gebhart/patrepeval huggingface dataset:
Quantum control of I2 in the gas phase and in condensed phase solid Kr matrix (1997)

We present experimental results and theoretical simulations for an example of quantum control in both gas and condensed phase environments. Specifically, we show that the natural spreading of vibrational wavepackets in anharmonic potentials can be counteracted when the wavepackets are prepared with properly tailored ultrafast light pulses, both for gas phase I2 and for I2 embedded in a cold Kr matrix. We use laser induced fluorescence to probe the evolution of the shaped wavepacket. In the gas phase, at 313 K, we show that molecular rotations play an important role in determining the localization of the prepared superposition. In the simulations, the role of rotations is taken into account using both exact quantum dynamics and nearly classical theory. For the condensed phase, since the dimensionality of the system precludes exact quantum simulations, nearly classical theory is used to model the process and to interpret the data. Both numerical simulations and experimental results indicate that a properly tailored ultrafast light field can create a localized vibrational wavepacket which persists significantly longer than that from a general non-optimal ultrafast light field. The results show that, under suitable conditions, quantum control of vibrational motion is indeed possible in condensed media. Such control of vibrational localization may then provide the basis for controlling the outcome of chemical reactions.
Inactivation of food-borne enteropathogenic bacteria and spoilage fungi using pulsed-light (2000)

The lethality of high-intensity pulsed-light emissions from low and high ultraviolet (UV) light sources on predetermined microbial populations has been investigated. Prior to treatment, the bacterial enteropathogens Bacillus cereus, Escherichia coli, and Salmonella enteritidis and the food-spoilage fungi Aspergillus niger and Fusarium culmorum were seeded separately onto the surface of either tryptone soya yeast extract or malt extract agar plates. Prescribed microbial population densities were applied to the test media and these samples were exposed to one of two light sources. These were low-pressure, xenon filled, flash lamps that produced either high or low UV intensities. They were operated in pulsed mode, being driven by a stacked Blurnlein table generator. Microbial samples were treated by exposure to different numbers of light pulses. The treated bacterial populations were reduced by /spl sim/8 log orders after 1000 light-pulses of the higher UV intensity light and the fungal counts had a corresponding reduction of 4.5 log orders. The fungus, Aspergillus niger, was shown to be significantly more resistant in spore form to the intense UV light compared with Fusarium culmorum. This resistance has been attributed to the high level of UV absorbance associated with the dark pigment present in A. niger. The pulsed light source of lower UV intensity was shown to be significantly less effective in reducing microbial populations.
Cytogenetic analysis by chromosome painting using dop‐pcr amplified flow‐sorted chromosomes (1992)

A novel polymerase chain reaction (PCR) technique has been combined with chromosome flow sorting to characterise two lymphoblastoid cell lines and one medullary thyroid carcinoma cell line carrying translocations close to the locus for multiple endocrine neoplasia type 2A (MEN 2A). Five hundred copies of the derivative chromosome(s) were flow sorted from each cell line and amplified by degenerate oligonucleotide-primed-polymerase chain reaction (DOP-PCR). This generated pools of DNA sequences corresponding to the abnormal chromosomes, which were then used as probes in fluorescence in situ hybridisation (FISH) experiments on normal metaphase cells. The resultant chromosome paints revealed the portions of the normal chromosomes related to those involved in the translocations. By this technique, translocation breakpoints in bands p15, q11.2, and q21 of chromosome 10 were defined in the above cell lines, in two cases refining previous cytogenetic data. This study shows that flow sorting of aberrant chromosomes and chromosome painting can be used as a rapid aid to cytogenetic analysis, particularly in cases of difficult karyotypes, such as tumours. Furthermore, the DOP-PCR technique described here will have applications to other areas of genome analysis, such as cloning of new markers; its design will allow a general and representative amplification to occur from any starting DNA in any species.
Correction: Intracellular Water Exchange for Measuring the Dry Mass, Water Mass and Changes in Chemical Composition of Living Cells (2013)

We present a method for direct non-optical quantification of dry mass, dry density and water mass of single living cells in suspension.Dry mass and dry density are obtained simultaneously by measuring a cell's buoyant mass sequentially in an H 2 O-based fluid and a D 2 O-based fluid.Rapid exchange of intracellular H 2 O for D 2 O renders the cell's water content neutrally buoyant in both measurements, and thus the paired measurements yield the mass and density of the cell's dry material alone.Utilizing this same property of rapid water exchange, we also demonstrate the quantification of intracellular water mass.In a population of E. coli, we paired these measurements to estimate the percent dry weight by mass and volume.We then focused on cellular dry density -the average density of all cellular biomolecules, weighted by their relative abundances.Given that densities vary across biomolecule types (RNA, DNA, protein), we investigated whether we could detect changes in biomolecular composition in bacteria, fungi, and mammalian cells.In E. coli, and S. cerevisiae, dry density increases from stationary to exponential phase, consistent with previously known increases in the RNA/protein ratio from up-regulated ribosome production.For mammalian cells, changes in growth conditions cause substantial shifts in dry density, suggesting concurrent changes in the protein, nucleic acid and lipid content of the cell.
Effect of hydration on methotrexate plasma concentrations in children with acute lymphocytic leukemia. (1988)

Hydration and urinary alkalinization are used with high-dose methotrexate (HDMTX) to minimize renal toxicity resulting from methotrexate (MTX) precipitation in the kidney tubules. The effect of two hydration and alkalinization schedules on MTX plasma concentrations were evaluated in 100 children with acute lymphocytic leukemia (ALL) following two courses of MTX, 2 g/m2. The mean 21- and 44-hour MTX plasma concentrations were significantly lower in the group receiving the greater hydration and alkalinization schedule: 0.79 (0.90 SD) v 1.39 (1.99 SD) mumol/L for 21-hour MTX plasma concentrations, P = .01; and 0.18 (0.38 SD) v 0.25 (0.50 SD) mumol/L for 44-hour MTX plasma concentrations, P = .01. Although the overall incidence of toxic events was similar in both groups, the incidence of severe toxicity was reduced in the group that received the greater hydration and alkalinization, 6% v 16%. This study demonstrated that the amount of hydration and alkalinization can affect MTX plasma concentrations. Optimizing the hydration and alkalinization schedule is important for minimizing the incidence of severe toxicity associated with HDMTX.
HIV-associated neurocognitive disorders persist in the era of potent antiretroviral therapy (2010)

The most severe HAND diagnosis (HAD) was rare, but milder forms of impairment remained common, even among those receiving CART who had minimal comorbidities. Future studies should clarify whether early disease events (e.g., profound CD4 decline) may trigger chronic CNS changes, and whether early CART prevents or reverses these changes.
Autonomic Modification of the Atrioventricular Node During Atrial Fibrillation (1999)

These studies confirmed that PGVS applied during AF could produce substantial VR slowing because of acetylcholine-induced depression of conduction in the AVN.
Adapting Selected Nucleic Acid Ligands (Aptamers) to Biosensors (1998)

A flexible biosensor has been developed that utilizes immobilized nucleic acid aptamers to specifically detect free nonlabeled non-nucleic acid targets such as proteins. In a model system, an anti-thrombin DNA aptamer was fluorescently labeled and covalently attached to a glass support. Thrombin in solution was selectively detected by following changes in the evanescent-wave-induced fluorescence anisotropy of the immobilized aptamer. The new biosensor can detect as little as 0.7 amol of thrombin in a 140-pL interrogated volume, has a dynamic range of 3 orders of magnitude, has an inter-sensing-element measurement precision of better than 4% RSD over the range 0-200 nM, and requires less than 10 min for sample analysis. The aptamer-sensor format is generalizable and should allow sensitive, selective, and fast determination of a wide range of analytes.
A novel family of transmembrane proteins interacting with β subunits of the Na,K-ATPase (2007)

We characterized a family consisting of four mammalian proteins of unknown function (NKAIN1, 2, 3 and 4) and a single Drosophila ortholog dNKAIN. Aside from highly conserved transmembrane domains, NKAIN proteins contain no characterized functional domains. Striking amino acid conservation in the first two transmembrane domains suggests that these proteins are likely to function within the membrane bilayer. NKAIN family members are neuronally expressed in multiple regions of the mouse brain, although their expression is not ubiquitous. We demonstrate that mouse NKAIN1 interacts with the beta1 subunit of the Na,K-ATPase, whereas Drosophila ortholog dNKAIN interacts with Nrv2.2, a Drosophila homolog of the Na,K-ATPase beta subunits. We also show that NKAIN1 can form a complex with another beta subunit-binding protein, MONaKA, when binding to the beta1 subunit of the Na,K-ATPase. Our results suggest that a complex between mammalian NKAIN1 and MONaKA is required for NKAIN function, which is carried out by a single protein, dNKAIN, in Drosophila. This hypothesis is supported by the fact that dNKAIN, but not NKAIN1, induces voltage-independent amiloride-insensitive Na(+)-specific conductance that can be blocked by lanthanum. Drosophila mutants with decreased dNKAIN expression due to a P-element insertion in the dNKAIN gene exhibit temperature-sensitive paralysis, a phenotype also caused by mutations in the Na,K-ATPase alpha subunit and several ion channels. The neuronal expression of NKAIN proteins, their membrane localization and the temperature-sensitive paralysis of NKAIN Drosophila mutants strongly suggest that this novel protein family may be critical for neuronal function.
Targeted Disruption of the Pemphigus Vulgaris Antigen (Desmoglein 3) Gene in Mice Causes Loss of Keratinocyte Cell Adhesion with a Phenotype Similar to Pemphigus Vulgaris (1997)

In patients with pemphigus vulgaris (PV), autoantibodies against desmoglein 3 (Dsg3) cause loss of cell-cell adhesion of keratinocytes in the basal and immediate suprabasal layers of stratified squamous epithelia. The pathology, at least partially, may depend on protease release from keratinocytes, but might also result from antibodies interfering with an adhesion function of Dsg3. However, a direct role of desmogleins in cell adhesion has not been shown. To test whether Dsg3 mediates adhesion, we genetically engineered mice with a targeted disruption of the DSG3 gene. DSG3 -/- mice had no DSG3 mRNA by RNase protection assay and no Dsg3 protein by immunofluorescence (IF) and immunoblots. These mice were normal at birth, but by 8-10 d weighed less than DSG3 +/- or +/+ littermates, and at around day 18 were grossly runted. We speculated that oral lesions (typical in PV patients) might be inhibiting food intake, causing this runting. Indeed, oropharyngeal biopsies showed erosions with histology typical of PV, including suprabasilar acantholysis and "tombstoning" of basal cells. EM showed separation of desmosomes. Traumatized skin also had crusting and suprabasilar acantholysis. Runted mice showed hair loss at weaning. The runting and hair loss phenotype of DSG3 -/- mice is identical to that of a previously reported mouse mutant, balding (bal). Breeding indicated that bal is coallelic with the targeted mutation. We also showed that bal mice lack Dsg3 by IF, have typical PV oral lesions, and have a DSG3 gene mutation. These results demonstrate the critical importance of Dsg3 for adhesion in deep stratified squamous epithelia and suggest that pemphigus autoantibodies might interfere directly with such a function.
Using Gene Expression Profiling to Differentiate Benign versus Malignant Thyroid Tumors (2004)

DNA microarrays allow quick and complete evaluation of a cell's transcriptional activity. Expression genomics is very powerful in that it can generate expression data for a large number of genes simultaneously across multiple samples. In cancer research, an intriguing application of expression arrays includes assessing the molecular components of the neoplastic process and utilizing the data for cancer classification (Miller LD, et al. Cancer Cell 2002;2:353-61). Classification of human cancers into distinct groups based on their molecular profile rather than their histological appearance may prove to be more relevant to specific cancer diagnoses and cancer treatment regimes. Several attempts to formulate a consensus about classification and treatment of thyroid carcinoma based on standard histopathological analysis have resulted in published guidelines for diagnosis and initial disease management (Sherman SI. Lancet 2003;361:501-11). In the past few decades, no improvement has been made in the differential diagnosis of thyroid tumors by fine needle aspiration biopsy, specifically suspicious or indeterminate thyroid lesions, suggesting that a new approach to this should be explored. Therefore, in this study, we developed a gene expression approach to diagnose benign versus malignant thyroid lesions in 73 patients with thyroid tumors. We successfully built a 10 and 6 gene model able to differentiate benign versus malignant thyroid tumors. Our results support the premise that a molecular classification system for thyroid tumors is possible, and this in turn may provide a more accurate diagnostic tool for the clinician managing patients with suspicious thyroid lesions.
Oncogenic and tumor suppressor functions of Notch in cancer: it’s NOTCH what you think (2011)

Notch signaling is often considered a model hematopoietic proto-oncogene because of its role as the main trigger of T cell acute lymphoblastic leukemia (T-ALL). Although its role in T-ALL is well characterized and further supported by a high frequency of activating NOTCH1 mutations in T-ALL patients, it still remains an open question whether the effects of Notch signaling are causative in other types of cancer, including solid tumors. Growing evidence supported by recent studies unexpectedly shows that Notch signaling can also have a potent tumor suppressor function in both solid tumors and hematological malignancies. We discuss the intriguing possibility that the pleiotropic functions of Notch can be tumor suppressive or oncogenic depending on the cellular context.
Confronting the scientific obstacles to global control of tuberculosis (2008)

Tuberculosis (TB) is a major threat to global health, recently exacerbated by the emergence of highly drug-resistant forms of the disease-causing pathogen and synergy with HIV/AIDS. In 2006, the Stop TB Partnership published "The global plan to stop TB: 2006--2015," which set out a vision of halving the prevalence of and mortality caused by the disease by 2015, followed by eliminating the disease as a public health problem by 2050. This vision depends on the development of improved diagnostics, simpler treatment, and more effective vaccination. Recently, active translational research pipelines directed toward each of these goals have been established, but improved understanding of the fundamental biology of this complex disease will prove to be the key to radical advances in TB control.
Inversion of seismic velocities for the pore aspect ratio spectrum of a rock (1979)

Laboratory measured seismic velocities of various rocks as a function of pressure and saturation are inverted to obtain their spectra of pore shapes. The inversion is based on the theory of closing of the pores as a function of pressure and the velocity changes that result. The rocks are modeled in terms of a matrix and spheroidal pores of different aspect ratios. To obtain the volume concentration of pores of each aspect ratio, two inversion schemes were formulated and examined. The linearized iterative inversion scheme gave a better result. The inversion was applied to both high‐porosity sedimentary rocks and low‐porosity igneous rocks. It worked well for all the rocks considered. The method has the power to resolve different aspect‐ratio cracks. It is predictive, i.e., using the pore aspect ratio spectrum from the inversion of velocity of a rock under one saturation condition, the velocities under a different saturation condition can be predicted via the direct problem. There are significant differences between the pore aspect ratio spectra of different rock types. For the Westerly granite, the pore aspect ratio spectrum obtained from velocity data is comparable to direct SEM observations.
Hemifacial Spasm Treated With Botulinum A Toxin Injection (1985)

Fifteen patients with hemifacial spasm were treated with botulinum A toxin injections. All patients experienced relief from spasm, with the effect lasting an average of 12.2 weeks. Complications were tearing in four patients, inability to close the involved eye in three patients, corneal exposure in one patient, and ectropion in one patient. All complications were transient and deemed minor by the patients.
Independent and overlapping transcriptional activation during liver development and regeneration in mice (2002)

Liver development and regeneration share the requirement for simultaneous proliferation and acquisition of highly specialized cellular functions. However, little is known about molecules with regulatory roles in both processes. We hypothesized that transcriptional reprogramming induced by regeneration recapitulates that of developing liver. To address this hypothesis, we determined global hepatic gene expression at embryonic day 14.5, postnatal day 14, and 6 to 24 hours following partial hepatectomy using microarrays containing 8,635 cDNAs. Analysis of genes overexpressed during these conditions revealed 3 unique expression patterns. The first was predominantly signature gene clusters specific for each growth phase. Major groups were hematopoiesis-related genes in embryonic livers, metabolic genes during postnatal liver development, and growth/inflammation and metabolic genes during regeneration. The second pattern consisted of dual overexpression during regeneration and at least one phase of development. Consistent with potential regulatory roles in liver growth, most of these transcripts control cell-cell contact, membrane trafficking, cell growth, metabolism, and inflammatory response. The third pattern, revealed by surveying their expression across 76 hepatic and extra-hepatic tissues, uncovered a restricted temporospatial pattern of liver overexpression for CD14, orosomucoid 1, hepcidin, Spi 2.1, Ith3, and Tim-44. In conclusion, these results provide a basis for the identification of gene and gene groups that play critical roles at different phases of liver development and regeneration, and underscore the importance of maintaining metabolic demands during organ growth.
Homologous pairing and strand exchange promoted by the Escherichia coli RecT protein. (1994)

RecT protein of Escherichia coli promotes the formation of joint molecules between homologous linear double-stranded M13mp19 replicative-form bacteriophage DNA and circular single-stranded M13mp19 DNA in the presence of exonuclease VIII, the recE gene product. The joint molecules were formed by a mechanism involving the pairing of the complementary strand of the linear double-stranded DNA substrate with the circular single-stranded DNA substrate coupled with the displacement of the noncomplementary strand. When the homologous linear double-stranded DNA substrate had homologous 3' or 5' single-stranded tails, then RecT promoted homologous pairing and strand exchange in the absence of exonuclease VIII. Histone H1 could substitute for RecT protein; however, joint molecules formed in the presence of histone H1 did not undergo strand exchange. These results indicate that under the reaction conditions used, the observed strand exchange reaction is promoted by RecT and is not the result of spontaneous branch migration. These results are consistent with the observation that expression of RecE (exonuclease VIII) and RecT substitutes for RecA in some recombination reactions in E. coli.
Nanopore-Based Conformational Analysis of a Viral RNA Drug Target (2014)

Nanopores are single-molecule sensors that show exceptional promise as a biomolecular analysis tool by enabling label-free detection of small amounts of sample. In this paper, we demonstrate that nanopores are capable of detecting the conformation of an antiviral RNA drug target. The hepatitis C virus uses an internal ribosome entry site (IRES) motif in order to initiate translation by docking to ribosomes in its host cell. The IRES is therefore a viable and important drug target. Drug-induced changes to the conformation of the HCV IRES motif, from a bent to a straight conformation, have been shown to inhibit HCV replication. However, there is presently no straightforward method to analyze the effect of candidate small-molecule drugs on the RNA conformation. In this paper, we show that RNA translocation dynamics through a 3 nm diameter nanopore is conformation-sensitive by demonstrating a difference in transport times between bent and straight conformations of a short viral RNA motif. Detection is possible because bent RNA is stalled in the 3 nm pore, resulting in longer molecular dwell times than straight RNA. Control experiments show that binding of a weaker drug does not produce a conformational change, as consistent with independent fluorescence measurements. Nanopore measurements of RNA conformation can thus be useful for probing the structure of various RNA motifs, as well as structural changes to the RNA upon small-molecule binding.
Intra-arterial thrombolytic therapy: a combined approach with angioplasty and/or minor surgery. (1993)

Low-dose intra-arterial treatment was performed in 124 patients who underwent a total of 142 procedures. The series included 87 occluded arteries and 55 occluded grafts. In only 29 instances (21%) was thrombolysis alone sufficient. In another 77 procedures (54%) the thrombolysis was followed by either angioplasty or minor surgery. In the remaining 36 treatments (25%) lysis of the occlusion failed. A successful end result of combined treatment was achieved in 67 of 77 (87%) procedures. Including the 29 patients in whom thrombolysis alone sufficed, a total of 96 of the 142 procedures (67%) were successful, with the overall success rate being better in grafts (78%) than in arteries (61%). The suprainguinal lesions had a significantly better response compared to the infra-inguinal ones. The evaluation of all procedures was done at the time of discharge from hospital. Complications were related either to local or systemic hemorrhage or distal embolization. Death related to treatment occurred in three patients.