gebhart/patrepeval huggingface dataset:
In-depthN-glycome profiling of paired colorectal cancer and non-tumorigenic tissues reveals cancer-, stage- and EGFR-specific protein N-glycosylation (2015)

Glycomics may assist in uncovering the structure-function relationships of protein glycosylation and identify glycoprotein markers in colorectal cancer (CRC) research. Herein, we performed label-free quantitative glycomics on a carbon-liquid chromatography-tandem mass spectrometry-based analytical platform to accurately profile the N-glycosylation changes associated with CRC malignancy. N-Glycome profiling was performed on isolated membrane proteomes of paired tumorigenic and adjacent non-tumorigenic colon tissues from a cohort of five males (62.6 ± 13.1 y.o.) suffering from colorectal adenocarcinoma. The CRC tissues were typed according to their epidermal growth factor receptor (EGFR) status by western blotting and immunohistochemistry. Detailed N-glycan characterization and relative quantitation identified an extensive structural heterogeneity with a total of 91 N-glycans. CRC-specific N-glycosylation phenotypes were observed including an overrepresentation of high mannose, hybrid and paucimannosidic type N-glycans and an under-representation of complex N-glycans (P < 0.05). Sialylation, in particular α2,6-sialylation, was significantly higher in CRC tumors relative to non-tumorigenic tissues, whereas α2,3-sialylation was down-regulated (P < 0.05). CRC stage-specific N-glycosylation was detected by high α2,3-sialylation and low bisecting β1,4-GlcNAcylation and Lewis-type fucosylation in mid-late relative to early stage CRC. Interestingly, a novel link between the EGFR status and the N-glycosylation was identified using hierarchical clustering of the N-glycome profiles. EGFR-specific N-glycan signatures included high bisecting β1,4-GlcNAcylation and low α2,3-sialylation (both P < 0.05) relative to EGFR-negative CRC tissues. This is the first study to correlate CRC stage and EGFR status with specific N-glycan features, thus advancing our understanding of the mechanisms causing the biomolecular deregulation associated with CRC.
Long-term marrow culture of cells from patients with acute myelogenous leukemia. Selection in favor of normal phenotypes in some but not all cases. (1985)

Long-term cultures were initiated with leukemic marrow aspirate cells from each of 13 newly diagnosed acute myelogenous leukemia (AML) patients. Initial assessment of the clonogenic potential of the marrow suggested that normal hemopoietic progenitors were reduced in most cases and progenitors of abnormal colonies and clusters were present in 10 cases. Subsequent assays of both nonadherent and adherent fractions of long-term cultures revealed two patterns of progenitor cell behavior. The most common pattern (nine cases) featured the detection after 1-4 wk of near normal numbers of typical erythroid, granulopoietic, and mixed colony-forming progenitor cells. Progenitors of abnormal (blast) colonies and clusters initially demonstrable in eight of these nine cases were, in these cases, not sustained in long-term culture and could not be found after 4 wk. Conversion to cytogenetic normalcy in long-term culture was confirmed in two experiments in this group. The second pattern (four cases) was characterized by the failure of progenitors capable of normal differentiation to become detectable in long-term cultures, and the concomitant maintenance of blast progenitors in the two cases in this group where such cells were initially demonstrable. Although progenitors capable of producing abnormal (blast) colonies or clusters in methylcellulose were not detected in either of the other two experiments, the maintenance for 6 wk of a hypercellular nonadherent blast population in one of these suggested the persisting activity of an "adherent layer-dependent" leukemic progenitor cell. Taken together, these findings indicate a strong correlation between the presence of leukemic blasts and their progenitors and a decreased level of normal hemopoiesis. In addition, the failure of leukemic cells to be maintained in long-term marrow cultures from some (but not all) AML patients suggests new applications of this methodology for studies of early stages of leukemic cell development.
Electrochemistry of Sulfur Adlayers on the Low-Index Faces of Silver (1996)

The formation and reactivity of sulfur adlayers on single-crystal Ag electrodes ((111), (110), and (100) orientations) in aqueous solutions (pH = 13) containing HS- are reported. Oxidative adsorption of HS- (Ag + HS- → AgSH + e-) occurs on all three low-index surfaces at potentials ranging between −0.5 and −0.7 V of the thermodynamic value for bulk Ag2S formation. Voltammetric and electrochemical quartz crystal measurements demonstrate that the resulting AgSH adlayer undergoes a second one-electron oxidation (AgSH + Ag + OH- → Ag2S + H2O + e-) at the (111) and (110) surfaces prior to bulk Ag2S formation, yielding an underpotential deposited Ag2S adlayer (surface coverages (S/Ag): θAg(111) = 0.46 ± 0.02 and θAg(110) = 0.54 ± 0.03). In contrast, the AgSH adlayer on Ag(100) is chemically inert prior to bulk Ag2S formation. Structural models indicate that the formation of a nearly stoichiometric Ag2S adlayer (i.e., θ ∼ 0.5) is feasible on the (111) and (110) surfaces without significant reconstruction of the outermost atomic layers of the substrate, but not on the (100) surface. The results suggest that the formation of a Ag2S monolayer is allowed only when the number density of S and Ag atoms at the interface is nearly coincident with the reaction stoichiometry.
Vascular targeting agents enhance chemotherapeutic agent activities in solid tumor therapy (2002)

The utility of combining the vascular targeting agents 5,6-dimethyl-xanthenone-4 acetic acid (DMXAA) and combretastatin A-4 disodium phosphate (CA4DP) with the anticancer drugs cisplatin and cyclophosphamide (CP) was evaluated in experimental rodent (KHT sarcoma), human breast (SKBR3) and ovarian (OW-1) tumor models. Doses of the vascular targeting agents that led to rapid vascular shutdown and subsequent extensive central tumor necrosis were identified. Histologic evaluation showed morphologic damage of tumor cells within a few hours after treatment, followed by extensive hemorrhagic necrosis and dose-dependent neoplastic cell death as a result of prolonged ischemia. Whereas these effects were induced by a range of CA4DP doses (10-150 mg/kg), the dose response to DMXAA was extremely steep; doses < or = 15 mg/kg were ineffective and doses > or = 20 mg/kg were toxic. DMXAA also enhanced the tumor cell killing of cisplatin, but doses > 15 mg/kg were required. In contrast, CA4DP increased cisplatin-induced tumor cell killing at all doses studied. This enhancement of cisplatin efficacy was dependent on the sequence and interval between the agents. The greatest effects were achieved when the vascular targeting agents were administered 1-3 hr after cisplatin. When CA4DP (100 mg/kg) or DMXAA (17.5 mg/kg) were administered 1 hr after a range of doses of cisplatin or CP, the tumor cell kill was 10-500-fold greater than that seen with chemotherapy alone. In addition, the inclusion of the antivascular agents did not increase bone marrow stem cell toxicity associated with these anticancer drugs, thus giving rise to a therapeutic gain.
Axillary hidradenitis suppurativa successfully treated with infliximab in a Crohn's disease patient (2002)

Axillary hidradenitis suppurativa successfully treated with infliximab in a Crohn's disease patient
Double-stranded RNA-dependent protein kinase activates transcription factor NF-kappa B by phosphorylating I kappa B. (1994)

The induction of interferon (IFN) genes by viruses or double-stranded RNA (dsRNA) requires the assembly of a complex set of transcription factors on responsive DNA elements of IFN gene promoters. One of the factors necessary for regulating IFN-beta gene transcription is nuclear factor NF-kappa B, the activation of which is triggered by dsRNA. It has previously been suggested that the dsRNA-activated p68 protein kinase (PKR) may act as an inducer-receptor, transducing the signal from dsRNA to NF-kappa B through phosphorylation of the inhibitor I kappa B. We present direct evidence that PKR can phosphorylate I kappa B-alpha (MAD-3) and activate NF-kappa B DNA binding activity in vitro. We further show that dsRNA induces an unusual phosphorylated form of I kappa B-alpha. The expression of a transdominant mutant PKR is able to perturb the dsRNA-mediated signaling pathway in vivo, suggesting a role for this kinase in IFN-beta gene induction.
On Terrorism: Reflections on Violence and The Outlaw (1994)

Scarcely a week goes by without at least one terrorist related incident making the headlines. The subject of terrorism has, meanwhile, engendered a vast and growing expert literature. Much of this vast body of literature is pragmatic in nature, in the sense that the authors are concerned with developing policy proposals. They present and analyze the problem of terrorism and then promote what they think is the appropriate response to terrorists-a response that often involves changing the legal framework. The bulk of what I call "terrorism literature" is produced in the "West." For the most part, it is written from the perspective of terrorism as a threat to western liberal democracies. For purposes of this paper, I have limited my inquiry to such literature and to terrorism as a western phenomenon. I am interested in exploring the repetition of rhetorical structures in terrorism literature and their reproduction in media reports of terrorist incidents. The choice of focus was dictated by the belief that terrorism is not just an objective "something" out there to be located with a telescope and examined with a microscope, but that it is also, less obviously, a creation or by-product of western liberal democracies; that it is intimately linked with the self-image or self-understanding of western liberal democracies.
An Accurate, Clinically Practical System For Spatial Vectorcardiography (1956)

This paper describes a news improved system of spatial vectorcardiography that is practical for clinical use. It represents an optimum compromise among such factors as soundness of theoretic basis, accuracy, reproducibility, signal-to-noise ratio, and speed of application. Some of its advantages over currently employed systems include a rational physical basis, corrections for torso shape, avoidance of left arm, insensitivity to individual variability of ventricle location, and accuracy comparable to applicability of 3-dimensional torso-model data to the human subject. Detailed description of electrode placement, practical procedures, and useful technics is included.
Glucagon-like Peptide-1, AGastrointestinalHormone with aPharmaceutical Potential (1999)

Glucagon-like peptide-1 (GLP-1) is an insulinotropic hormone secreted from endocrine cells in the gut mucosa in response to meal ingestion. It is an important incretin hormone; mice with a null mutation in the GLP-1 receptor gene develop glucose intolerance. In addition, it inhibits gastrointestinal secretion and motility and is thought to be part of the "ileal brake" mechanism. Perhaps because of the latter actions it inhibits food intake, but intracerebral injection of GLP-1 also inhibits food intake. The insu­ linotropic effect is preserved in patients with type 2 diabetes mellitus, in whom also glucagon secretion is inhibited. Thus upon iv GLP-1 infusion blood glucose may be completely normalised. Because its actions are glucose-dependent hypoglycaemia does not develop. However, GLP-1 is metabolised extremely rapidly in vivo, initially by a mechanism that involves the enzyme dipeptidyl peptidase-IV. It is currently being investigated how GLP-1 or analogues thereof can be employed in practical diabetes therapy. Promising solutions include the development of stable analogues and inhibitors of the degrading enzyme.
Reliability of estrogen receptors in predicting response to antiestrogens. (1997)

Fujii et al reported that Uracil potentiated the antitumor activity of fluorouracil (5-FU) and 1-(2-tetrahydrofuryl)-5-fluorouracil (tegafur). This effect was due to inhibition of the degradation of 5-FU, yet the phosphorylation of 5-FU was unaffected. The molar ratio of tegafur and uracil was 1:4, a combination that has since been widely prescribed in Japan for the treatment of cancer patients. We present here our experimental and clinical results when investigating the antineoplastic effects of this combination of drugs--known as UFT--and provide evidence that UFT is an effective treatment for patients with cancer.
Analytical framework for dynamic light pulse atom interferometry at short interrogation times (2011)

High-precision inertial sensing demonstrations with light pulse atom interferometry have typically used Raman pulses having durations orders of magnitude shorter than the dwell time between interferometer pulses. Environmentally robust sensors operating at high-bandwidth will be required to operate at short (millisecond scale) dwell times between Raman pulses. In such an operational mode, the Raman pulse duration becomes an appreciable fraction of the dwell time between pulses. In addition, high-precision inertial sensing applications have typically been demonstrated in mildly dynamic or nondynamic environments having low rate of change of inertial input, ensuring that applied Raman pulses satisfy the Raman resonance condition. Application of nonresonant pulses will be inevitable in sensors registering time-varying inertial input. We present a diagrammatic technique for calculation of atomic output state populations for multipulse atom optics manipulations that explicitly account for the effects of finite pulse duration and finite Raman detuning effects on the laser-induced atomic phase. We analyze several atom interferometer sequences. We report accelerometer and gyroscope phase evolution for fixed Raman laser frequency difference incorporating corrections in powers of the ratio of pulse duration to time interval between interferometer pulses. Our accelerometer result agrees with other published results.
A Unified Query-based Generative Model for Question Generation and Question Answering (2017)

We propose a query-based generative model for solving both tasks of question generation (QG) and question an- swering (QA). The model follows the classic encoder- decoder framework. The encoder takes a passage and a query as input then performs query understanding by matching the query with the passage from multiple per- spectives. The decoder is an attention-based Long Short Term Memory (LSTM) model with copy and coverage mechanisms. In the QG task, a question is generated from the system given the passage and the target answer, whereas in the QA task, the answer is generated given the question and the passage. During the training stage, we leverage a policy-gradient reinforcement learning algorithm to overcome exposure bias, a major prob- lem resulted from sequence learning with cross-entropy loss. For the QG task, our experiments show higher per- formances than the state-of-the-art results. When used as additional training data, the automatically generated questions even improve the performance of a strong ex- tractive QA system. In addition, our model shows bet- ter performance than the state-of-the-art baselines of the generative QA task.
Comparison between Ranitidine and Omeprazole for Protection against Gastroduodenal Damage Caused by Naproxen (1992)

Acute gastroduodenal injury is commonly associated with the use of nonsteroidal anti-inflammatory drugs. The mechanism of injury is not well understood. The objectives of this study were to evaluate the protective effect of two drugs that give different degrees of acid inhibition against naproxen-induced gastroduodenal injury. Fifteen volunteers aged 22-28 years underwent pre- and post-treatment gastroduodenoscopies during three treatment periods (that is, six examinations), and mucosal injury was graded on a Lanza scale ranging from 0 to 4. The subjects received placebo, 150 mg rantidine twice daily, or 40 mg omeprazole in a double-blind, random-order design for 7 days. Plain naproxen, 500 mg twice daily, was given on days 3-7. The mean injury score for the stomach during placebo treatment was 1.53, and ranitidine gave 44% and omeprazole 40% reduction compared with placebo, which did not reach statistical significance. About 70% of the stomach injury was located in the antrum. The mean injury score during placebo for the duodenum was 1.93, and ranitidine gave 80% and omeprazole 90% reduction (p = 0.004). In conclusion, a correlation between different degrees of acid suppression and a protective effect on the gastroduodenal mucosa could not be shown. The study suggests that acid plays a major role in acute naproxen-induced injury to the duodenal mucosa, and a moderate acid reduction is adequate for protection. In the stomach acid seems to play a minor role in the mucosal injury, but physiochemical contact with naproxen in the antrum and a cyclooxygenase inhibition are of greater importance.
First Clinical Application of the DuraHeart Centrifugal Ventricular Assist Device for a Japanese Patient (2009)

The DuraHeart ventricular assist device (VAD) is a third-generation implantable centrifugal pump with a magnetically levitated impeller. Since February 2007, the device has been clinically applied with excellent results as a bridge to heart transplantation in Europe. As of this writing, however, the device has yet to be approved by the Ministry of Health, Labour and Welfare for clinical use in Japan. We herein report the first clinical application of this device for a Japanese patient. A 31-year-old man with dilated cardiomyopathy was transferred to the Heart and Diabetes Center NRW (HDZ-NRW) in Bad Oeynhausen, Germany, where he was to await heart transplantation. The transfer was safely completed under management with low-dose dopamine. His condition gradually deteriorated at HDZ-NRW, and the DuraHeart left ventricular assist device was implanted for the left ventricle at 7 weeks after admission. Shortly thereafter, however, on POD 7, a Thoratec VAD had to be inserted on the right side due to refractory right heart failure. The right ventricular assist device could be explanted after a 3-month assist, and the patient is now waiting for heart transplantation at home in Germany.
Synthesis of podophyllotoxin and related analogues .9. Synthesis of ethylenedioxy and indan analogues of picropodophyllone and their antimitotic activity (1996)

Furo 3',4' : 6,7]-naphtho 2,3-e]-1, 4-dioxin-7-one-6, 6a-tetrahydro-10-one-6-phenyl (9) and furo 3', 4',:6, 7]-naphtho 2,3-d]-2,3-cyclopentenyl-6-one-5, 5a, 8, 8a-tetrahydro-9-one-5-phenyl (10) have been synthesised by bishydroxymethylation of tetralone acids (5 &amp; 6) using formaldehyde in alkali followed by Jones oxidation using chromium trioxide in sulphuric acid.
The influence of age and sex on the relationship between heart rate variability, haemodynamic variables and subjective measures of acute post-operative pain (2011)

Acute pain influences the sympathovagal balance. This response is significantly influenced by age and sex.
Porcine Reproductive and Respiratory Syndrome: NEB-1 PRRSV Infection did not Potentiate Bacterial Pathogens (1995)

A 2-phase study was conducted to evaluate the ability of the NEB-1 strain of porcine reproductive and respiratory syndrome virus (PRRSV) to potentiate common bacterial pathogens of swine. In phase I, 25 of 50 4-5-week-old specific-pathogen-free (SPF) pigs were exposed to NEB-1 PRRSV (day 0). Seven days after virus inoculation, 8 groups received 1 of 4 bacterial pathogens: Haemophilus parasuis, Streptococcus suis, Salmonella cholerasuis, and Pasteurella multocida. The ability of NEB-1 PRRSV to produce clinical disease, viremia, neutralizing antibody, gross and microscopic lesions and to potentiate bacterial pathogens was assessed. Response to NEB-1 PRRSV was similar among inoculated pigs; prolonged hyperthermia, lethargy, mild to moderate dyspnea, and cutaneous erythema were consistent clinical signs. No clinical differences were observed in groups after bacterial challenge. Virus was isolated from serum at weekly intervals through the end of the study, and all PRRSV-inoculated pigs had seroconverted by study termination. Two of 5 pigs died in non-PRRSV-inoculated groups challenged with H. parasuis and Streptococcus suis. Mortality in PRRSV-infected pigs was limited to 1 of 5 pigs from the Salmonella cholerasuis-challenged group. Gross lesions were seen in pigs dying after inoculation in H. parasuis- and Streptococcus suis-inoculated groups, in Salmonella cholerasuis- and P. multocida-challenged pigs, and in 1 non-PRRSV-inoculated control pig. Microscopic lesions consisted of mild to moderate proliferative interstitial pneumonia, nonsuppurative myocarditis, lymphoid hyperplasia, and nonsuppurative encephalitis in PRRSV-inoculated pigs. Findings in phase I indicated that NEB-1 PRRSV does not potentiate bacterial disease while inducing consistent clinical signs, viremia, seroconversion, and microscopic lesions.(ABSTRACT TRUNCATED AT 250 WORDS)
Chemical Genetic Control of Protein Levels:  Selective in Vivo Targeted Degradation (2004)

Genetic loss of function analysis is a powerful method for the study of protein function. However, some cell biological questions are difficult to address using traditional genetic strategies often due to the lack of appropriate genetic model systems. Here, we present a general strategy for the design and syntheses of molecules capable of inducing the degradation of selected proteins in vivo via the ubiquitin-proteasome pathway. Western blot and fluorometric analyses indicated the loss of two different targets: green fluorescent protein (GFP) fused with FK506 binding protein (FKBP12) and GFP fused with the androgen receptor (AR), after treatment with PROteolysis TArgeting Chimeric moleculeS (PROTACS) incorporating a FKBP12 ligand and dihydrotestosterone, respectively. These are the first in vivo examples of direct small molecule-induced recruitment of target proteins to the proteasome for degradation upon addition to cultured cells. Moreover, PROTAC-mediated protein degradation offers a general strategy to create "chemical knockouts," thus opening new possibilities for the control of protein function.
Dynamic Lens Compensation for Active Color Imaging and Constant Magnification Focusing (1991)

Vision researchers base their work on assumptions that lenses behave ideally. In practice, the image formation process is complex and camera lenses have many non-ideal behaviors that can cause problems in simple vision tasks like color image analysis and range from focus. For example, unlike the ideal lens, the refractive power of a real lens is actually a function of wavelength. This means that images of a scene taken under different wavelengths will have slightly different focus and magnification. The resulting misregistration between the images when they are superimposed to form a composite color image can cause significant problems in color image analysis. Another property of real lenses is that focusing the lens also changes its magnification. In range from focus, these changes in image magnification can bias the position of a sharpness criterion function's peak leading to errors in the range estimates. By precisely controlling the lens during imaging, it is possible to make lenses behave more ideally. We have developed a procedure we call Active Color Imaging in which lens magnification and focus are precisely compensated to produce color images that are over ten times better registered than uncompensated color images. We have also developed a procedure we call Constant Magnification Focusing which allows a user to focus a lens without changing the image magnification, eliminating focus magnification induced errors in range from focus tasks.