gebhart/patrepeval huggingface dataset:
IL-8 and IFN-γ in Tear Fluid of Patients with Cystic Fibrosis (2006)

Cystic fibrosis (CF) is inherited as an autosomal recessive disorder. It is caused by mutations in the protein-coding gene of chromosome 7, resulting in chronic pulmonary disease and pancreatic insufficiency. The disease affects all secretory epithelia, including the eye. The pathogenesis of ocular changes in CF is still unknown, but the involvement of immunologic processes in patients with CF has been studied in recent years. We measured interleukin-8 (IL-8) and interferon-gamma (IFN-gamma) levels in tears in a group of patients and a group of normal controls to determine if the levels of these cytokines are elevated in CF. The levels of these cytokines in tears and the clinical severity of CF and eye disease were compared. Tear samples were collected from 24 patients with CF at the department of pediatric diseases, Medical University of Bialystok, Poland. Cytokine levels were determined by ELISA. Ophthalmic examinations, including tests for keratoconjunctivitis sicca (dry eye), were used to study the ocular surface. The tear levels of IL-8 and IFN-gamma in the CF patients were significantly higher than those in controls. The clinical severity of CF correlated significantly with the IL-8 and IFN-gamma levels. We found positive correlation between the tear levels of IFN-gamma and dry eye findings in CF patients. Our results suggest that the inflammatory cytokines IL-8 and IFN-gamma may play key roles in the regulation of ocular surface inflammation and the immunologic reaction in patients with CF. The tear levels of IL-8 and IFN-gamma may be candidate markers for evaluation of the clinical status of CF and eye disease. These findings help to provide a new insight into the pathogenesis of dry eye in patients with CF and provide potential targets for therapy.
Characterization of the Import Process of a Transit Peptide into Chloroplasts (1995)

In order to get insight into the functioning of transit sequences in chloroplast protein transport, the import of the full-length transit peptide of ferredoxin (trfd) was investigated. trfd rapidly associated with chloroplasts under import conditions and becomes protected against externally added proteases. Import of radiolabeled trfd is inhibited equally efficiently by nonlabeled trfd as well as by the intact precursor of ferredoxin. This strongly suggests that trfd enters the general import pathway of proteins into chloroplasts. trfd import was stimulated by ATP, which is the first demonstration that ATP is involved in membrane translocation of a targeting signal. Imported trfd was membrane-associated but was also partially degraded by internal proteases, most likely present in the stroma, indicating that the membrane-associated fraction of trfd is en route to its functional localization. The degradation products are exported out of the organelle. In contrast to the import of the precursor of ferredoxin, the import of trfd was independent of protease-sensitive components on the chloroplast surface, indicating that the initial binding of precursor proteins may be facilitated by transit sequence-lipid interactions.
Thoracic Pedicle Screw Fixation in Spinal Deformities (2001)

Thoracic pedicle screw fixation is a reliable method of treating spinal deformities, with an excellent deformity correction and a high margin of safety.
An on-die CMOS leakage current sensor for measuring process variation in sub-90nm generations (2005)

This paper describes an on-die leakage current sensor in 1.2V, 90nm dual-V/sub t/ CMOS technology for accurately measuring process variation. Results based on measured leakage data show higher signal-to-noise ratio and reduced sensitivity to supply and P/N skew variations compared to prior designs.
Deficiency of Growth Differentiation Factor 3 Protects against Diet-Induced Obesity by Selectively Acting on White Adipose (2008)

Growth differentiation factor 3 (GDF3) is a member of the TGFbeta superfamily. White adipose is one of the tissues in which Gdf3 is expressed, and it is the only tissue in which expression increases in response to high-fat diet. We generated Gdf3-/- mice, which were indistinguishable from wild-type mice and had normal weight curves on regular diet. However, on high-fat diet Gdf3-/- mice were resistant to the obesity that normally develops in wild-type mice. Herein we investigate the physiological and molecular mechanisms that underlie this protection from diet-induced obesity and demonstrate that GDF3 deficiency selectively affects white adipose through its influence on basal metabolic rates. Our results are consistent with a role for GDF3 in adipose tissue, with consequential effects on energy expenditure that ultimately impact adiposity.
Light-activated heterotrophic growth of the cyanobacterium Synechocystis sp. strain PCC 6803: a blue-light-requiring process (1991)

A glucose-tolerant strain of Synechocystis sp. strain 6803 will not grow on glucose under complete darkness unless given a daily pulse of white light, typically 5 min of 40 mumol m-2 s-1 (light-pulsed conditions). The light pulse is insufficient for photoautotrophy, as glucose is required and growth yield is dependent on glucose concentration. Growth rate is independent of fluence, but growth yield is dependent on fluence, saturating at 40 to 75 mumol m-2 s-1. A Synechocystis strain 6803 psbA mutant strain grows under light-pulsed conditions at rates similar to those for the glucose-tolerant strain, indicating that photosystem II is not required for growth. The relative spectral sensitivity of the growth of light-pulsed cultures (growth only in blue light, 400 to 500 nm, maximum at 450 nm) precludes energetic contribution from cyclic electron transport around photosystem I. Pulses of long-wavelength light (i.e., 550 and 650 nm) did not support the growth of Synechocystis strain 6803 and, when supplied before or after a blue-light pulse, did not inhibit blue-light-stimulated growth of Synechocystis strain 6803. We conclude that the required blue-light pulse does not support growth via photosynthetic electron transport but appears instead to function as an environmental signal regulating heterotrophic metabolism, cell division, or other photomorphogenic processes. We have termed the growth of Synechocystis strain 6803 pulsed with light and kept otherwise in complete darkness light-activated heterotrophic growth. This observation of a blue-light requirement for the growth of Synechocystis strain 6803 represents a novel blue light effect on the growth of a cyanobacterium.
Ventilator-associated pneumonia: Breaking the vicious circle of antibiotic overuse* (2007)

A rational empirical antimicrobial therapy for ventilator-associated pneumonia using limited-spectrum antibiotics is possible if local ecology and patient medical history and clinical status are considered. In addition, de-escalation is feasible in 42% of patients. This integrative approach may reduce the emergence of resistant bacteria, which in turns reduces the need for broad-spectrum antibiotics, breaking the vicious circle of antibiotic overuse.
Multicenter Double‐Blind, Randomized, Placebo‐Controlled Trial of Levetiracetam as Add‐On Therapy in Patients with Refractory Partial Seizures (2000)

The antiepileptic efficacy and tolerability of LEV (1,000 mg/d and 2,000 mg/d, administered in two divided doses) as add-on therapy was established in patients with refractory partial seizures in this clinical study.
Inheritable Silencing of Endogenous Genes by Hit-and-Run Targeted Epigenetic Editing (2016)

Gene silencing is instrumental to interrogate gene function and holds promise for therapeutic applications. Here, we repurpose the endogenous retroviruses' silencing machinery of embryonic stem cells to stably silence three highly expressed genes in somatic cells by epigenetics. This was achieved by transiently expressing combinations of engineered transcriptional repressors that bind to and synergize at the target locus to instruct repressive histone marks and de novo DNA methylation, thus ensuring long-term memory of the repressive epigenetic state. Silencing was highly specific, as shown by genome-wide analyses, sharply confined to the targeted locus without spreading to nearby genes, resistant to activation induced by cytokine stimulation, and relieved only by targeted DNA demethylation. We demonstrate the portability of this technology by multiplex gene silencing, adopting different DNA binding platforms and interrogating thousands of genomic loci in different cell types, including primary T lymphocytes. Targeted epigenome editing might have broad application in research and medicine.
Sparse Sampling of Signal Innovations (2008)

Sparse sampling of continuous-time sparse signals is addressed. In particular, it is shown that sampling at the rate of innovation is possible, in some sense applying Occam's razor to the sampling of sparse signals. The noisy case is analyzed and solved, proposing methods reaching the optimal performance given by the Cramer-Rao bounds. Finally, a number of applications have been discussed where sparsity can be taken advantage of. The comprehensive coverage given in this article should lead to further research in sparse sampling, as well as new applications. One main application to use the theory presented in this article is ultra-wide band (UWB) communications.
A μ‐Oxo‐μ‐η2:η2‐Peroxo Titanium Complex as a Reservoir of Active Species in Asymmetric Epoxidation Using Hydrogen Peroxide (2008)

In the on-deck circle: A μ-oxo-μ-η2:η2-peroxo titanium(salan) complex (see structure; Ti purple, O red, N blue, C gray) was synthesized from the corresponding di-μ-oxo titanium(salan) complex using 30 % hydrogen peroxide. The μ-oxo-μ-η2:η2-peroxo complex is slowly converted into an active species involved in the catalytic cycle of asymmetric epoxidation.
Incidence of Cutaneous T-Cell Lymphoma in the United States, 1973-2002 (2007)

The continued rise in incidence of CTCL is substantial, and the cause of this increase is unknown. The racial, ethnic, sex, and geographic differences in incidence may be of etiologic importance. Changes in ICD-O definitions have made it difficult to evaluate incidence trends for subclassifications of CTCL such as mycosis fungoides. In addition, these changes resulted in the creation of ambiguous histologic codes, which may have caused coding errors. These errors along with the lack of independent verification are limitations of our study. An epidemiological investigation using population-based data is important to better understand this disorder.
Synthesis and Characterization of Highly Fluorinated Gemini Pyridinium Surfactants (2009)

Abstract A series of fluorinated gemini pyridinium amphiphiles have been prepared, purified and fully characterized. The synthesis was performed using alkyl trifluoromethanesulfonates as the quaternizing agents, provided very good yields and overcame problems arising with other less powerful alkylating agents. The use of different characterization techniques, such as conductivity and surface tension measurements, shed light on the aggregation process. The title products showed interesting, unusual properties, which could be interpreted in view of a peculiar aggregating behaviour. This family of compounds is very interesting for their possible transfection activity and application in gene therapy. (© Wiley‐VCH Verlag GmbH &amp; Co. KGaA, 69451 Weinheim, Germany, 2009)
New compounds based on anthracene as a good candidate for organic dye-sensitized solar cells: Theoretical investigations (2012)

The specific properties of organic-conjugated molecules and polymers are of great importance since they have become the most promising materials for the optoelectronic device technology such as solar cells. The use of low band gap materials is a viable method for better harvesting of the solar spectrum and increasing its efficiency. The control of the parameter of these materials is a research issue of ongoing interest. In this work, quantum chemical investigation was performed to explore the optical and electronic properties of a series of different compounds based on anthracene. Different electron side groups were introduced to investigate their effects on the electronic structure. The theoretical knowledge of the highest occupied molecular orbital (HOMO) and lowest unoccupied molecular orbital (LUMO) energy levels of the components is basic in studying organic solar cells; so the HOMO, LUMO, Gap energy and open circuit voltage (Voc) of the studied compounds have been calculated and reported. These properties suggest these materials as good candidate for organic dye-sensitized solar cells.

	 

	Key words: p-Conjugated molecules, anthracene, organic solar cells, density function theory (DFT), low band-gap, electronic properties.
Multi-scale rigid registration to detect damage in micro-CT images of progressively loaded bones (2011)

We present a method to detect damage in time-lapsed, micro-CT images of progressively loaded bone. The method we have developed splits the image into regions and performs registration on each region individually. The procedure is repeated with progressively smaller regions until either a minimum size or a maximum number of levels is reached. The regions are then classified as damaged or undamaged. This method has been successfully applied to three sets of images and tested with simulated damage. It will allow us to determine the characteristics of trabecular architecture that provide strength and to predict regions that are most likely to be damaged based on their structure.
Ion dynamics and mixed mobile ion effect in fluoride glasses (2005)

We report the ionic relaxation and mixed mobile ion effect in 50ZrF4−10BaF2−10YF3−(30−x)LiF−xNaF fluoride glass series, where fluorine anions participate in the diffusion process in addition to alkali cations, unlike mixed alkali oxide glasses and crystals. By analyzing the ion dynamics in the framework of a power-law model as well as modulus formalism we have observed mixed mobile ion effect in the dc conductivity and its activation energy, the crossover frequency and its activation energy, the conductivity relaxation frequency and its activation energy, and also in the decoupling index. We have correlated these phenomena with the fractal dimension of the conduction pathways in the mixed alkali fluoride glasses compared to the single alkali glasses. We have shown that the relaxation dynamics in mixed alkali fluoride glasses is independent of temperature but dependent on glass composition.
Effects of interleukin-3 and c-kit ligand on the survival of various classes of human hematopoietic progenitor cells (1994)

Abstract We examined the effects of interleukin-3 (IL-3) and c-kit ligand (KL) on the survival of differentiated hematopoietic progenitor cells (HPC), the burst-forming unit-erythroid (BFU-E); colony-forming unit- granulocyte, erythroid, monocyte, megakaryocyte (CFU-GEMM); and CFU- granulocyte-monocyte (CFU-GM) and more primitive hematopoietic cells that give rise to these progenitor cells (pre-colony-forming cells [pre- CFC]). CD34+ HLA-DR+ cells, which are highly enriched for committed HPC, and CD34+ HLA-DR- c-kit+ cells, which contain the most primitive assayable hematopoietic cells, including long-term bone marrow culture- initiating cells, high proliferative potential-CFC, the CFU-blast, and the BFU-megakaryocyte, were suspended in serum-free medium in the presence or absence of IL-3 or KL. CD34+ HLA-DR+ cells incubated under serum-free conditions or in the presence of KL for 96 hours lost greater than 90% of assayable unilineage or multilineage HPC, whereas those cells incubated in the presence of IL-3 retained 40% of the number of HPC present at time 0. The effect of IL-3 on HPC survival was most pronounced on the BFU-E and CFU-GEMM present within CD34+ HLA-DR+ cells. Addition of IL-3, but not of KL, to CD34+ HLA-DR+ cells delayed the appearance of morphologic changes and DNA fragmentation patterns associated with cell death occurring by apoptosis. CD34+ HLA-DR-c-kit+ cells were incubated under similar serum-free conditions in the presence or absence of IL-3 or KL, and the frequency of pre-CFC was determined by limiting dilution analysis. The frequency of pre-CFC in cells incubated for 48 hours in the absence of serum was similar to that of cells incubated in the presence of IL-3 and approximately doubled when CD34+ HLA-DR- c-kit+ cells were incubated in the presence of KL. Addition of KL to serum-free suspension cultures of CD34+ HLA-DR- c-kit+ cells delayed the appearance of DNA fragmentation patterns associated with apoptosis to a greater extent than did the addition of IL-3. These studies suggests that IL-3, but not KL, promotes HPC survival, whereas KL plays a greater role than IL-3 in sustaining more primitive HPC, such as pre-CFC. The effects of both cytokines in mediating HPC and primitive hematopoietic cell survival appear to be related, in part, to their ability to suppress apoptosis.
Highly sensitive detection of early‐stage pancreatic cancer by multimodal near‐infrared molecular imaging in living mice (2008)

Pancreatic cancer is a serious disease with poor patient outcome, often as a consequence of late diagnosis in advanced stages. This is in large part due to the lack of diagnostic tools for early detection. To address this deficiency, we have investigated novel molecular near-infrared fluorescent (NIRF) in vivo imaging techniques in clinically relevant mouse models of pancreatic cancer. Genome wide gene expression profiling was used to identify cathepsin cystein proteases and matrix metalloproteinases (MMP) as targets for NIRF imaging. Appropriate protease activatable probes were evaluated for detection of early-stage pancreatic cancer in mice with orthotopically implanted pancreatic cancer cell lines. Mice with pancreatitis served as controls. Whole body in vivo NIRF imaging using activatable cathepsin sensitive probes specifically detected pancreatic tumors as small as 1-2 mm diameter. Imaging of MMP activity demonstrated high specificity for MMP positive tumors. Intravital flexible confocal fluorescence lasermicroscopy of protease activity enabled specific detection of pancreatic tumors at the cellular level. Importantly, topical application of NIRF-probes markedly reduced background without altering signal intensity. Taken together, macroscopic and confocal lasermicroscopic molecular in vivo imaging of protease activity is highly sensitive, specific and allows discrimination between normal pancreatic tissue, inflammation and pancreatic cancer. Translation of this approach to the clinic could significantly improve endoscopic and laparoscopic detection of early-stage pancreatic cancer.
Observation of single‐cell fluorescence spectra in laser flow cytometry (1996)

We report the first demonstration of directly recording fluorescence spectra of single cells in flow cytometry. An intensified, 512-element photodiode array was used in conjunction with a dispersing prism to capture the fluorescence emission spectra of Coulter ImmunoCheck calibration beads and Dictyostelium discoideum spores stained with the indocarbocyanine derivative CY3, fluorescein isothiocyanate, or R-phycoerythrin. The demonstration was made feasible by enhancing the signal-to-noise ratio of the detection process by using a fast gating technique applied to the detector. Results show that the complete fluorescence spectra of individual stained cells contain information that is normally not captured by conventional flow cytometers. By using the spectrographic flow cytometer, all this information is recorded, allowing small features and shifts in the fluorescence spectra of labelled particles to be studied. © 1996 Wiley-Liss, Inc.
Oxidative processes in red blood cells from normal and diabetic individuals. (1995)

The oxidation processes in normal and diabetic erythrocytes after cell exposure to H2O2 and t-butyl hydroperoxide, as well as the effect of malondialdehyde (a stable end product of lipid peroxidation) on erythrocyte membrane structure and stability were studied. The malondialdehyde level began to increase only after oxidation of most of the red blood cell glutathione by peroxides. The activation energy of malondialdehyde was 53 +/- 7 kj/mol. Sodium azide inhibited the oxidation processes induced by t-butyl hydroperoxide. The modification of erythrocytes by malondialdehyde decreased the fluidity of the membrane lipid bilayer measured by fluorescence anisotropy and increased the osmotic stability of the cells. The level of endogenous thiobarbituric acid-reactive species was higher and antioxidative activity was lower in diabetic cells. It seems likely that oxidation processes and accumulation of malondialdehyde can contribute directly to changes in the properties of ¿diabetic¿ red blood cells and may cause the development of long-term complications.
Determinants of the inherent strength of human 5′ splice sites (2005)

We previously showed that the authentic 5' splice site (5'ss) of the first exon in the human beta-globin gene is intrinsically stronger than a cryptic 5'ss located 16 nucleotides upstream. Here we examined by mutational analysis the contribution of individual 5'ss nucleotides to discrimination between these two 5'ss. Based on the in vitro splicing efficiencies of a panel of 26 wild-type and mutant substrates in two separate 5'ss competition assays, we established a hierarchy of 5'ss and grouped them into three functional subclasses: strong, intermediate, and weak. Competition between two 5'ss from different subclasses always resulted in selection of the 5'ss that belongs to the stronger subclass. Moreover, each subclass has different characteristic features. Strong and intermediate 5'ss can be distinguished by their predicted free energy of base-pairing to the U1 snRNA 5' terminus (DeltaG). Whereas the extent of splicing via the strong 5'ss correlates well with the DeltaG, this is not the case for competition between intermediate 5'ss. Weak 5'ss were used only when the competing authentic 5'ss was inactivated by mutation. These results indicate that extensive complementarity to U1 snRNA exerts a dominant effect for 5'ss selection, but in the case of competing 5'ss with similarly modest complementarity to U1, the role of other 5'ss features is more prominent. This study reveals the importance of additional submotifs present in certain 5'ss sequences, whose characterization will be critical for understanding 5'ss selection in human genes.
Pharmacokinetic Characteristics, Efficacy, and Safety of Buccal Testosterone in Hypogonadal Males: A Pilot Study (1998)

Transbuccal administration of drugs provides an easy route of administration. To test the safety and efficacy of a novel testosterone (T) product, we performed a randomized, double blind, placebo-controlled study in a parallel design. Men with serum T levels below 250 ng/dL were administered either an active buccal tablet containing 10 mg T (n = 7) or a buccal placebo tablet (n = 6) containing 3 mg pseudoephedrine HCl for taste matching. Men were studied while taking a standard T enanthate dose, after 6 weeks of a wash-out period, and after 8 weeks of therapy. The men were matched for age (mean +/- SD, 41 +/- 16 vs. 47 +/- 16) and type of hypogonadism (three primary testicular failures in each group, with the remainder having a central etiology). Acute pharmacokinetic testing showed peak serum hormone levels at 30 min, with a mean serum T concentration of 2688 +/- 147 ng/dL (range, 1820-3770 ng/dL). Levels returned to baseline in 4-6 h, resulting in a total T area under the curve level of 3865 ng/hn.dL, less than that using other available forms of T administration. Similar pharmacokinetics were observed for the hormone's metabolites, bioavailable T, free T, and estradiol. After 8 weeks of treatment, the results of nocturnal penile tumescence studies evaluating rigidity and circumference were significantly different from those in the placebo group (P < 0.05) and comparable to those during T enanthate therapy. In conclusion, transbuccal T therapy was sufficient to maintain normal sexual function while minimizing the total time of exposure to elevated circulating serum T levels.