gebhart/patrepeval huggingface dataset:
Peptide binding specificity of HLA-DR4 molecules: correlation with rheumatoid arthritis association. (1995)

We have investigated whether sequence 67 to 74 shared by beta chains of rheumatoid arthritis (RA)-associated HLA-DR molecules imparts a specific pattern of peptide binding. The peptide binding specificity of the RA-associated molecules, DRB1*0401, DRB1*0404, and the closely related, RA nonassociated DRB1*0402 was, therefore, determined using designer peptide libraries. The effect of single key residues was tested with site-directed mutants of DRB1*0401. The results have demonstrated striking differences between RA-linked and unlinked DR allotypes in selecting the portion of peptides that interacts with the 67-74 area. Most differences were associated with a single amino acid exchange at position 71 of the DR beta chain, and affected the charge of residues potentially contacting position 71. The observed binding patterns permitted an accurate prediction of natural protein derived peptide sequences that bind selectively to RA-associated DR molecules. Thus, the 67-74 region, in particular position 71, induces changes of binding specificity that correlate with the genetic linkage of RA susceptibility. These findings should facilitate the identification of autoantigenic peptides involved in the pathogenesis of RA.
Plasma N-Terminal Pro–Brain Natriuretic Peptide and Adrenomedullin (1998)

Plasma N-BNP measured 2 to 4 days after myocardial infarction independently predicted left ventricular function and 2-year survival. Stratification of patients into low- and high-risk groups can be facilitated by plasma N-BNP or BNP measurements, and one of these could reasonably be included in the routine clinical workup of patients after myocardial infarction.
Production of human papillomavirus type 16 virions in a keratinocyte cell line (1990)

Human papillomavirus type 16 (HPV-16) is strongly associated with carcinoma of the cervix, but the complete life cycle of the virus cannot be studied because no experimental system is available in which HPV-16 progeny are produced, and there is currently no source of HPV-16 virus particles. Most cell lines that harbor HPV-16 DNA contain the viral genome as integrated or concatenated DNA in which open reading frames are disrupted or deleted, but a human cervical keratinocyte cell line has been described which maintains HPV-16 DNA in monomeric episomal form (M.A. Stanley, H.M. Brown, M.W. Appleby, and A.C. Minson, Int. J. Cancer 43:672-676, 1989). This cell line was induced to form a stratified differentiating epithelium by grafting onto nude mice. Long-term grafts displayed the histological features of a low-grade cervical dysplasia, and terminally differentiated cells contained amplified levels of HPV-16 DNA, virus capsid antigen, and virus particles. This experimental system appears to permit the completion of the HPV-16 life cycle in virus-containing keratinocytes.
Measurement of T‐Cell Telomere Length Using Amplified‐Signal FISH Staining and Flow Cytometry (2017)

Exposure to pathogen-associated molecular patterns (PAMPS), damage-associated molecular patterns (DAMPS), and physiologically challenging stimuli either positively or negatively affect leukocyte maturity. Cellular maturity has implications for the effectiveness of host response to bacterial or viral infection and/or tissue injury. Thus, the ability to accurately assess cellular maturity and health is important to fully understand immune status and function. The most common technique for measuring cellular maturity is to measure telomere length; however, existing techniques are not optimized for single-cell measurements using flow cytometry. Specifically, existing methods used to measure telomere length are PCR-based, making it difficult for a researcher to measure maturity within specific leukocyte subsets (e.g., T cells). In this report, we describe a new approach for the measurement of telomere length within individual T cells using an amplified fluorescence in situ hybridization (FISH) technique (PrimeFlow RNA Assay). The unique aspect of this technique is that it amplifies the fluorescent signal rather than the target up to 3000-fold, resulting in the detection of as few as 1 copy of the target nucleic acid. While the current technique focuses on human T cells, this method can be broadly applied to a variety of cell types and disease models. © 2017 by John Wiley & Sons, Inc.
Current Perceptions of Students Following the September 11, 2001 Terrorist Attacks (2003)

This research looked at perceptions of college students following the events of September 11, 2001. Results showed that students have made substantial changes in their arrival time prior to their flight leaving, and 49.7% are “slightly more concerned” over flying. A majority of students (77.1%) have changed their mail handling procedures. A sizable portion (17.8%) said a company recruiter, that they would like to interview with, cancelled their campus semester visit because of the events of September 11. Hospitality and Tourism Management students had significantly lower salary expectations than non-HTM students now as compared to before September 11.
COIL CENTERING OF THE KOLKATA SUPERCONDUCTING CYCLOTRON MAGNET (2007)

The superconducting Nb-Ti coil is wound on a stainless steel bobbin of about 1.5 m diameter and 1.2 m height. The bobbin acts as the liquid helium chamber inside which the coil is dipped. It is suspended with nine support links - six vertical and three horizontal, inside the iron vacuum chamber. These support links can be adjusted in length externally so that the coil can be moved inside the vacuum chamber. The annular cryostat, including the coil, is placed inside the pill box type iron yoke around the upper and lower poles. The cryostat is placed inside the yoke with two locating pins. A jig was made to measure the deviations of the vacuum chamber inner wall with respect to the magnet pole center and the locating pins were adjusted to place it accurately. The coil was then cooled to liquid helium temperature and energized. During energisation process, the coil was centered using the lowest force criterion. After the full current was achieved, the final centering was checked with the magnet field measurement data analysis. This paper summarizes the methodologies and procedures followed in this work.
Complete Characterization of the Seventeen Step Moenomycin Biosynthetic Pathway (2009)

The moenomycins are phosphoglycolipid antibiotics produced by Streptomyces ghanaensis and related organisms. The phosphoglycolipids are the only known active site inhibitors of the peptidoglycan glycosyltransferases, an important family of enzymes involved in the biosynthesis of the bacterial cell wall. Although these natural products have exceptionally potent antibiotic activity, pharmacokinetic limitations have precluded their clinical use. We previously identified the moenomycin biosynthetic gene cluster in order to facilitate biosynthetic approaches to new derivatives. Here, we report a comprehensive set of genetic and enzymatic experiments that establish functions for the 17 moenomycin biosynthetic genes involved in the synthesis of moenomycin and variants. These studies reveal the order of assembly of the full molecular scaffold and define a subset of seven genes involved in the synthesis of bioactive analogues. This work will enable both in vitro and fermentation-based reconstitution of phosphoglycolipid scaffolds so that chemoenzymatic approaches to novel analogues can be explored.
Position-Independent Transgene Expression Mediated by Boundary Elements from the Apolipoprotein B Chromatin Domain (1995)

The human apolipoprotein B (apoB) gene resides within a 47.5-kb chromatin domain that is flanked by sequences that bind to the nuclear matrix. These matrix attachment regions (MARs) are boundaries between nuclease-sensitive and -resistant chromatin. As domain boundaries are thought to function as insulator elements, shielding sequences between them from effects of neighboring chromatin, this raised the possibility that the apoB MARs have functions that could be assayed by transfection. To test this possibility, we examined effects of the apoB MARs on transgene expression in transiently and stably transfected rat and human hepatoma cells. The apoB MARs had no effects on expression of transiently transfected reporters, but they altered expression of stably integrated transgenes in dramatic and reproducible ways. Single integrated copies of transgenes that contained the apoB promoter and second intron enhancer, which are sufficient for high-level expression in transient assays, were expressed at low and variable levels in stable transfectant clones. In contrast, transgenes containing the apoB 5' and 3' MARs were expressed at levels nearly 200-fold higher than levels of the minimal reporters in stable transfectants, and expression was position independent. Transgenes that contained the apoB MARs and an additional 3.3 kb of apoB 5' flanking sequence were also expressed in an elevated, position-independent manner. Surprisingly, tandem transgene arrays in multicopy transfectants were transcriptionally inactive. These observations suggest that the apoB MARs function as insulator elements, shielding transgene expression from effects of neighboring chromatin domains.
Nonuniform High-Gamma (60–500 Hz) Power Changes Dissociate Cognitive Task and Anatomy in Human Cortex (2011)

High-gamma-band (>60 Hz) power changes in cortical electrophysiology are a reliable indicator of focal, event-related cortical activity. Despite discoveries of oscillatory subthreshold and synchronous suprathreshold activity at the cellular level, there is an increasingly popular view that high-gamma-band amplitude changes recorded from cellular ensembles are the result of asynchronous firing activity that yields wideband and uniform power increases. Others have demonstrated independence of power changes in the low- and high-gamma bands, but to date, no studies have shown evidence of any such independence above 60 Hz. Based on nonuniformities in time-frequency analyses of electrocorticographic (ECoG) signals, we hypothesized that induced high-gamma-band (60-500 Hz) power changes are more heterogeneous than currently understood. Using single-word repetition tasks in six human subjects, we showed that functional responsiveness of different ECoG high-gamma sub-bands can discriminate cognitive task (e.g., hearing, reading, speaking) and cortical locations. Power changes in these sub-bands of the high-gamma range are consistently present within single trials and have statistically different time courses within the trial structure. Moreover, when consolidated across all subjects within three task-relevant anatomic regions (sensorimotor, Broca's area, and superior temporal gyrus), these behavior- and location-dependent power changes evidenced nonuniform trends across the population. Together, the independence and nonuniformity of power changes across a broad range of frequencies suggest that a new approach to evaluating high-gamma-band cortical activity is necessary. These findings show that in addition to time and location, frequency is another fundamental dimension of high-gamma dynamics.
Galectin-3 in Renal Pathology: More Than Just an Innocent Bystander? (2016)

Due to its multifunctional character, galectin-3 plays a pivotal role in interstitial fibrosis and progression of chronic kidney disease. Inhibition of galectin-3 may be a promising therapeutic strategy to prevent end-stage renal disease.
Sequence-specific DNA Binding Activity of RNA Helicase A to the p16 Promoter (2001)

p16(INK4a) is frequently altered in human cancer, often through epigenetically mediated transcriptional silencing. However, little is known about the transcriptional regulation of this gene. To learn more about such control, we initiated studies of proteins that bind to the promoter in cancer cells that do, and do not, express the gene. We identify RNA helicase A (RHA) as a protein that binds much better to the p16(INK4a) promoter in the expressing cells. RHA has not previously been characterized to manifest sequence-specific DNA interaction but does so to the sequence 5' CGG ACC GCG TGC GC 3' in the p16(INK4a) promoter. The Drosophila homologue to RHA, maleless (Mle), functions in the fly for 2-fold activation of male X-chromosome genes. In our experimental setting, RHA induces a similar modest up-regulation of the p16(INK4a) promoter that is dependent upon its sequence-specific interaction. Mle colocalizes with hyperacetylated H4Ac16 on the X-chromosome and some autosomal loci. The decreased binding of RHA to p16(INK4a) in our cells, where the gene is transcriptionally inactive, is associated with decreased amounts of RHA that immunoprecipitate with acetylated lysine antibodies. Finally, we show RHA to be a cellular substrate for caspase-3, which decreases its sequence-specific binding to p16(INK4a) by cleavage of the N terminus. Thus, we have identified a new protein interaction with the p16(INK4a) promoter that involves an important protein for transcriptional modulation. This interaction is decreased in cancer cells, where this gene is aberrantly transcriptionally silent.
Protein Secretion in Escherichia Coli (1985)

Human coronavirus (HCoV) infection causes respiratory diseases with mild to severe outcomes. In the last 15 years, we have witnessed the emergence of two zoonotic, highly pathogenic HCoVs: severe acute respiratory syndrome coronavirus (SARS-CoV) and ...Read More
An American Academy of Sleep Medicine Review (2000)

Summary: Insomnia is a condition which affects millions of individuals, giving rise to emotional distress, daytime fatigue, and loss of productivity. Despite its prevalence, it has received scant clinical attention. An adequate evaluation of persistent insomnia requires detailed historical information as well as medical, psychological and psychiatric assessment. Use of a classification system for sleep disorders and familiarity with major diagnostic groups will facilitate the clinician's evaluation and treatment. Thorough assessment also requires attention to the unique aspects of presentation and specific set of etiologies which are associated with particular age groups.
Lentiviral Vpx Accessory Factor Targets VprBP/DCAF1 Substrate Adaptor for Cullin 4 E3 Ubiquitin Ligase to Enable Macrophage Infection (2008)

Vpx is a small virion-associated adaptor protein encoded by viruses of the HIV-2/SIVsm lineage of primate lentiviruses that enables these viruses to transduce monocyte-derived cells. This probably reflects the ability of Vpx to overcome an as yet uncharacterized block to an early event in the virus life cycle in these cells, but the underlying mechanism has remained elusive. Using biochemical and proteomic approaches, we have found that Vpx protein of the pathogenic SIVmac 239 strain associates with a ternary protein complex comprising DDB1 and VprBP subunits of Cullin 4-based E3 ubiquitin ligase, and DDA1, which has been implicated in the regulation of E3 catalytic activity, and that Vpx participates in the Cullin 4 E3 complex comprising VprBP. We further demonstrate that the ability of SIVmac as well as HIV-2 Vpx to interact with VprBP and its associated Cullin 4 complex is required for efficient reverse transcription of SIVmac RNA genome in primary macrophages. Strikingly, macrophages in which VprBP levels are depleted by RNA interference resist SIVmac infection. Thus, our observations reveal that Vpx interacts with both catalytic and regulatory components of the ubiquitin proteasome system and demonstrate that these interactions are critical for Vpx ability to enable efficient SIVmac replication in primary macrophages. Furthermore, they identify VprBP/DCAF1 substrate receptor for Cullin 4 E3 ubiquitin ligase and its associated protein complex as immediate downstream effector of Vpx for this function. Together, our findings suggest a model in which Vpx usurps VprBP-associated Cullin 4 ubiquitin ligase to enable efficient reverse transcription and thereby overcome a block to lentivirus replication in monocyte-derived cells, and thus provide novel insights into the underlying molecular mechanism.
Fabrication of BESOI-materials using implanted nitrogen as an effective etch stop barrier (2003)

Summary form only given. Silicon sensors with membrane structures or fabrication of bonding and etch-back silicon-on-insulator (BESOI) materials are commonly produced using p/sup +/-doped silicon as an effective etch stop in EDP or KOH solutions. It is shown that an implanted dose of nitrogen (/sup 14/N/sup +/) in the silicon can also act as an effective etch barrier in EDP solutions. The results show that a dose of 4*10/sup 16/ cm/sup -2/ at 120 keV is enough to drastically decrease the silicon etch rate, from 1.4 mu m/min to practically zero. There are two major advantages to the use of implanted nitrogen as an etch stop. Since the diffusion constant for nitrogen in silicon (at this concentration) is very low as compared to the diffusion of boron and phosphorus, it is easier to get a well-defined thickness if the following process steps includes high-temperature steps. Also, the nitrogen is not an effective electrically active dopant.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Multi router traffic grapher (MRTG) for body area network (BAN) surveillance (2004)

Wireless sensors are capable of gathering real-time data not only from the environment, but also from the signals that the human body can generate. These tiny and smart tags may act as another layer of infrastructure between the physical world and the Internet. However, a complete system of software tools, gateway devices and reliable communication channels are needed to achieve this bridging. In our testbed we tested the limits of implementing a motes based system using commodity based hardware In this paper, the authors discuss a portable and remote health monitoring system using wireless sensors, based on a persistent monitoring of bio-signals from an unwell or elderly person, using the concept of Body Area Network (BAN). All the signals not only from the body but also from the environment, will be stored in a web server and displayed graphically using an existing tool for monitoring network traffic, namely MRTG (Multi Router Traffic Grapher). The aim is to allow secure remote access to certain health parameters in order to alert carers to abnormal body signs, and provide a complete data collection at doctor's disposal. Consequently MRTG can facilitate the determination of how changes in the environment affect vital signs (e.g. correlation between weather and health). The researchers demonstrate that wireless sensors have a very high level of integration with existing tools related to network monitoring. This will enable a new and powerful method for joining physical and networks layers.
Endothelin-1 in Adult Respiratory Distress Syndrome (1993)

Endothelin-1 (ET-1), a potent vasoconstrictor peptide produced by endothelial cells and degraded predominantly in the pulmonary vasculature, has been implicated in the development of various organ dysfunctions. To determine the pathophysiologic role of ET-1 in adult respiratory distress syndrome (ARDS) and the impact of impaired lung function on transpulmonary peptide handling, we compared plasma levels and pulmonary ET-1 balance in 14 patients with ARDS and in seven healthy control subjects. To obtain comparable conditions in both groups, the ET-1 level was raised in the control group by exogenous infusion (0.4 pmol/kg/min) to 9.4 +/- 0.8 pmol/L. ARDS was accompanied by a hyperdynamic circulatory pattern with increased cardiac output and depressed total vascular resistance but, simultaneously, pulmonary hypertension. Venous ET-1 concentration was massively increased in ARDS (9.8 +/- 1.2 versus 2.1 +/- 0.2 pmol/L, p < 0.001). In control subjects, the lung cleared the major fraction of ET-1 (fractional extraction 43 +/- 8.8%, uptake 12.5 +/- 2.5 pmol/min). In contrast, in ARDS there was a pronounced pulmonary releases into the circulation (32.8 +/- 10.3 pmol/min). We conclude that ET-1 concentrations are elevated in ARDS as the result of both increased formation and decreased disposal. Lung failure affects not only gas exchange but also nonrespiratory, metabolic pulmonary functions.
Stability of pantoprazole in an extemporaneously compounded oral liquid (2002)

Journal Article Stability of pantoprazole in an extemporaneously compounded oral liquid Get access Paul J. Dentinger, M.S., Paul J. Dentinger, M.S. Chemist Department of Pharmacy, Strong Memorial Hospital, Rochester Search for other works by this author on: Oxford Academic Google Scholar Chad F. Swenson, B.S., Chad F. Swenson, B.S. Supervisor of Manufacturing Department of Pharmacy, Strong Memorial Hospital, Rochester Search for other works by this author on: Oxford Academic Google Scholar Nasr H. Anaizi, Ph.D. Nasr H. Anaizi, Ph.D. Clinical Pharmacist, Associate Professor Department of Pharmacy, Department of Pharmacology and Physiology, University of Rochester, Rochester. Address correspondence to Dr. Anaizi at the Department of Pharmacy, Box 638, University of Rochester Medical Center, 601 Elmwood Avenue, Rochester, NY 14642 (nasr_anaizi@urmc.rochester.edu). Search for other works by this author on: Oxford Academic Google Scholar American Journal of Health-System Pharmacy, Volume 59, Issue 10, 15 May 2002, Pages 953–956, https://doi.org/10.1093/ajhp/59.10.953 Published: 15 May 2002
Induction of myelodysplasia by myeloid-derived suppressor cells (2013)

Myelodysplastic syndromes (MDS) are age-dependent stem cell malignancies that share biological features of activated adaptive immune response and ineffective hematopoiesis. Here we report that myeloid-derived suppressor cells (MDSC), which are classically linked to immunosuppression, inflammation, and cancer, were markedly expanded in the bone marrow of MDS patients and played a pathogenetic role in the development of ineffective hematopoiesis. These clonally distinct MDSC overproduce hematopoietic suppressive cytokines and function as potent apoptotic effectors targeting autologous hematopoietic progenitors. Using multiple transfected cell models, we found that MDSC expansion is driven by the interaction of the proinflammatory molecule S100A9 with CD33. These 2 proteins formed a functional ligand/receptor pair that recruited components to CD33's immunoreceptor tyrosine-based inhibition motif (ITIM), inducing secretion of the suppressive cytokines IL-10 and TGF- by immature myeloid cells. S100A9 transgenic mice displayed bone marrow accumulation of MDSC accompanied by development of progressive multilineage cytopenias and cytological dysplasia. Importantly, early forced maturation of MDSC by either all-trans-retinoic acid treatment or active immunoreceptor tyrosine-based activation motif-bearing (ITAM-bearing) adapter protein (DAP12) interruption of CD33 signaling rescued the hematologic phenotype. These findings indicate that primary bone marrow expansion of MDSC driven by the S100A9/CD33 pathway perturbs hematopoiesis and contributes to the development of MDS.