gebhart/patrepeval huggingface dataset:
Vertebrate Marine Species as Model Systems for Studying Telomeres and Telomerase (2005)

Due to the limitations of in vitro human tissue culture systems, it has long been recognized that in vivo model organisms are critically necessary for studying important biological processes related to human disease. Telomere shortening and dysfunction have been shown as a contributing factor in aging using tissue culture systems and after 6 generations in inbred strains of mice. Currently, there are no models and little or no data defining the role of telomeres and telomerase in toxicological response, metal-induced carcinogenesis, or aging in marine animals. One of our primary objectives has been to determine if fish have similar utility to mouse models of aging and cancer, at least related to telomere biogenesis and telomerase function. We have found that the vast majority of tissues from marine species have functional telomerase activity, and that several of these vertebrates, although telomerase-expressing, have telomere lengths that resemble those found in human cells and tissues. Thus, because aquatic species have "normal" telomere sizes, marine animals may be more biologically relevant and cost-effective models for studying stem cells, aging, and cancer than inbred strains of rodents.
Early alterations in airway mucociliary clearance and inflammation of the lamina propria in CF mice (1997)

In cystic fibrosis (CF), whether cystic fibrosis transmembrane conductance regulator (CFTR) dysfunction leads to decreased mucociliary clearance and mucus hypersecretion, before bacterial infection, remains an open question. To answer this question, we quantified in a blind trial the mucociliary transport velocity, the histological state, and the degree of inflammation of the tracheal mucosa in 23 cftr(m1HGU/cftr(m1HGU) transgenic mice (Dorin, J. R., P. Dickinson, E. W. F. W. Alton, S. N. Smith, D. M. Geddes, B. J. Stevenson, W. L. Kimber, S. Fleming, A. R. Clark, M. L. Hooper, L. Anderson, R. S. P. Beddington, and D. J. Porteous. Nature Lond. 359: 211-215, 1992) and in 30 control littermates housed in pathogen-free conditions. The nasal and tracheal transepithelial potential difference (PD) measured in basal conditions was significantly more negative in the cftr(m1HGU) mutant mice as compared with the control mice (nasal PD: -7.1 +/- 0.6 and -4.6 +/- 0.5 mV, respectively, P < 0.01; tracheal PD: -30.8 +/- 2.1 and -21.4 +/- 1.8 mV, respectively, P < 0.04). In the cftr(m1HGU)/cftr(m1HGU) mice, the mucociliary transport velocity was significantly lower (14.2 +/- 4.4 microm/mm, P < 0.04) compared with the control mice (30.6 +/- 5.9 microm/mm). The number of inflammatory cells in the lamina propria was significantly higher in the cftr(m1HGU)/cftr(m1HGU) mice (1048.7 +/- 124.7 cells/mm2, P < 0.03) compared with the control mice (640.5 +/- 58.2 cells/mm2). These results suggest that in CF, decreased airway mucociliary clearance and airway submucosal inflammation represent early alterations, before any airway infection.
Printed Circuit Technology for Fabrication of Plastic-Based Microfluidic Devices (2004)

One of the primary advantages of using plastic-based substrates for microfluidic systems is the ease with which devices can be fabricated with minimal dependence on specialized laboratory equipment. These devices are often produced using soft lithography techniques to cast replicas of a rigid mold or master incorporating a negative image of the desired surface structures. Conventional photolithographic micromachining processes are typically used to construct these masters in either thick photoresist, etched silicon, or etched glass substrates. The speed at which new masters can be produced using these techniques, however, can be relatively slow and often limits the rate at which new device designs can be built and tested. In this paper, we show that inexpensive photosensitized copper clad circuit board substrates can be employed to produce master molds using conventional printed circuit technology. This process offers the benefits of parallel fabrication associated with photolithography without the need for cleanroom facilities, thereby providing a degree of speed and simplicity that allows microfluidic master molds with well-defined and reproducible structural features to be constructed in approximately 30 min in any laboratory. Precise control of channel heights ranging from 15 to 120 microm can be easily achieved through selection of the appropriate copper layer thickness, and channel widths as small as 50 microm can be reproducibly obtained. We use these masters to produce a variety of plastic-based microfluidic channel networks and demonstrate their suitability for DNA electrophoresis and microfluidic mixing studies.
Circular dichroism changes in galactosyltransferase upon substrate binding (1975)

Circular dichroism studies with the galactosyltransferase isolated from bovine skim milk are described. Addition of UDP-galactose to the galactosyltransferase-Mn-2+ complex causes a decrease in the negative mean residue ellipticity in the 205-220-nm range and positive increases in the 265- and 275-290-nm ellipticity. These date are consistent with the view that a conformation change involving aromatic amino acid residues occurs upon the binding of UDP-galactose to the galactosyltransferase-Mn-2+ complex. No effects in the near-ultraviolet circular dichroism spectrum were observed upon the addition of UDP or glucose to the galactosyltransferase-Mn-2+ complex.
Expression of the human papillomavirus type 11 L1 capsid protein in Escherichia coli: characterization of protein domains involved in DNA binding and capsid assembly (1997)

The L1 major capsid protein of human papillomavirus type 11 (HPV-11) was expressed in Escherichia coli, and the soluble recombinant protein was purified to near homogeneity. The recombinant L1 protein bound DNA as determined by the Southwestern assay method, and recombinant mutant L1 proteins localized the DNA-binding domain to the carboxy-terminal 11 amino acids of L1. Trypsin digestion of the full-length L1 protein yielded a discrete 42-kDa product (trpL1), determined by sodium dodecyl sulfate-polyacrylamide gel electrophoresis, resulting from cleavage at R415, 86 amino acids from the L1 carboxy terminus. Sucrose gradient sedimentation analysis demonstrated that trpL1 sedimented at 11S, while L1 proteins with amino-terminal deletions of 29 and 61 residues sedimented at 4S. Electron microscopy showed that the full-length L1 protein appeared as pentameric capsomeres which self-assembled into capsid-like particles. The trpL1 protein also had a pentameric morphology but was unable to assemble further. In an enzyme-linked immunosorbent assay, the trpL1 and L1 capsids reacted indistinguishably from virus-like particles purified after expression of HPV-11 L1 in insect cells. The carboxy terminus of L1 therefore constitutes the interpentamer linker arm responsible for HPV-11 capsid formation, much like the carboxy-terminal domain of the polyomavirus VP1 protein. The trypsin susceptibility of HPV-11 L1 capsids suggests a possible mechanism for virion disassembly.
“Live high–train low” using normobaric hypoxia: a double-blinded, placebo-controlled study (2011)

The combination of living at altitude and training near sea level [live high-train low (LHTL)] may improve performance of endurance athletes. However, to date, no study can rule out a potential placebo effect as at least part of the explanation, especially for performance measures. With the use of a placebo-controlled, double-blinded design, we tested the hypothesis that LHTL-related improvements in endurance performance are mediated through physiological mechanisms and not through a placebo effect. Sixteen endurance cyclists trained for 8 wk at low altitude (<1,200 m). After a 2-wk lead-in period, athletes spent 16 h/day for the following 4 wk in rooms flushed with either normal air (placebo group, n = 6) or normobaric hypoxia, corresponding to an altitude of 3,000 m (LHTL group, n = 10). Physiological investigations were performed twice during the lead-in period, after 3 and 4 wk during the LHTL intervention, and again, 1 and 2 wk after the LHTL intervention. Questionnaires revealed that subjects were unaware of group classification. Weekly training effort was similar between groups. Hb mass, maximal oxygen uptake (VO(2)) in normoxia, and at a simulated altitude of 2,500 m and mean power output in a simulated, 26.15-km time trial remained unchanged in both groups throughout the study. Exercise economy (i.e., VO(2) measured at 200 W) did not change during the LHTL intervention and was never significantly different between groups. In conclusion, 4 wk of LHTL, using 16 h/day of normobaric hypoxia, did not improve endurance performance or any of the measured, associated physiological variables.
Ultrasound-accelerated immunoassay, as exemplified by enzyme immunoassay of choriogonadotropin. (1984)

The rate-limiting step in many solid-phase immunoassays is associated with the slow kinetics of binding of macro-molecular antigen and conjugate to the immobilized phase. We demonstrate that the use of ultrasonic energy to enhance mass transport across liquid/solid interfaces can dramatically accelerate antigen binding to immobilized antibodies. We use an ultrasound-accelerated procedure with an enzyme-channelling test strip containing glucose oxidase and specific antibody to the alpha-subunit of human choriogonadotropin (HCG) co-immobilized onto a cellulose support. A horseradish peroxidase conjugate of monospecific antibody to the beta-subunit of HCG is used in the liquid phase to complete the immune "sandwich." Use of ultrasound to accelerate binding and of enzyme channelling to eliminate wash steps result in a simple two-incubation protocol by which 25 int. units of urinary HCG per liter can be detected visually in less than 20 min of assay time.
Characterization of the coupling activity for the binding of inter-alpha-trypsin inhibitor to hyaluronan in human and bovine follicular fluid (2002)

The plasma proteinase inter-alpha-trypsin inhibitor is necessary for normal expansion of the cumulus-oocyte complex (COC) and lack of inter-alpha-trypsin inhibitor results in severe infertility. After diffusion from the circulation into the follicles, inter-alpha-trypsin inhibitor is incorporated into the extracellular hyaluronan network of the expanding COC. However, mixing isolated inter-alpha-trypsin inhibitor with hyaluronan in vitro does not result in coupling to hyaluronan. Other components must be present. A recently developed electrophoretic technique by which hyaluronan-bound inter-alpha-trypsin inhibitor is immobilized was used to demonstrate coupling activity in human and bovine follicular fluid that is necessary for the formation of a firm binding between inter-alpha-trypsin inhibitor heavy chains and hyaluronan, as observed in vivo. No coupling activity could be detected in human serum. Coupling occurred only in the presence of follicular fluid. The coupling activity of follicular fluid was irreversibly destroyed by heat treatment, lowering of pH or tryptic digestion, indicating that the coupling activity is associated with a protein. Calcium ions are essential for the coupling reaction. The binding reaction in vitro using intact inter-alpha-trypsin inhibitor is slow and occurs over 24 h. The early-formed complexes between inter-alpha-trypsin inhibitor and hyaluronan contain small amounts of bikunin, whereas the end product contains heavy chains and essentially no bikunin. The heavy chains released from inter-alpha-trypsin inhibitor by NaOH treatment bound immediately to hyaluronan, indicating that the dissociation of heavy chains from inter-alpha-trypsin inhibitor is the rate-limiting step. In conclusion, at least four components are essential for the covalent binding of heavy chains to hyaluronan: inter-alpha-trypsin inhibitor and calcium from plasma, hyaluronan and one or more proteins found in follicular fluid.
The Ets family of transcription factors (1993)

Interest in the Ets proteins has grown enormously over the last decade. The v-ets oncogene was originally discovered as part of a fusion protein expressed by a transforming retrovirus (avian E26), and later shown to be transduced from a cellular gene. About 30 related proteins have now been found in species ranging from flies to humans, that resemble the vEts protein in the so-called 'ets domain'. The ets domain has been shown to be a DNA-binding domain, that specifically interacts with sequences containing the common core trinucleotide GGA. Furthermore, it is involved in protein-protein interactions with co-factors that help determine its biological activity. Many of the Ets-related proteins have been shown to be transcription activators, like other nuclear oncoproteins and anti-oncoproteins (Jun, Fos, Myb, Myc, Rel, p53, etc.). However, Ets-like proteins may have other functions, such as in DNA replication and a general role in transcription activation. Ets proteins have been implicated in regulation of gene expression during a variety of biological processes, including growth control, transformation, T-cell activation, and developmental programs in many organisms. Signals regulating cell growth are transmitted from outside the cell to the nucleus by growth factors and their receptors. G-proteins, kinases and transcription factors. We will discuss how several Ets-related proteins fit into this scheme, and how their activity is regulated both post- and pre-translationally. Loss of normal control is often associated with conversion to an oncoprotein. vEts has been shown to have different properties from its progenitor, which might explain how it has become oncogenic. Oncogene-related products have been implicated in the control of various developmental processes. Evidence is accumulating for a role for Ets family members in Drosophila development, Xenopus oocyte maturation, lymphocyte differentiation, and viral infectious cycles. An ultimate hope in studying transformation by oncoproteins is to understand how cells become cancerous in humans, which would lead to more effective treatments. vEts induces erythroblastosis in chicken. Cellular Ets-family proteins can be activated by proviral insertion in mice and, most interestingly, by chromosome translocation in humans. We are at the beginning of understanding the multiple facets of regulation of Ets activity. Future work on the Ets family promises to provide important insights into both normal control of growth and differentiation, and deregulation in illness.
Override of the Radiation-induced Mitotic Block in Human Tumour Cells by Methylxanthines and Its Relationship to the Potentiation of Cytotoxicity (1990)

The four methylated xanthine derivatives, caffeine, theophylline, theobromine and paraxanthine, were tested for their ability to override the mitotic block induced by ionizing radiation in the human bladder carcinoma cell line RT112. All four agents were found to partially override the block, ranking in terms of potency at a concentration of 1 mM in the order caffeine greater than theophylline greater than theobromine = paraxanthine. However, the effects of the four agents on the clonal survival of irradiated cells failed to correlate with the extent of override, both in terms of the relative effects of the four agents and the dose-response relationships; at a concentration of 1 mM only caffeine was found to potentiate cell killing as well as causing block override, whilst at higher concentrations all the agents had a significant effect on survival but little or no further influence on the degree of block override. It is therefore concluded that override of a mitotic block is not in itself sufficient to cause the increased killing seen when irradiated cells are incubated in the presence of caffeine, and that caffeine exerts its potentiating effect either by directly inhibiting repair of damage in DNA or by causing override of the radiation-induced inhibition of DNA synthesis.
Synthesis and Evaluation of CC-1065 and Duocarmycin Analogues Incorporating the Iso-CI and Iso-CBI Alkylation Subunits:  Impact of Relocation of the C-4 Carbonyl (1997)

The synthesis of 2-(tert-Butyloxycarbonyl)-1,2,9,9a-tetrahydrocyclopropa[c]benzo[f]indol-8-one (31, N-BOC-iso-CBI) and 1-(tert-Butyloxycarbonyl)-4-hydroxy-3-[[(methanesulfonyl)oxy]methyl]-2,3-dihydroindole (19, seco-N-BOC-iso-CI) containing an isomeric structural modification in the CC-1065 and duocarmycin alkylation subunits and their incorporation into analogues of the natural products are detailed. The approach was based on a directed ortho metalation of an appropriately functionalized benzene (13) or naphthalene (24) precursor to regiospecifically install iodine at the C-2 position. Conversion of these respective intermediates to the dihydroindole skeleton utilized an established 5-exo-trig aryl radical cyclization onto an unactivated alkene with subsequent TEMPO trap or the more recent 5-exo-trig aryl radical cyclization onto a vinyl chloride for direct synthesis of the immediate precursors. Closure of the activated cyclopropane to complete the iso-CBI nucleus was accomplished by a selective ortho spirocyclization. The evaluation of the iso-CBI-based agents revealed a significant stability comparable to that of CC-1065 and duocarmycin A, but that it is more reactive than duocarmycin SA (6−7×) or the direct comparison CBI-based agents (5×) for which X-ray structure comparisons served to establish the basis for their inherent reaction regioselectivity and reactivity. Resolution and synthesis of a full set of natural product analogues and subsequent evaluation of their DNA alkylation properties revealed that the iso-CBI analogues, even with the relocation of the C-4 carbonyl and the most substantial structural modifications to the alkylation subunit to date, reacted at comparable rates and retain the identical and characteristic sequence selectivity of CC-1065 and the duocarmycins. This observation is inconsistent with the proposal that a sequence-dependent C-4 carbonyl protonation by strategically located DNA backbone phosphates controls the DNA alkylation selectivity but is consistent with the proposal that it is determined by the AT-rich noncovalent binding selectivity of the agents and the steric accessibility of the N3 alkylation site. Confirmation that the DNA alkylation reaction is derived from adenine N3 addition to the least substituted carbon of the activated cyclopropane, and its quantitation (95%) was established by isolation and characterization of the depurination adenine N3 adduct. Consistent with past studies and despite the deep-seated structural change in the alkylation subunit, the agents were found to exhibit potent cytotoxic activity that correlates with their inherent reactivity.
Clinicopathologic manifestations and breakpoints of the t(3;5) in patients with acute nonlymphocytic leukemia. (1989)

Acquired chromosomal rearrangements in acute nonlymphocytic leukemia (ANLL) have been linked to specific clinicopathologic features that suggest new disease subtypes. In this collaborative study, we report five patients with ANLL and a t(3;5) in their leukemic cells. At diagnosis, four of the patients had a t(3;5) as their sole karyotypic anomaly; the remaining patient had additional structural and numerical abnormalities. Careful cytogenetic analysis indicated that the breakpoints of this rearrangement are 3q25.1 and 5q34, in contrast to the various breakpoints reported in earlier studies (3q21----3q25 and 5q31----5q35). The karyotypic, morphologic, and clinical characteristics of this group, as well as those of 14 previously reported patients with the t(3;5), were compared to identify any features that might warrant consideration of a specific syndrome. The available information indicates a worldwide distribution and a nearly equal male:female ratio for patients with this translocation. The median age of the group, 37 years, was younger than that of all patients with ANLL, 49 years. A preceding myelodysplastic syndrome was observed in three patients. The limited numbers of observations on leukocyte count, hemoglobin level, and platelet count precluded meaningful comparison with data for ANLL patients in general. Although each FAB morphologic subtype, except M3, occurred in patients with a t(3;5), the frequency of M6 was much greater than expected. Bone marrows from each of the five patients we report showed increased numbers of megakaryocytes; trilineage dysplasia was observed in the marrow of each of the four patients for whom it could be assessed. Taken together, these findings suggest that the t(3;5) may affect cells capable of differentiation into multiple lineages.
Understanding Natural Language Commands for Robotic Navigation and Mobile Manipulation (2011)

This paper describes a new model for understanding natural language commands given to autonomous systems that perform navigation and mobile manipulation in semi-structured environments. Previous approaches have used models with fixed structure to infer the likelihood of a sequence of actions given the environment and the command. In contrast, our framework, called Generalized Grounding Graphs, dynamically instantiates a probabilistic graphical model for a particular natural language command according to the command's hierarchical and compositional semantic structure. Our system performs inference in the model to successfully find and execute plans corresponding to natural language commands such as "Put the tire pallet on the truck." The model is trained using a corpus of commands collected using crowdsourcing. We pair each command with robot actions and use the corpus to learn the parameters of the model. We evaluate the robot's performance by inferring plans from natural language commands, executing each plan in a realistic robot simulator, and asking users to evaluate the system's performance. We demonstrate that our system can successfully follow many natural language commands from the corpus.
PLATELET CD62p EXPRESSION AND MICROPARTICLE FORMATION IN MURINE ACQUIRED IMMUNE DEFICIENCY SYNDROME AND CHRONIC ETHANOL CONSUMPTION (2003)

Elevated platelet CD62p and PMPs may represent a pro-thrombotic status that have important pathological consequences.