gebhart/patrepeval huggingface dataset:
Bactenecin 7 peptide fragment as a tool for intracellular delivery of a phosphorescent oxygen sensor (2010)

Research on cell-penetrating peptides for the intracellular delivery of porphyrin compounds has mainly focused on the use of trans-activator of transcription (TAT)-derived peptides and, to a lesser extent, on proline-rich peptides and phosphorescent metalloporphyrins. In this article, we describe a novel phosphorescent oxygen-sensitive probe for intracellular use which comprises a bactenecin 7 peptide fragment (15-24) conjugated with the uncharged monofunctional derivative of Pt(II) coproporphyrin I (PEPP0). This probe provides efficient loading of various mammalian cells, including PC12, HCT116, SH-SY5Y and HeLa, via cell-type-dependent uptake mechanisms. The conjugate displays a similar distribution in cytoplasm and mitochondria which allows local oxygen levels to be monitored. Respiratory responses of PC12 cells loaded with the conjugate, measured on a time-resolved fluorescent reader, showed significant cell deoxygenation in response to uncoupling by carbonyl cyanide 4-(trifluoromethoxy)phenylhydrazone and external hypoxia. Treatment with mitochondrial inhibitors led to a decrease in cell deoxygenation. Although the biophysical properties of this conjugate are similar to those of the phosphorescent intracellular oxygen-sensitive probes described previously, it possesses a number of advantages, including ease of synthesis, high loading efficiency and reliability in physiological experiments with cells. This intracellular probe can be employed for the measurement of intracellular O(2) levels in samples containing mammalian cells using the phosphorescence quenching technique. In addition, the responses to metabolic stimuli can be assessed in a wide range of cells, as can the levels of relative cell oxygenation under external hypoxia.
Performance guarantees for cluster-based internet services (2003)

As web-based transactions become an essential element of everyday corporate and commerce activities, it becomes increasingly important that the performance of web-based services be predictable and guaranteed even in the presence of wildly fluctuating input loads. In this paper, we propose a general implementation framework to provide quality of service (QoS) guarantee for cluster-based Internet services, such as E-commerce or directory service. We describe the design, implementation, and evaluation of a web request distribution system called Gage, which can provide every subscriber with distinct guarantee on the number of generic web requests that are serviced per second regardless of the total input loads at run time. Gage is one of the first systems that can support QoS guarantee involving multiple system resources, i.e., CPU, disk, and network. The frontend request distribution server of Gage distributes incoming requests among a cluster of back-end web server nodes so as to maintain per-subscriber QoS guarantee and load balance among the back-end servers. Each back-end web server node includes a Gage module, which performs distributed TCP splicing and detailed resource usage accounting. Performance evaluation of the fully operational Gage prototype demonstrates that the proposed architecture can indeed provide the guaranteed request throughput for different classes of web accesses, even in the presence of excessive input loads. The additional performance overhead associated with QoS support in Gage is merely 3.06%.
Embryo development after successful somatic cell nuclear transfer to in vitro matured human germinal vesicle oocytes (2007)

To our knowledge, this is the first report describing development of cloned human embryos using IVM oocytes and non-autologous transfer using a conventional method of SCNT.
Ferritin as an Endogenous MRI Reporter for Noninvasive Imaging of Gene Expression in C6 Glioma Tumors (2005)

The heavy chain of murine ferritin, an iron storage molecule with ferroxidase activity, was developed as a novel endogenous reporter for the detection of gene expression by magnetic resonance imaging (MRI). Expression of both enhanced green fluorescent protein (EGFP) and influenza hemagglutinin (HA)-tagged ferritin were tightly coregulated by tetracycline (TET), using a bidirectional expression vector. C6 cells stably expressing a TET-EGFP-HA-ferritin construct enabled the dynamic detection of TET-regulated gene expression by MRI, followed by independent validation using fluorescence microscopy and histology. MR relaxation rates were significantly elevated both in vitro and in vivo on TET withdrawal, and were consistent with induced expression of ferritin and increase in intracellular iron content. Hence, overexpression of ferritin was sufficient to trigger cellular response, augmenting iron uptake to a degree detectable by MRI. Application of this novel MR reporter gene that generates significant contrast in the absence of exogenously administered substrates opens new possibilities for noninvasive molecular imaging of gene expression by MRI.
Automated DNA diagnostics using an ELISA-based oligonucleotide ligation assay. (1990)

DNA diagnostics, the detection of specific DNA sequences, will play an increasingly important role in medicine as the molecular basis of human disease is defined. Here, we demonstrate an automated, nonisotopic strategy for DNA diagnostics using amplification of target DNA segments by the polymerase chain reaction (PCR) and the discrimination of allelic sequence variants by a colorimetric oligonucleotide ligation assay (OLA). We have applied the automated PCR/OLA procedure to diagnosis of common genetic diseases, such as sickle cell anemia and cystic fibrosis (delta F508 mutation), and to genetic linkage mapping of gene segments in the human T-cell receptor beta-chain locus. The automated PCR/OLA strategy provides a rapid system for diagnosis of genetic, malignant, and infectious diseases as well as a powerful approach to genetic linkage mapping of chromosomes and forensic DNA typing.
Inhibition of Histone Deacetylase Activity Suppresses Epithelial-to-Mesenchymal Transition Induced by TGF-β1 in Human Renal Epithelial Cells (2006)

Histone acetylation plays an important role in regulating gene expressions by modulating chromatin structure. Histone deacetylase (HDAC) inhibitors have been reported to have an antifibrogenic effect in some organs, such as the liver, skin, and lung, but the underlying mechanisms remain to be clarified. In the kidney, bone morphologic protein 7 (BMP-7) and hepatocyte growth factor are reported to antagonize TGF-beta1-induced tubular epithelial-to-mesenchymal transition (EMT), but nothing is known concerning the effect of HDAC inhibitors on EMT. It was shown that trichostatin A (TSA), an HDAC inhibitor, prevented TGF-beta1-induced EMT in cultured human renal proximal tubular epithelial cells. Treatment with TGF-beta1 induced morphologic changes such as EMT in human renal proximal tubular epithelial cells. However, co-treatment with TSA completely prevented TGF-beta1-induced morphologic changes and significantly prevented TGF-beta1-induced downregulation of E-cadherin and upregulation of collagen type I. Treatment with TSA did not alter TGF-beta1-induced phosphorylation of Smad2 and Smad3 but induced several inhibitory factors of TGF-beta1 signals, such as inhibitors of DNA binding/differentiation 2 (Id2) and BMP-7. Chromatin immunoprecipitation assay confirmed that histone acetylation was involved in the downregulation of E-cadherin and upregulation of Id2 and BMP-7. These results suggest that TSA and other HDAC inhibitors could be new therapeutic agents for tubular EMT.
RENAL RESEARCH INSTITUTE SYMPOSITUM: Characteristics and Effects of Inflammation in End‐Stage Renal Disease (2003)

Malnutrition and cardiovascular disease are associated with end-stage renal disease (ESRD) and both are closely associated with one another, both in cross-sectional analysis and when the courses of individual patients are followed over time. Inflammation, by suppressing synthesis of albumin, transferrin, and other negative acute-phase proteins and increasing their catabolic rates, either combines with modest malnutrition or mimics malnutrition, resulting in decreased levels of these proteins in dialysis patients. Inflammation also leads to reduced muscle mass by increasing muscle protein catabolism and blocking synthesis of muscle protein. More importantly, inflammation alters plasma protein composition and endothelial structure and function so as to promote vascular disease. Markers of inflammation, C-reactive protein (CRP), and interleukin (IL)-6 powerfully predict death from all causes and from cardiovascular disease in dialysis patients as well as progression of vascular injury. The causes of inflammation are likely multifactorial, including oxidative modification of plasma proteins, interaction of blood with nonbiocompatible membranes and lipopolysaccharides in dialysate, subclinical infection of vascular access materials, oxidative catabolism of endothelium-derived nitric oxide, and other infectious processes. Treatment should be focused on identifying potential causes of inflammation, if obvious, and reduction of other risk factor for cardiovascular disease.
Multiresolution Coding Of Image And Video Signals (1998)

Publication in the conference proceedings of EUSIPCO, Rhodes, Greece, 1998
Control of hepatocyte replication by two serum factors. (1984)

Serum proteins from hepatectomized or control rats were separated by gel permeation chromatography and assayed for stimulation of hepatocyte proliferation in primary cultures of hepatocytes. Two peaks of activity were seen in the areas of large (greater than 120,000) and small (less than 3,000) molecular weight. These activities are different from insulin, epidermal growth factor, or vasopressin and are empirically termed hepatopoietin A and B, respectively. The two activities interact in a synergistic manner to stimulate hepatocyte proliferation at rates comparable to that of the whole serum.
Microglial activation correlates with severity in Huntington disease (2006)

These [(11)C](R)-PK11195 PET findings show that the level of microglial activation correlates with Huntington disease (HD) severity. They lend support to the view that microglia contribute to the ongoing neuronal degeneration in HD and indicate that [(11)C](R)-PK11195 PET provides a valuable marker when monitoring the efficacy of putative neuroprotecting agents in this relentlessly progressive genetic disorder.
Transthyretin-Related Familial Amyloidotic Polyneuropathy (2005)

Transthyretin-related familial amyloidotic polyneuropathy (FAP) is a fatal hereditary amyloidosis. Until 20 years ago, FAP was thought to be restricted to endemic occurrence in certain areas. However, owing to progress in biochemical and molecular genetic analyses, FAP is now believed to occur worldwide. As of today, reports of about 100 different points of single or double mutations, or a deletion in the transthyretin gene, have been published, and several different phenotypes of FAP have been documented, even for the same mutation in the transthyretin gene. We present herein the current clinicopathological, biochemical, molecular genetic, and epidemiological aspects of transthyretin-related FAP, and we introduce a new diagnostic procedure for the disease.
Safety and feasibility of contrast echocardiography for the evaluation of patients with HeartMate 3 left ventricular assist devices (2017)

Routine use of a contrast agent appears safe when used in patients having a new third generation LVAD and may enhance the diagnostic accuracy of transthoracic echocardiography in these patients. LV size determination can be obtained more often due to improved LV visualization using contrast agent.
Human exhaled air analytics: biomarkers of diseases (2007)

Over the last few years, breath analysis for the routine monitoring of metabolic disorders has attracted a considerable amount of scientific interest, especially since breath sampling is a non-invasive technique, totally painless and agreeable to patients. The investigation of human breath samples with various analytical methods has shown a correlation between the concentration patterns of volatile organic compounds (VOCs) and the occurrence of certain diseases. It has been demonstrated that modern analytical instruments allow the determination of many compounds found in human breath both in normal and anomalous concentrations. The composition of exhaled breath in patients with, for example, lung cancer, inflammatory lung disease, hepatic or renal dysfunction and diabetes contains valuable information. Furthermore, the detection and quantification of oxidative stress, and its monitoring during surgery based on composition of exhaled breath, have made considerable progress. This paper gives an overview of the analytical techniques used for sample collection, preconcentration and analysis of human breath composition. The diagnostic potential of different disease-marking substances in human breath for a selection of diseases and the clinical applications of breath analysis are discussed.
Ischemic and nephrotoxic acute renal failure are distinguished by their broad transcriptomic responses (2006)

Acute renal failure (ARF) has a high morbidity and mortality. In animal ARF models, effective treatments must be administered before or shortly after the insult, limiting their clinical potential. We used microarrays to identify early biomarkers that distinguish ischemic from nephrotoxic ARF or biomarkers that detect both injury types. We compared rat kidney transcriptomes at 2 and 8 h after ischemia/reperfusion and after mercuric chloride. Quality control and statistical analyses were necessary to normalize microarrays from different lots, eliminate outliers, and exclude unaltered genes. Principal component analysis revealed distinct ischemic and nephrotoxic trajectories and clear array groupings. Therefore, we used supervised analysis, t-tests, and fold changes to compile gene lists for each group, exclusive or nonexclusive, alone or in combination. There was little network connectivity, even in the largest group. Some microarray-identified genes were validated by TaqMan assay, ruling out artifacts. Western blotting confirmed that heme oxygenase-1 (HO-1) and activating transcription factor-3 (ATF3) proteins were upregulated; however, unexpectedly, their localization changed within the kidney. HO-1 staining shifted from cortical (early) to outer stripe of the outer medulla (late), primarily in detaching cells, after mercuric chloride but not ischemia/reperfusion. ATF3 staining was similar, but with additional early transient expression in the outer stripe after ischemia/reperfusion. We conclude that microarray-identified genes must be evaluated not only for protein levels but also for anatomical distribution among different zones, nephron segments, or cell types. Although protein detection reagents are limited, microarray data lay a rich foundation to explore biomarkers, therapeutics, and the pathophysiology of ARF.
Emerging Applications of Superhydrophilic‐Superhydrophobic Micropatterns (2013)

Water on superhydrophilic surfaces spreads or is absorbed very quickly, and exhibits water contact angles close to zero. We encounter superhydrophilic materials in our daily life (e.g., paper, sponges, textiles) and they are also ubiquitous in nature (e.g., plant and tree leaves, Nepenthes pitcher plant). On the other hand, water on completely non-wettable, superhydrophobic surfaces forms spherical droplets and rolls off the surface easily. One of the most well-known examples of a superhydrophobic surface is the lotus leaf. Creating novel superhydrophobic surfaces has led to exciting new properties such as complete water repellency, self-cleaning, separation of oil and water, and antibiofouling. However, combining these two extreme states of superhydrophilicity and superhydrophobicity on the same surface in precise two-dimensional micropatterns opens exciting new functionalities and possibilities in a wide variety of applications from cell, droplet, and hydrogel microarrays for screening to surface tension confined microchannels for separation and diagnostic devices. In this Progress Report, we briefly describe the methods for fabricating superhydrophilic-superhydrophobic patterns and highlight some of the newer and emerging applications of these patterned substrates that are currently being explored. We also give an outlook on current and future applications that would benefit from using such superhydrophilic-superhydrophobic micropatterns.
Analytical model for variable partition duplexing (1993)

An analytical model to describe the statistical multiplexing performance in a variable partition duplexing (VPD) multiple access scheme is described. The analytical and simulation results are shown to agree closely for a variety of conditions.
Hormone-Specific Inhibitory Influence of α-Subunit Asn56 Oligosaccharide on In Vitro Subunit Association and Follicle-Stimulating Hormone Receptor Binding of Equine Gonadotropins1 (1998)

Hybrid hormones were created using combinations of equine (e) LH, eFSH, and eCG alpha- and beta-subunit preparations. The efficiency of eFSH beta association was highest with eLH alpha (64-72%) and was lowest with eCG alpha (37-50%). Selective removal of alphaAsn56 oligosaccharide increased heterodimerization efficiency by 9-20% for eLH alpha, by 21-28% for eFSH alpha, and by 28-41% for eCG alpha. Both alpha and beta subunits contributed significantly to FSH receptor-binding activities of the hybrids. Purified hybrid hormone preparations consisting of either eFSH beta or eLH beta combined with eLH alpha, eFSH alpha, or eCG alpha were prepared. Equine FSH beta hybrids were more active in the FSH radioreceptor assay than eLH beta hybrids; within each beta-subunit group the eLH alpha hybrids were the most active, followed by eFSH alpha hybrids, while the least active were eCG alpha hybrids. A truncated, des(121-149) eLH beta derivative (eLH beta t) combined with native alpha-subunit preparations exhibited the same effect of alpha-subunit type on FSH receptor binding. Hybrids combining the eLH beta t derivative with Asn56-deglycosylated (N56dg-)eLH alpha, N56dg-eFSH alpha, and N56dg-eCG alpha preparations possessed 2.2- to 4.3-fold increased FSH receptor-binding activities as compared with the same hybrid preparations possessing the Asn56 carbohydrate. Granulosa cell bioassay of purified native eFSH beta and eLH beta hybrid hormones indicated no significant effect of the alpha-subunit carbohydrate differences on progesterone production. The alpha-subunit Asn56 oligosaccharide exerts a hormone-specific inhibitory influence on in vitro subunit reassociation and FSH receptor binding related to the size of its Man(alpha1-6)Man antenna.
Humanized Anti-Interleukin-6 Receptor Antibody Suppresses Tumor Angiogenesis and In vivo Growth of Human Oral Squamous Cell Carcinoma (2009)

Therapeutic approaches targeting IL-6R by tocilizumab may be effective for OSCC treatment by at least inhibiting angiogenesis.
Emerging Therapies: Spectrum of Applications of Monoclonal Antibody Therapy (2000)

This article focuses on the recent dramatic advances in the applications of monoclonal antibody therapy to hematopoietic and neoplastic disease. The increase in the understanding of the role of growth factors and their receptors in the pathogenesis of malignancy and other undesirable hematological events taken in conjunction with the ability to produce humanized chimeric monoclonal antibodies to these targets is providing a new perspective for the treatment of leukemia, lymphoma and breast cancer, autoimmune disease and for prevention of ischemic complications. Dr. Waldmann describes approaches targeting the Her2/neu and the II-2/IL-15 receptor systems. The Her2/neu receptor is overexpressed in select breast, ovarian, gastric and pancreatic neoplasms. The use of trastuzumab (Herceptin) in the treatment of patients with breast cancer whose tumors overexpress this receptor are reviewed. The IL-2 receptor (Tac) is expressed on select malignant cells (adult T cell leukemia, hairy cell leukemia) and activated T cells involved in autoimmune disease and organ rejection. Humanized anti-Tac alone (daclizumab, Zenapax) or armed with toxins or radionuclides have been used successfully in the treatment of leukemia. Dr. Levy updates the experience with rituximab targeting CD20 on B cell lymphomas and reviews the antibodies to CD3, CD22, CD33, CD52, HLA-DR beta chain and HLA-D currently in or proposed for clinical trials, including radiolabelled antibodies. In the last section, Dr. Coller reviews the therapeutic results achieved with abciximab (ReoPro), an antagonist of platelet receptor GPIIbIIIa for the prevention of restenosis in percutaneous coronary interventions and the treatment of unstable angina. The mechanism of action, pharmacology and safety and efficacy of abciximab are reviewed.
Functional interactions between herpes simplex virus immediate-early proteins during infection: gene expression as a consequence of ICP27 and different domains of ICP4 (1995)

Two of the five immediate-early gene products, ICP4 and ICP27, expressed by herpes simplex virus type 1 have profound effects on viral gene expression and are absolutely essential for virus replication. Functional interactions between ICP4 and ICP27 may contribute to establishing the program of viral gene expression that ensues during lytic infection. To evaluate this possibility, viral mutants simultaneously deleted for ICP27 and defined functional domains of ICP4 were constructed. These mutant viruses allowed a comparison of gene expression as a function of different domains of ICP4 in the presence and absence of ICP27. Gene expression in the absence of both ICP4 and ICP27 was also examined. The results of this study demonstrate a clear involvement for ICP27 in the induction of early genes, in addition to its known role in enhancing late gene expression during viral infection. In the absence of both ICP4 and ICP27, viral early gene expression, as measured by the accumulation of thymidine kinase and ICP6 messages was dramatically reduced relative to the amounts of these messages seen in the absence of only ICP4. Therefore, elevated levels of early gene expression as a consequence of ICP27 occurred in the absence of any ICP4 activity. Evidence is also presented regarding the modulation of the ICP4 repression function by ICP27. When synthesized in the absence of ICP27, a mutant ICP4 protein was impaired in its ability to repress transcription from the L/ST promoter in the context of viral infection and in vitro. This defect correlated with the loss of the ability of this mutant protein to bind to its recognition sequence when produced in infected cells in the absence of ICP27. These observations indicate that ICP27 can regulate the activity of at least one domain of the ICP4 protein as well as contribute to elevated early gene expression independently of ICP4.
Cyanide Production and Degradation During Growth of Chromobacterium violaceum (1978)

Cyanogenesis by growing cultures of Chromobacterium violaceum was stimulated by the inclusion of glycine and methionine in the growth medium. Increases in the ferrous ion and phosphate concentrations of the growth medium stimulated cyanide production. Chromobacterium violaceum possesses a number of cyanide-utilizing enzymes: β-cyanoalanine synthase, γ-cyano-α-aminobutyric acid synthase and rhodanese. Studies on the activities of these enzymes in cell-free extracts of cultures growing under both high and low cyanide-evolving conditions are presented. Addition of chloramphenicol to high and low cyanide-evolving cultures towards the end of exponential growth had a profound effect on the medium cyanide concentrations. These observations are shown to have been caused by chloramphenicol blocking the induction of the cyanide-utilizing enzymes.