulated lymphocytes were karyotypically normal, but two independent abnormalities were found in marrow--47,XX, +8 and 46,XX,del(11)(q23). None of 14 type B G6PD lymphoblastoid lines analyzed in detail contained these karyotypic abnormalities, which strongly suggests that a visible chromosomal alteration is not the sole step in the development of this disease. We hypothesize that at least two events are involved in the pathogenesis of this patient's myelodysplasia: one causing proliferation of a clone of genetically unstable pluripotent stem cells and another inducing chromosomal abnormalities in its descendants.
On-the-Go Mapping of Soil pH Using Antimony Electrodes (2008)

Glass-membrane ion-selective electrodes represent the most common measurement means to determine the pH of an aquatic media. Automated engagement of such electrodes with naturally moist soil samples allows implementation of on-the-go mapping of soil pH. However, some early adopters of this technology reported heavy electrode abuse and occasional breakage in soils with course texture and/or hard impurities. Antimony electrodes provide an alternative suitable for on-the-go mapping of soil pH. This paper illustrates the results of laboratory and field experiments comparing soil pH measurements obtained using glass-based and antimony-based ion-selective electrodes. It was concluded that measurements produced using an antimony electrode were of similar quality to the measurements done with a conventional glass electrode. However, the ability to withstand abrasion was much higher when soil was engaged with an antimony electrode than with a glass membrane.
The Interdomain Region of Dengue NS5 Protein That Binds to the Viral Helicase NS3 Contains Independently Functional Importin β1 and Importin α/β-Recognized Nuclear Localization Signals (2002)

Dengue virus NS5 protein is a multifunctional RNA-dependent RNA polymerase that is essential for virus replication. We have shown previously that the 37- amino acid interdomain spacer sequence (residues (369)X(2)KKX(14)KKKX(11)RKX(3)405) of Dengue2 NS5 contains a functional nuclear localization signal (NLS). In this study, beta-galactosidase fusion proteins carrying point mutations of the positively charged residues or truncations of the interdomain linker region (residues 369-389 or residues 386-405) were analyzed for nuclear import and importin binding activities to show that the N-terminal part of the linker region (residues 369-389, a/bNLS) is critical for nuclear localization and is recognized with high affinity by the conventional NLS-binding importin alpha/beta heterodimeric nuclear import receptor. We also show that the importin beta-binding site (residues 320-368, bNLS) adjacent to the a/bNLS, previously identified by yeast two-hybrid analysis, is functional as an NLS, recognized with high affinity by importin beta, and able to target beta-galactosidase to the nucleus. Intriguingly, the bNLS is highly conserved among Dengue and related flaviviruses, implying a general role for the region and importin beta in the infectious cycle.
The craniocervical venous system in relation to cerebral venous drainage. (2002)

The lateral, posterior, and anterior condylar veins and the mastoid and occipital emissary veins connect the dural venous sinuses of the posterior cranial fossa with the vertebral venous systems. These connections are clinically relevant, because encephalic drainage occurs preferentially through the vertebral venous system in the upright position. The ACC is a constant anatomic structure that may play an important role in the redirection of cerebral blood in the craniocervical region.
Endotoxemia is common following abdominal organ transplantation and is associated with reperfusion and rejection (2009)

Objective. Patients undergoing orthotopic liver transplantation (OLT) and multi-visceral transplantation (MVT) may have an increased incidence of endotoxemia due to translocation of endotoxin from the intestine, in combination with impaired hepatic clearance. We sought to evaluate the presence of endotoxemia in the perioperative period, using the Endotoxin Activity Assay™ (EAA) to understand the association of endotoxin activity (EA) with clinical course and outcome. Material and methods. In this prospective observational pilot study we measured EA in 40 patients undergoing OLT or MVT during the perioperative period. As a control, the EAA was performed on 10 healthy adult volunteers. We analyzed the relationships between EA and graft function, episodes of rejection, infection and outcome. Results. Mean EA in the control group was 0.21±0.05 u (range 0.16–0.27 u). For patients, baseline pre-transplant EA was significantly greater than that in controls at 0.50±0.17 u (range 0.10–0.80 u) (p=0.001) and further increased post-reperfusion (p=0.018) during OLT, especially in patients who developed post-reperfusion syndrome (PRS) (p=0.029). In the postoperative phase, EA remained elevated (>0.40 u) in nearly 75% of patients for up to 1 month post-surgery but was greatest (>0.60 u) for patients who developed infection. However, postoperative EA did not correlate with length of hospital or intensive care unit stay or with 90-day survival. Conclusions. High EA is common before, during and after abdominal organ transplantation and is associated with PRS, infection and rejection. However, unlike other critically ill patients, high EA in this cohort does not necessarily affect short-term prognosis. Further study will delineate the utility of measuring EA in the abdominal transplant population.
Pharmacological Elevation of Circulating Bioactive Phosphosphingolipids Enhances Myocardial Recovery After Acute Infarction (2015)

Acute myocardial infarction (AMI) initiates innate immune and reparatory mechanisms through which bone marrow-derived stem/progenitor cells (BMSPCs) are mobilized toward the ischemic myocardium and contribute to myocardial regeneration. Although it is clear that the magnitude of BMSPC mobilization after AMI correlates with cardiac recovery, the molecular events driving BMSPC mobilization and homing are poorly understood. The present study confirms the role of bioactive lipids in BMSPC mobilization after AMI and proposes a new strategy that improves cardiac recovery. Inhibiting sphingosine-1 phosphate (S1P) lyase (SPL) allows for the augmentation of the plasma levels of S1P and stem cell mobilization. These findings demonstrate that early transient SPL inhibition after MI correlates with increased stem cell mobilization and their homing to the infarct border zones. Augmenting BMSPC mobilization correlated with the formation of new blood vessels and cardiomyocytes and c-Kit cell proliferation. These novel findings on the cellular level were associated with functional cardiac recovery, reduced adverse remodeling, and a decrease in scar size. Taken together, these data indicate that pharmacological elevation of bioactive lipid levels can be beneficial in the early phase after cardiac ischemic injury. These findings provide the first evidence that a carefully timed transient pharmacological upregulation of bioactive lipids after AMI could be therapeutic, because it results in significant cardiac structural and functional improvements.
Lidocaine Concentration in Oral Tissue by the Addition of Epinephrine (2016)

The vasoconstrictive effect due to the addition of epinephrine to local anesthetic has been clearly shown by measuring blood-flow volume or blood anesthetic concentration in oral mucosal tissue. However, there are no reports on the measurement of anesthetic concentration using samples directly taken from the jawbone and oral mucosal tissue. Consequently, in this study, the effect of lidocaine concentration in the jawbone and oral mucosal tissue by the addition of epinephrine to the local anesthetic lidocaine was considered by quantitatively measuring lidocaine concentration within the tissue. Japanese white male rabbits (n = 96) were used as test animals. General anesthesia was induced by sevoflurane and oxygen, and then cannulation to the femoral artery was performed while arterial pressure was constantly recorded. Infiltration anesthesia was achieved by 0.5 mL of 2% lidocaine containing 1 : 80,000 epinephrine in the upper jawbone (E(+)) and 0.5 mL of 2% of epinephrine additive-free lidocaine (E(0)) under the periosteum. At specified time increments (10, 20, 30, 40, 50, and 60 minutes), samples from the jawbone, oral mucosa, and blood were collected, and lidocaine concentration was directly measured by high-performance liquid chromatography. No significant differences in the change in blood pressure were observed either in E(+) or E(0). In both E(+) and E(0) groups, the serum lidocaine concentration peaked 10 minutes after local anesthesia and decreased thereafter. At all time increments, serum lidocaine concentration in E(+) was significantly lower than that in E(0). There were no significant differences in measured lidocaine concentration between jawbone and mucosa within either the E(+) or the E(0) groups at all time points, although the E(0) group had significantly lower jawbone and mucosa concentrations than the E(+) group at all time points when comparing the 2 groups to each other. Addition of epinephrine to the local anesthetic inhibited systemic absorption of local anesthetic into the blood such that a high concentration could be maintained in the tissue. Epinephrine-induced vasoconstrictive effect was observed not only in the oral mucosa but also in the jawbone.
PROPKA3: Consistent Treatment of Internal and Surface Residues in Empirical p<i>K</i><sub>a</sub>Predictions (2011)

In this study, we have revised the rules and parameters for one of the most commonly used empirical pKa predictors, PROPKA, based on better physical description of the desolvation and dielectric response for the protein. We have introduced a new and consistent approach to interpolate the description between the previously distinct classifications into internal and surface residues, which otherwise is found to give rise to an erratic and discontinuous behavior. Since the goal of this study is to lay out the framework and validate the concept, it focuses on Asp and Glu residues where the protein pKa values and structures are assumed to be more reliable. The new and improved implementation is evaluated and discussed; it is found to agree better with experiment than the previous implementation (in parentheses): rmsd = 0.79 (0.91) for Asp and Glu, 0.75 (0.97) for Tyr, 0.65 (0.72) for Lys, and 1.00 (1.37) for His residues. The most significant advance, however, is in reducing the number of outliers and removing unreasonable sensitivity to small structural changes that arise from classifying residues as either internal or surface.
Intermediate Progenitors in Adult Hippocampal Neurogenesis: Tbr2 Expression and Coordinate Regulation of Neuronal Output (2008)

Neurogenesis in the adult hippocampus is a highly regulated process that originates from multipotent progenitors in the subgranular zone (SGZ). Currently, little is known about molecular mechanisms that regulate proliferation and differentiation in the SGZ. To study the role of transcription factors (TFs), we focused on Tbr2 (T-box brain gene 2), which has been implicated previously in developmental glutamatergic neurogenesis. In adult mouse hippocampus, Tbr2 protein and Tbr2-GFP (green fluorescent protein) transgene expression were specifically localized to intermediate-stage progenitor cells (IPCs), a type of transit amplifying cells. The Tbr2+ IPCs were highly responsive to neurogenic stimuli, more than doubling after voluntary wheel running. Notably, the Tbr2+ IPCs formed cellular clusters, the average size of which (Tbr2+ cells per cluster) likewise more than doubled in runners. Conversely, Tbr2+ IPCs were selectively depleted by antimitotic drugs, known to suppress neurogenesis. After cessation of antimitotic treatment, recovery of neurogenesis was paralleled by recovery of Tbr2+ IPCs, including a transient rebound above baseline numbers. Finally, Tbr2 was examined in the context of additional TFs that, together, define a TF cascade in embryonic neocortical neurogenesis (Pax6 --> Ngn2 --> Tbr2 --> NeuroD --> Tbr1). Remarkably, the same TF cascade was found to be linked to stages of neuronal lineage progression in adult SGZ. These results suggest that Tbr2+ IPCs play a major role in the regulation of adult hippocampal neurogenesis, and that a similar transcriptional program controls neurogenesis in adult SGZ as in embryonic cerebral cortex.
A Review of the Comparative Mammalian Toxicity of Ethylene Glycol and Propylene Glycol (1999)

The purpose of this article is to review and interpret the scientific literature on the mammalian toxicity of ethylene glycol (EG) and propylene glycol (PG), with the goal of comparing the toxicity of the two chemicals. This type of review may serve as the basis for risk management decision-making. Because EG is not a GRAS (generally recognized as safe) chemical, its uses are restricted when compared with PG; thus, certain routes of exposure are not relevant here for toxicological comparison (e.g., subcutaneous, intramuscular, and intravenous). Therefore, this review is focused on the oral, inhalation, and dermal routes of exposure. However, where toxicological data derived from an alternative route of exposure serve to eludicate mechanisms of toxicity, data from these routes are considered. Based on the review provided herein, the following conclusions can be drawn. From the standpoint of lethality, acute effects, and reproductive, developmental, and kidney toxicity, the toxicity of EG exceeds that of PG. Further, localized dermal effects from EG and PG are both mild, with data suggesting that PG may have a skin contact sensitization potential. Finally, PG exposure in laboratory animals has been associated with reversible hematological changes; no data were located for EG from which to draw a toxicological comparison.