gebhart/patrepeval huggingface dataset:
TMPRSS2-ERG Fusion Prostate Cancer: An Early Molecular Event Associated With Invasion (2007)

Prostate cancer (PCA) is one of the most prevalent cancers and a major leading cause of morbidity and mortality in the Western world. The TMPRSS2-ERG fusion was recently identified as a common recurrent chromosomal aberration in this malignancy. In our study, we interrogated a broad spectrum of benign, precursor, and malignant prostatic lesions to assess the TMPRSS2-ERG fusion status using a multicolor interphase fluorescence in situ hybridization assay. Samples from hospital-based cohorts consisted of 237 clinically localized PCA, 34 hormone naive metastases, 9 hormone refractory metastases, 26 high grade prostatic intraepithelial neoplasia lesions, 15 samples of benign prostatic hyperplasia, 38 of proliferative inflammatory atrophy, and 47 of benign prostatic tissue. The TMPRSS2-ERG fusion was present in 48.5% of clinically localized PCA, 30% of hormone naive metastases, 33% of hormone refractory metastases, and in 19% of high grade prostatic intraepithelial neoplasia lesions in intermingling to cancer foci. Almost all these fusion positive cases show a homogenous distribution of the fusion pattern. In contrast, none of the other samples harbored this genetic aberration. If we consider the high incidence of PCA and the high frequency of this gene fusion, TMPRSS2-ERG is the most common genetic aberration so far described in human malignancies. Furthermore, its clinical application as a biomarker and ancillary diagnostic test is promising given its high specificity.
Injection of a novel synthetic hydrogel preserves left ventricle function after myocardial infarction (2008)

Abstract Myocardial infarction (MI) and the subsequent heart failure remain one of the leading causes of morbidity and mortality world wide. A number of studies have demonstrated that bioderived materials improve cardiac function after implantation because of their angiogenic potential. In this study, we hypothesized that injection of biomaterials into infarcted myocardium can preserve left ventricular (LV) function through its prevention of paradoxical systolic bulging. To test this hypothesis, infarction was induced in rabbit myocardium by coronary artery ligation. After 1 week, 200‐μL α‐cyclodextrin (α‐CD)/MPEG‐PCL‐MPEG hydrogel was injected into the infarcted myocardium. Injection of phosphate buffered saline (PBS) served as controls. Twenty‐eight days after the treatment, histological analysis indicated that the injection of hydrogel prevented scar expansion and wall thinning compared with the control ( p &lt; 0.05) without more microvessel density in infarcted myocardium ( p = 0.70). LV ejection fraction, determined by echocardiography, was significantly greater in the hydrogel‐treated group (56.09% ± 8.42%) than the control group (37.26% ± 6.36%, p = 0.001). The LV end‐diastolic and end‐systolic diameters were 2.07 ± 0.33 cm and 1.74 ± 0.30 cm, respectively, in the control group. Smaller LV end‐diastolic diameter (1.61 ± 0.26 cm, p = 0.005) and smaller end‐systolic diameter (1.17 ± 0.23 cm, p = 0.001) were found in the hydrogel‐treated group. These results suggest that α‐CD/MPEG‐PCL‐MPEG hydrogel could serve as an injectable biomaterial that prevents LV remodeling and dilation for the treatment of MI. © 2008 Wiley Periodicals, Inc. J Biomed Mater Res, 2009
Autologous Stem Cell Transplantation As Post-Remission Therapy in Adult Acute Myelogenous Leukemia: Does Platelet Contamination of Peripheral Blood Mobilized Stem Cell Grafts Influence the Risk of Leukemia Relapse? (2000)

Conventional chemotherapy of acute myelogenous leukemia (AML) results in an overall long-term disease-free survival of less than 50%, but for selected subsets of younger patients the prognosis can be improved by allogeneic stem cell transplantation. The use of autologous stem cell transplantation is now investigated as an alternative to allotransplantation due to its lower risk of serious complications. However, autotransplantation is associated with a relatively high risk of post-transplant AML relapse that can be derived from contaminating leukemia cells in the autograft. Peripheral blood mobilized stem cell (PBSC) grafts usually contain a higher number of platelets. The degree of platelet contamination is determined by the peripheral blood platelet count at the time of harvesting, and the platelets become activated and release soluble mediators during the ex vivo handling of PBSC grafts. Many of these platelet-derived mediators can bind to specific receptors expressed by AML blasts, and the platelet contamination may then alter AML blast survival and thereby influence the risk of post-transplant leukemia relapse. Therefore, we conclude that the platelet contamination of autologous stem cell grafts is possibly of clinical importance, but the effect of this nonstandardized parameter is difficult to predict in individual patients because the number of graft-contaminating platelets, the degree of platelet activation, and the effects of platelet-derived mediators on AML blasts differ between patients.
Specific cellular stimulation in the primary immune response: experimental test of a quantized model. (1982)

Dose-response and dose-suppression curves have been measured for the primary immune response in mice, in vivo and in vitro, by using size-fractionated linear polymers of acrylamide substituted with hapten. The results are in general agreement with a simple theory based on the premise that the specific primary immunological response is quantized at some fundamental and limiting step, requiring a minimum number of linked antigen receptors for response.
The basic science of memory as it applies to epilepsy (2007)

The mechanisms of memory delineated by the model of long-term potentiation (LTP) are similar to those underlying epileptogenesis by kindling. Memory is impaired by seizures and epilepsy. High frequency neural activity is important in both memory formation and seizures. Both kindling and LTP are most effectively induced by high-frequency stimuli, involve synaptic facilitation, and share overlapping molecular mechanisms, such as N-methyl-d-aspartate (NMDA) receptor-induced calcium cascade and protein synthesis. The hippocampus contributes to both through its role in memory formation and its low seizure threshold.
Music alters constitutively expressed opiate and cytokine processes in listeners. (2004)

Taken together, it appears that music-listeners exhibit plasma signal molecule changes consistent with the physiological changes associated with the reported actions of music, i.e, lower blood pressure.
Apolipoprotein B-100: conservation of lipid-associating amphipathic secondary structural motifs in nine species of vertebrates (1998)

Development of a computer program called LOCATE allowed us to show that human apolipoprotein B-100 is composed of five domains, NH2-alpha1-beta1-alpha2-beta2-alpha3-COOH, enriched, alternately, in amphipathic alpha helixes and amphipathic beta strands. Using updated versions of this program, here we compare the complete sequence of human apolipoprotein B-100 with partial sequences from eight additional species of vertebrates (chicken, frog, hamster, monkey, mouse, pig, rat, and rabbit). The lipid-associating amphipathic alpha helixes cluster in domains alpha2 (between residues 2075 +/- 25 and 2575 +/- 25) and alpha3 (between residues 4100 +/- 100 and 4550 +/- 50) in all species for which those regions have been sequenced but with little conservation of individual helixes. Lipid-associating amphipathic beta strands cluster in domains beta1 (approximately residues 827-2000) and beta2 (approximately residue 2571 to residue 4000 +/- 50) in all species for which these regions have been sequenced, with conservation of several individual amphipathic beta strands. Hydrophobic segments are present in apolipoprotein B-100 sequences of all nine species but the frequency of occurrence is no greater than generally found in beta sheet-containing proteins. We conclude that four alternating lipid-associating domains, -beta1-alpha2-beta2-alpha3-COOH, are common supramolecular features of apolipoprotein B-100 in nine vertebrate species.
Hepatocyte Nuclear Factor 3/fork head Homolog 11 Is Expressed in Proliferating Epithelial and Mesenchymal Cells of Embryonic and Adult Tissues (1997)

The hepatocyte nuclear factor 3alpha (HNF-3alpha) and 3beta proteins have homology in the winged helix/fork head DNA binding domain and regulate cell-specific transcription in hepatocytes and in respiratory and intestinal epithelia. In this study, we describe two novel isoforms of the winged helix transcription factor family, HNF-3/fork head homolog 11A (HFH-11A) and HFH-11B, isolated from the human colon carcinoma HT-29 cell line. We show that these isoforms arise via differential splicing and are expressed in a number of epithelial cell lines derived from tumors (HT-29, Caco-2, HepG2, HeLa, A549, and H441). We demonstrate that differentiation of Caco-2 cells toward the enterocyte lineage results in decreased HFH-11 expression and reciprocal increases in HNF-3alpha and HNF-3beta mRNA levels. In situ hybridization of 16 day postcoitus mouse embryos demonstrates that HFH-11 expression is found in the mesenchymal and epithelial cells of the liver, lung, intestine, renal cortex, and urinary tract. Although HFH-11 exhibits a wide cellular expression pattern in the embryo, its adult expression pattern is restricted to epithelial cells of Lieberkühn's crypts of the intestine, the spermatocytes and spermatids of the testis, and the thymus and colon. HFH-11 expression is absent in adult hepatocytes, but its expression is reactivated in proliferating hepatocytes at 4, 24, and 48 h after partial hepatectomy. Consistent with these findings, we demonstrate that HFH-11 mRNA levels are stimulated by intratracheal administration of keratinocyte growth factor in adult lung and its expression in an adult endothelial cell line is reactivated in response to oxidative stress. These experiments show that the HFH-11 transcription factor is expressed in embryonic mesenchymal and epithelial cells and its expression is reactivated in these adult cell types by proliferative signals or oxidative stress.
Does medication overuse headache represent a behavior of dependence? (2005)

Medication overuse is relatively common in patients with frequent headache. To explore the prevalence of patients who meet the criteria for substance dependence in Diagnostic and Statistical Manual of Mental Disorders, Edition IV (DSM-IV), and to identify variables of substance dependence among patients with chronic daily headache, we recruited consecutive patients with chronic daily headache at a headache clinic from November 1999 to June 2004. Each patient completed a headache intake form, a dependence questionnaire modified from DSM-IV, and the Hospital Anxiety and Depression Scale (HADS). The presence of probable medication overuse headache (pMOH) was defined on the basis of the International Classification of Headache Disorders, 2nd edition, 2004. A total of 1,861 patients with chronic daily headache (1,369 women, 492 men; mean age, 49.6+/-15.4 years) were recruited. Almost half (895/1,861, 48%) met criteria of pMOH, and 606 of these patients (606/895, 68%) met three of five DSM-IV substance dependence criteria. In contrast, only 191 of 968 patients without pMOH (20%) met the DSM-IV criteria (OR=8.6, [7.0-10.6], chi-square test, P<0.001). Patients who fulfilled DSM-IV criteria of dependence had higher numbers of physician appointments in the past year. Multivariate logistic regression analyses revealed that migraine headache, frequent physician consultation, intensity of headache, and presence of a higher anxiety score were significant independent variables for substance dependence. Among patients with chronic daily headache, pMOH was associated with behaviors of substance dependence.
Hormone replacement therapy and the endometrium (2001)

Modern hormone replacement therapy (HRT) regimens contain oestrogen and progestogen, given either in a cyclical or continuous combined manner. Most endometrial biopsies from women on sequential HRT show weak secretory features. Approximately 15% show proliferative activity, although this figure may be less if more than nine days of progestogen is given in each cycle. A small proportion will show an inactive or atrophic endometrium. Up to 50% of biopsies from women on continuous combined HRT contain minimal endometrial tissue for histopathological analysis: this correlates well with an atrophic endometrium with no appreciable pathology. Of the 50% with more substantial material, approximately one half will show endometrial atrophy, and one half will show weak secretory features. Proliferative, menstrual, and pseudodecidual changes are rare. Approximately 20% of women given unopposed oestrogen for one year develop endometrial hyperplasia. The relative risk of endometrial carcinoma is two to three. This is dramatically reduced by the addition of progestogen to the regimen, but cyclical progestogen as part of a sequential HRT regimen does not completely eliminate the risk of carcinoma. The prevalence of endometrial hyperplasia associated with sequential HRT is 5.4%, and that of atypical hyperplasia (endometrial intraepithelial neoplasia) is 0.7%. Continuous combined HRT is not associated with the development of hyperplasia or carcinoma, and may normalise the endometrium of women who have developed complex hyperplasia on sequential HRT. The probability of a histopathologist finding clinically relevant pathology in an endometrial biopsy specimen of a patient on HRT is low and is more likely to be a manifestation of pre-existing disease.
Immunoassay for B. globigii spores as a model for detecting B. anthracis spores in finished water (2005)

The 2001 anthrax alarm in the US raised concerns about the Nation's preparedness to the threat of bioterrorism, and the demand for early warning systems that might be used in the case of a biological attack continues to grow. Here we develop an ultra-sensitive rapid detection method for B. globigii(BG) spores, the simulant of B. anthracis(BA) spores. BG spores were detected by a bead-based sandwich immunoassay with fluorescence detection. Paramagnetic Dynal beads were used as a solid support, primary antibody was attached to the beads by streptavidin-biotin coupling and the secondary antibody had an alkaline phosphatase (AP) enzyme label. Enzymatic conversion of fluorescein diphosphate (FDP) to fluorescein by AP was measured in real time with lambda(ex)= 490 nm and lambda(em)= 520 nm. The assay was linear from 2.6 x 10(3)-5.6 x 10(5) BG spores mL(-1), and the detection limit was 2.6 x 10(3) spores mL(-1) or 78 spores. All reagent concentrations and incubation times were optimized. The assay time from the moment the spores were introduced to the system was 30 min, and real-time fluorescence detection was done in less than 1 min. Formation of the BG spores-capture beads complex was confirmed by environmental scanning electron microscopy (ESEM). BG spores were detected successfully when doped into Cincinnati tap water to demonstrate the applicability of the developed method to detect the spores in non-buffered media.
Nonhypotensive Dose of Telmisartan Attenuates Cognitive Impairment Partially Due to Peroxisome Proliferator-Activated Receptor-γ Activation in Mice With Chronic Cerebral Hypoperfusion (2010)

Background and Purpose— The effect of telmisartan, an angiotensin II Type 1 receptor blocker with peroxisome proliferator-activated receptor-γ-modulating activity, was investigated against spatial working memory disturbances in mice subjected to chronic cerebral hypoperfusion. Methods— Adult C57BL/6J male mice were subjected to bilateral common carotid artery stenosis using external microcoils. Mice received a daily oral administration of low-dose telmisartan (1 mg/kg per day), high-dose telmisartan (10 mg/kg per day), or vehicle with or without peroxisome proliferator-activated receptor-γ antagonist GW9662 (1 mg/kg per day) for all treatments for 30 days after bilateral common carotid artery stenosis. Cerebral mRNA expression of monocyte chemoattractant protein-1 and tumor necrosis factor-α was measured 30 days after bilateral common carotid artery stenosis, and postmortem brains were analyzed for demyelinating change with Klüver-Barrera staining and immunostained for glial, oxidative stress, and vascular endothelial cell markers. Spatial working memory was assessed by the Y-maze test. Results— Mean systolic blood pressure and cerebral blood flow did not decrease with low-dose telmisartan but significantly decreased with high-dose telmisartan. Low-dose telmisartan significantly attenuated, but high-dose telmisartan provoked, spatial working memory impairment with glial activation, oligodendrocyte loss, and demyelinating change in the white matter. Such positive effects of low-dose telmisartan were partially offset by cotreatment with GW9662. Consistent with this, low-dose telmisartan reduced the degree of oxidative stress of vascular endothelial cells and the mRNA levels of monocyte chemoattractant protein-1 and tumor necrosis factor-α compared with vehicle. Conclusions— Anti-inflammatory and antioxidative effects of telmisartan that were exerted in part by peroxisome proliferator-activated receptor-γ activation, but not its blood pressure-lowering effect, have protective roles against cognitive impairment and white matter damage after chronic cerebral hypoperfusion.
Frustum-traced raster shadows: revisiting irregular z-buffers. (2015)

We present a real-time system that renders antialiased hard shadows using irregular z-buffers (IZBs). For subpixel accuracy, we use 32 samples per pixel at roughly twice the cost of a single sample. Our system remains interactive on a variety of game assets and CAD models while running at 1080p and 2160p and imposes no constraints on light, camera or geometry, allowing fully dynamic scenes without precomputation. Unlike shadow maps we introduce no spatial or temporal aliasing, smoothly animating even subpixel shadows from grass or wires.Prior irregular z-buffer work relies heavily on GPU compute. Instead we leverage the graphics pipeline, including hardware conservative raster and early-z culling. We observe a duality between irregular z-buffer performance and shadow map quality; this allows common shadow map algorithms to reduce our cost. Compared to state-of-the-art ray tracers, we spawn similar numbers of triangle intersections per pixel yet completely rebuild our data structure in under 2 ms per frame.
Identification of Porcine Reproductive and Respiratory Syndrome Virus in Semen and Tissues from Vasectomized and Nonvasectomized Boars (1998)

Previous studies have indicated that porcine reproductive and respiratory syndrome virus (PRRSV) can be identified in and transmitted through boar semen. However, the site(s) of replication indicating the origin of PRRSV in semen has not been identified. To determine how PRRSV enters boar semen, five vasectomized and two nonvasectomized PRRSV-seronegative boars were intranasally inoculated with PRRSV isolate VR-2332. Semen was collected three times weekly from each boar and separated into cellular and cell-free (seminal plasma) fractions. Both fractions were evaluated by reverse transcriptase nested polymerase chain reaction (RT-nPCR) for the presence of PRRSV RNA. Viremia and serostatus were evaluated once weekly, and boars were euthanatized 21 days postinoculation (DPI). Tissues were collected and evaluated by RT-nPCR, virus isolation (VI), and immunohistochemistry to identify PRRSV RNA, infectious virus, or viral antigen, respectively. PRRSV RNA was identified in semen from all vasectomized and nonvasectomized boars and was most consistently found in the cell fraction, within cells identified with a macrophage marker. Viral replication as determined by VI was predominately found within lymphoid tissue. However, PRRSV RNA was widely disseminated throughout many tissues, including the reproductive tract at 21 DPI. These results indicate that PRRSV can enter semen independent of testicular or epididymal tissues, and the source of PRRSV in semen is virus-infected monocytes/macrophages or non-cell-associated virus in serum. PRRSV-infected macrophages in semen may result from infection of local tissue macrophages or may originate from PRRSV-infected circulating monocytes or macrophages.
The saga of IMAC and MIT (1989)

Immobilized Metal-ion Affinity Chromatography, IMAC, has been gaining in popularity as the purification technique of choice for proteins and peptides. IMAC of proteins on transition metals (Co, Ni, Cu, Zn) can be rationalized in terms of the coordination of histidine residues. Brief accounts of the principles of IMAC, its anticipated development and plausible applications are presented. Metal Ion Transfer, MIT, may offer an efficient means to deplete a metal ion from a metalloprotein or, conversely, to charge its apo form with a metal.
Polydopamine—a nature-inspired polymer coating for biomedical science (2011)

Polymer coatings are of central importance for many biomedical applications. In the past few years, poly(dopamine) (PDA) has attracted considerable interest for various types of biomedical applications. This feature article outlines the basic chemistry and material science regarding PDA and discusses its successful application from coatings for interfacing with cells, to drug delivery and biosensing. Although many questions remain open, the primary aim of this feature article is to illustrate the advent of PDA on its way to become a popular polymer for bioengineering purposes.
Effects of weight and definiteness on speakers’ choice of clausal ordering in English (2012)

No abstract.
Rat Sperm 2B1 Glycoprotein (PH20) Contains a C-Terminal Sequence Motif for Attachment of a Glycosyl Phosphatidylinositol Anchor. Effects of Endoproteolytic Cleavage on Hyaluronidase Activity1 (2000)

Rat sperm 2B1 antigen (the orthologue of guinea pig sperm PH20) is a plasma membrane-bound glycoprotein that is endoproteolytically cleaved during passage through the epididymis and subsequently migrates from the tail to the acrosomal domain during capacitation. Unlike guinea pig PH20, however, sperm surface 2B1 is insensitive to phosphatidylinositol phospholipase C, nor is it known how endoproteolytic cleavage affects its hyaluronidase activity. In this investigation we have expressed 2B1 cDNA in Chinese hamster ovary cells; we have shown that it contains an internal sequence motif for attachment of a glycosyl phosphatidylinositol (GPI) anchor and that cleavage from a single- into a two-chain molecule causes a significant shift in the optimum pH for hyaluronidase activity. Functionally, these results suggest that 1) 2B1 glycoprotein on rat spermatozoa is attached to the plasma membrane via a GPI anchor and that this is an important factor in its ability to migrate from the tail to the acrosomal domain during capacitation; and 2) endoproteolytic cleavage of 2B1 serves to optimize its hyaluronidase activity immediately before fertilization, thereby facilitating penetration of spermatozoa through the cumulus oophorus.