gebhart/patrepeval huggingface dataset:
Small Noncleaved, Non-Burkitt's (Burkitt-Like) Lymphoma: Cytogenetics Predict Outcome and Reflect Clinical Presentation (1999)

SNC-NB lymphoma is a clinically and cytogenetically heterogenous disease. Dual translocation of c-myc and bcl-2 is characterized by a rapid clinical course and extremely poor outcome. This latter entity may represent the most clinically aggressive lymphoma thus far characterized and warrants intensive investigational treatment where feasible.
Molecular mechanisms of bone resorption by the osteoclast (1989)

The osteoclast is a multinucleated cell that is actively engaged in the synthesis of lysosomal enzymes, their vectorial transport toward the apical membrane, and the secretion of these enzymes at its apical pole. These secreted enzymes are targeted to the apical ruffled-border membrane by mechanisms that involve cation-independent mannose-6-phosphate receptors. These receptors bind to an enzyme-linked mannose-6-phosphate recognition marker in the Golgi complex, and the enzyme-ligand-receptor complex, carried within small coated transport vesicles, dissociates upon reaching the low pH established in the bone-resorbing compartment by the osteoclast. The apical bone-resorbing compartment is sealed off by the attachment of the osteoclast to the calcified matrix and is actively acidified by the osteoclast. The plasma membrane of the cell is divided into distinct domains. The apical membrane at the ruffled-border shares common antigenic determinants with lysosomal and endosomal membranes, including a 100 kD protein and proton pumps that may be involved in the acidification of the extracellular resorbing compartment. The basolateral membrane is highly enriched in carbonic anhydrase, and bicarbonate-chloride exchange appears to regulate the intracellular pH of this cell. These observations are consistent with a scheme in which, in the low pH environment of the bone-resorbing lacuna produced by the osteoclast, the mineral phase dissolves, exposing the organic matrix to the action of the secreted enzymes. The activity of these enzymes is in turn presumably favored by the acidic milieu. All constituents of the matrix, whether mineral or organic, then would be reduced to their elemental forms (ions and amino acids) extracellularly.(ABSTRACT TRUNCATED AT 250 WORDS)
Magnetic-Resonance-Based Electrical Properties Tomography: A Review (2014)

Frequency-dependent electrical properties (EPs; conductivity and permittivity) of biological tissues provide important diagnostic information (e.g., tumor characterization), and also play an important role in quantifying radiofrequency (RF) coil induced specific absorption rate (SAR), which is a major safety concern in high- and ultrahigh-field magnetic resonance imaging (MRI) applications. Cross-sectional imaging of EPs has been pursued for decades. Recently introduced electrical properties tomography (EPT) approaches utilize the measurable RF magnetic field induced by the RF coil in an MRI system to quantitatively reconstruct the EP distribution in vivo and noninvasively with a spatial resolution of a few millimeters or less. This paper reviews the EPT approach from its basic theory in electromagnetism to the state-of-the-art research outcomes. Emphasizing on the imaging reconstruction methods rather than experimentation techniques, we review the developed imaging algorithms, validation results in physical phantoms and biological tissues, as well as their applications in in vivo tumor detection and subject-specific SAR prediction. Challenges for future research are also discussed.
Separation and analysis of free ceramides containing 2-hydroxy fatty acids in Sphingobacterium species (1983)

The occurrence of free ceramides was shown in the chloroform-methanol extractable lipids of 16 strains of Sphingobacterium including three species: S. versatilis, S. multivorum and S. mizutae. The predominant long-chain base was identified as a branched-chain, saturated dihydroxy base with a carbon chain consisting of 17 carbon atoms, while the most abundant fatty acid was 2-hydroxy-13-methyltetradecanoic acid. The major molecular species of the intact ceramides were identified as LCB-d-iso-17 : 0-2-OHiso-15 : 0FA, LCB-d-iso-17 : 0-iso-15 : 0FA and LCB-d-n16 : 0-iso-15 : 0FA.
Mycobacterium tuberculosis Infects Dendritic Cells with High Frequency and Impairs Their Function In Vivo (2007)

Mycobacterium tuberculosis (Mtb) is thought to reside in macrophages, although infected dendritic cells (DCs) have been observed. Thus, although cellular associations have been made, global characterization of the cells harboring Mtb is lacking. We have performed temporal and quantitative characterization of the cells harboring Mtb following aerosol infection of mice by using GFP-expressing bacteria and flow cytometry. We discovered that Mtb infects phagocytic cells of diverse phenotypes, that the predominant infected cell populations change with time, and that myeloid DCs are the major cell population infected with Mtb in the lungs and lymph nodes. We also found that the bacteria in the lung-draining lymph node are transported there from the lungs by a CCL19/21-dependent mechanism and that the transport of bacteria to the lymph node is a transient phenomenon despite chronic infection. In addition, we found that the lymph node cell subsets that are most efficacious in stimulating Mtb-specific, TCR-transgenic CD4(+) T lymphocytes are not infected with the bacteria and are scarce or absent from the lungs of infected mice. Finally, we found that the lung cell populations that are infected with Mtb at high frequency are relatively ineffective at stimulating Ag-specific CD4(+) T lymphocytes, and we have obtained evidence that live Mtb can inhibit MHC class II Ag presentation without a decrease in the surface expression of MHC class II. These results indicate that Mtb targets DC migration and Ag presentation in vivo to promote persistent infection.
Navigating the cell: how motors function in vivo (2014)

The Company of Biologists Workshop entitled 'Navigating the Cell: How Motors Function in vivo' was held in March 2014 at Wiston House in Steyning, West Sussex, UK. The meeting was an opportunity for a diverse group of experts in the biology and physics of cytoskeletal dynamics, and molecular motors to come together in a setting that promoted scientific interactions and the development of new collaborations. Here, we summarize the highlights of the meeting, one of which was the unique organizational principle that promoted cross-fertilization of ideas and approaches among the participants.
APE2 promotes DNA damage response pathway from a single-strand break (2018)

As the most common type of DNA damage, DNA single-strand breaks (SSBs) are primarily repaired by the SSB repair mechanism. If not repaired properly or promptly, unrepaired SSBs lead to genome stability and have been implicated in cancer and neurodegenerative diseases. However, it remains unknown how unrepaired SSBs are recognized by DNA damage response (DDR) pathway, largely because of the lack of a feasible experimental system. Here, we demonstrate evidence showing that an ATR-dependent checkpoint signaling is activated by a defined plasmid-based site-specific SSB structure in Xenopus HSS (high-speed supernatant) system. Notably, the distinct SSB signaling requires APE2 and canonical checkpoint proteins, including ATR, ATRIP, TopBP1, Rad9 and Claspin. Importantly, the SSB-induced ATR DDR is essential for SSB repair. We and others show that APE2 interacts with PCNA via its PIP box and preferentially interacts with ssDNA via its C-terminus Zf-GRF domain, a conserved motif found in >100 proteins involved in DNA/RNA metabolism. Here, we identify a novel mode of APE2-PCNA interaction via APE2 Zf-GRF and PCNA C-terminus. Mechanistically, the APE2 Zf-GRF-PCNA interaction facilitates 3'-5' SSB end resection, checkpoint protein complex assembly, and SSB-induced DDR pathway. Together, we propose that APE2 promotes ATR-Chk1 DDR pathway from a single-strand break.
Science for all Americans (2002)

Abstract Setting goals for student learning in fields of science, technology, and mathematics must receive institutionwide attention, setting expectations for what graduates should know and developing departmental and programmatic course offerings that ensure those expectations will be met.
Maintenance of Serological Memory by Polyclonal Activation of Human Memory B Cells (2002)

Production of antibodies can last for a lifetime, through mechanisms that remain poorly understood. Here, we show that human memory B lymphocytes proliferate and differentiate into plasma cells in response to polyclonal stimuli, such as bystander T cell help and CpG DNA. Furthermore, plasma cells secreting antibodies to recall antigens are produced in vivo at levels proportional to the frequency of specific memory B cells, even several years after antigenic stimulation. Although antigen boosting leads to a transient increase in specific antibody levels, ongoing polyclonal activation of memory B cells offers a means to maintain serological memory for a human lifetime.
Prospective study of the Acri.LISA bifocal intraocular lens (2007)

The Acri.LISA 366D IOL provided a satisfactory full range of vision; a high level of uncorrected and corrected distance, intermediate, and near acuity; and improved contrast sensitivity under photopic and mesopic conditions.
Level of sustained entorhinal activity at study correlates with subsequent cued-recall performance: A functional magnetic resonance imaging study with high acquisition rate (1999)

Functional magnetic resonance imaging (fMRI) with high acquisition rate was performed during the intentional memorizing of words to specify which medial temporal lobe structure is important in determining what words are subsequently remembered in a cued-recall test and to characterize the time course of activation in that structure. Functional images of six healthy young subjects were analyzed by two subject- and voxel-wise statistics: First, to identify brain areas transiently engaged in encoding of words, brain activity during memorizing visually presented words and watching a fixation cross was compared by a Kolmogorov-Smirnov statistic (KS-test). Second, to identify brain areas whose activity correlates with memory encoding success, a Kendall's correlation was calculated between signal intensity at study and performance in a subsequent cued-recall test. Averaged signal intensities were plotted as a function of time to depict the time course of brain activity detected by both statistical tests. The level of slowly modulated, sustained activity in Brodmann area 28 (entorhinal cortex) did not respond transiently as study words appeared, but did correlate positively with subsequent test performance. More left than right activity in Brodmann area 45 (dorso-lateral prefrontal cortex) and bilateral activity in Brodmann area 44 (premotor cortex) exhibited transient hemodynamic responses that did not show any relation to subsequent memory performance. Thus, the study identified a novel pattern of slowly modulated brain activity in human entorhinal cortex that may represent a declarative memory encoding state whose level predicts whether experiences will be remembered or forgotten.
Hydroxytyrosol Prevents Oxidative Deterioration in Foodstuffs Rich in Fish Lipids (2008)

Hydroxytyrosol, a natural phenolic compound obtained from olive oil byproduct, was characterized as an antioxidant in three different foodstuffs rich in fish lipids: (a) bulk cod liver oil (40% of omega-3 PUFAs), (b) cod liver oil-in-water emulsions (4% of omega-3 PUFAs), and (c) frozen minced horse mackerel ( Trachurus trachurus) muscle. Hydroxytyrosol was evaluated at different concentration levels (10, 50, and 100 ppm), and its antioxidant capacity was compared against that of a synthetic phenolic, propyl gallate. Results proved the efficiency of hydroxytyrosol to inhibit the formation of lipid oxidation products in all tested food systems, although two different optimal antioxidant concentrations were observed. In bulk oil and oil-in-water emulsions, a higher oxidative stability was achieved by increasing the concentration of hydroxytyrosol, whereas an intermediate concentration (50 ppm) showed more efficiency, delaying lipid oxidation in frozen minced fish muscle. The endogenous depletion of alpha-tocopherol and omega-3 polyunsaturated fatty acids (omega-3 PUFAs) was also inhibited by supplementing hydroxytyrosol in minced muscle; however, the consumption of the endogenous total glutathione was not efficiently reduced by either hydroxytyrosol or propyl gallate. A concentration of 50 ppm of hydroxytyrosol was best to maintain a longer initial level of alpha-tocopherol (approximately 300 microg/g of fat), whereas both 50 and 100 ppm of hydroxytyrosol were able to preserve completely omega-3 PUFAs. Hydroxytyrosol and propyl gallate showed comparable antioxidant activities in emulsions and frozen fish muscle, and propyl gallate exhibited better antioxidant efficiency in bulk fish oil.
Antibacterial spectrum of lactoferricin B, a potent bactericidal peptide derived from the N ‐terminal region of bovine lactoferrin (1992)

A physiologically diverse range of Gram-positive and Gram-negative bacteria was found to be susceptible to inhibition and inactivation by lactoferricin B, a peptide produced by gastric pepsin digestion of bovine lactoferrin. The list of susceptible organisms includes Escherichia coli, Salmonella enteritidis, Klebsiella pneumoniae, Proteus vulgaris, Yersinia enterocolitica, Pseudomonas aeruginosa, Campylobacter jejuni, Staphylococcus aureus, Streptococcus mutans, Corynebacterium diphtheriae, Listeria monocytogenes and Clostridium perfringens. Concentrations of lactoferricin B required to cause complete inhibition of growth varied within the range of 0.3 to 150 micrograms/ml, depending on the strain and the culture medium used. The peptide showed activity against E. coli O111 over the range of pH 5.5 to 7.5 and was most effective under slightly alkaline conditions. Its antibacterial effectiveness was reduced in the presence of Na+, K+, Mg2+ or Ca2+ ions, or in the presence of various buffer salts. Lactoferricin B was lethal, causing a rapid loss of colony-forming capability in most of the species tested. Pseudomonas fluorescens, Enterococcus faecalis and Bifidobacterium bifidum strains were highly resistant to this peptide.
[Endoluminal percutaneous thrombectomy as a treatment for acute vascular access thrombosis: long-term results of 123 procedures]. (2001)

mean age: 63 +/- 15 years (18-84), previous VA: 3.3 +/- 2.5 (0-9). The mean follow-up was 10.5 +/- 8.6 months (3-35). Percutaneous thrombectomy was able to remove the clots in 120 instances (technical success: 97.5%). After the thrombectomy 15 patients (16.3%) were immediately referred to the surgeon to perform a new VA due to vascular lesions in which percutaneous treatment was not indicated. Thirteen cases (14.1%) showed early thrombosis (< 72 hours). During the follow-up, 27 cases developed thrombosis (30%) and 26 VA were still patent (28.3%). In 23% of perfusion lung scans and in 2 of the 5 angiographies performed after thrombectomy, subsegmentary or segmentary perfusion defects were detected, without clinical significance. There were no relevant undesirable effects related to the technique and no symptomatic pulmonary embolism. In summary, percutaneous thrombectomy, whether hydrodynamic or mechanical, has shown to be an efficacious treatment of VA thrombosis for HD, preserving the VA with satisfactory long-term results.
The irreversible gamma-aminobutyric acid (GABA) transaminase inhibitor gamma-vinyl-GABA blocks cocaine self-administration in rats. (1999)

gamma-Vinyl gamma-aminobutyric acid (GABA) (GVG) is an irreversible inhibitor of GABA transaminase, the primary enzyme involved in GABA metabolism. Acute administration of GVG increases brain GABA levels and blocks cocaine-induced locomotor activity, cocaine-induced lowering of brain stimulation reward thresholds, and cocaine-induced conditioned place preference. To further evaluate the effects of GVG on cocaine-induced reward, we examined its effects on cocaine self-administration in male Wistar rats on fixed ratio 5 and progressive ratio schedules of reinforcement. Additionally, the effects of GVG on operant responding for a food reward were examined on the same two schedules to determine whether the effects of GVG were specific to cocaine reward or generalized to other types of reward. GVG dose dependently decreased responding for cocaine on both schedules of reinforcement, suggesting that GVG attenuated the reward value of the cocaine. Responding for food was also decreased by GVG, suggesting that the effects of increased GABA levels induced by GVG may have a general effect on central reward systems. Data from this and other studies indicate that GVG does not induce motor impairment, decrease spontaneous locomotor activity, or induce catalepsy. Taken together, these data suggest that increases in GABAergic activity induced by GVG have an attenuating effect on centrally mediated reward systems and that the GABA system may be a useful target in the development of new therapeutic strategies for cocaine addiction.
FOSTERING DEVELOPMENT, EVALUATION, AND DEPLOYMENT OF FORWARD CRASH AVOIDANCE SYSTEM (FOCAS) (1995)

This work is part of a three year program to foster the development, evaluation, and deployment of forward crash avoidance systems. The work performed during the first and second years of the program has addressed adaptive cruise control and warnings based upon the motion and proximity of preceding vehicles in the path of travel. The work for this second year has emphasized features of ACC systems that could make them either more convenient and comfortable through the use of adjustable headway or safer through the use of warnings. The second year of the project presents detailed information on: driver-adjustable headway time, observations concerning drivers, neural network methods for finding driving episodes, an audio prompt for ACC intervention (crash warning), implementation of a brake-assisted lo-decel-cue, and use of an ACC test vehicle with 0.18 g deceleration authority. This year's work has included the development of an audio warning based upon using range and range-rate data to compute the deceleration needed to meet selected headway goal. Another type of warning, as well as an extension of the control authority of the ACC, was provided by downshifting the transmission when a deceleration greater than that of coastdown was required. An additional warning system called a lo-decel-cue was also studied. This system used the foundation brakes, though only in a constrained manner, to warn the driver.
Accumulation of Chromosomal Imbalances From Intraductal Proliferative Lesions to Adjacent In Situ and Invasive Ductal Breast Cancer (2000)

Carcinoma of the breast is thought to evolve through a sequential progression from normal to proliferative epithelium and eventually into carcinoma. Here lumpectomy specimens from five patients were studied, selected for the presence of ductal hyperplasia without atypia, atypical ductal hyperplasia, ductal carcinoma in situ, and invasive ductal carcinoma. Laser microdissection of tissue allowed precise sampling and direct correlation of phenotypic and genotypic changes. Analyses of the samples revealed an increasing mean number of chromosomal changes occurring with increasing histologic severity, and for the first time chromosomal abnormalities were demonstrated in ductal hyperplasia without atypia. Chromosomal changes found in each of the four histologic entities included gains on 10q, 12q, 16p, and 20q and loss on 13q. In ductal hyperplasia without atypia, gain on 20q as well as loss on 13q was detected with high frequency (four of five samples). Alterations identified in more than 50% of atypical ductal hyperplasia samples included gains on 3p, 8q, 15q, and 22q and loss on 16q. In ductal carcinoma in situ, gain of DNA on 1q and 17q and loss on 4q were additionally found, and in invasive ductal carcinoma, further gains on 6p, 10q, 11q13, and 17p were identified. The chromosomal alterations occurring in the different histopathologic lesions strongly suggest that these regions harbor tumor suppressor genes or oncogenes significant for the development of ductal carcinoma of the breast.
Real-time simulation and supervisory control; the next logical step after system monitoring (2002)

Power monitoring systems, with all the benefits they provide, are partial solutions in the modernization of industrial power systems. Massive data is collected and logged for the system historian to trend and display on command. This paper presents, by use of on-line/off-line simulation of real-time data and by supervisory control, an approach that allows the monitored data to be used to assist operators in predicting system response and behavior for automating system control and providing operator training.
Predicted structure of the bovine calcitonin gene-related peptide and the carboxy-terminal flanking peptide of bovine calcitonin precursor (1991)

We have isolated from a bovine genomic library a clone which contains the calcitonin (CT) and CT gene-related peptide (CGRP) sequences, using probes representing the human CT and CGRP sequences. Sequence analysis has identified the nucleotide sequence coding for bovine CT, its C-terminal flanking peptide and bovine CGRP. The deduced amino acid sequence of bovine CGRP revealed a significant homology with other CGRPs so far reported. It differs by only one amino acid from rat CGRP alpha and porcine CGRP, and by three and four amino acids from human CGRP beta and alpha respectively. Bovine CT has, however, only 14 out of 32 residues in common with human CT. As in the human CT precursor, the C-terminal flanking peptide of bovine CT precursor is a 21 amino acid peptide. It shares only 11 residues in common with its human counterpart. This study thus provides further evidence that CGRP, in contrast to CT and its C-terminal flanking peptide, is a highly conserved molecule.
En Route to a Plant Scale Synthesis of the Promising Antitumor Agent 12,13-Desoxyepothilone B (2000)

[reaction--see text] Efficient and processable syntheses of key building blocks of the antitumor agent 12,13-desoxyepothilone B (dEpoB) by catalytic asymmetric induction are herein described.
TREM2 Variants in Alzheimer's Disease (2012)

Heterozygous rare variants in TREM2 are associated with a significant increase in the risk of Alzheimer's disease. (Funded by Alzheimer's Research UK and others.).
Serological Properties of γG and γM Antibodies to the Somatic Antigen of Vibrio cholerae During the Course of Immunization of Rabbits (1971)

Direct- and passive-agglutinating, complement-fixing, and bactericidal properties of gammaG and gammaM antibodies produced in rabbits inoculated with live Vibrio cholerae were determined at intervals over a period of 345 days. Although gammaM antibody titers increased more rapidly than gammaG during the initial stages of antibody production, the titers of gammaG and gammaM declined proportionally during a 3-month rest period and increased proportionally after a booster injection. The relative titers of gammaM as determined in the four serological procedures remained fairly constant throughout the period of observation. In contrast, early gammaG was less effective than late gammaG in vibriocidal, complement-fixing, and passive-hemagglutinating activity. At no stage of immunization was the agglutinating ability of gammaG affected by 2-mercaptoethanol, but its complement-dependent activity was markedly reduced, more so in early serum than in late. The heat lability of early gammaG approached that of gammaM, but gammaG became more resistant to heat in later stages of immunization.