gebhart/patrepeval huggingface dataset:
Production of monoclonal antibody against amyloid fibril protein and its immunohistochemical application. (1985)

An autopsy case of multiple myeloma (IgA-lambda) with extensive amyloid arthropathy of the systemic joints was described. Heavy deposits of amyloid (amyloidoma) were observed in the articular cavities of the joints. Furthermore, numerous amyloid deposits were found in the walls of small blood vessels in the general organs. Incubation of the paraffin sections of amyloid with potassium permanganate produced little loss of Congo red affinity and apple-green birefringence under polarized light. A crude preparation of amyloid protein was isolated from a frozen intra-articular mass, which had been obtained at necropsy, and injected into the footpads of BALB/c mice with complete Freund's adjuvant. The immune spleen cells were fused with myeloma cells (P3 X 63-Ag8.653) under the presence of polyethylene glycol. Hybridoma cell lines, producing supernatants which reacted not only with amyloid substances but also with normal human tissues, were omitted from the subjects of recloning, and one hybridoma cell line (Am-1) producing a specific monoclonal antibody (MAb) against the immunized amyloid substance was finally obtained. Using the indirect immunoperoxidase method, the specificity of MAb Am-1 was confirmed in the cryostat sections as well as in the formalin-fixed paraffin sections of various organs of the case from which the crude amyloid protein was obtained and used for immunization. Amyloid deposits in 25 cases with amyloidosis or amyloid deposits were examined with MAb Am-1, and 2 cases showed positive reactivity with Am-1. These 2 cases presented primary amyloidosis and focal amyloid deposits in the oral cavity, respectively; Congo red staining of amyloid in these cases showed resistance to treatment with potassium permanganate, as observed in the amyloid of the original case used for immunization. Trypsin treatment of the sections resulted in a loss of positive reactivity with MAb Am-1 in all these cases. This result indicates that Am-1 recognizes a substance composed of protein molecules. Furthermore, the immunohistochemical distribution of Am-1 positive reaction was consistent with the histological distribution of substance which could be stained by Congo red and showed apple-green birefringence under polarized light. These results have suggested that Am-1 reacts with a portion of amyloid protein which is resistant to treatment with potassium permanganate followed by Congo red staining.
Activation of Group III mGluRs Inhibits GABAergic and Glutamatergic Transmission in the Substantia Nigra Pars Reticulata (2001)

The GABAergic projection neurons of the substantia nigra pars reticulata (SNr) exert an important influence on the initiation and control of movement. The SNr is a primary output nucleus of the basal ganglia (BG) and is controlled by excitatory inputs from the subthalamic nucleus (STN) and inhibitory inputs from the striatum and globus pallidus. Changes in the output of the SNr are believed to be critically involved in the development of a variety of movement disorders. Anatomical studies reveal that metabotropic glutamate receptors (mGluRs) are highly expressed throughout the BG. Interestingly, mRNA for group III mGluRs are highly expressed in STN, striatum, and globus pallidus, and immunocytochemical studies have shown that the group III mGluR proteins are present in the SNr. Thus it is possible that group III mGluRs play a role in the modulation of synaptic transmission in this nucleus. We performed whole cell patch-clamp recordings from nondopaminergic SNr neurons to investigate the effect of group III mGluR activation on excitatory and inhibitory transmission in the SNr. We report that activation of group III mGluRs by the selective agonist L(+)-2-amino-4-phosphonobutyric acid (L-AP4, 100 microM) decreases inhibitory synaptic transmission in the SNr. Miniature inhibitory postsynaptic currents studies and paired-pulse studies reveal that this effect is mediated by a presynaptic mechanism. Furthermore we found that L-AP4 (500 microM) also reduces excitatory synaptic transmission at the STN-SNr synapse by action on presynaptically localized group III mGluRs. The finding that mGluRs modulate the major inputs to SNr neurons suggests that these receptors may play an important role in motor function and could provide new targets for the development of pharmacological treatments of movement disorders.
Tissue Factor Pathway Inhibitor-2 Is Upregulated by Vascular Endothelial Growth Factor and Suppresses Growth Factor-Induced Proliferation of Endothelial Cells (2006)

Our data suggest that VEGF-upregulation of TFPI-2 expression in endothelial cells may represent a mechanism for negative feedback regulation and modulation of its pro-angiogenic action on endothelial cells. TFPI-2, or derivatives of TFPI-2, may be novel therapeutics for treatment of angiogenic disease processes.
Hepcidin and Disorders of Iron Metabolism (2010)

The hepatic peptide hormone hepcidin is the principal regulator of iron absorption and its tissue distribution. Pathologically increased hepcidin concentrations cause or contribute to iron-restrictive anemias including anemias associated with inflammation, chronic kidney disease and some cancers. Hepcidin deficiency results in iron overload in hereditary hemochromatosis and ineffective erythropoiesis. The hepcidin-ferroportin axis is the principal regulator of extracellular iron homeostasis in health and disease, and is a promising target for the diagnosis and treatment of iron disorders and anemias.
Lipopolysaccharide, tumor necrosis factor-alpha, and IL-1 beta prevent programmed cell death (apoptosis) in human peripheral blood monocytes (1991)

Human peripheral blood monocytes progressively lose viability when cultured in the absence of serum, cytokines, or other stimuli. In this study, we investigated whether monocyte death results from membrane damage (i.e., necrosis) or internally regulated processes [i.e., programmed cell death (PCD) or apoptosis]. Our results clearly indicated that monocytes die by PCD when cultured without stimulation. Death was associated with fragmentation of DNA into integer multiples of approximately 200 bp, a decrease in cell size, condensation of the nucleus and cytoplasmic organelles, and membrane blebbing, all of which are cardinal features of PCD. Monocytes exposed to nonphysiologic conditions such as acidic media (pH 4.2), 56 degrees C for 30 min, or freezing and thawing were killed without concomitant DNA fragmentation, indicating that DNA fragmentation was not a result of cell death per se. Addition of Escherichia coli LPS, a potent monocyte activating agent, in concentrations as low as 0.1 ng/ml caused a marked increase in monocyte survival and prevented DNA fragmentation. Moreover, exogenous human rTNF-alpha or IL-1 beta also prevented PCD, suggesting that PCD is regulated by certain cytokines released from LPS-stimulated monocytes. The results indicate that in the absence of appropriate stimulation, monocytes are programmed to undergo a sequence of molecular events leading to cell death. Regulation of PCD may be an important homeostatic mechanism for controlling the number of monocytes available to respond to infection, wound healing, and tumor growth.
A Trial of 17 Alpha-Hydroxyprogesterone Caproate to Prevent Prematurity in Twins (2007)

Treatment with 17 alpha-hydroxyprogesterone caproate did not reduce the rate of preterm birth in women with twin gestations. (ClinicalTrials.gov number, NCT00099164 [ClinicalTrials.gov].).
GRP78 as a Novel Predictor of Responsiveness to Chemotherapy in Breast Cancer (2006)

The discovery of predictive factors for chemoresistance is critical for improving adjuvant therapy for cancer patients. The 78-kDa glucose-regulated protein (GRP78), widely used as an indicator of the unfolded protein response (UPR), is induced in the tumor microenvironment. In vitro studies suggest that GRP78 confers chemoresistance to topoisomerase inhibitors, such as Adriamycin (doxorubicin). Here, we report on a retrospective cohort study of 127 stage II and III breast cancer patients who were treated with Adriamycin-based chemotherapy. Archival tumor specimens were available for analysis and the relationship of GRP78 expression level to "time to recurrence" (TTR), used as a surrogate marker for drug resistance, was examined. Our data show that 67% of the study subjects expressed high level of GRP78 in their tumors before the initiation of chemotherapy and suggest an association between GRP78 positivity and shorter TTR [hazard ratio (HR), 1.78; P = 0.16]. Interestingly, subgroup analysis reveals that the HR for the GRP78-positive group increased significantly among patients who did not receive further taxane treatment (HR, 3.00; P = 0.022) and among mastectomy patients (HR, 3.33; P = 0.027). The HR was even stronger among mastectomy patients who did not receive further taxane treatment (HR, 4.82; P = 0.010). The use of GRP78 as a predictor for chemoresponsiveness and the potential interaction of GRP78 and/or the UPR pathways with taxanes warrant larger studies.
Linear ion traps in mass spectrometry (2004)

Linear ion traps are finding new applications in many areas of mass spectrometry. In a linear ion trap, ions are confined radially by a two-dimensional (2D) radio frequency (RF) field, and axially by stopping potentials applied to end electrodes. This review focuses on linear ion trap instrumentation. Potentials and ion motion in linear multipole fields and methods of ion trapping, cooling, excitation, and isolation are described. This is followed by a description of various mass discrimination effects that have been reported with linear ion traps. Linear ion traps combined in various ways with three-dimensional (3D) traps, time-of-flight (TOF) mass analyzers, and Fourier transform ion cyclotron resonance mass spectrometers are then given. Linear ion traps can be used as stand alone mass analyzers, and their use for mass analysis by Fourier transforming image currents, by mass selective radial ejection, and by mass selective axial ejection are reviewed.
Effects of Vasopressin in Septic Shock (2008)

Septic shock continues to be one of the leading causes of death in the intensive care unit today. The confluence of many factors contributes to the deterioration of patients' condition in septic shock. Increased levels of nitric oxide, in part, mediate the cardiovascular effects of septic shock. Nitric oxide is major mediator of vasodilation and hypotension as well as myocardial depression. It also contributes to decreased production and release of endogenous vasopressin. Vasopressin effects are actualized by stimulation of V1, V2, and V3 receptors located in various parts of the body. The response is dose dependent. Endogenous vasopressin and angiotensin II act synergistically to preserve and restore blood pressure levels. Decreased circulating vasopressin contributes to adrenal insufficiency via hypothalamic-pituitary-adrenal axis suppression and increased catecholamine resistance to vasopressors. Exogenous vasopressin supplementation in physiologic doses has been shown to improve blood pressure levels and decrease vasopressor needs in patients with septic shock.
Long-term promoter activity during herpes simplex virus latency (1994)

The ability to direct foreign gene expression from the herpes simplex virus type 1 (HSV-1) genome during an acute or latent infection is a subject of increasing importance in the utilization of HSV vectors for gene therapy. Little is known about the types of transcription factors present in neurons or about whether different neuronal populations within a ganglion vary in their complement of these factors. With respect to HSV-1 latency, it is not known how or why the latency-associated transcript (LAT) promoter is able to function continually during latency while all other viral promoters are inactive. To further studies of these two phenomena, we constructed seven recombinant viruses with various promoter constructs driving expression of the lacZ reporter gene. Each construct was inserted into HSV-1 at the glycoprotein C locus, and recombinant viruses were evaluated for the ability to express beta-galactosidase during acute and latent viral infections in murine dorsal root ganglia. During acute infection of murine dorsal root ganglia, the activities of the promoters varied over a wide range. Constructs containing the murine metallothionein promoter (MT1), the phosphoglycerate kinase promoter, the Moloney murine leukemia virus long terminal repeat (LTR), or the region upstream of and including the HSV LAT core promoter (LAT) were active during the acute but not the latent phase of infection. The addition of transcription factor binding sites present in the upstream LAT region to the MT1 and LTR promoters (LAT-MT1 and LAT-LTR, respectively) significantly increased acute-phase expression. Despite these high initial rates of transcription, of all the promoter constructs only LAT-LTR was able to remain transcriptionally active after the establishment of a latent state. Thus, the Moloney murine leukemia virus LTR provides a DNA element which functions to prevent promoter inactivation during latency. An analogous HSV long-term-expression element is evidently not present in the upstream LAT promoter, indicating that the HSV long-term-expression function is provided by a region outside of that which gives high-level neuronal expression during the acute phase of infection.
Rapid and Sensitive Protein Similarity Searches (1985)

An algorithm was developed which facilitates the search for similarities between newly determined amino acid sequences and sequences already available in databases. Because of the algorithm's efficiency on many microcomputers, sensitive protein database searches may now become a routine procedure for molecular biologists. The method efficiently identifies regions of similar sequence and then scores the aligned identical and differing residues in those regions by means of an amino acid replacability matrix. This matrix increases sensitivity by giving high scores to those amino acid replacements which occur frequently in evolution. The algorithm has been implemented in a computer program designed to search protein databases very rapidly. For example, comparison of a 200-amino-acid sequence to the 500,000 residues in the National Biomedical Research Foundation library would take less than 2 minutes on a minicomputer, and less than 10 minutes on a microcomputer (IBM PC).
Chemical Ionization Mass Spectrometry. II. Esters (1966)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTChemical Ionization Mass Spectrometry. II. EstersM. S. B. Munson and F. H. FieldCite this: J. Am. Chem. Soc. 1966, 88, 19, 4337–4345Publication Date (Print):October 1, 1966Publication History Published online1 May 2002Published inissue 1 October 1966https://pubs.acs.org/doi/10.1021/ja00971a007https://doi.org/10.1021/ja00971a007research-articleACS PublicationsRequest reuse permissionsArticle Views328Altmetric-Citations83LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-Alertsclose Get e-Alerts
Turn Residue Sequence Determines β-Hairpin Conformation in Designed Peptides (1997)

A series of linear peptides designed to fold into different β-hairpin conformations in aqueous solution has been studied by 1H NMR with the aim of understanding the role played by the turn residue sequence in defining β-hairpin structure. The designed peptides differ only in the amino acid sequence of the putative turn region and have identical strand residues. Our results clearly demonstrate that the turn residue sequence determines the turn conformation and, thereby, other features of the β-hairpin conformation, such as the pattern of interstrand residue pairing and the type of hydrogen-bonding register between β-strand backbone atoms. Furthermore, two key structural factors responsible for the stability of different types of turns were identified. Thus, a side-chain−side-chain interaction between Asn at position i and Thr at position i + 4 stabilizes five-residue turns, whereas a four-residue turn is stabilized when the first residue of the turn has high tendency to populate the αR region of the Ramachandran map. Our results highlight the relevance of turn structures in the early events of protein folding.
Therapeutic Strategy for Acute Spinal Cord Contusion Injury: Cell Elimination Combined with Microsurgical Intervention (2007)

The data suggest that a clinical protocol could be developed to treat acute human spinal cord injury through conventional clinical procedures, a combination of microsurgical manipulation and radiation therapy. These also suggest it is imperative to first prevent the secondary damage caused by fluid accumulation for a cure to be possible.
HiTRACE: high-throughput robust analysis for capillary electrophoresis (2011)

We propose a computational method called high-throughput robust analysis for capillary electrophoresis (HiTRACE) to automate the key tasks in large-scale nucleic acid CE analysis, including the profile alignment that has heretofore been a rate-limiting step in the highest throughput experiments. We illustrate the application of HiTRACE on 13 datasets representing 4 different RNAs, 3 chemical modification strategies and up to 480 single mutant variants; the largest datasets each include 87 360 bands. By applying a series of robust dynamic programming algorithms, HiTRACE outperforms prior tools in terms of alignment and fitting quality, as assessed by measures including the correlation between quantified band intensities between replicate datasets. Furthermore, while the smallest of these datasets required 7-10 h of manual intervention using prior approaches, HiTRACE quantitation of even the largest datasets herein was achieved in 3-12 min. The HiTRACE method, therefore, resolves a critical barrier to the efficient and accurate analysis of nucleic acid structure in experiments involving tens of thousands of electrophoretic bands.
Pentoxifylline blocks hepatic stellate cell activation independently of phosphodiesterase inhibitory activity (1997)

Activated, but not quiescent, hepatic stellate cells (lipocytes) have a high level of collagen type I and smooth muscle actin (SMA) gene expression. Therefore, stellate cell activation is a critical step in hepatic fibrosis. The mechanisms leading to stellate cell activation in vivo are unknown. The characteristic hepatic oxidative stress cascade induced in rats by CCl4 markedly stimulated stellate cell entry into S phase, nuclear factor (NF)-kappa B activity, and c-myb expression. These changes were prevented by pentoxifylline, which also decreased CCl4-induced hepatic injury. As expected, cAMP-mediated phosphorylation of CREB-Ser133 was induced in vivo in stellate cells by pentoxifylline but not by its metabolite 5, an N-1 carboxypropyl derivative, which lacks phosphodiesterase inhibitory activity. Stellate cell nuclear extracts from CCl4-treated, but not from control, animals formed a complex with the critical promoter E box of the alpha-SMA gene, which was disrupted by c-myb antibodies and competed with by c-myb cognate DNA. Treatment with pentoxifylline or metabolite 5 prevented the molecular abnormalities characteristic of stellate cell activation induced by CCl4. These results suggest that induction of c-myb plays an important role in the in vivo activation of stellate cells. Pentoxifylline blocks stellate cell activation in vivo independently of its inhibitory effects on phosphodiesterases by interfering with the oxidative stress cascade and the activation of NF-kappa B and c-myb.
Local recurrence model of malignant pleural mesothelioma for investigation of intrapleural treatment☆ (2007)

With this new recurrence model for investigation of malignant pleural mesothelioma in rats, we were able to investigate new intrapleural therapies after pneumonectomy. The intrapleural application of cisplatin-Vivostat significantly reduced the extent of local recurrence.
Synthesis, Cloning and Expression of Recombinant Aprotinin (1987)

Synthetic DNA fragments containing the coding sequence for the serine proteinase inhibitor aprotinin, also known as bovine pancreatic trypsin inhibitor (BPTI) a Kunitz type inhibitor were fused to form a synthetic aprotinin gene by the method of Khorana and cloned into E. coli. The synthetic gene is characterized by the presence of certain restriction sites. These restriction sites are unique within the used cloning system. Therefore, a great number of modifications can be achieved easily by exchange of appropriate restriction fragments. Using this method the variant [Glu52]aprotinin was obtained starting from the aprotinin gene. Both genes were successfully expressed in E. coli as fusion proteins with beta-galactosidase using vector pUR 278. No translation products could be detected in four other expression system (pUR 108, pDR 540, pKK 223-3 and pUC 8). [Glu52]aprotinin was purified and renatured after cyanogen bromide cleavage of the fusion protein. This recombinant [Glu52]aprotinin shows exactly the same trypsin-inhibitory profile as natural aprotinin.
Structure of 3′ Terminal Region of Type II Human T Lymphotropic Virus: Evidence for New Coding Region (1984)

The sequence of the 3' terminus of the human T lymphotropic virus type II (HTLV-II) was determined and compared to the corresponding sequence of HTLV-I. The 1557-nucleotide-long sequence can be divided into a 5' region that is not conserved between the two viruses, and a 3', 1011-nucleotide-long region that is highly conserved and that corresponds precisely with a long open reading frame for both HTLV-I and -II. The proteins that could be encoded by these open reading frames have a molecular weight of about 38,000 and are closely related in primary amino acid sequence. The genomic structure in the 3' region of HTLV was found to be similar to that of bovine leukemia virus.
Analysis of biologic surrogate markers from a Children's Oncology Group Phase I trial of gefitinib in pediatric patients with solid tumors (2006)

This trial evaluated the effect of gefitinib on the plasma circulating levels of epidermal growth factor receptor (EGFR), vascular endothelial growth factor (VEGF), matrix metalloproteinases (MMP)-2 and -9 of patients treated on a pediatric Phase I trial. Complete plasma correlative studies were obtained from 16 of the 25 enrolled patients. There was a trend for lower MMP-2 baseline levels in patients with partial response or stable disease. The Ewing sarcoma from the only patient with partial response lacked egfr mutations. Gefitinib did not induce any significant variation in the levels of the assessed parameters, and none of these determinations showed significant predictive or prognostic value.
Development and psychometric assessment of the COPD and Asthma Sleep Impact Scale (CASIS) (2009)

The CASIS shows good internal consistency, test-retest reliability, and construct validity and may be useful in helping to understand the impact that COPD and asthma have on sleep outcomes.