gebhart/patrepeval huggingface dataset:
An Antimicrobial Stewardship Program’s Impact with Rapid Polymerase Chain Reaction Methicillin‐ResistantStaphylococcus aureus/S. aureusBlood Culture Test in Patients withS. aureusBacteremia (2010)

Rapid organism detection of Staphylococcus aureus bacteremia and communication to clinicians expedites antibiotic optimization. We evaluated clinical and economic outcomes of a rapid polymerase chain reaction methicillin‐resistant S. aureus/S. aureus blood culture test (rPCR). This single‐center study compared inpatients with S. aureus bacteremia admitted from 1 September 2008 through 31 December 2008 (pre‐rPCR) and those admitted from 10 March 2009 through 30 June 2009 (post‐rPCR). An infectious diseases pharmacist was contacted with results of the rPCR; effective antibiotics and an infectious diseases consult were recommended. Multivariable regression assessed clinical and economic outcomes of the 156 patients. Mean time to switch from empiric vancomycin to cefazolin or nafcillin in patients with methicillin‐susceptible S. aureus bacteremia was 1.7 days shorter post‐rPCR (P = .002). In the post‐rPCR methicillin‐susceptible and methicillin‐resistant S. aureus groups, the mean length of stay was 6.2 days shorter (P = .07) and the mean hospital costs were $21,387 less (P = .02). rPCR allows rapid differentiation of S. aureus bacteremia, enabling timely, effective therapy and is associated with decreased length of stay and health care costs.
Measuring Alertness (2008)

A generation of research in cognitive psychology has given rise to many tasks that tap at various aspects of attention. It is now widely agreed that attention is not a single thing and that its measurement needs a strategy to study each of its various aspects. While there is no widely agreed taxonomy of attentional operations, there is an important distinction between functions of obtaining and maintaining the alert state (alerting network), orienting to sensory events (orienting network), and regulating thoughts and behaviors (executive network). Neuroimaging has confirmed that these functions involve separate but overlapping areas of brain activity. Neurochemical and genetic studies have also provided some distinctions between brain networks involved in attention. Alertness as a function of one important attentional network is emphasized and methods to activate phasic and tonic alerting are reviewed and individual or group differences in the efficiency of network operations are discussed.
Axonal Regeneration and Functional Recovery after Complete Spinal Cord Transection in Rats by Delayed Treatment with Transplants and Neurotrophins (2001)

Little axonal regeneration occurs after spinal cord injury in adult mammals. Regrowth of mature CNS axons can be induced, however, by altering the intrinsic capacity of the neurons for growth or by providing a permissive environment at the injury site. Fetal spinal cord transplants and neurotrophins were used to influence axonal regeneration in the adult rat after complete spinal cord transection at a midthoracic level. Transplants were placed into the lesion cavity either immediately after transection (acute injury) or after a 2-4 week delay (delayed or chronic transplants), and either vehicle or neurotrophic factors were administered exogenously via an implanted minipump. Host axons grew into the transplant in all groups. Surprisingly, regeneration from supraspinal pathways and recovery of motor function were dramatically increased when transplants and neurotrophins were delayed until 2-4 weeks after transection rather than applied acutely. Axonal growth back into the spinal cord below the lesion and transplants was seen only in the presence of neurotrophic factors. Furthermore, the restoration of anatomical connections across the injury site was associated with recovery of function with animals exhibiting plantar foot placement and weight-supported stepping. These findings suggest that the opportunity for intervention after spinal cord injury may be greater than originally envisioned and that CNS neurons with long-standing injuries can reinitiate growth, leading to improvement in motor function.
Adaptive Graph Cut Based Binarization of Video Text Images (2012)

Interactive image segmentation which needs the user to give certain hard constraints has shown promising performance for object segmentation. In this paper, we consider characters in text image as a special kind of object, and propose an adaptive graph cut based text binarization method to segment text from background. The main contributions of the paper lie in: 1) in order to make the binarization local adaptive with uneven background, the text region image is firstly roughly split into several sub-images on which graph cut is applied, and 2) considering the unique characteristics of the text, we propose to automatically classify some pixels as text or background with high confidence, severed as hard constraints seeds for graph cut to extract text from background by spreading the seeds into the whole sub-image. The experimental results show that our approach could get better performance in both character extraction accuracy and recognition accuracy.
Preparation of Mixed Self-Assembled Monolayers (SAMs) That Resist Adsorption of Proteins Using the Reaction of Amines with a SAM That Presents Interchain Carboxylic Anhydride Groups (2000)

This paper describes a procedure for preparing mixed self-assembled monolayers (mixed SAMs) on gold that resist the nonspecific adsorption of proteins from solution. This method was tested using α-amino derivatives of ω-hydroxy- and ω-methoxy-oligo(ethylene glycols): H2N(CH2CH2O)nCH3 and H2N(CH2CH2O)nH (n = 3, 6). Mixed SAMs were prepared by allowing these amines to react with a SAM presenting interchain carboxylic anhydride groups. The resistance of the resulting surfaces to adsorption of several proteinscarbonic anhydrase (EC 4.2.1.1), ribonuclease A (EC 3.1.27.5), lysozyme (EC 3.2.1.17), and fibrinogenwas examined using surface plasmon resonance (SPR) spectroscopy. These mixed SAMs resist the nonspecific adsorption of proteins approximately as effectively as single-component SAMs prepared using the conventional method involving chemisorption of oligo(ethylene glycol)-terminated alkanethiols on gold. Characterization of the mixed SAM that presents a 1:1 mixture of −OCNH(CH2CH2O)6CH3 and CO2H/CO2- groups by polarized infrared external reflectance spectroscopy indicates that the ethylene glycol units are in an amorphous conformation. A model surface for use in studies of biospecific adsorption was synthesized by reacting the anhydride groups with a mixture of H2N(CH2CH2O)6H and H2N(CH2CH2O)6CH2CONH(CH2)6NHCOC6H4SO2NH2; the resulting system was examined for its ability to bind bovine carbonic anhydrase by SPR. The values of the relevant constants were koff = 0.0054 s-1, kon = 13 000 M-1 s-1, and Kd = 0.42 μM. These values agree with values obtained by other means. The reaction of amines with SAMs that present interchain carboxylic anhydrides provides an experimentally simple route to the formation of mixed SAMs that resist the nonspecific adsorption of proteins or that adsorb a protein of interest biospecifically.
A Study of the Immunological Response to Tumor Ablation with Irreversible Electroporation (2007)

Immune cell recruitment during the treatment of sarcoma tumors in mice with irreversible electroporation was studied by immunohistochemistry. Irreversible electroporation is a non-thermal tissue ablation technique in which certain short duration electrical fields are used to permanently permeabilize the cell membrane, presumably through the formation of nanoscale defects in the membrane. Employing irreversible electroporation parameters known to completely ablate the tumors without thermal effects we did not find infiltration of immune cells probably because of the destruction of infiltration routes. We confirm here that immune response is not instrumental in irreversible electroporation efficacy, and we propose that irreversible electroporation may be, therefore, a treatment modality of interest to immunodepressed cancer patients.
ALX148 blocks CD47 and enhances innate and adaptive antitumor immunity with a favorable safety profile (2018)

CD47 is a widely expressed cell surface protein that functions as an immune checkpoint in cancer. When expressed by tumor cells, CD47 can bind SIRPα on myeloid cells, leading to suppression of tumor cell phagocytosis and other innate immune functions. CD47-SIRPα signaling has also been implicated in the suppression of adaptive antitumor responses, but the relevant cellular functions have yet to be elucidated. Therapeutic blockade of the CD47 pathway may stimulate antitumor immunity and improve cancer therapy. To this end, a novel CD47-blocking molecule, ALX148, was generated by fusing a modified SIRPα D1 domain to an inactive human IgG1 Fc. ALX148 binds CD47 from multiple species with high affinity, inhibits wild type SIRPα binding, and enhances phagocytosis of tumor cells by macrophages. ALX148 has no effect on normal human blood cells in vitro or on blood cell parameters in rodent and non-human primate studies. Across several murine tumor xenograft models, ALX148 enhanced the antitumor activity of different targeted antitumor antibodies. Additionally, ALX148 enhanced the antitumor activity of multiple immunotherapeutic antibodies in syngeneic tumor models. These studies revealed that CD47 blockade with ALX148 induces multiple responses that bridge innate and adaptive immunity. ALX148 stimulates antitumor properties of innate immune cells by promoting dendritic cell activation, macrophage phagocytosis, and a shift of tumor-associated macrophages toward an inflammatory phenotype. ALX148 also stimulated the antitumor properties of adaptive immune cells, causing increased T cell effector function, pro-inflammatory cytokine production, and a reduction in the number of suppressive cells within the tumor microenvironment. Taken together, these results show that ALX148 binds and blocks CD47 with high affinity, induces a broad antitumor immune response, and has a favorable safety profile.
Expression of Tumor‐rejection Antigens in Gynecologic Cancers (2000)

We recently reported the four tumor-rejection antigens (SART1(259), SART2, SART3, and ART4) that possess tumor epitopes capable of inducing HLA-A2402-restricted cytotoxic T lymphocytes (CTLs) in cancer patients. This study investigated the expression of these tumor antigens in gynecologic cancers, including 33 ovarian cancers, 38 cervical cancers, and 40 endometrial cancers. SART1(259) antigen was detected in 56%, 35%, and 30% of ovarian, cervical and endometrial cancers, while SART2 antigen was detected in 46%, 66%, and 30% of these cancers, respectively. Both SART3 and ART4 antigens were detectable in the majority of these gynecologic cancers tested. In contrast, none of these antigens was detectable in any of the normal ovarian and uterine tissues tested. Peripheral blood mononuclear cells (PBMCs) of HLA-A24(+) patients with gynecologic cancers were found to produce significant levels of interferon-gamma in response to HLA-A24(+) SART3(+) gynecologic cancer cells after having been stimulated three times in vitro with either SART3(109 - 118) or SART3(315 - 323) peptide. These PBMCs lysed HLA-A24(+) SART3(+) gynecologic cancer cells, but not HLA-A24(-) SART3(+) gynecologic cancer cells or HLA-A24(+) normal cells. Therefore, these four antigens and their peptides, including SART3 peptides, would be appropriate molecules for use in specific immunotherapy of HLA-A24(+) gynecologic cancer patients.
Molecular Biology of Osmoregulation (1984)

The drought of 1983 resulted in some 10 billion dollars in agricultural losses and has focused attention on the vulnerability of our major crops to this devastating form of environmental stress. This article is concerned with the molecular biology of a new class of genes, called osm (osmotic tolerance) genes, that protect bacteria like Escherichia coli against osmotic stress and may work in a similar manner in plants and animals. Osm genes govern the production of a class of molecules, such as betaine and proline, that protect the cell and its constituents against dehydration. These osmoprotectant molecules have been known for many years to accumulate in plants but have only recently been shown to have potent antistress activity for bacteria.
Eyelash Removal Method for Human Iris Recognition (2006)

A novel eyelash removal method for preprocessing of human iris images in a human iris recognition system is presented. The method filters each occluded pixel along an axis perpendicular to the eyelash direction, and accepts the filtered value if it changes by more than a certain threshold. This allows partially occluded regions of the iris to be included in iris coding which would previously have been excluded. The method is applied with three iris coding algorithms on an extended 308 class CASIA database and large improvements are shown in the matching performance of two methods, with a modest improvement in the third.
Cloning, Characterization, and Transcription of Three Laccase Genes from Gaeumannomyces graminis var. tritici , the Take-All Fungus (2002)

Gaeumannomyces graminis var. tritici, a filamentous ascomycete, is an important root pathogen of cereals that causes take-all disease and results in severe crop losses worldwide. Previously we identified a polyphenol oxidase (laccase) secreted by the fungus when induced with copper. Here we report cloning and partial characterization of three laccase genes (LAC1, LAC2, and LAC3) from G. graminis var. tritici. Predicted polypeptides encoded by these genes had 38 to 42% amino acid sequence identity and had conserved copper-binding sites characteristic of laccases. The sequence of the LAC2 predicted polypeptide matched the N-terminal sequence of the secreted laccase that we purified in earlier studies. We also characterized expression patterns of these genes by reverse transcription-PCR. LAC1 was transcribed constitutively, and transcription of LAC2 was Cu inducible. All three genes were transcribed in planta; however, transcription of LAC3 was observed only in planta or in the presence of host (wheat) plant homogenate.
Subclinical Hypothyroidism Is an Independent Risk Factor for Atherosclerosis and Myocardial Infarction in Elderly Women: The Rotterdam Study (2000)

Subclinical hypothyroidism is a strong indicator of risk for atherosclerosis and myocardial infarction in elderly women.
Safety and Efficacy of an Injectable Extracellular Matrix Hydrogel for Treating Myocardial Infarction (2013)

New therapies are needed to prevent heart failure after myocardial infarction (MI). As experimental treatment strategies for MI approach translation, safety and efficacy must be established in relevant animal models that mimic the clinical situation. We have developed an injectable hydrogel derived from porcine myocardial extracellular matrix as a scaffold for cardiac repair after MI. We establish the safety and efficacy of this injectable biomaterial in large- and small-animal studies that simulate the clinical setting. Infarcted pigs were treated with percutaneous transendocardial injections of the myocardial matrix hydrogel 2 weeks after MI and evaluated after 3 months. Echocardiography indicated improvement in cardiac function, ventricular volumes, and global wall motion scores. Furthermore, a significantly larger zone of cardiac muscle was found at the endocardium in matrix-injected pigs compared to controls. In rats, we establish the safety of this biomaterial and explore the host response via direct injection into the left ventricular lumen and in an inflammation study, both of which support the biocompatibility of this material. Hemocompatibility studies with human blood indicate that exposure to the material at relevant concentrations does not affect clotting times or platelet activation. This work therefore provides a strong platform to move forward in clinical studies with this cardiac-specific biomaterial that can be delivered by catheter.
Deep Sequencing of the Vaginal Microbiota of Women with HIV (2010)

Illumina based microbial profiling enabled high though-put analyses of microbial samples at a high phylogenetic resolution. The vaginal microbiota among women living with HIV in Sub-Saharan Africa constitutes several profiles associated with a normal microbiota or BV. Recurrence of BV frequently constitutes a different BV-associated profile than before antibiotic treatment.
Characterization and immunoassay of human tumor-associated galactosyltransferase isoenzyme II. (1988)

Galactosyltransferase (GT) (EC 2.4.1.38) was purified to homogeneity from human ovarian tumor effusion fluid and normal human serum by chromatography on alpha-lactalbumin and anti-human immunoglobulin affinity (to selectively absorb contaminating IgG) columns. Both preparations showed a single, broad band on sodium dodecyl sulfate-polyacrylamide gel electrophoresis centered at a molecular weight of 48,000, but nondenaturing polyacrylamide gel electrophoresis of GT isolated from tumor effusion fluid revealed the presence of a series of oligomeric proteins possessing GT activity, which were barely detectable in normal human serum. Sodium dodecyl sulfate-polyacrylamide gel electrophoresis of N-glycanase- and O-glycanase-treated GT revealed that each endoglycanase removed carbohydrate with an approximate molecular weight of 3,000, revealing the presence of both N-linked and O-linked oligosaccharide substitutions on GT. Purified GT (containing a mixture of GT isoenzymes) was used to immunize BALB/c mice for monoclonal antibody (MAb) preparation. Four of the MAb isolated reacted with GT. MAb 3872 (patent pending; an IgG1) was determined to be specific for a cancer-associated GT isoenzyme (GT-II) by immunostaining of Western blots and nondenaturing polyacrylamide gel electrophoresis of GT specifically eluted from a MAb 3872 affinity column. Two 125I-labeled cyanogen bromide peptides (Mr 8,400 and 7,400) prepared from 125I-GT were specifically bound and eluted from a MAb 3872 affinity column, demonstrating that the MAb 3872 GT-II-specific antigenic epitope resides on these peptides. MAb 3872 was immobilized on 1,1'-carbonyldiimidazole-activated trisacryl GF-2000 and used to specifically assay serum GT-II levels in 29 individual normal human serum samples and 77 serum samples from 38 patients with advanced ovarian tumors. The normal serum GT-II level was found to be 85.3 +/- 30.9 milliunits/ml, with a range of 17 to 160 milliunits/ml. Of the 38 tumor patients, 33 showed GT-II values in excess of 200 milliunits/ml, with a range of 216 to 8,469 milliunits/ml. Serial samples obtained from the ovarian tumor patients suggested that the serum GT-II level reflected the tumor burden of the patient.
Speculative multithreaded processors (2001)

Speculation will overcome the limitations in dividing a single program into multiple threads that can execute on the multiple logical processing elements needed to enhance performance through parallelization.
Recognition and Prevention of Tumor Metastasis by the NK Receptor NKp46/NCR1 (2012)

NK cells employ a variety of activating receptors to kill virally infected and tumor cells. Prominent among these receptors are the natural cytotoxicity receptors (NCRs) (NKp30, NKp44, and NKp46), of which only NKp46 has a mouse ortholog (NCR1). The tumor ligand(s) of NKp46/NCR1 is still unknown, but it was shown that the human NKp46 and the mouse NCR1 are involved in tumor eradication both in vitro and in vivo. Whether any of the NK activating receptors is involved in the prevention of tumor metastasis is unknown. To address this question, we studied the activity of the NK cell receptor NKp46/NCR1 in two spontaneous metastasis models, the B16F10.9 melanoma (B16) and the Lewis lung carcinoma (D122) in the NCR1 knockout mouse that was generated by our group, in various in vitro and in vivo assays. We demonstrated that all B16 and D122 tumors, including those generated in vivo, express an unknown ligand(s) for NKp46/NCR1. We have characterized the properties of the NKp46/NCR1 ligand(s) and demonstrated that NKp46/NCR1 is directly involved in the killing of B16 and D122 cells. Importantly, we showed in vivo that NKp46/NCR1 plays an important role in controlling B16 and D122 metastasis. Thus, to our knowledge, in this study we provide the first evidence for the direct involvement of a specific NK killer receptor in preventing tumor metastasis.
Post-challenge hyperinsulinaemia rather than hyperglycaemia is associated with the severity of coronary artery disease in patients without a previous diagnosis of diabetes mellitus (2005)

Patients with CAD without a previous diagnosis of DM had a high prevalence of abnormal glucose tolerance. Post-challenge hyperinsulinaemia was associated with the number of diseased coronary arteries and the presence of previous MI. The insulin response to the glucose challenge test requires further investigation as a potential risk factor for CAD and a potential target for intervention.
Cell transformation by the epidermal growth factor receptor and v-erbB. (1991)

It has become increasingly apparent that growth factor receptors can function as oncogenic proteins and play causal roles in cell transformation. A prime example is the epidermal growth factor receptor (EGFR), which belongs to the ligand-activated tyrosine kinase receptor family and is overexpressed in certain human tumors. The transforming gene of avian erythroblastosis virus, v-erbB, encodes a truncated form of the EGFR whose kinase domain is constitutively activated by deletion of the ligand binding domain. Recent comparative studies of the v-erbB gene in different viral isolates have revealed that subtle sequence changes (point mutations, small deletions) can alter both the pathogenic spectrum of the virus and the range of cell types susceptible to transformation in vitro. Therefore, the possibility exists that similar, as-yet-unidentified, mutations may exist in the EGFR gene; if so, the EGFR may be an oncogenic factor in tumors other than those with which it has been associated to date.
The Use of Althesin in Drug‐Resistant Status Epilepticus (1979)

The properties of Althesin (anticonvulsant activity, depression of oxygen consumption, lowering of ICP, rapid excretion) led us to use this steroid combination to treat 11 patients in status epilepticus resistant to the standard drugs (benzodiazepines and barbiturates). The administration of Althesin by slow intravenous injection was ineffective in 2 of the 3 patients thus treated. The doses used (2--10 ml) were probably too small. One only administration of a 10% solution of Althesin in 10% fructose by intravenous drip (the rate was calculated so as to obtain the burst suppression stage at the EEG) stopped status epilepticus in 7 of the 9 patients thus treated. In this group the doses used varied from 25 to 50 ml. The 2 patients in whom it was necessary to repeat Althesin administration and combine it with other drugs had both been operated on for severe brain injuries involving marked cerebral edema. In spite of the very small number of cases, the definitive arrest of status epilepticus obtained in 8 out of 11 patients first treated with other drugs is encouraging: Althesin probably may be regarded as an adjunct in the treatment of status epilepticus.
Pd/C-Catalyzed Chemoselective Hydrogenation in the Presence of Diphenylsulfide (2006)

[Structure: see text] A Pd/C-catalyzed chemoselective hydrogenation using diphenylsulfide as a catalyst poison has been developed. This methodology selectively hydrogenates olefin and acetylene functionalities without hydrogenolysis of aromatic carbonyls and halogens, benzyl esters, and N-Cbz protective groups.