gebhart/patrepeval huggingface dataset:
Surface fucosylation of human cord blood cells augments binding to P-selectin and E-selectin and enhances engraftment in bone marrow (2004)

Murine hematopoietic stem and progenitor cells (HSPCs) home to bone marrow in part by rolling on P-selectin and E-selectin expressed on endothelial cells. Human adult CD34(+) cells, which are enriched in HSPCs, roll on endothelial selectins in bone marrow vessels of nonobese diabetic/severe combined immune deficiency (NOD/SCID) mice. Many human umbilical cord blood (CB) CD34(+) cells do not roll in these vessels, in part because of an uncharacterized defect in binding to P-selectin. Selectin ligands must be alpha1-3 fucosylated to form glycan determinants such as sialyl Lewis x (sLe(x)). We found that inadequate alpha1-3 fucosylation of CB CD34(+) cells, particularly CD34(+)CD38(-/low) cells that are highly enriched in HSPCs, caused them to bind poorly to E-selectin as well as to P-selectin. Treatment of CB CD34(+) cells with guanosine diphosphate (GDP) fucose and exogenous alpha1-3 fucosyltransferase VI increased cell-surface sLe(x) determinants, augmented binding to fluid-phase P- and E-selectin, and improved cell rolling on P- and E-selectin under flow. Similar treatment of CB mononuclear cells enhanced engraftment of human hematopoietic cells in bone marrows of irradiated NOD/SCID mice. These observations suggest that alpha1-3 fucosylation of CB cells might be a simple and effective method to improve hematopoietic cell homing to and engraftment in bone marrows of patients receiving CB transplants.
Acute renal failure in hospitalized patients with HIV: risk factors and impact on in-hospital mortality (2006)

Acute renal failure remains common among hospitalized patients with HIV and is associated with chronic kidney disease, liver disease, and increased mortality.
The correlation between insulin-like growth factor II mRNA binding protein 3 expression in hepatocellular carcinoma and prognosis. (2013)

IMP3, which is associated with tumor formation, invasion, tumor cell proliferation and so on, may become the target for inhabiting cell proliferation and the biomarker for predicting prognosis.
The central role of chromatin in autoimmune responses to histones and DNA in systemic lupus erythematosus. (1994)

To gain insight into the mechanisms of autoantibody induction, sera from 40 patients with systemic lupus erythematosus (SLE) were tested by ELISAs for antibody binding to denatured individual histones, native histone-histone complexes, histone-DNA subnucleosome complexes, three forms of chromatin, and DNA. Whole chromatin was the most reactive substrate, with 88% of the patients positive. By chi-square analysis, only the presence of anti-(H2A-H2B), anti-[(H2A-H2B)-DNA], and antichromatin were correlated with kidney disease measured by proteinuria > 0.5 g/d. SLE patients could be divided into two groups based on their antibody-binding pattern to the above substrates. Antibodies from about half of the patients reacted with chromatin and the (H2A-H2B)-DNA subnucleosome complex but displayed very low or no reactivity with native DNA or the (H3-H4)2-DNA subnucleosome complex. An additional third of the patients had antibody reactivity to chromatin, as well as to both subnucleosome structures and DNA. Strikingly, all sera that bound to any of the components of chromatin also bound to whole chromatin, and adsorption with chromatin removed 85-100% of reactivity to (H2A-H2B)-DNA, (H3-H4)2-DNA, and native DNA. Individual sera often bound to several different epitopes on chromatin, with some epitopes requiring quaternary protein-DNA interactions. These results are consistent with chromatin being a potent immunogenic stimulus in SLE. Taken together with previous studies, we suggest that antibody activity to the (H2A-H2B)-DNA component signals the initial breakdown of immune tolerance whereas responses to (H3-H4)2-DNA and native DNA reflect subsequent global loss of tolerance to chromatin.
Novel Application of 7-Chloro-4-nitrobenzo-2-oxa-1,3-diazole To Identify Cysteine Sulfenic Acid in the AhpC Component of Alkyl Hydroperoxide Reductase (1997)

The trapping of a sulfenic acid within the fully active C165S mutant of the AhpC peroxidase protein from Salmonella typhimurium was investigated. The electrophilic reagent employed in these studies, 7-chloro-4-nitrobenz-2-oxa-1,3-diazole (NBD-Cl), has previously been used to modify thiol, amino, and tyrosine hydroxyl groups in proteins; at neutral pH only cysteinyl residues of AhpC proteins are modified. The peroxide-oxidized C165S mutant of AhpC incubated with NBD-Cl gave a product with an absorbance maximum at 347 nm, whereas the thiol-NBD conjugate formed from the reduced protein absorbed maximally at 420 nm. Electrospray ionization mass spectrometry of the modified proteins allowed identification of the species absorbing at 347 nm as a Cys-S(O)-NBD derivative containing one additional oxygen relative to the Cys-S-NBD product. The C165S conjugates with Cys-S(O)-NBD and Cys-S-NBD had no peroxidase activity when compared to unreacted C165S and wild-type AhpC, but were both reactivated through removal of NBD by DTT. Oxidized C165S was also modified by dimedone, a common sulfenic acid reagent, to give the expected inactivated conjugate of higher mass. This reagent was not removed by DTT and blocked any further reaction of the protein with NBD-Cl. NBD modification of Enterococcus faecalis NADH peroxidase, a well-characterized flavoprotein with an active-site sulfenic acid (Cys-SOH), also yielded the spectrally-distinguishable NBD conjugates following incubation of NBD-Cl with oxidized and reduced forms of the denatured peroxidase, indicating a general utility for this reagent with other sulfenic acid-containing proteins. A significant advantage of NBD-Cl over previously-used sulfenic acid reagents such as dimedone is in the retention of the sulfenic acid oxygen in the modified product; differentiation between protein-associated thiols and sulfenic acids is therefore now possible by means of both visible absorbance properties and mass analyses of the NBD-modified proteins.
Pertussigen Treatment Retards, but fails to Prevent, the Development of type I, Insulin-Dependent Diabetes Mellitus (IDDM) in NOD Mice (1991)

Current evidence supports an autoimmune etiopathogenesis for Type I, insulin-dependent diabetes mellitus (IDDM) in which the pancreatic beta (beta) cell is the specific target tissue. Recently, the NOD (non-obese diabetic) mouse has become an important model for IDDM, exhibiting many of the pathological features observed in man, including a progressive pancreatic islet leukocytic inflammation referred to as insulitis. The present study was carried out to determine the efficacy of the bacterial-derived bio-product, pertussigen, to retard the progression of insulitis and thereby prevent overt diabetes. Results revealed that (1) the rapid onset of IDDM in female NOD mice is absent if the mothers are treated with pertussigen prior to mating, (2) treatment of young prediabetic NOD mice with repeated injections of pertussigen results in the retardation of onset of IDDM when compared to untreated control NOD mice, and (3) the severity of insulitis in pertussigen-treated NOD mice not developing IDDM was noticeably less severe than age and sex-matched untreated control mice. Since earlier work had shown that pertussis vaccine, which contains pertussigen, could prevent development of IDDM in mice treated with streptozotocin, the present results may indicate basic differences in the inflammatory responses in the genetically-predisposed NOD mice and IDDM-nonsusceptible mice with streptozotocin-induced diabetes.
Early treatment of subarachnoid hemorrhage after preventing rerupture of an aneurysm (1995)

Twelve patients with Hunt and Hess neurological Grades III to V underwent thrombosis of aneurysms using cellulose acetate polymer within 23 hours of aneurysm rupture. On computerized tomography (CT), nine of these patients had difuse or localized thick subarachnoid blood clots, two had diffuse thin clots and one had intraventricular clots. Immediately after thrombosis, all patients were administered tissue plasminogen activator (TPA) through spinal or ventricular catheters. The pressure of the lumbar cerebrospinal fluid was maintained at 100 to 150 mm H2O. The TPA was given as multiple injections of 2 mg on Day 0 and 1 to 2 mg on the following 1 to 2 days. In two patients the second injection of TPA was not given because of severe brain damage resulting from the initial subarachnoid hemorrhage. Ten patients showed complete clearance of the cisternal clot on CT within 72 hours after thrombosis. Seven partially thrombosed aneurysms and five multiple aneurysms were clipped during delayed surgery. Only one patient experienced mild vasospasm as shown on the follow-up angiogram. Eight patients improved clinically and had a good recovery, two had severe disability, and two died. Urgent thrombosis of a ruptured aneurysm followed by immediate postthrombotic administration of TPA may be a safe and reasonable means of preventing vasospasm and improving patient outcome.
BugFix: A learning-based tool to assist developers in fixing bugs (2009)

We present a tool called BugFix that can assist developers in fixing program bugs. Our tool automatically analyzes the debugging situation at a statement and reports a prioritized list of relevant bug-fix suggestions that are likely to guide the developer to an appropriate fix at that statement. BugFix incorporates ideas from machine learning to automatically learn from new debugging situations and bug fixes over time. This enables more effective prediction of the most relevant bug-fix suggestions for newly-encountered debugging situations. The tool takes into account the static structure of a statement, the dynamic values used at that statement by both passing and failing runs, and the interesting value mapping pairs [17] associated with that statement. We present a case study illustrating the efficacy of BugFix in helping developers to fix bugs.
Radical deoxygenation of tert-alcohols in 2'-branched-chain sugar pyrimidine nucleosides: Synthesis and antileukemic activity of 2'-deoxy-2'(S)-methylcytidine. (1987)

We have synthesized 2'-deoxy-2' (S) -methylcytidine (7), a new antileukemic nucleoside. The carbonyl methylation of 2'-ketonucleoside (1) with MeLi, Me3Al and MeMgX was examined. Only in the reaction with MeMgX, did the more hindered β-attack afford the 2'-methyl-t-alcohol (2b). Compound 2b was converted into the methyl oxalate (4), which was subjected to radical deoxygenation to give the 2'-deoxy-2' (S) -methyl derivative (5). The deprotection of 5 followed by substitution with NH3 furnished 7. The structure-activity relationships of 7 and some other 2'-branched-chain sugar cytidines against L1210 cells are also described.
Assembly of functional antibodies from immunoglobulin heavy and light chains synthesised inE. coli (1984)

Genes for a murine mu heavy chain and a lambda light chain immunoglobulin have been inserted into bacterial expression plasmids containing the Escherichia coli trp promoter and ribosome binding site. Induction of transcription from the trp promoter results in accumulation of both light and heavy chain polypeptides in appropriate host strains. Both proteins were found as insoluble products. Following extraction and purification of the immunoglobulin containing fractions, antigen binding activity was recovered. The activity demonstrates essentially the same properties as the antibody from the hybridoma from which the genes were cloned.
Generating sparse partial inductance matrices with guaranteed stability (1995)

This paper proposes a definition of magnetic vector potential that can be used to evaluate sparse partial inductance matrices. Unlike the commonly applied procedure of discarding the smallest matrix terms, the proposed approach maintains accuracy at middle and high frequencies and is guaranteed to be positive definite for any degree of sparsity (thereby producing stable circuit solutions). While the proposed technique is strictly based upon potential theory (i.e. the invariance of potential differences on the zero potential reference choice), the technique is, nevertheless, presented and discussed in both circuit and magnetic terms. The conventional and the proposed sparse formulation techniques are contrasted in terms of eigenvalues and circuit simulation results on practical examples.
SS-FDMA channelization and routing in advanced multibeam mobile satellite systems (1988)

Resumes the investigations carried out in the frame of INMARSAT Contract INM/86-218/HK: 'Study of Channelization and Routing in an INMARSAT 3rd Generation Satellite Transponder' dealing with the design of a satellite-switched frequency division multiple access (SS-FDMA) onboard router for multibeam mobile satellite systems of next decade (1991 technology has been taken as a reference). SS-FDMA is basically an adaptation of FDMA to multibeam satellite systems, re-proposed in the early 1980s as a consequence of significant breakthroughs achieved in the field of HPA linearization-to reduce multicarrier intermodulation and thus the amount of required backoff-and forward error correction (FEC) codecs implementation, necessary to balance link budget deficiencies in the presence of small (low-cost) terminals. A number of technology issues are present in such user-oriented systems, including narrowband filtering, large switching matrices and low phase noise programmable mixers. They are discussed and limitations/emerging trends indicated.
Immune checkpoint inhibitors: An innovation in immunotherapy for the treatment and management of patients with cancer (2017)

Cancer survival rates are generally increasing in the United States. These trends have been partially attributed to improvement in therapeutic strategies. Cancer immunotherapy is an example of one of the newer strategies used to fight cancer, which primes or activates the immune system to produce antitumor effects. The first half of this review paper concisely describes the cell mechanisms that control antitumor immunity and the major immunotherapeutic strategies developed to target these mechanisms. The second half of the review discusses in greater depth immune checkpoint inhibitors that have recently demonstrated tremendous promise for the treatment of diverse solid tumor types, including melanoma, non-small cell lung cancer, and others. More specifically, the mechanisms of action, side effects, and patient and family management and education concerns are discussed to provide oncology nurses up-to-date information relevant to caring for cancer-affected patients treated with immune checkpoint inhibitors. Future directions for cancer immunotherapy are considered.
The Genetic Control of HLA‐A and B Antigens in Somatic Cell Hybrids: Requirement for β2 Microglobulin (1978)

The lymphoblastoid cell line Daudi lacks both HLA-A and B antigens and beta2 microglobulin. Somatic cell hybrids derived from a fusion between this line and D98/AH--2 were shown to express four HLA antigens not detectable on either parent cell, A1, A10(Aw26), Bw16(Bw38, Bw17. The initial definition by direct cytotoxicity assay was confirmed by absorption of reactions against target T lymphocytes, thus avoiding problems due to contaminating Ia antibodies, and by blocking the reactions by pretreatment with a chicken anti-human beta2 microglobulin serum. That the new specificities were due to the Daudi HLA region was confirmed by the finding that interspecific hybrids between Daudi and A9L, containing a single human chromosome 6, expressed A10 and Bw17. This also defined the haplotypes of Daudi as A10(Aw26), Bw17 and A1, Bw16(Bw38). The re-expression of the Daudi HLA-A and B antigens in two independent sets of hybrids indicates that it does not carry a mutation in the HLA region. It has previously been reported that somatic cell hybrids with Daudi, which contain chromosome 15, do not express human beta2 microglobulin. These results suggest that the reason for the lack of HLA-A and B antigens on Daudi is a secondary effect due to the mutation(s) in the beta2 microglobulin gene.
Design and evaluation of spoken dialog systems (2002)

Interactive spoken dialog systems extend the range of automated telecommunication services beyond simple limited-choice form-filling applications to goal-directed tasks covering richer, more complex domains. Creating effective and efficient dialog systems requires not only accurate and robust speech recognition and language modeling, but also iterative, principled design of the user interface (UI), coupled with system evaluation with real users. This paper focusses on the design and evaluation of spoken dialog systems, first discussing how general UI principles that are well-understood for graphical UIs are also relevant for spoken language interfaces, and then describing the PARADISE framework for evaluating spoken dialog systems.
Semantic Image Browser: Bridging Information Visualization with Automated Intelligent Image Analysis (2006)

Browsing and retrieving images from large image collections are becoming common and important activities. Semantic image analysis techniques, which automatically detect high level semantic contents of images for annotation, are promising solutions toward this problem. However, few efforts have been made to convey the annotation results to users in an intuitive manner to enable effective image browsing and retrieval. There is also a lack of methods to monitor and evaluate the automatic image analysis algorithms due to the high dimensional nature of image data, features, and contents. In this paper, we propose a novel, scalable semantic image browser by applying existing information visualization techniques to semantic image analysis. This browser not only allows users to effectively browse and search in large image databases according to the semantic content of images, but also allows analysts to evaluate their annotation process through interactive visual exploration. The major visualization components of this browser are multi-dimensional scaling (MDS) based image layout, the value and relation (VaR) display that allows effective high dimensional visualization without dimension reduction, and a rich set of interaction tools such as search by sample images and content relationship detection. Our preliminary user study showed that the browser was easy to use and understand, and effective in supporting image browsing and retrieval tasks
THE NATIONWIDE NOSOCOMIAL INFECTION RATE (1985)

From a random sample of patients and hospitals and extrapolation ratios derived from the best available sources of data, the authors estimate that the nationwide nosocomial infection rate among the 6,449 acute-care US hospitals in 1975-1976 was 5.7 nosocomial infections per 100 admissions and that over 2 million nosocomial infections occurred in a 12-month period in these hospitals. Nosocomial urinary tract infections constituted 42% of the infections, surgical wound infections 24%, nosocomial pneumonia 10%, nosocomial bacteremia 5%, and nosocomial infections at all other sites 19%. If adjustments are made for the accuracy of the diagnostic method, the increasing nationwide secular trend, and the number of nosocomial infections in nursing homes, however, as many as 4 million nosocomial infections per year may now be occurring. This greatly exceeds previous estimates and calls for timely and accurate vital statistics on the problem.
The hem of the embryonic cerebral cortex is defined by the expression of multiple Wnt genes and is compromised in Gli3-deficient mice (1998)

In the developing vertebrate CNS, members of the Wnt gene family are characteristically expressed at signaling centers that pattern adjacent parts of the neural tube. To identify candidate signaling centers in the telencephalon, we isolated Wnt gene fragments from cDNA derived from embryonic mouse telencephalon. In situ hybridization experiments demonstrate that one of the isolated Wnt genes, Wnt7a, is broadly expressed in the embryonic telencephalon. By contrast, three others, Wnt3a, 5a and a novel mouse Wnt gene, Wnt2b, are expressed only at the medial edge of the telencephalon, defining the hem of the cerebral cortex. The Wnt-rich cortical hem is a transient, neuron-containing, neuroepithelial structure that forms a boundary between the hippocampus and the telencephalic choroid plexus epithelium (CPe) throughout their embryonic development. Indicating a close developmental relationship between the cortical hem and the CPe, Wnt gene expression is upregulated in the cortical hem both before and just as the CPe begins to form, and persists until birth. In addition, although the cortical hem does not show features of differentiated CPe, such as expression of transthyretin mRNA, the CPe and cortical hem are linked by shared expression of members of the Bmp and Msx gene families. In the extra-toesJ (XtJ) mouse mutant, telencephalic CPe fails to develop. We show that Wnt gene expression is deficient at the cortical hem in XtJ/XtJ mice, but that the expression of other telencephalic developmental control genes, including Wnt7a, is maintained. The XtJ mutant carries a deletion in Gli3, a vertebrate homolog of the Drosophila gene cubitus interruptus (ci), which encodes a transcriptional regulator of the Drosophila Wnt gene, wingless. Our observations indicate that Gli3 participates in Wnt gene regulation in the vertebrate telencephalon, and suggest that the loss of telencephalic choroid plexus in XtJ mice is due to defects in the cortical hem that include Wnt gene misregulation.
Antibodies against human neutrophil LECAM-1 (LAM-1/Leu-8/DREG-56 antigen) and endothelial cell ELAM-1 inhibit a common CD18-independent adhesion pathway in vitro (1991)

Neutrophil adhesion to interleukin-1 (IL-1)-stimulated human umbilical vein endothelial cells (HUVEC) involves the CD18 family of leukocyte integrins (lymphocyte function-associated antigen-1 [LFA-1], Mac-1, and p150,95) and LECAM-1 (DREG-56/LEU-8/LAM-1 antigen) on neutrophils and intercellular adhesion molecule-1 (ICAM-1) and endothelial leukocyte adhesion molecule-1 (ELAM-1) on the endothelium. In this study, we compare CD18-independent adhesion pathways mediated by neutrophil LECAM- 1 and endothelial ELAM-1 and find that these two pathways overlap in a variety of assays: (1) anti-LECAM-1 and anti-ELAM-1 monoclonal antibody (MoAb) inhibit neutrophil binding to HUVEC, and the inhibitory effect is not additive; (2) anti-LECAM-1 MoAb, like anti-ELAM-1 MoAb, inhibits neutrophil binding to HUVEC stimulated for 3 hours with IL-1, but not to HUVEC stimulated for 8 hours, by which time ELAM-1 expression is downregulated; (3) anti-ELAM-1 MoAb has no effect on transendothelial migration, a CD18-dependent, LECAM-1-independent neutrophil function. Interestingly, anti-ELAM MoAb has a reduced but significant inhibitory effect on the adhesion of activated neutrophils that have shed their cell-surface LECAM-1. We also show that neutrophil binding to ELAM-1- transfected L cells is inhibited not only by anti-ELAM-1 but also by anti-LECAM-1 MoAb. These results suggest that LECAM-1 and ELAM-1 can operate in the same adhesion pathway, possibly as a receptor- counterreceptor pair. LECAM-1 and ELAM-1 are likely to interact with other ligands as well, perhaps through carbohydrate determinants that modify more than one glycoprotein.