gebhart/patrepeval huggingface dataset:
The roles of human viruses in the pathogenesis of lymphoma. (1998)

There are two families of viruses that contribute to lymphomagenesis in humans: herpesviruses and retroviruses. The two herpesviruses are the Epstein-Barr virus (EBV) and human herpesvirus-8 (HHV-8). EBV is an extremely well-characterized transforming agent: nine viral proteins contribute to transformation in vitro. In contrast, in vivo, the pattern of EBV gene expression varies with different types of malignancies. EBV is associated with endemic Burkitt's lymphoma, acquired immune deficiency syndrome (AIDS)-related lymphoma, post-transplantation lymphoproliferative disease, Hodgkin's disease (HD), and rare T-cell lymphomas. We have summarized studies on the different patterns of viral gene expression and signaling in different EBV-related malignancies, which have begun to reveal how EBV variably contributes to the malignant phenotype in different diseases. HHV-8 is associated with primary effusion lymphomas in patients with AIDS, and the rapidly accumulating information on this virus is summarized. Human T-cell leukemia virus-1 (HTLV-1) is a retrovirus which is the causative agent of adult T-cell leukemia/lymphoma (ATL). The specific mechanism of HTLV-1-mediated T-cell transformation is unclear, but the effects of HTLV-1 on interleukin-2 signaling are reviewed.
U.S. District Court Southern District of New York (Foley Square) (2006)

Miller v. Independent Energy, et al Assigned to: Judge Shira A. Scheindlin Referred to: Magistrate Judge Michael H. Dolinger Demand: $0 Lead case: 1:00-cv-06689-SAS-MHD Member cases: 1:00-cv-07161-SAS 1:00-cv-07451-SAS 1:00-cv-07455-SAS 1:00-cv-07488-SAS 1:00-cv-07495-SAS 1:00-cv-07496-SAS 1:00-cv-07683-SAS 1:00-cv-07950-SAS 1:00-cv-08004-SAS 1:00-cv-08009-SAS 1:00-cv-08010-SAS 1:00-cv-08336-SAS 1:00-cv-08494-SAS 1:01-cv-00926-SAS 1:01-cv-00927-SAS 1:01-cv-00928-SAS Related Case: 1:00-cv-08564-SAS Cause: 15:77 Securities Fraud Date Filed: 09/06/2000 Jury Demand: Both Nature of Suit: 850 Securities/Commodities Jurisdiction: Federal Question
The level of serum secretory IgA of patients with IgA nephropathy is elevated and associated with pathological phenotypes (2007)

It was concluded that mesangial IgA, at least partly, was originated from mucosal immune sites. The levels of serum SIgA were significantly increased in patients with IgAN and were closely associated with pathological phenotypes.
An in vitro assessment of the role of Tooth Mousse in preventing wine erosion (2008)

TM may have significant role in the management of wine erosion, which is under-recognized as an occupational hazard by the Australian wine industry. Future studies are needed to compare the relative benefits of TM and other remineralizing agents, when used individually or in combination, in preventing dental erosion.
Analysis of Heterogeneous βA4 Peptides in Human Cerebrospinal Fluid and Blood by a Newly Developed Sensitive Western Blot Assay (1996)

The betaA4 peptide, a major component of senile plaques in Alzheimer's disease (AD) brain, has been found in cerebrospinal fluid (CSF) and blood of both AD patients and normal subjects. Although betaA4 1-40 is the major form produced by cell metabolism and found in CSF, recent observations suggest that the long-tailed betaA4 1-42 plays a more crucial role in AD pathogenesis. Here, we established new monoclonal antibodies against the C-terminal end of betaA4 1-40 and 1-42, and used them for the specific Western blot detection. After optimizing the assay conditions, these antibodies detected low picogram amount of betaA4, and both betaA4 1-40 and 1-42 levels in CSF could be determined by direct loading of the samples. Blood levels of betaA4 1-40 and 1-42 were also determined by specific immunoprecipitation followed by Western blot detection. We found that CSF betaA4 1-42 level is lower in AD patients compared with non-demented controls, although there was a significant overlap between the groups. The level of betaA4 1-40 in CSF, and of betaA4 1-40 as well as betaA4 1-42 in plasma, were not different between AD patients and controls. Besides the 4-kDa full-length betaA4 band, we could also detect several N-terminal variants of betaA4 in CSF and plasma of both AD patients and controls. Two N-terminally truncated betaA4 species migrating at the position of 3.3 and 3.7 kDa were found in CSF, while 3.7- and 5-kDa forms were found in plasma. The relative abundance of these various species were considerably different in the CSF and plasma, suggesting that the cellular source and/or clearance of betaA4 is different in these two compartments.
Sheathotomy without separation of venule overlying arteriole at occlusion site in uncommon branch retinal vein occlusion. (2005)

Two cases of uncommon branch retinal vein occlusion (BRVO) with vein overlying artery at occlusion site that can be found in less than 1% who underwent retinal venule sheathotomy without separation of retinal vessel for decompression of BRVO were reported. Both patients had macular hemorrhage, edema, and area of macular capillary nonperfusion. Visual acuity (VA) worsened to 6/60 in both cases. The retinal venules were dissected around the crossing site without separation of retinal vessels. Intraoperative dilation, pulsation and restoration of downstream blood flow of the involved venules were observed. In the first patient, at 1 day, 2 weeks, and 6 weeks postoperatively, VA improved to 6/36, 6/9, and 6/6, respectively, and remained unchanged at 12 months postoperatively. In the second patient, VA improved to 6/24 on the first day postoperatively and improved to 6/18 at 1 week follow up and continuously improved to nearly normal at 2 months postoperatively then patient lost contact. Postoperative fundus fluorescein angiogram showed dilated and improved perfusion with decreased macular edema in both cases. Optical coherent tomography confirmed remarkable reduction of retinal thickness (from 874 microns preoperatively to 420 microns at 1 week postoperatively) in the second patient. Retinal venule sheathotomy without separation of retinal vessel for decompression of BRVO with venule overlying arteriole at occlusion site could be effective for improving VA and decreased macular edema.
A computational study of the effect of vocal-fold asymmetry on phonation (2010)

Unilateral laryngeal paralysis leads to tension imbalance and hence to asynchronous movements between the two vocal folds during phonation. In the current study, a computational model of phonation that couples a two-mass model of the vocal folds with a Navier-Stokes model of the glottal airflow, has been used to examine the dynamics of vocal fold configurations with tension imbalance and its implications for phonation. The simulations show that tension imbalance influences phonation onset, intensity as well as the fundamental phonation frequency. Distinct non-linear effects such as period-doubling bifurcation and preferential frequency selection are also observed.
Engineering Control in Reservoir Simulation: Part I (1988)

ABSTRACT This paper presents a broad critique of the current state of reservoir simulation and its applications with an emphasis on its three key shortcomings: (1) lack of established industry standards for simulation (2) non-uniqueness, and (3) inherent uncertainties in reservoir modeling. Examples are discussed to demonstrate how these factors can and have led to misinterpretation and misuse of simulation results.
Comprehensive analysis of loss of heterozygosity events in glioblastoma using the 100K SNP mapping arrays and comparison with copy number abnormalities defined by BAC array comparative genomic hybridization (2007)

We have undertaken an extensive high-resolution analysis of loss of heterozygosity (LOH) in 30 high grade gliomas using the Affymetrix 100K SNP mapping array. Only 70% of LOH events were accompanied by a copy number loss (CNA(loss)), and of the other 30%, the distal region of 17p preferentially showed copy number neutral (CNN)-associated LOH. Combined analysis of CNA(loss) and LOH using MergeLevels analysis software predicts whether the observed losses occurred on a diploid or tetraploid background. In a side-by-side comparison between SNP and bacterial artificial chromosome (BAC) arrays, the overall identification of CNAs was similar on both platforms. The resolution provided by the SNP arrays, however, allowed a considerably more accurate definition of breakpoints as well as defining small events within the cancer genomes, which could not be detected on BAC arrays. CNN LOH was only detected by the SNP arrays, as was ploidy prediction. From our analysis, therefore, it is clear that simultaneously defining CNAs and CNN-LOH using the SNP platform provides a higher resolution and more complete analysis of the genetic events that have occurred within tumor cells. Our extensive analysis of SNP array data has also allowed an objective assessment of threshold LOH scores that can accurately predict LOH. This capability has important implications for interpretation of LOH events since they have consistently been used to localize potential tumor suppressor genes within the cancer genome.
High time-resolution measurement and analysis of LAN traffic: Implications for LAN interconnection (1991)

In order to study the interactions between LANs and proposed interconnection networks, a high time-resolution hardware monitor for Ethernet LANs is presented that avoids the shortcomings of previous monitoring tools, such as traffic burst clipping and timestamp jitter. Using data recorded by a monitor for several hundred million Ethernet packets, an overview of the short-range time correlations in external LAN traffic is presented. The analysis shows that LAN traffic is extremely bursty across time domains spanning six orders of magnitude. This behavior is compared with simple formal traffic models. The results suggest that the pronounced short-term traffic correlations, together with the extensive time regime of traffic burstiness, strongly influence the patterns of loss and delay induced by LAN interconnection.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Signature for heavy Majorana neutrinos in hadronic collisions (2000)

The production and decay of new possible heavy Majorana neutrinos are analyzed in hadronic collisions. New bounds on the mixing of these particles with standard neutrinos are estimated according to a fundamental representation suggested by grand unified models. A clear signature for these Majorana neutrinos is given by same-sign dileptons plus a charged weak vector boson in the final state. We discuss the experimental possibilities for the future Large Hadron Collider (LHC) at CERN.
Programmes of cell death and autolysis in tracheary elements: when a suicidal cell arranges its own corpse removal (2014)

Tracheary element (TE) differentiation represents a unique system to study plant developmental programmed cell death (PCD). TE PCD occurs after deposition of the secondary cell walls when an unknown signal induces tonoplast rupture and the arrest of cytoplasmic streaming. TE PCD is tightly followed by autolysis of the protoplast and partial hydrolysis of the primary cell walls. This review integrates TE differentiation, programmed cell death (PCD), and autolysis in a biological and evolutionary context. The collective evidence from the evolutionary and molecular studies suggests that TE differentiation consists primarily of a programme for cell death and autolysis under the direct control of the transcriptional master switches VASCULAR NAC DOMAIN 6 (VND6) and VND7. In this scenario, secondary cell walls represent a later innovation to improve the water transport capacity of TEs which necessitates transcriptional regulators downstream of VND6 and VND7. One of the most fascinating features of TEs is that they need to prepare their own corpse removal by expression and accumulation of hydrolases that are released from the vacuole after TE cell death. Therefore, TE differentiation involves, in addition to PCD, a programmed autolysis which is initiated before cell death and executed post-mortem. It has recently become clear that TE PCD and autolysis are separate processes with separate molecular regulation. Therefore, the importance of distinguishing between the cell death programme per se and autolysis in all plant PCD research and of careful description of the morphological, biochemical, and molecular sequences in each of these processes, is advocated.
Effect of Adsorbates on Field Emission from Carbon Nanotubes (2001)

Recent experiments indicate that water molecules adsorbed on carbon nanotube tips significantly enhance field-emission current. Through first-principles density-functional theory calculations we show that the water-nanotube interaction is weak in zero electric field. However, under emission conditions large electric field present at the tube tip: (a) increases the binding energy appreciably, thereby stabilizing the adsorbate; and (b) lowers the ionization potential (IP), thereby making it easier to extract electrons. Lowering of IP is enhanced further through the formation of a water cluster on the nanotube tip.
Treatment in advanced colorectal cancer: what, when and how? (2009)

Treatment of advanced colorectal cancer (CRC) increasingly requires a multidisciplinary approach and multiple treatment options add to the complexity of clinical decision-making. Recently novel targeted therapy against angiogenesis and epidermal growth factor receptor completed a plethora of phase III studies. The addition of bevacizumab to chemotherapy improved the efficacy over chemotherapy alone in both first and second line settings, although the magnitude of benefit may not be as great when a more optimal chemotherapy platform is used. Studies performed thus far did not address conclusively whether bevacizumab should be continued in subsequent lines of treatment. Anti-angiogenesis tyrosine kinase inhibitors have not shown any additional benefit over chemotherapy alone so far. Although some benefits were seen with cetuximab in all settings of treating advanced CRC, K-ras mutation status provides an important determinant of who would not benefit from such a treatment. Caution should be exercised in combining anti-angiogenesis with anti-EGFR strategy until further randomised data become available. In this review, we have focused on the implications of these trial results on the everyday management decisions of treating advanced CRC.
Characterization of the putative maltose transporters encoded by YDL247w and YJR160c (2002)

The maltose permease family of Saccharomyces cerevisiae comprises five proteins, three of which are characterized, MAL31, MAL61 and AGT1 and two putative permeases, YDL247w (MPH2) and YJR160c (MPH3). The two uncharacterized permeases share 100% identity and have 75% identity with MAL31 and MAL61 and 55% identity with AGT1. Characterization of the genes YDL247w and YJR160c confirmed that they encode alpha-glucoside permeases capable of transporting maltose, maltotriose, alpha-methylglucoside and turanose. Analysis of the promoter regions identified regulatory elements, binding sites for the transcriptional activator, Malx3p and the inhibitory protein, Mig1p. Further analysis of the flanking sequences located blocks of identity covering five open reading frames, indicating that this region was involved in chromosomal block duplication. The members of the maltose permease family are proteins that have strongly overlapping but nevertheless distinct functions, which is a selective advantage for yeast, as it reflects successful adaptation to the variety of environmental conditions to which the yeast cells are exposed; such adaptability is very important in an industrial context.
SUMMARY OF TRAVEL TRENDS: 1990 NATIONWIDE PERSONAL TRANSPORTATION SURVEY (1992)

To further our understanding of travel behavior, the U.S. Department of Transportation (US DOT) conducts the Nationwide Personal Transportation Survey (NPTS) to obtain information on personal travel of U.S. households with respect to why, how, when, where from, where to, how frequently, how long, and with whom. The NPTS also provides information by subgroups of the population, e.g., by age, gender, race, zero-vehicle households, which allows important policy analyses of how transportation serves these groups. The NPTS has been conducted in 1969, 1977, 1983, 1990, and 1995.\n
Proteomics Analysis of A33 Immunoaffinity-purified Exosomes Released from the Human Colon Tumor Cell Line LIM1215 Reveals a Tissue-specific Protein Signature (2009)

Exosomes are 40-100-nm-diameter nanovesicles of endocytic origin that are released from diverse cell types. To better understand the biological role of exosomes and to avoid confounding data arising from proteinaceous contaminants, it is important to work with highly purified material. Here, we describe an immunoaffinity capture method using the colon epithelial cell-specific A33 antibody to purify colorectal cancer cell (LIM1215)-derived exosomes. LC-MS/MS revealed 394 unique exosomal proteins of which 112 proteins (28%) contained signal peptides and a significant enrichment of proteins containing coiled coil, RAS, and MIRO domains. A comparative protein profiling analysis of LIM1215-, murine mast cell-, and human urine-derived exosomes revealed a subset of proteins common to all exosomes such as endosomal sorting complex required for transport (ESCRT) proteins, tetraspanins, signaling, trafficking, and cytoskeletal proteins. A conspicuous finding of this comparative analysis was the presence of host cell-specific (LIM1215 exosome) proteins such as A33, cadherin-17, carcinoembryonic antigen, epithelial cell surface antigen (EpCAM), proliferating cell nuclear antigen, epidermal growth factor receptor, mucin 13, misshapen-like kinase 1, keratin 18, mitogen-activated protein kinase 4, claudins (1, 3, and 7), centrosomal protein 55 kDa, and ephrin-B1 and -B2. Furthermore, we report the presence of the enzyme phospholipid scramblase implicated in transbilayer lipid distribution membrane remodeling. The LIM1215-specific exosomal proteins identified in this study may provide insights into colon cancer biology and potential diagnostic biomarkers.
Botulinum neurotoxins are zinc proteins. (1992)

The available amino acid sequences of 150-kDa botulinum and tetanus neurotoxins show the presence of a closely homologous segment in the middle of the light chain (NH2-terminal 50 kDa), which is the intracellularly active portion of the toxin. This segment contains the zinc binding motif of metalloendopeptidases, HEXXH. Atomic adsorption analysis of botulinum neurotoxins (serotypes A, B, and E) made on the basis of this observation demonstrated the presence of one zinc atom/molecule of 150-kDa neurotoxin. Conditions were found for the removal of the zinc ion with chelating agents and for the restoration of the normal metal content. The conserved segment, which includes the zinc binding motif, was synthesized and shown to bind [65Zn]2+. Chemical modification experiments indicated that two histidines and no cysteines are involved in Zn2+ coordination in agreement with a probable catalytic role for the zinc ion. The present findings suggest the possibility that botulinum neurotoxins are zinc proteases.
Induction of a major histocompatibility complex class I-restricted cytotoxic T-lymphocyte response to a highly conserved region of human immunodeficiency virus type 1 (HIV-1) gp120 in seronegative humans immunized with a candidate HIV-1 vaccine (1994)

Efforts to induce broadly reactive immunity against human immunodeficiency virus type 1 (HIV-1) have been impaired by the extent of sequence variation exhibited by this lentivirus. Cytotoxic T lymphocytes (CTL) specific for other viruses such as influenza virus have been shown to mediate immunity against divergent viral strains, a property that is related to the ability of CTL to recognize processed antigen derived from conserved viral proteins. A recent candidate HIV-1 vaccine regimen has been described in which subjects receive a primary immunization with a recombinant vaccinia virus expressing gp160 and then a booster immunization with recombinant gp160. Volunteers immunized with this regimen have exhibited augmented humoral responses and have also developed CD4+ and CD8+ CTL specific for gp160. In this report, we have identified the epitopes recognized by CD4+ and CD8+ CTL obtained from two vaccines. An immunodominant CD8+ CTL response was HLA-A3.1 restricted and recognized a 10-amino-acid epitope (gp120/38-47) in a highly conserved region of gp120. CTL specific for the epitope gp120/38-47 were able to lyse targets sensitized with peptides corresponding to all known natural sequence variants in this region. In addition, other HLA class I-restricted CTL epitopes were identified in relatively conserved regions of gp120 and gp41, and CD4+ CTL were shown to recognize two different regions of gp120. Thus, in these two volunteers, immunization with a single strain of HIV-1 induced CD4+ and CD8+ CTL that are specific for multiple conserved regions of HIV-1 and would be expected to recognize a broad range of viral isolates.
A modified technique of stent fenestration of the interatrial septum improves patients with pulmonary hypertension (2008)

The modified stent fenestration technique is feasible and safe in patients with severe pulmonary hypertension. In a selected group of patients, functional capacity might improve although disease progression continues.
Molecular and immunohistochemical evaluation of epidermal growth factor receptor and c-erb-B-2 gene product in transitional cell carcinomas of the urinary bladder: a study in Greek patients. (1995)

In this study, the expression of epidermal growth factor receptor (EGFr) and c-erb-B-2 was evaluated in 35 formalin-fixed, paraffin-embedded cases of transitional cell carcinomas of the urinary bladder (TCCs). EGFr and c-erb-B-2 expression was assessed with immunohistochemistry, and molecular analysis of the respective genes was performed with the differential polymerase chain reaction. The results were statistically analyzed in relationship to histologic grade, stage, and clinical outcome. Strong cytoplasmic expression of the EGFr using the polyclonal antibody Ab-4 was found in three (25%) Grade 2 and eight (67%) Grade 3 TCCs (P < 0.01). Two Grade 2 (17%) and 11 (92%) Grade 3 TCCs strongly expressed the anti-c-erb-B-2 Ab-3 antibody. None of Ta/T1 TCCs cases showed strong expression against EGFr, in contrast to c-erb-B-2 where two cases (18%) were found to express an intense immunosignal. Eleven (85%) T2/T3 cases showed strong positivity either against EGFr or c-erb-B-2 (P < 0.001). Eleven patients died within 12 months after the diagnosis, and all of them showed strong expression of EGFr and c-erb-B-2. Amplification of EGFr and c-erb-B-2 genes was identified in one (3%) and four (11%) TCCs cases, respectively. All patients with amplified genes died within 12 months from the date of diagnosis. Our results indicate that simultaneous expression of EGFr and c-erb-B-2 occurs in TCCs, is related to the histologic grade and the stage of the disease, and denotes aggressive biologic behavior.