gebhart/patrepeval huggingface dataset:
Localization of O-GlcNAc modification on the serum response transcription factor. (1992)

A unique form of nucleoplasmic and cytoplasmic protein glycosylation, O-linked GlcNAc, has previously been detected, using Gal transferase labeling techniques, on a myriad of proteins (for review see Hart, G. W., Haltiwanger, R. S., Holt, G. D., and Kelly, W. G. (1989a) Annu. Rev. Biochem. 58, 841-874), including many RNA polymerase II transcription factors (Jackson, S. P., and Tjian, R. (1988) Cell 55, 125-133). However, virtually nothing is known about the degree of glycosylation at individual sites, or, indeed, the actual sites of attachment of O-GlcNAc on transcription factors. In this paper we provide rigorous evidence for the occurrence and locations of O-GlcNAc on the c-fos transcription factor, serum response factor (SRF), expressed in an insect cell line. Fast atom bombardment mass spectrometry (FAB-MS) of proteolytic digests of SRF provides evidence for the presence of a single substoichiometric O-GlcNAc residue on each of four peptides isolated after sequential cyanogen bromide, tryptic, and proline specific enzyme digestion: these peptides are 306VSASVSP312, 274GTTSTIQTAP283, 313SAVSSADGTVLK324, and 374DSSTDLTQTSSSGTVTLP391. Using an array of techniques, including manual Edman degradation, aminopeptidase, and elastase digestion, together with FAB-MS, the major sites of O-GlcNAc attachment were shown to be serine residues within short tandem repeat regions. The highest level of glycosylation was found on the SSS tandem repeat of peptide (374-391) which is situated within the transcriptional activation domain of SRF. The other glycosylation sites observed in SRF are located in the region of the protein between the DNA binding domain and the transcriptional activation domain. Glycosylation of peptides (274-283) and (313-324) was found to occur on the serine in the TTST tandem repeat and on serine 316 in the SS repeat, respectively. The lowest level of glycosylation was recovered in peptide (306-312) which lacks tandem repeats. All the glycosylation sites identified in SRF are situated in a relatively short region of the primary sequence close to or within the transcriptional activation domain which is distant from the major sites of phosphorylation catalyzed by casein kinase II.
Human Ig superfamily CTLA‐4 gene: chromosomal localization and identity of protein sequence between murine and human CTLA‐4 cytoplasmic domains (1988)

The mouse CTLA-4 gene has been shown to code for an activated lymphocyte-associated sequence belonging to the Ig gene superfamily. We now report on the molecular cloning and study of the human corresponding gene isolated from a genomic library and designated Hu-CTLA-4. The Hu-CTLA-4 gene exists as a single copy per human haploid genome and maps to band q33 of chromosome 2. It comprises 3 exons notwithstanding the leader sequence. The first exon encodes a V-like domain of 116 amino acids, the second one a hydrophobic putative transmembrane region of 37 amino acids and the third one a 34 amino acid putative cytoplasmic domain. Whereas the overall homology between the human and murine CTLA-4 proteins is 76%, there is, remarkably, a complete identity of their cytoplasmic domains. This complete interspecies conservation comes in support of an important role for this domain in CTLA-4 function.
The SCID-hu Mouse: A Small Animal Model for HIV Infection and Pathogenesis (1991)

The SCID-hu mouse is a heterochimeric small animal model designed to support hematopoietic differentiation and function in vivo. Multiple organs of the human hematolymphoid system have been successfully engrafted into the immunodeficient C.B-17 scid scid mouse, including fetal liver, thymus, lymph node, and skin. Co-implantation of human fetal liver and human fetal thymus results in long-term, multilineage human hematopoiesis in vivo. Mature human lymphocytes within the SCID-hu mouse are phenotypically and functionally normal. HIV infection of the SCID-hu mouse reflects a tropism similar to that found in humans: only human organs with CD4+ cells are infected. Viral replication can thereafter be monitored with assays that are safe, reproducible, and quantitative. Given this small animal model, it is now possible to study systematically the infective process of HIV and to address questions about the efficacy of novel antiviral compounds or vaccines in vivo.
Identification of Promoter Regions and Regulatory Sites (2010)

Promoter sequences are the main regulatory elements of gene expression. Their recognition by computer algorithms is fundamental for understanding gene expression patterns, cell specificity and development. This chapter describes the advanced approaches to identify promoters in animal, plant and bacterial sequences. Also, we discuss an approach to identify statistically significant regulatory motifs in genomic sequences.
Diagnosis of Ovarian Cancer Using Decision Tree Classificationof Mass Spectral Data (2003)

Recent reports from our laboratory and others support the SELDI ProteinChip technology as a potential clinical diagnostic tool when combined with n ‐dimensional analyses algorithms. The objective of this study was to determine if the commercially available classification algorithm biomarker patterns software (BPS), which is based on a classification and regression tree (CART), would be effective in discriminating ovarian cancer from benign diseases and healthy controls. Serum protein mass spectrum profiles from 139 patients with either ovarian cancer, benign pelvic diseases, or healthy women were analyzed using the BPS software. A decision tree, using five protein peaks resulted in an accuracy of 81.5% in the cross‐validation analysis and 80%in a blinded set of samples in differentiating the ovarian cancer from the control groups. The potential, advantages, and drawbacks of the BPS system as a bioinformatic tool for the analysis of the SELDI high‐dimensional proteomic data are discussed.
High-Q enhancement of attractive and repulsive optical forces between coupled whispering-gallery-mode resonators (2005)

We have calculated the optically-induced force between coupled high-Q whispering gallery modes of microsphere resonators. Attractive and repulsive forces are found, depending whether the bi-sphere mode is symmetric or antisymmetric. The magnitude of the force is linearly proportional to the total power in the spheres and consequently linearly enhanced by Q. Forces on the order of 100 nN are found for Q=108, large enough to cause displacements in the range of 1mum when the sphere is attached to a fiber stem with spring constant 0.004 N/m.
A case-control study of oxidized low density lipoproteins and preeclampsia risk (2005)

Diffuse vascular endothelial dysfunction, secondary to oxidative stress, is an important pathological feature of preeclampsia. Oxidative conversion of low density lipoproteins (LDL) to oxidized-LDL (Ox-LDL) is considered an important step in transforming macrophages into lipid-laden foam cells destined to develop into early atherosclerotic-like lesions. In our study of 95 women with preeclampsia and 100 controls, we evaluated the association between maternal plasma Ox-LDL concentrations and preeclampsia risk. Ox-LDL concentrations were measured using a solid phase two-site enzyme immunoassay. Plasma lipids were measured using standard enzymatic procedures. We used logistic regression to estimate odds ratios (OR) and 95% confidence intervals (CI) adjusted for confounders. Plasma Ox-LDL concentrations were positively correlated with cholesterol, triglyceride (TG), and LDL concentrations in cases and controls, (Spearman's r ranging from 0.39-0.48, p-values all <0.01). There was no evidence of an increased risk of preeclampsia across increasing quartiles of Ox-LDL. The ORs for successive quartiles, with the lowest as the reference group, were as follows: 1.0, 1.1, 0.6, and 1.2. Women with extremely high concentrations of Ox-LDL (> or =73 U/L, the upper decile), as compared with those with lower values (<73 U/L) had a 2.7-fold increased risk of preeclampsia (95% CI 1.0-6.8). Women with high Ox-LDL and high TG concentrations (> or =284 mg/dl), as compared with those without these two factors, had a 9.6-fold increased preeclampsia risk (95% CI 2.0-45.6). Elevated Ox-LDL, particularly in conjunction with elevated TG, appears to be a risk factor of preeclampsia.
Vascular responses of dura mater (1989)

The goal of this study was to examine vascular responses of the dura mater. Microspheres were used to measure blood flow to the dura and brain in anesthetized dogs. Under control conditions, blood flow to the dura was 38 +/- 3 (SE) ml.min-1.100 g-1. Values for blood flow to the dura obtained with simultaneous injection of 15- and 50-microns microspheres were similar, which suggests that shunting of 15-microns spheres was minimal. Left atrial infusion of substance P (100 ng.kg-1.min-1) and serotonin (40 micrograms.kg-1.min-1), two agonists that have been reported to increase vascular permeability in the dura, increased blood flow to the dura two- to threefold. Adenosine (iv) produced vasodilatation in the dura. Adenosine and serotonin did not affect cerebral blood flow, but substance P increased blood flow to the brain by approximately 40%. Seizures, which produce pronounced dilatation of cerebral vessels despite activation of sympathetic nerves, produced vasoconstriction in the dura. Thus 1) the dura is perfused at a relatively high level of blood flow under normal conditions and is very responsive to vasoactive stimuli, and 2) substance P and serotonin, which have been implicated in the pathogenesis of vascular headache, produce pronounced vasodilator responses in the dura mater.
Lymph circulation in the breast after radiotherapy and breast conservation. (2006)

The aim of this study was to investigate the breast lymph circulation and skin blood circulation after radiotherapy and breast conservation. In 23 patients who had undergone lumpectomy for breast cancer (mean age 58 years, range 44-75) and 12 patients with lumpectomy for benign lesions (mean age 51 years, range 33-72), lymph circulation in the breast was measured by 99mTc-nanocolloid clearance and skin circulation by Laser Doppler Fluxmetry (LDF). Measurements were made 2-5 years after radiotherapy (50 Gy) in the former group and at a corresponding time in the latter. The lymph circulation was measured 2 cm above and medial or lateral to the areolar border in the quadrant not operated on for carcinoma. Skin circulation was measured at corresponding sites. The lymph circulation expressed as the ratio of 99mTc-nanocolloid clearance in the operated irradiated to that in the non-operated (radiation 2-4 Gy) breast was 2.33 (2.66) (median, interquartile range) (p value 0.01) and the skin circulation ratio over the corresponding area was 0.92 (0.21). Corresponding ratios in the non-radiotherapy group were 2.07 (1.96) (p value 0.03) and 1.04 (0.18) respectively. Compared with the control breast (i.e., the non-operated non-irradiated breast), there was a 4-fold increase in lymph flow in the operated, irradiated breast, a 2.5-fold increase in the contralateral non-operated (2-4 Gy) breast and a 1.5-fold increase in the operated non-irradiated breast. Radiotherapy after breast conservation surgery leads to increased long-term changes in basal lymph circulation and smaller increases in lymph flow in the contralateral breast receiving 2-4 Gy and after surgery. If maximal lymph transport capacity is unchanged, edema may be more likely in this circumstance of reduced lymphatic transport reserve.
The C-terminal SH2 domain of p85 accounts for the high affinity and specificity of the binding of phosphatidylinositol 3-kinase to phosphorylated platelet-derived growth factor beta receptor. (1992)

Upon stimulation by its ligand, the platelet-derived growth factor (PDGF) receptor associates with the 85-kDa subunit of phosphatidylinositol (PI) 3-kinase. The 85-kDa protein (p85) contains two Src homology 2 (SH2) domains and one SH3 domain. To define the part of p85 that interacts with the PDGF receptor, a series of truncated p85 mutants was analyzed for association with immobilized PDGF receptor in vitro. We found that a fragment of p85 that contains a single Src homology domain, the C-terminal SH2 domain (SH2-C), was sufficient for directing the high-affinity interaction with the receptor. Half-maximal binding of SH2-C to the receptor was observed at an SH2-C concentration of 0.06 nM. SH2-C, like full-length p85, was able to distinguish between wild-type PDGF receptor and a mutant receptor lacking the PI 3-kinase binding site. An excess of SH2-C blocked binding of full-length p85 and PI 3-kinase to the receptor but did not interfere with the binding of two other SH2-containing proteins, phospholipase C-gamma and GTPase-activating protein. These results demonstrate that a region of p85 containing a single SH2 domain accounts both for the high affinity and specificity of binding of PI 3-kinase to the PDGF receptor.
Reshaping a human antibody to inhibit the interleukin 6-dependent tumor cell growth. (1993)

The mouse PM-1 monoclonal antibody binds to the human interleukin 6 receptor, inhibits IL-6 functions, and shows strong antitumor cell activity against multiple myeloma cells. In order to be effective as a therapeutic agent administered to human patients in repeated doses, reshaped human PM-1 antibodies consisting of human REI-based light chain and NEW-based heavy chain variable regions were designed and constructed with the assistance of a structural model of the mouse PM-1 variable regions. The best reshaped human PM-1 antibody is equivalent to mouse or chimeric PM-1 antibody in terms of antigen binding and growth inhibition against multiple myeloma cells. Only a few minor changes in the human framework regions were required to recreate the mouse PM-1 antigen-binding site within a human antibody. The reshaped human PM-1 antibody, therefore, could be efficacious in human multiple myeloma patients.
A Poxvirus Protein That Binds to and Inactivates IL-18, and Inhibits NK Cell Response (2000)

IL-18 induces IFN-gamma and NK cell cytotoxicity, making it a logical target for viral antagonism of host defense. We demonstrate that the ectromelia poxvirus p13 protein, bearing homology to the mammalian IL-18 binding protein, binds IL-18, and inhibits its activity in vitro. Binding of IL-18 to the viral p13 protein was compared with binding to the cellular IL-18R. The dissociation constant of p13 for murine IL-18 is 5 nM, compared with 0.2 nM for the cellular receptor heterodimer. Mice infected with a p13 deletion mutant of ectromelia virus had elevated cytotoxicity for YAC-1 tumor cell targets compared with control animals. Additionally, the p13 deletion mutant virus exhibited decreased levels of infectivity. Our data suggest that inactivation of IL-18, and subsequent impairment of NK cell cytotoxicity, may be one mechanism by which ectromelia evades the host immune response.
Translocation 4; 11 in acute lymphoblastic leukemia: clinical characteristics and prognostic significance (1982)

Abstract Banded bone marrow chromosome analyses have been done on 83 unselected patients with acute lymphoblastic leukemia (ALL). Seven patients, all with non-T, non-B ALL, had a translocation involving the long arms of chromosomes 4 and 11. Five of these patients, 4 children and 1 adult, were first studied at diagnosis, and the t(4;11) (q21;q23) was the only karyotypic abnormality. All 5 presented with a marked leukocytosis (greater than 150 X 10(9)/liter). Four of these 5 patients achieved a complete remission following the same intensive treatment regimen; however, remission duration and survival were very short (medians 2.5 and 8 mo, respectively). The fifth patient is currently receiving induction chemotherapy. The remaining 2 patients, both adults, were studied in relapse only, and had other karyotypic abnormalities in addition to the t(4;11). One of these relapse patients was a female whose clinical presentation and course were similar to those above. The last patient was a male who presented with a leukocyte count of 7 X 10(9)/liter and maintained an initial complete remission for 37 mo. Our data suggest that patients who have a t(4;11) (q21;q23) at the time of diagnosis of ALL have a poor prognosis with conventional therapy and require a new therapeutic approach.
Evidence for a role for protein kinase C in the stimulation of protein synthesis by insulin in swiss 3T3 fibroblasts (1993)

We have examined the role of protein kinase C (PKC) in the stimulation of protein synthesis by insulin using two complementary approaches. In the first, fibroblasts were pretreated with phorbol esters to down-regulate PKC. In these cells, the effects of insulin and of phorbol esters on protein synthesis were completely abolished, although serum still elicited an effect approaching that seen in control cells. Secondly, we used newly developed inhibitors of PKC which, again, blocked the effects of insulin and phorbol esters without greatly reducing the response to serum. Thus PKC apparently plays an important role in the stimulation of translation by insulin.
Improving Arterial Pulsatility by Feedback Control of a Continuous Flow Left Ventricular Assist Device via in Silico Modeling (2014)

This study shows the possibility of obtaining more physiological pulsatile hemodynamics in the arteries by applying output-driven varying speed control to a CF-LVAD.
Multiple sclerosis among United Kingdom-born children of immigrants from the Indian subcontinent, Africa and the West Indies. (1990)

Multiple sclerosis (MS) is very uncommon among ethnic Asians in the Indian subcontinent, among Asians and Africans resident in the New Commonwealth countries of Africa and in the West Indies. It is also very uncommon among those who have migrated to England from those countries. In contrast, the children born in the United Kingdom of Asian, African and West Indian immigrants have, in the age groups available for study, a high prevalence of MS of a similar order to that occurring in the general population of England.
[Acute invasive fungal rhinosinusitis--case report]. (2002)

A case report of acute invasive fungal rhinosinusitis in 28 year old woman with acute myeloid leukemia is described in this paper. The diagnosis of the fungal disease was based on clinical presentation, endoscopic evaluation of nasal cavity, computed tomography and magnetic resonance imaging of the paranasal sinuses and histopathological findings. An aggressive treatment including antifungal therapy (amphotericin B), antibiotics and the surgery of paranasal sinuses was implemented. Unfortunately the underlying disease and the fungal invasion progressed rapidly and the patient died on the forth week post-op due to cardiorespiratory failure.
MRI Abnormalities Associated with Mild Cognitive Impairments of Vascular (VMCI) Versus Neurodegenerative (NMCI) Types Prodromal for Vascular and Alzheimers Dementias (2005)

Compared with persistently cognitively normal subjects, MCI subjects and converted dementias were significantly older without significant gender differences, but cognitively impaired subjects were older than the CN group since age is a risk factor for cognitive decline. Histories of hypertension, heart disease, diabetes mellitus, TIAs and strokes were more frequent among subjects with VMCI and VaD, confirming that all vascular risk factors contribute to vascular cognitive decline, but since vascular risk factors were treated, not all progressed to VAD. Family history of neurodegenerative disease, particularly DAT, were more prevalent among NMCI and converted DAT subjects. VMCI showed more extensive leucoaraiosis and lacunar infarcts than subjects with NMCI. NMCI, prodromal for dementia of Alzheimer's type (DAT), showed more medial temporal lobe atrophy with enlarged temporal horns, and fewer vascular lesions.
Reassessment of 79B actin gene expression in the abdomen of adult Drosophila melanogaster (1997)

The expression pattern of the 79B actin gene in Drosophila melanogaster has been inferred previously by means of a reporter gene in which 79B actin promoter sequences drive the lacZ coding sequences. Although the 79B actin gene is expressed primarily in muscles of the thorax and first abdominal segment of the adults of both sexes, expression in the remaining abdominal segments appears limited to the male genital muscles and the male-specific Muscle of Lawrence (MOL). This reported abdominal expression pattern has been reassessed. By varying parameters of tissue preparation and lacZ reporter gene detection, expression of the 79B actin gene has been revealed in most dorsal abdominal longitudinal fibres and genital muscles of both females and males. These new results suggest that there are differences in the level of 79B actin gene expression among the various abdominal muscles of both sexes, and that abdominal expression is not limited primarily to male sex structures.
Prevalence of Broad-Host-Range Lytic Bacteriophages of Sphaerotilus natans , Escherichia coli , and Pseudomonas aeruginosa (1998)

Two bacteriophage collections were examined with regard to their ability to form plaques on multiple bacterial host species. Nine of 10 phages studied were found to be broad-host-range bacteriophages. These phages fell into two groups. Group 1, the SN series, was isolated from sewage treatment plant samples with Sphaerotilus natans ATCC 13338 as a host. The DNAs of these bacteriophages contained modified bases and were insensitive to cleavage by type I and II restriction endonucleases. The efficiency of plating of these bacteriophages was changed only slightly on the alternate host. Group 2, the BHR series, was isolated by a two-host enrichment protocol. These bacteriophages were sensitive to restriction, and their efficiency of plating was dramatically reduced on the alternate host. Our results suggest that a multiple-host enrichment protocol may be more effective for the isolation of broad-host-range bacteriophages by avoiding the selection bias inherent in single-host methods. At least two of the broad-host-range bacteriophages mediated generalized transduction. We suggest that broad-host-range bacteriophages play a key role in phage ecology and gene transfer in nature.
The sedative effects and the attenuation of cardiovascular and arousal responses during anesthesia induction and intubation in pediatric patients: a randomized comparison between two different doses of preoperative intranasal dexmedetomidine (2013)

Intranasal DEX 2 μg·kg(-1) administered 30 min before anesthesia induction provides considerable effect to attenuate the increase in MAP caused by intubation response. Changes in HR and BIS also demonstrate that this kind of premedication provides effective attenuation of intubation response. And preoperative intranasal DEX 2 μg·kg(-1) produces optimal-sedation, more favorable anesthesia induction course in pediatric patients. Premedication of intranasal DEX is a considerable way to blunt cardiovascular and arousal responses to endotracheal intubation.