gebhart/patrepeval huggingface dataset:
Defining a <i>rob</i> Regulon in <i>Escherichia coli</i> by Using Transposon Mutagenesis (2000)

The Rob protein of Escherichia coli is a member of the AraC-XylS family of prokaryotic transcriptional regulators and is expressed constitutively. Deletion of the rob gene increases susceptibility to organic solvents, while overexpression of Rob increases tolerance to organic solvents and resistance to a variety of antibiotics and to the superoxide-generating compound phenazine methosulfate. To determine whether constitutive levels of Rob regulate basal gene expression, we performed a MudJ transposon screen in a rob deletion mutant containing a plasmid that allows for controlled rob gene expression. We identified eight genes and confirmed that seven are transcriptionally activated by normal expression of Rob from the chromosomal rob gene (inaA, marR, aslB, ybaO, mdlA, yfhD, and ybiS). One gene, galT, was repressed by Rob. We also demonstrated by Northern analysis that basal expression of micF is significantly higher in wild-type E. coli than in a rob deletion mutant. Rob binding to the promoter regions of most of these genes was substantiated in electrophoretic mobility shift assays. However, Mu insertions in individual Rob-regulated genes did not affect solvent sensitivity. This phenotype may depend on changes in the expression of several of these Rob-regulated genes or on other genes that were not identified. Rob clearly affects the basal expression of genes with a broad range of functions, including antibiotic resistance, acid adaptation, carbon metabolism, cell wall synthesis, central intermediary metabolism, and transport. The magnitudes of Rob's effects are modest, however, and the protein may thus play a role as a general transcription cofactor.
Beam steering and monopulse processing of probe-fed dielectric resonator antennas (1999)

It is shown that the azimuth radiation pattern direction of a multi-probe dielectric resonator antenna (DRA) can be changed by exciting different probes within the dielectric when the other probes are open-circuited. When two probes are excited simultaneously, smaller steering increments can be obtained without significantly changing the beamwidths. In some combinations, a pair of probes has a significantly greater bandwidth than a single probe. Driving pairs of probes with unequal power division is shown to steer the beam by the expected amount, thus forming the basis for future electronic beam steering of DRAs and creating the possibility of obtaining any desired steering angle. DRA monopulse processing, using two beams to form sum and difference patterns, is also demonstrated. These results have obvious applications for radar systems where control of the radiation pattern is desirable. The efficiency of DRAs make them well suited to these applications, except where large bandwidths are required.
Osteopontin expression profiles predict pathological and clinical outcome in breast cancer. (2009)

OPN expression profiles are significantly associated with tumour grade, stage and patient prognosis in breast cancer. OPN-c is likely to be of particular utility as a prognostic marker and should be included in future validation studies.
Querying continuous functions in a database system (2008)

Many scientific, financial, data mining and sensor network applications need to work with continuous, rather than discrete data e.g., temperature as a function of location, or stock prices or vehicle trajectories as a function of time. Querying raw or discrete data is unsatisfactory for these applications -- e.g., in a sensor network, it is necessary to interpolate sensor readings to predict values at locations where sensors are not deployed. In other situations, raw data can be inaccurate owing to measurement errors, and it is useful to fit continuous functions to raw data and query the functions, rather than raw data itself -- e.g., fitting a smooth curve to noisy sensor readings, or a smooth trajectory to GPS data containing gaps or outliers. Existing databases do not support storing or querying continuous functions, short of brute-force discretization of functions into a collection of tuples. We present FunctionDB, a novel database system that treats mathematical functions as first-class citizens that can be queried like traditional relations. The key contribution of FunctionDB is an efficient and accurate algebraic query processor - for the broad class of multi-variable polynomial functions, FunctionDB executes queries directly on the algebraic representation of functions without materializing them into discrete points, using symbolic operations: zero finding, variable substitution, and integration. Even when closed form solutions are intractable, FunctionDB leverages symbolic approximation operations to improve performance. We evaluate FunctionDB on real data sets from a temperature sensor network, and on traffic traces from Boston roads. We show that operating in the functional domain has substantial advantages in terms of accuracy (15-30%) and up to order of magnitude (10x-100x) performance wins over existing approaches that represent models as discrete collections of points.
Stabilization of Peptide Fibrils by Hydrophobic Interaction (2006)

Hydrophobic interactions play an important role in assembly processes in aqueous environments. In case of peptide amphiphiles, hydrophobicity is combined with hydrogen bonding to yield well-defined peptide-based aggregates. Here, we report a systematic study after the role of hydrophobic interactions on both stabilization and morphology of a peptide fibrillar assembly. For this purpose, alkyl tails were connected to a known beta-sheet forming peptide with the sequence KTVIIE. The introduction of n-alkyl groups induced thermal stability to the assemblies without affecting the morphology of the peptide aggregates.
Neurons arise in the basal neuroepithelium of the early mammalian telencephalon: A major site of neurogenesis (2004)

Neurons of the mammalian CNS are thought to originate from progenitors dividing at the apical surface of the neuroepithelium. Here we use mouse embryos expressing GFP from the Tis21 locus, a gene expressed throughout the neural tube in most, if not all, neuron-generating progenitors, to specifically reveal the cell divisions that produce CNS neurons. In addition to the apical, asymmetric divisions of neuroepithelial (NE) cells that generate another NE cell and a neuron, we find, from the onset of neurogenesis, a second population of progenitors that divide in the basal region of the neuroepithelium and generate two neurons. Basal progenitors are most frequent in the telencephalon, where they outnumber the apically dividing neuron-generating NE cells. Our observations reconcile previous data on the origin and lineage of CNS neurons and show that basal, rather than apical, progenitors are the major source of the neurons of the mammalian neocortex.
Microcell-mediated transfer of chromosome 6 into metastatic human C8161 melanoma cells suppresses metastasis but does not inhibit tumorigenicity. (1994)

Structural alterations of chromosome 6, including del(6q), are often associated with metastatic melanoma; therefore, we hypothesized that a metastasis-suppressor gene could be coded on human chromosome 6. Highly metastatic C8161 human malignant melanoma cells exhibit chromosomal changes typical of late-stage melanomas. Using microcell-mediated chromosome transfer, a copy of a normal human chromosome 6 was introduced into C8161. Three randomly selected hybrid clones (neo6/C8161.1, neo6/C8161.2 and neo6/C8161.3) were assayed for metastasis in athymic nude mice. All controls - parental C8161 cells, randomly-selected single cell clones, neo-transfected cell clones, neo11/C8161.2 and neo11/C8161.3 - were tumorigenic (270/272 mice) and metastatic (208/272 mice). neo6/C8161 hybrid cells were still tumorigenic (91/93 mice) but were not metastatic (0/195 mice). The presence of the added chromosomes was verified in cultured and tumor cells by amplification of polymorphic (CA)n markers using PCR-RFLP. The neo6/C8161 hybrids display growth and morphological patterns of more differentiated cells than C8161. In Northern blot analysis an inverse relationship between metastatic ability and metastasis-suppressor gene, nm23-H1, expression is observed - with clone neo6/C8161.1 expressing the highest level of nm23 transcripts, neo6/C8161.2 and neo6/C8161.3 expressing intermediate levels, and barely detectable levels are seen in C8161. Collectively, these results suggest that a malignant melanoma metastasis-regulatory gene may be located on human chromosome 6. These results further demonstrate that tumorigenicity and metastatic ability are distinct phenotypes.
Model for a transcript map of human chromosome 21: isolation of new coding sequences from exon and enriched cDNA libraries (1995)

The construction of a transcriptional map for human chromosome 21 requires the generation of a specific catalogue of genes, together with corresponding mapping information. Towards this goal, we conducted a pilot study on a pool of random chromosome 21 cosmids representing 2 Mb of non-contiguous DNA. Exon-amplification and cDNA selection methods were used in combination to extract the coding content from these cosmids, and to derive expressed sequences libraries. These libraries and the source cosmid library were arrayed at high density for hybridisation screening. A strategy was used which related data obtained by multiple hybridisations of clones originating from one library, screened against the other libraries. In this way, it was possible to integrate the information with the physical map and to compare the gene recovery rate of each technique. cDNAs and exons were grouped into bins delineated by EcoRI cosmid fragments, and a subset of 91 cDNAs and 29 exons have been sequenced. These sequences defined 79 non-overlapping potential coding segments distributed in 24 transcriptional units, which were mapped along 21q. Northern blot analysis performed for a subset of cDNAs indicated the existence of a cognate transcript. Comparison to databases indicated three segments matching to known chromosome 21 genes: PFKL, COL6A1 and S100B and six segments matching to unmapped anonymous expressed sequence tags (ESTs). At the translated nucleotide level, strong homologies to known proteins were found with ATP-binding transporters of the ABC family and the dihydroorotase domain of pyrimidine synthetases. These data strongly suggest that bona fide partial genes have been isolated. Several of the newly isolated transcriptional units map to clinically important regions, in particular those involved in Down's syndrome, progressive myoclonus epilepsia and auto-immune polyglandular disease. The study presented here illustrates the complementarity of exon-amplification and cDNA selection techniques for generating a large resource of new expressed landmarks, which contribute to the construction of a chromosome 21 transcript map.
A Portal for Software Security (2005)

One of the real challenges facing the emerging field of software security is the lack of an easily accessible common body of knowledge. We describe a software security portal that the USA Department of Homeland Security (DHS) National Cyber Security Division (NCSD) is developing (along with the Carnegie Mellon Software Engineering Institute (SEI) and Cigital). The launch of this portal is scheduled for October 2005 as part of the US-CERT Web site. The portal aims to provide a common, accessible, well-organized set of information for practitioners wishing to do software security.
Time resolved spectroscopy of InMnAs using differential transmission technique in mid-infrared (2010)

InMnAs grown by MOVPE is a room temperature ferromagnetic semiconductor with a Tc of 330 K. The origin of the ferromagnetism and the interactions between itinerant carriers and localized spins in these structures are open questions. To address these questions, the carrier and spin life time in these structures were probed in mid-infrared region. The approach in this work was focused on the time and polarization-resolved differential transmission measurements suggesting a T1 of ∼1 ps. We compare our results with reported spin relaxations in InAs and MBE grown InMnAs.
Onychomycosis: current treatment and future challenges (1999)

Onychomycosis is a fungal infection of the nails, more often of the toenails. It is a common condition, with an estimated overall prevalence of 3-10% in European populations. Dermatophytes, especially Trichophyton rubrum and Trichophyton mentagrophytes, are the usual pathogens. Some 50% of infected patients fail to seek medical advice. Medically confirmed onychomycosis should be treated. This recommendation is based on several disease-specific considerations: cosmetic and functional disability, lack of spontaneous remission, impairment of health and wellbeing in elderly patients and the need to reduce contamination in communal bathing places. Current treatments for onychomycosis include oral antifungal agents such as terbinafine (Lamisil) and itraconazole (Sporanox). They offer significantly improved rates of cure, shorter treatment regimens and a lower level of adverse events than was previously the case. Comparative studies have shown that terbinafine is more effective than griseofulvin, fluconazole or itraconazole in the treatment of this condition, providing a cure rate of 70-80% and an excellent tolerability profile. Terbinafine is also the most cost-effective agent. However, several problems remain that will provide future challenges in the treatment of onychomycosis, not least the consistent treatment failure rate of 20%. In many of these cases, surgery may need to precede drug therapy in order to maximise the prospects of clinical and mycological cure. In addition, duration of treatment also needs to be more closely adjusted to the individual case by prior identification of severity and extent of toenail infection, and combined oral and topical therapy also requires further investigation.
Hydrodynamic Focusing on a Silicon Chip: Mixing Nanoliters in Microseconds (1998)

We describe the formation and control of nanoscale, submerged fluid jets. The focusing process necessary to achieve these small length scales is characterized experimentally and theoretically. Fast mixing is one important application of nanoscale fluid control: We demonstrate this with a continuous-flow mixer capable of mix times of less than $10\ensuremath{\mu}\mathrm{s}$ and sample consumption rates of nanoliters per second. This new technique facilitates the study of fast reaction kinetics on time scales unattainable with conventional mixing technology.
Characterization of Orphan Human Cytochromes P450 (2007)

Of the 57 human cytochromes P450 (P450) and 58 pseudogenes discovered to date, (http://drnelson.utmem.edu/CytochromeP450.html ), 1/4 still remain "orphans" in the sense that their function, expression sites, and regulation are still largely not elucidated. The post-human genome-sequencing project era has presented the research community with novel challenges. Despite many insights gathered about gene location and genetic variations in our human genome, we still lack important knowledge about these novel P450 enzymes and their functions in endogenous and exogenous metabolism, as well as their possible roles in the metabolism of toxicants and carcinogens. Our own list of such orphans currently consists of 13 members: P450 2A7, 2S1, 2U1, 2W1, 3A43, 4A22, 4F11, 4F22, 4V2, 4X1, 4Z1, 20A1, and 27C1. Some of the orphans, e.g. P450s 2W1 and 2U1, already have putative assigned functions in arachidonic acid metabolism and may activate carcinogens. However, at this point, for the majority of them more knowledge is available about their genes and single nucleotide polymorphisms than of their biological functions. It is noteworthy that most P450 orphans express high interspecies sequence conservation and have orthologs in rodents (e.g. CYP4X1/Cyp4x1, CYP4V2/Cyp4v3). This review summarizes recent knowledge about the P450 orphans and questions remaining about their specific roles in human metabolism.
A Visual, Histological, and Enzymatic Study of Regenerating Rheumatoid Synovium in the Synovectomized Knee (1973)

In the knees of twenty-five patients with rheumatoid arthritis who had had synovectomy an average of thirty-one months previously (range one to 120), arthroscopy, aspiration, and biopsy were done. The findings were that the regenerated synovium became histologically indistinguishable from that found in patients not operated on—grossly and microscopically active areas alternated with inactive ones, lysosomal glycosidases were elevated and rose with time, and the synovium of eighteen of twenty-one of the patients two years after synovectomy met the criteria for rheumatoid disease.
Spectroscopic characterization of microscopic hydrogen-bonding disparities in supercritical water (2005)

The local hydrogen-bonding environment in supercritical water (380 degrees C, 300 bars, density 0.54 gcm3) was studied by x-ray Raman scattering at the oxygen K edge. The spectra are compared to those of the gas phase, liquid surface, bulk liquid, and bulk ice, as well as to calculated spectra. The experimental model systems are used to assign spectral features and to quantify specific local hydrogen-bonding situations in supercritical water. The first coordination shell of the molecules is characterized in more detail with the aid of the calculations. Our analysis suggests that approximately 65% of the molecules in supercritical water are hydrogen bonded in configurations that are distinctly different from those in liquid water and ice. In contrast to liquid water the bonded molecules in supercritical water have four intact hydrogen bonds and in contrast to ice large variations of bond angles and distances are observed. The remaining approximately 35% of the molecules exhibit two free O-H bonds and are thus either not involved in hydrogen bonding at all or have one or two hydrogen bonds on the oxygen side. We determine an average O-O distance of 3.1+/-0.1 A in supercritical water for the H bonded molecules at the conditions studied here. This and the corresponding hydrogen bond lengths are shown to agree with neutron- and x-ray-diffraction data at similar conditions. Our results on the local hydrogen-bonding environment with mainly two disparate hydrogen-bonding configurations are consistent with an extended structural model of supercritical water as a heterogeneous system with small patches of bonded molecules in various tetrahedral configurations and surrounding nonbonded gas-phase-like molecules.
Trehalose: an intriguing disaccharide with potential for medical application in ophthalmology (2011)

Trehalose is a naturally occurring disaccharide comprised of two molecules of glucose. The sugar is widespread in many species of plants and animals, where its function appears to be to protect cells against desiccation, but is not found in mammals. Trehalose has the ability to protect cellular membranes and labile proteins against damage and denaturation as a result of desiccation and oxidative stress. Trehalose appears to be the most effective sugar for protection against desiccation. Although the exact mechanism by which trehalose protects labile macromolecules and lipid membranes is unknown, credible hypotheses do exist. As well as being used in large quantities in the food industry, trehalose is used in the biopharmaceutical preservation of labile protein drugs and in the cryopreservation of human cells. Trehalose is under investigation for a number of medical applications, including the treatment of Huntington's chorea and Alzheimer's disease. Recent studies have shown that trehalose can also prevent damage to mammalian eyes caused by desiccation and oxidative insult. These unique properties of trehalose have thus prompted its investigation as a component in treatment for dry eye syndrome. This interesting and unique disaccharide appears to have properties which may be exploited in ophthalmology and other disease states.
Quantification of nitric oxide synthase activity in microdissected segments of the rat kidney (1999)

This study was designed to quantify nitric oxide synthase (NOS) activity in microdissected glomeruli (Glm), pars convoluta, pars recta, cortical collecting duct, cortical thick ascending limb, outer medullary collecting duct, medullary thick ascending limb and thin limb, inner medullary collecting duct (IMCD) and thin limb, and vasa recta (VR). Total protein from microdissected segments was incubated with L-[3H]arginine and appropriate cofactors, and the L-arginine and converted L-citrulline were separated by reverse-phase HPLC and radiochemically quantitated. NOS activity was found to be greatest in IMCD (11.5 +/- 1.0 fmol citrulline. mm-1. h-1) and moderate in Glm (1.9 +/- 0.3 fmol. glomerulus-1. h-1) and VR (3.2 +/- 0.8 fmol. mm-1. h-1). All other renal structures studied exhibited significantly less NOS activity. The mRNA for NOS isoforms in the NOS activity-positive segments was then identified by RT-PCR. The IMCD contained mRNA for neuronal (nNOS), endothelial (eNOS), and inducible NOS (iNOS), but Glm and VR only expressed the mRNA for nNOS and eNOS. These experiments demonstrate that the greatest enzymatic activity for NO production in the kidney is in the IMCD, three- to sixfold less activity is present in the Glm and VR, and minimal NOS activity is found in other segments studied.
Preparation of Solid-Supported Lipid Bilayers by Spin-Coating (2002)

A new method to deposit lipid bilayers on solid substrates by spin-coating of lipid solutions is presented, leading to highly aligned and homogeneous bilayers probably nucleating at the interface. Importantly, the total number of bilayers can be controlled by the deposition parameters. The samples have been characterized by X-ray reflectivity, both at partial and at full hydration in the presence of excess water.
Revised amino acid sequence of the B‐chain of ricin D due to loss of tryptophan in the cyanogen bromide cleavage (1985)

The complete amino acid sequence of the ricin D B‐chain was redetermined using the DABITC/PITC double‐coupling method. By comparing the presently established amino add sequence with the sequence reported earlier which was determined by the manual Edman degradation technique, it was found that the identification of 26 amino acid residues had to be revised. Furthermore, the ricin D B‐chain was shown to consist of 262 amino acid residues rather than 260 as previously described. In addition, based on the new amino acid sequence, the sequence homology between the N‐ and C‐terminal domain of this chain was found to be 31%.