gebhart/patrepeval huggingface dataset:
Molybdenum-sensitive transcriptional regulation of the chlD locus of Escherichia coli (1987)

The chlD gene in Escherichia coli is required for the incorporation and utilization of molybdenum when the cells are grown with low concentrations of molybdate. We constructed chlD-lac operon fusions and measured expression of the fusion, Mo cofactor, and nitrate reductase activities under a variety of growth conditions. The chlD-lac fusion was highly expressed when cells were grown with less than 10 nm molybdate. Increasing concentrations of molybdate caused loss of activity, with less than 5% of the activity remaining at 500 nM molybdate; when tungstate replaced molybdate, it had an identical affect on chlD expression. Expression of chlD-lac was increased in cells grown with nitrate. Strains with chlD-lac plus an additional mutation in a chl or nar gene were constructed to test whether the regulation of chlD-lac required the concerted action of gene products involved with Mo cofactor or nitrate reductase synthesis. Mutations in narL prevented the increase in activity in response to nitrate; mutations in chlB, narC, or narI resulted in partial constitutive expression of the chlD-lac fusion: the fusion was regulated by molybdate, but it no longer required the presence of nitrate for maximal activity. Mutations in chlA, chlE, or chlG which affect Mo cofactor metabolism, did not affect the expression of chlD-lac.
Cigarette Smoking and the Periodontal Patient (2004)

Evidence from cross-sectional and case-control studies in various populations demonstrates that adult smokers are approximately three times as likely as non-smokers to have periodontitis. The association between smoking and attachment loss is even stronger when the definition of periodontitis is restricted to the most severely affected subjects. Smokers have a diminished response to periodontal therapy and show approximately half as much improvement in probing depths and clinical attachment levels following non-surgical and various surgical modalities of therapy. Implant failures in smokers are twice those of non-smokers, with a higher failure rate in the maxillary arch accounting for the majority of the difference. Tobacco-induced alterations in microbial and host factors contribute to these deleterious effects of smoking on the periodontium. In longitudinal studies, the rate of periodontal disease progression is increased in smokers, but decreases to that of a non-smoker following tobacco cessation. Likewise, recent non-smokers respond to periodontal therapy in a manner similar to patients who have never smoked. Data regarding the impact of smoking on periodontal status included in this review will be helpful to dental health professionals as they counsel their patients regarding tobacco use. The role of dental health professionals in tobacco cessation is discussed, including the use of the five A's: ask--identify tobacco users; advise--advise them to quit; assess--evaluate the patient's readiness to quit; assist--offer assistance in cessation; and arrange--follow up on the patient's cessation efforts. The addition of pharmacotherapy to behavioral therapy, including nicotine replacement therapy and bupropion, can increase cessation rates. The most popular form of nicotine replacement therapy is the patch, and its use has been shown to double cessation rates compared to behavioral therapy alone. Use of bupropion in combination with nicotine replacement therapy may be particularly helpful for heavy smokers or smokers who have experienced multiple failed attempts at cessation. The American Academy of Periodontology Parameters of Care include tobacco cessation as a part of periodontal therapy, and the 2000 Surgeon General's Report on Oral Health in America encourages dental professionals to become more active in tobacco cessation counseling. Doing so will have far-reaching positive effects on our patients' oral and general health.
Molecular Basis of Bone Morphogenetic Protein-15 Signaling in Granulosa Cells (2002)

Bone morphogenetic protein-15 (BMP-15), an oocyte growth factor belonging to the transforming growth factor-beta superfamily, has recently been shown to be necessary for normal female fertility in mammals. We have previously demonstrated that BMP-15 regulates granulosa cell (GC) proliferation and differentiation; namely, BMP-15 promotes GC mitosis, suppresses follicle-stimulating hormone (FSH) receptor expression, and stimulates kit ligand expression. Although the role of BMP-15 in female reproduction has progressively deserved much attention, there is nothing known to date about the signaling pathway and receptors for BMP-15. Using rat primary GCs and a human GC cell line, COV434, we have now found that administration of BMP-15 causes a rapid and transient phosphorylation, thus activation, of the Smad1/5/8 pathway. BMP-15 also stimulated promoter activity of a selective BMP-responsive reporter construct, further demonstrating the stimulation of Smad1/5/8 signaling by BMP-15. In contrast, BMP-15 stimulation of Smad2 phosphorylation was very weak. To identify the receptors for BMP-15, we utilized recombinant extracellular domains of individual transforming growth factor-beta superfamily receptors and found that activin receptor-like kinase-6 extracellular domain most effectively co-immunoprecipitates with BMP-15, whereas BMP receptor type II extracellular domain was most effective in inhibiting BMP-15 bioactivity on FSH-induced progesterone production and GC thymidine incorporation. We also investigated whether activation of the MAPK pathway is necessary for BMP-15 biological activity and found that the addition of U0126, an inhibitor of ERK1/2 phosphorylation, suppresses BMP-15 activity on GC mitotsis but not on FSH-induced progesterone production, suggesting a selective signaling cascade in GC proliferation and differentiation.
Motion prediction for moving objects: a statistical approach (2004)

This paper proposes a technique to obtain long term estimates of the motion of a moving object in a structured environment. Objects moving in such environments often participate in typical motion patterns which can be observed consistently. Our technique learns those patterns by observing the environment and clustering the observed trajectories using any pairwise clustering algorithm. We have implemented our technique using both simulated and real data coming from a vision system. The results show that the technique is general, produces long-term predictions and is fast enough for its use in real time applications.
Basic Aspects of Radiofrequency Catheter Ablation (1994)

Radiofrequency (RF) catheter ablation has become the treatment of choice for many symptomatic cardiac arrhythmias. It is presumed that the primary cause of tissue injury by RF ablation is thermally mediated, resulting in a relatively discrete homogeneous lesion. The mechanism by which RF current heats tissue is resistive heating of a narrow rim (< 1 mm) of tissue that is in direct contact with the ablation electrode. Deeper tissue heating occurs as a result of passive heat conduction from this small region of volume heating. Lesion size is proportional to the temperature at the electrode-tissue interface and the size of the ablation electrode. Temperatures above 50 degrees C are required for irreversible myocardial injury, but temperatures above 100 degrees C result in coagulum formation on the ablation electrode, a rapid rise in electrical impedance, and loss of effective tissue heating. Lesion formation is also dependent on optimal electrode-tissue contact and duration of RF delivery. Newer developments in RF ablation include temperature monitoring, longer ablation electrodes coupled to high-powered RF generators, and novel ablation electrode designs.
Propagative Sidewall Alkylcarboxylation that Induces Red-Shifted Near-IR Photoluminescence in Single-Walled Carbon Nanotubes (2013)

Semiconducting single-walled carbon nanotubes (SWCNTs) are direct band gap materials in which exciton photoluminescence (PL) occurs at the same wavelength as excitation. Here, we show that propagative sidewall alkylation can induce a new PL peak in (6,5) SWCNTs red-shifted from the E11 near-infrared exciton excitation and emission by ∼140 meV. The magnitude of the red-shift is weakly dependent on the terminal functional group. This new emission peak is relatively bright even after a high degree of functionalization because the reaction occurs by propagating outward from initial defects, creating bands of functional groups while maintaining the number of effective defect sites. Density functional theory computations suggest that the covalently attached alkyl functional groups introduce a new, optically allowed, low-lying state from which this new emission may arise. This method of shifting nanotube PL away from the bare nanotube excitation may find applications in near-infrared (IR) fluorescence imaging by allowing both excitation and emission to occur in the optically transparent window for biological tissues.
Yeast ADA2 protein binds to the VP16 protein activation domain and activates transcription. (1994)

Previously it was shown that yeast ADA2 protein is necessary for the full activity of some activation domains, such as VP16 and GCN4, in vivo and in vitro. These results suggest that ADA2 protein functions as a transcriptional coactivator or adaptor that bridges the interaction between certain acidic activation domains and the basal transcription machinery. Here we present two findings consistent with this model. (i) ADA2 protein interacts with a region of the VP16 acidic activation domain that requires ADA2 for activity in vivo. (ii) ADA2 protein, when fused to a heterologous DNA-binding domain, can stimulate the activity of the basal transcription factors in vivo. This ability of ADA2 to activate transcription is mediated by ADA3, a gene with properties similar to ADA2. These findings suggest that ADA2 protein has at least some of the properties expected of a transcriptional adaptor.
A new method for evaluating experimental cryptosporidial parasite loads using immunofluorescent flow cytometry. (1995)

A flow cytometric method for the quantification of Cryptosporidium parvum oocysts in stool specimens was developed to replace conventional microscopic immunofluorescent assays. Fecal pellets were collected from control (uninfected) severe combined immune-deficient mice, suspended in 2.5% potassium dichromate at a ratio of 400 microliter per pellet, and homogenized by vortexing. Purified oocytes were added to the samples (10(5), 10(4), 10(3), and 10(2)/ml). Aliquots (200 microliters) of the vortexed samples were centrifuged over microscale discontinuous sucrose gradients. The oocyst-containing fractions were collected, washed, and incubated with an oocyst-specific monoclonal antibody (labeled with fluorescein isothiocyanate) for 30 min at 37 degrees C. Sample volumes were adjusted to 600 microliters with phosphate-buffered saline and assayed by using logical gating of forward/side scatter and fluorescence signal on a flow cytometer. Seeded samples showed a linear correlation with the number of oocysts recovered from the gradients. Analyses of stool samples from chronically infected mice demonstrated that the flow cytometry method was approximately 10 times more sensitive than conventional immunofluorescent assays.
A dual coordinate descent method for large-scale linear SVM (2008)

In many applications, data appear with a huge number of instances as well as features. Linear Support Vector Machines (SVM) is one of the most popular tools to deal with such large-scale sparse data. This paper presents a novel dual coordinate descent method for linear SVM with L1-and L2-loss functions. The proposed method is simple and reaches an ε-accurate solution in O(log(1/ε)) iterations. Experiments indicate that our method is much faster than state of the art solvers such as Pegasos, TRON, SVMperf, and a recent primal coordinate descent implementation.
Perfluoro Compounds as Blood Substitutes (1978)

Abstract Inconceivable as it is, it has been proved that animals can survive after having had their blood massively or even totally replaced by emulsions of perfluorinated compounds in salines. “Bloodles” rats charged with an emulsion of perfluorotri‐ n ‐butylamine survived a five hour period in an atmosphere containing 50% oxygen and 50% carbon monoxide, i.e. in conditions where the transport of oxygen by the red cells is entirely blocked. This review discusses: (1) the experiments which have demonstrated the capability of blood substitutes based on perfluorinated compounds to sustain life; (2) the characteristics and preparation of the relevant perfluoro compounds and the production and handling of their emulsions; (3) their “physiology”, i.e. toxicity, life‐span in the blood‐stream, effect on the organs and their functions, and excretion properties. Obstacles remaining to be overcome in order to provide a safe blood substitute for medical practice include the availability of numerous series of well‐defined pure and inert perfluorinated chemicals, the production of stable emulsions, the optimization of fluid balance, and the attainment of reasonable excretion rates. The accent is placed upon the role of the chemist in the progress of this research.
Matrix engineering (1991)

Matrix engineering is a technology that utilizes hyaluronan (HA, hyaluronic acid) based matrices to control, direct or augment tissue regenerative processes. Hyaluronan and the concept of matrix engineering have become established tools in ophthalmic and orthopaedic medicine. The clinical indications for HA are limited by the physical properties and short residence time of the natural HA molecule. To expand and improve upon its current medical applications, a family of HA derivatives was prepared by chemical modification and cross-linking. Relative to the non-modified HA molecule, the hylan family of polymers provides more versatile physical forms, improved mechanical properties and an extended residence time. Hylan can also be used as a surface coating to improve blood compatibility. The chemical, physical and biological properties of hylans will be reviewed, focusing on the specific therapeutic indications they enable.
Rational Design of Genetically Encoded Fluorescence Resonance Energy Transfer-Based Sensors of Cellular Cdc42 Signaling (2003)

The temporal and spatial control of Rho GTPase signaling pathways is a central issue in understanding the molecular mechanisms that generate complex cellular movements. The Rho protein Cdc42 induces a significant conformational change in its downstream effector, the Wiskott-Aldrich syndrome protein (WASP). On the basis of this conformational change, we have created a series of single-molecule sensors for both active Cdc42 and Cdc42 guanine nucleotide exchange factors (GEFs) that utilize fluorescence resonance energy transfer (FRET) between cyan and yellow fluorescent proteins. In vitro, the Cdc42 sensors produce up to 3.2-fold FRET emission ratio changes upon binding active Cdc42. The GEF sensors yield up to 1.7-fold changes in FRET upon exchange of GDP for GTP. The GEF-catalyzed rate of nucleotide exchange for the GEF sensor is indistinguishable from that of wild-type Cdc42, but GAP-catalyzed nucleotide hydrolysis is slowed approximately 16-fold. In vivo, both sensors faithfully report on Cdc42 and/or Cdc42-GEF activity. These results establish the successful creation of rationally designed and genetically encoded tools that can be used to image the activity of biologically and medically important molecules in living systems.
Concentrations of Thrombopoietin in Bone Marrow in Normal Subjects and in Patients With Idiopathic Thrombocytopenic Purpura, Aplastic Anemia, and Essential Thrombocythemia Correlate With Its mRNA Expression of Bone Marrow Stromal Cells (1998)

The function of bone marrow (BM) stromal thrombopoietin (TPO) in megakaryopoiesis remains unknown. In the present study we attempted to clarify the pathophysiological implications of stromal TPO in normal subjects (NS) and in patients with idiopathic thrombocytopenic purpura (ITP), aplastic anemia (AA), and essential thrombocythemia (ET) by measuring TPO concentrations in BM and peripheral blood (PB) and by estimating the levels of stromal TPO mRNA with TaqMan fluorescence-based post-reverse transcription-polymerase chain reaction product detection system. The results showed that TPO concentrations in PB were significantly elevated in patients with ITP (34.9 +/- 11.7 pg/mL) and AA (364.1 +/- 153.5 pg/mL) but within normal range in patients with ET (each 20.0 and 22.1; NS, 22.1 +/- 8.2 pg/mL). In all subjects, the TPO concentrations in BM correlated well with the PB levels, and the former were consistently higher than the latter. The concentrations of TPO in BM also correlated with the levels of TPO mRNA in stromal cells. Furthermore, expression levels of TPO mRNA clearly correlated with megakaryocyte counts in NS and patients with ITP, indicating that stromal TPO actually enhances megakaryopoiesis. Thus, our results in the present study indicate that TPO from BM stromal cells is considered to play an essential role for megakaryopoiesis under various patho-physiological conditions.
Oxidative Stress in the Regulation of Normal and Neoplastic Hematopoiesis (2008)

Recent evidence suggests that oxidative stress contributes significantly to the regulation of hematopoietic cell homeostasis. In particular, red blood cells and hematopoietic stem cells are highly sensitive to deregulated accumulation of reactive oxygen species (ROS). Unchecked ROS accumulation often leads to hemolysis, that is, to destruction and shortened life span of red blood cells. In addition, the process of erythroid cell formation is sensitive to ROS accumulation. Similarly, ROS buildup in hematopoietic stem cells compromises their function as a result of potential damage to their DNA leading to loss of quiescence and alterations of hematopoietic stem cell cycling. These abnormalities may lead to accelerated aging of hematopoietic stem cells or to hematopoietic malignancies.
The Leaderless Bacteriocin Enterocin K1 Is Highly Potent against Enterococcus faecium: A Study on Structure, Target Spectrum and Receptor (2017)

Enterocin K1 (EntK1), enterocin EJ97 (EntEJ97), and LsbB are three sequence related leaderless bacteriocins. Yet LsbB kills only lactococci while EntK1 and EntEJ97 target wider spectra with EntK1 being particularly active against <i>Enterococcus faecium</i>, including nosocomial multidrug resistant isolates. NMR study of EntK1 showed that it had a structure very similar to LsbB - both having an amphiphilic N-terminal α-helix and an unstructured C-terminus. The α-helix in EntK1 is, however, about 3-4 residues longer than that of LsbB. Enterococcal mutants highly resistant to EntEJ97 and EntK1 were found to have mutations within <i>rseP</i>, a gene encoding a stress response membrane-bound Zn-dependent protease. Heterologous expression of the enterococcal <i>rseP</i> rendered resistant cells of <i>Streptococcus pneumoniae</i> sensitive to EntK1 and EntEJ97, suggesting that RseP likely serves as the receptor for EntK1 and EntEJ97. It was also shown that the conserved proteolytic active site in <i>E. faecalis</i> RseP is partly required for EntK1 and EntEJ97 activity, since alanine substitutions of its conserved residues (HExxH) reduced the sensitivity of the clones to the bacteriocins. RseP is known to be involved in bacterial stress response. As expected, the growth of resistant mutants with mutations within <i>rseP</i> was severely affected when they were exposed to higher (stressing) growth temperatures, e.g., at 45°C, at which wild type cells still grew well. These findings allow us to design a hurdle strategy with a combination of the bacteriocin(s) and higher temperature that effectively kills bacteriocin sensitive bacteria and prevents the development of resistant cells.
Alprazolam, Propranolol, and Placebo in the Treatment of Panic Disorder and Agoraphobia with Panic Attacks (1989)

Fifty-five patients completed a 5-week double-blind study comparing alprazolam, propranolol, and placebo in the treatment of panic disorder and agoraphobia with panic attacks. There was no concomitant behavioral treatment. Patient and therapist rating scales included Sheehan's Panic and Anxiety Attack Scales, the Marks-Sheehan Phobia Scale, the Hamilton Anxiety Scale, the Hamilton Depression Scale, and the Side Effects Checklist. The results generally support the efficacy of alprazolam, but not propranolol, in the treatment of panic disorder and agoraphobia with panic attacks. The significance of the results are discussed, as well as a number of the unique aspects of our procedures and patient population.
Interactions between DNA-bound repressors govern regulation by the λ phage repressor (1979)

The lambda phage repressor binds cooperatively to the three sites in the right operator (O(R)) according to the following pattern. If the DNA is wild type, O(R)1 and O(R)2 are filled coordinately because of interactions between repressor dimers bound to these two sites. Site O(R)3 is filled only at higher repressor concentrations. In contrast, if O(R)1 is mutant, O(R)2 and O(R)3 are filled coordinately because of interactions between repressors bound to these sites. In this case, the affinity of O(R)3 is increased and that of O(R)2 is decreased relative to the wild type. We infer that a repressor dimer bound to the middle site O(R)2 can interact either with another repressor dimer bound to O(R)1 (wild-type case) or, alternatively, with one bound to O(R)3 (mutant O(R)1 case). We argue that these repressor interactions are mediated by protein-protein contacts between adjacent repressor dimers, because the isolated amino-terminal domains of repressor bind to the operator sites noncooperatively. The cro protein of phage lambda, a second regulatory protein, which recognizes the same three sites in O(R) as does repressor, binds non-cooperatively. Experiments performed in vivo show that regulation of gene expression by repressor can be influenced critically by cooperative interactions. We demonstrate that the effect of repressor in a lysogen on the activity of the promoter P(RM) can be changed from activation to repression by deletion of O(R)1. We explain this effect in terms of the alternative cooperative interactions described above.
Electrical nerve and muscle stimulation by radio frequency surgery: role of direct current loops around the active electrode (1993)

Tissue cutting by electrosurgery is often accompanied with stimulation of nerves and muscles, despite the high frequency of the alternating current being applied. The main source of this stimulation is thought to be the generation of low frequency current by the nonlinear sparking process. However, measurement of this low-frequency current, in the generator electrode's circuit, showed relatively small values, barely sufficient to support this hypothesis. In this study more powerful low frequency current could be identified, indeed also originating from the nonlinear sparking process. Local direct and low frequency currents, at a level of tens of milliamperes, appeared to be generated between different sites of the active electrode-tissue interface. Probably these local currents have not been noticed before as they cannot be detected in the outer chain of generator, electrodes, and connecting wires. This finding may explain why most measures, intended to prevent stimulation by modifying this outer chain, had only limited success.