gebhart/patrepeval huggingface dataset:
Comprehensive Assessment of Potential Multiple Myeloma Immunoglobulin Heavy Chain V-D-J Intraclonal Variation Using Massively Parallel Pyrosequencing (2012)

Multiple myeloma (MM) is characterized by the accumulation of malignant plasma cells (PCs) in the bone marrow (BM). MM is viewed as a clonal disorder due to lack of verified intraclonal sequence diversity in the immunoglobulin heavy chain variable region gene (IGHV). However, this conclusion is based on analysis of a very limited number of IGHV subclones and the methodology employed did not permit simultaneous analysis of the IGHV repertoire of non-malignant PCs in the same samples. Here we generated genomic DNA and cDNA libraries from purified MM BMPCs and performed massively parallel pyrosequencing to determine the frequency of cells expressing identical IGHV sequences. This method provided an unprecedented opportunity to interrogate the presence of clonally related MM cells and evaluate the IGHV repertoire of non-MM PCs. Within the MM sample, 37 IGHV genes were expressed, with 98.9% of all immunoglobulin sequences using the same IGHV gene as the MM clone and 83.0% exhibiting exact nucleotide sequence identity in the IGHV and heavy chain complementarity determining region 3 (HCDR3). Of interest, we observed in both genomic DNA and cDNA libraries 48 sets of identical sequences with single point mutations in the MM clonal IGHV or HCDR3 regions. These nucleotide changes were suggestive of putative subclones and therefore were subjected to detailed analysis to interpret: 1) their legitimacy as true subclones; and 2) their significance in the context of MM. Finally, we report for the first time the IGHV repertoire of normal human BMPCs and our data demonstrate the extent of IGHV repertoire diversity as well as the frequency of clonally-related normal BMPCs. This study demonstrates the power and potential weaknesses of in-depth sequencing as a tool to thoroughly investigate the phylogeny of malignant PCs in MM and the IGHV repertoire of normal BMPCs.
Increase in dicentric chromosome formation after a single CT scan in adults (2015)

Excess risk of leukemia and brain tumors after CT scans in children has been reported. We performed dicentric chromosome assay (DCAs) before and after CT scan to assess effects of low-dose ionizing radiation on chromosomes. Peripheral blood (PB) lymphocytes were collected from 10 patients before and after a CT scan. DCA was performed by analyzing either 1,000 or 2,000 metaphases using both Giemsa staining and centromere-fluorescence in situ hybridization (Centromere-FISH). The increment of DIC formation was compared with effective radiation dose calculated using the computational dosimetry system, WAZA-ARI and dose length product (DLP) in a CT scan. Dicentric chromosome (DIC) formation increased significantly after a single CT scan, and increased DIC formation was found in all patients. A good correlation between the increment of DIC formation determined by analysis of 2,000 metaphases using Giemsa staining and those by 2,000 metaphases using Centromere-FISH was observed. However, no correlation was observed between the increment of DIC formation and the effective radiation dose. Therefore, these results suggest that chromosome cleavage may be induced by one CT scan, and we recommend 2,000 or more metaphases be analyzed in Giemsa staining or Centromere-FISH for DCAs in cases of low-dose radiation exposure.
The electrode system in impedance-based ventilation measurement (1992)

In this paper, we determined which electrode types, sizes, and locations were best suited for impedance-based ventilation measurement. Optimal electrodes provide high signal-to-(motion) artifact ratio (SAR) and reliability by meeting the following criteria: 1) low baseline impedance, 2) high adhesion, 3) good physical stability, 4) large effective area, 5) thin with high flexibility. We compared 14 electrodes from two main groups: adhesive-gel and conductive rubber electrodes. Adhesive-gel electrodes are easy to apply, make good body contact, and do not slip during the course of an experiment. We found that higher SAR's are obtained when electrode area is increased by connecting several small electrodes together rather than by using a single electrode with a larger area. The peak SAR is achieved when two electrode arrays (area = 70 cm2) are centered at the 8th intercostal spaces on opposite midaxillary lines. To determine the optimal electrode locations, we placed 32 electrodes on the trunk and recorded impedance between 171 electrode combinations on ten normal adult subjects. Based on these data, we conclude that the SAR's are highest when one electrode is placed on the midpoint between the left and right second intercostal spaces on the sternum and the other electrode is placed in the opposite position on the back.
Activation and sensitisation of the vanilloid receptor: role in gastrointestinal inflammation and function (2004)

The exquisite specific excitatory and desensitising actions of capsaicin on a subpopulation of primary sensory neurons have been instrumental in identifying the roles of these neurons in nociception, reflex responses and neurogenic inflammation. Structure activity studies with capsaicin-like molecules have suggested that a "receptor" should mediate the effects of capsaicin on sensory neurons. The cloning of the vanilloid receptor-1 (VR1) has confirmed this hypothesis. VR1 (TRPV1) belongs to the transient receptor potential (TRP) family of channels, and its activation by various xenobiotics, noxious temperature, extracellular low pH and high concentration of certain lipid derivatives results in cation influx and sensory nerve terminal excitation. TRPV1 may dimerise or form tetramers or heteromers with PLC-gamma and TrkA or even with other TRPs. TRPV1 is markedly upregulated and/or "sensitised" under inflammatory conditions via protein kinase C-epsilon-, cAMP-dependent PK- and PLC-gamma-dependent pathways or by exposure to dietary agents as ethanol. TRPV1 is expressed on sensory neurons distributed in all the regions of the gastrointestinal tract in myenteric ganglia, muscle layer and mucosa. There is evidence of TRPV1 expression also in epithelial cells of the gastrointestinal tract. High expression of TRPV1 has been detected in several inflammatory diseases of the colon and ileum, whereas neuropeptides released upon sensory nerve stimulation triggered by TRPV1 activation seem to play a role in intestinal motility disorders. TRPV1 antagonists, which will soon be available for clinical testing, may undergo scrutiny for the treatment of inflammatory diseases of the gut.
The effect of grain size on thermal conductivity of quartz sands and silts (1998)

Synthetic samples of different grain size fractions of quartz were prepared and the thermal conductivities measured with a divided bar apparatus. The measurements were carried out on dried and water-saturated samples both perpendicular and parallel to the main stress direction during compaction of the samples. A clear correlation was observed between the porosity and the measured thermal conductivities. For water-saturated samples the thermal conductivity decreases more with increasing porosity than for ideal isotropic material as predicted by the geometric mean model. A clear positive correlation was also found between the thermal conductivity and the grain sizes of the samples. When the expected effect of porosity on the thermal conductivity was excluded, a linear correlation between the logarithm of the grain size and the measured thermal conductivities of the water-saturated samples was found. An anisotropy effect (a = k/k 1 ) in thermal conductivity was observed for the samples, being most prominent for the coarsest ones. The measured anisotropy is assumed to be mainly due to the thermal anisotropic nature of the quartz crystal.
Syndecan-1 restitution by plasma after hemorrhagic shock (2015)

From the Shock Trauma Center (R.A.K.), University of Maryland, Baltimore, Maryland; and Blood Systems Research Institute and the University of California (S.P.), San Francisco, California. Submitted: October 24, 2014, Revised: January 20, 2015, Accepted: February 2, 2015. Presented at the 4th Annual Remote Damage Control Resuscitation Symposium of the Trauma Hemostasis and Oxygenation Research Network, June 9–11, 2014, in Bergen, Norway. The opinions or assertions contained herein are the private views of the authors and are not construed as official or reflecting the views if the U.S. Department of Defense or the U.S. Government. Address for reprints: Rosemary Kozar, MD, PhD, Shock Trauma Center, 22 South Green St., S4D07 Baltimore, MD 21201; email: [email protected].
Hybrid intravascular ultrasound and optical coherence tomography catheter for imaging of coronary atherosclerosis (2012)

Preliminary ex vivo images using a hybrid IVUS-OCT catheter demonstrated feasibility in using the device for intracoronary imaging of atherosclerosis. Future studies will include in vivo imaging and larger samples sizes to enable quantitative comparisons of tissue characterization and feature identification using hybrid imaging catheters versus standalone IVUS and OCT imaging techniques. © 2012 Wiley Periodicals, Inc.
The effect of l-ascorbate on catecholamine biosynthesis (Short Communication) (1973)

l-Ascorbate stimulates the enzymic hydroxylation of phenylalanine in vitro by recycling tetrahydrobiopterin, which reduces O(2) utilized in the reaction. It is suggested that ascorbate might have a similar function in vivo; this would explain the apparent regulation of tyrosine hydroxylase and tryptophan hydroxylase activities by this vitamin.
Understanding consumer database marketing (1997)

As consumer marketers have become increasingly disenchanted with traditional “shotgun” mass‐media approaches to reaching customers, database marketing has emerged as the answer to marketers’ woes. Despite its widespread use by direct marketers, database marketing is relatively new to consumer marketers and, as such, leaves some consumer marketers confused as to why it works and how to implement a database program. Presents a managerially relevant introduction to database marketing. Defines database marketing, outlines its advantages and disadvantages and describes application examples. Provides managers with a practical approach to developing a database marketing program. Reviews some trends in database marketing to prepare the consumer marketer for changes in the database marketing program.
Initiation of Increased Pancreatic Islet Growth in Young Normoglycemic Mice (Umea +/?) (1999)

Pancreatic islets from obese hyperglycemic mice are large and contain a high proportion of normally functioning -cells.We have previously shown that young obese mice have an elevated -cell proliferation rate at 3 weeks of age.We now wanted to investigate possible factors involved in the initiation of islet growth, including blood glucose, C peptide, glucagon-like peptide-1, vasoactive intestinal polypeptide, and L-5-hydroxytryptophan.We found that the increased -cell proliferation on day 20 precedes the rise in blood glucose by 2 days.The islet cell proliferation, measured as the 5-bromo-2-de- Injection of animalsOn day 18, obese mice were separated from their lean littermates.In the evening of day 18, during the morning, midday, and evening of day 19, and during the morning of day 20, lean mice were injected with 13, 27, 40, and 53 nmol/kg BW GLP-1 (Sigma Chemical Co., St. Louis, MO); 1.8, 5.4, and 16 nmol/kg synthetic human C peptide (Sigma Chemical Co.); 400 nmol/kg vasoactive intestinal polypeptide (VIP; Sigma Chem-
Costs and predictors of costs in rheumatoid arthritis: A prevalence‐based study (2003)

Abstract Objective To analyze the annual cost of rheumatoid arthritis (RA) and its predictive factors. Methods Data were obtained from a 12‐month retrospective cohort of 201 RA patients, randomly selected from a rheumatology registry, through a structured interview and records of the Central Information System of the hospital. Results were divided into direct, indirect, and total costs in 2001 US dollars. A sensitivity analysis was performed. Multiple linear regression models for the different types of costs were carried out. Results The total cost was $2.2 million per year, with a cost attributable to RA of $2.07 million per year. The average cost per patient was $10,419 per year (ranging from $7,914 per patient per year in the best scenario to $12,922 per patient per year in the worst case). Direct costs represent nearly 70% of total costs. We found an average increment in total costs of $11,184 per year per unit of Health Assessment Questionnaire (HAQ) score ( P &lt; 0.0001) and an average annual increment of $621 per year of disease ( P &lt; 0.0001). After adjustment, the HAQ score, inability to perform housework tasks, and being permanently disabled for work were the only predictors of high costs. Conclusion Our data show a remarkable economic impact of RA over society and link the costs of the disease to its consequences in terms of functional disability, work disability, and housework disability.
Synthetic Modification of Silica Beads That Allows for Sequential Attachment of Two Different Oligonucleotides (2006)

We developed a simple and elegant synthesis strategy that enables us to attach controlled (equimolar) amounts of two different oligonucleotides onto one silica bead. The method involves addition of orthogonally protected lysine followed by activation and derivatization of each amino group with a different moiety. This sequential oligonucleotide attachment enables the use of a combinatorial scheme to generate millions of bead types, each characterized by its two oligo tags. (In our randomly assembled arrays each bead type can then be identified by a series of hybridizations of fluorescently labeled decoder oligos to the address tags.) To demonstrate feasibility of such a scheme we created over 1000 bead types, which were characterized by their two oligo tags. The method enables genotyping or gene expression assays at multiplex levels of hundreds of thousands to millions.
Down-regulation of G9a triggers DNA damage response and inhibits colorectal cancer cells proliferation (2015)

G9a, a histone methyltransferase, is aberrantly expressed in some human tumor types. By comparing 182 paired colorectal cancer and peritumoral tissues, we found that G9a was highly expressed in colorectal cancer (CRC). Overexpression of G9a promoted CRC cells proliferation and colony formation, whereas knockdown of G9a inhibited CRC cells proliferation. Depletion of G9a increased the rate of chromosome aberration, induced DNA double strand breaks and CRC cells senescence. G9a inhibition synergistically increased γH2AX expression induced by topoisomerase I inhibitors and ultimately led to CRC cell death. The findings that down-regulation of G9a triggers DNA damage response and inhibits colorectal cancer cells proliferation may define G9a as potential oncotarget in CRC.
Dietary fiber for dogs: IV. In vitro fermentation of selected fiber sources by dog fecal inoculum and in vivo digestion and metabolism of fiber-supplemented diets (1995)

Two experiments were conducted to evaluate single sources and blends of dietary fiber in dog food. In Exp. 1, 14 fibrous substrates were fermented in vitro using dog feces as the source of inoculum. Organic matter disappearance was lowest (P < .05; < 10%) for Solka Floc and oat fiber and greatest (P < .05; > 80%) for fructooligosaccharides (FOS) and lactulose. Solka Floc, oat fiber, gum karaya, and xanthan gum produced the least (P < .05; < 1 mmol/g of substrate OM) total short-chain fatty acids (SCFA). Lactulose, citrus pectin, and guar gum produced the greatest (P < .05; > 6.8 mmol/g of substrate OM) total SCFA. In Exp. 2, six diets were formulated based on results obtained in Exp. 1. Treatments included 1) beet pulp (BP), 2) Solka Floc (SF), 3) citrus pulp (CP), 4) stool blend (SB), 5) SCFA blend (SC), and 6) combination blend (CB). Digestibility of DM and total dietary fiber (TDF) was greatest (P < .05; 87.3 and 60.8%, respectively) for dogs consuming the SC diet. Feces from dogs fed SC were scored as more unformed and liquid in consistency than feces from dogs fed the other diets. Dogs consuming the SF and SB diets had the lowest (P < .05; 11.0 and 4.1%, respectively) TDF digestibilities. Organic matter disappearance values derived from substrates fermented in vitro reasonably predicted the fiber digestibility of diets fed to dogs. Moderately fermentable dietary fiber sources, such as BP, promote excellent stool characteristics without compromising nutrient digestibility, and may promote gastrointestinal tract health by optimizing SCFA production.
Use of Fluorescence Resonance Energy Transfer To Investigate the Conformation of DNA Substrates Bound to the Klenow Fragment (1998)

Fluorescence resonance energy transfer (FRET) has been used to investigate the conformation of the single stranded region for a series of fluorescent DNA template-primers bound to the Klenow fragment (KF) of Escherichia coli DNA polymerase I. Fluorescent derivatives of template-primer DNA, modified with tetramethylrhodamine (TMR), served as energy transfer acceptors to the donor fluorescein fluorophore used to modify cysteine 751 in the double mutant KF (S751C, C907S). Design of the template-primer allowed the probe's position within the DNA-protein complex to be varied by stepwise extension of the primer strand upon addition of the appropriate deoxynucleoside triphosphates (dNTP). The TMR acceptor probe occupied seven different positions in the template-primers, five in the single stranded region and two in the double stranded region. The efficiency of energy transfer was determined at each position by calculating the integrated area of the fluorescein emission peak in the presence and absence of acceptor. Results indicate that the FRET efficiency varied in a sinusoidal fashion with a periodicity of approximately 10 base pairs and that the data could be fitted to an equation derived from a simple model formulated on the basis of helical structure. The data support the conclusion that the single stranded template portion of a DNA template-primer adopts a helical conformation when bound to the KF. The results of this study further support FRET as a useful method for the determination of structure and conformation in protein-DNA complexes.
A prospective phase II trial exploring the association between tumor microenvironment biomarkers and clinical activity of ipilimumab in advanced melanoma (2011)

Baseline expression of immune-related tumor biomarkers and a post-treatment increase in TILs may be positively associated with ipilimumab clinical activity. The observed pharmacodynamic changes in gene expression warrant further analysis to determine whether treatment-emergent changes in gene expression may be associated with clinical efficacy. Further studies are required to determine the predictive value of these and other potential biomarkers associated with clinical response to ipilimumab.
Soluble TLT-1 modulates platelet–endothelial cell interactions and actin polymerization (2010)

Triggering receptor expressed on myeloid cells (TREM) like transcript-1 (TLT-1) is a membrane protein receptor found in alpha-granules of platelets and megakaryocytes. Upon platelet activation TLT-1 is rapidly brought to the surface of platelets. Recently, we demonstrated that activated platelets release a soluble form of TLT-1 (sTLT-1) that is found in serum but not in the plasma of healthy individuals and can enhance platelet aggregation in vitro. Furthermore, evaluation of patients diagnosed with inflammatory diseases, such as sepsis, show that these patients have significantly elevated levels of sTLT-1 in their blood. Accordingly, mice deficient in TLT-1 are predisposed to bleeding in response to an inflammatory challenge; however, the mechanism of TLT-1 function remains unknown. In this investigation, we demonstrate an increase in the amount of platelets that adhere to endothelial cell monolayers in the presence of recombinant sTLT-1 (rsTLT-1). Additionally, we present evidence that rsTLT-1 increases platelet adherence to glass slides by stimulating actin polymerization in platelets, as determined by increased staining of rodamine phalloidin. These results suggest that during inflammation, sTLT-1 may mediate hemostasis by enhancing actin polymerization, resulting in increased platelet aggregation and adherence to the endothelium.
The Biomedical Aspects of Lasers (1964)

THERE IS much to interest the physician in the development of that fascinating instrument of modern physics, the laser. Although the first working laser was produced as late as July, 1960,<sup>1</sup>laser development is now one of the greatest research fields of modern science. However, except for a few exceptions in the biomedical and microwelding fields, it remains a laboratory tool for scientific research. It is to medicine that most research workers in laser technology look for immediate practical developments, although up to the present there has not been much investigation of lasers in the field of medicine. The laser produces a beam of coherent electromagnetic radiation of a sharply defined wavelength in that region of the spectrum broadly described as optical. This range includes the near-violet, the visible, and the near and far regions in the infrared. The term "coherence" is to be emphasized because it is an
Bulk flow of cerebrospinal fluid into brain in response to acute hyperosmolality (1987)

Brain volume is regulated during acute hyperosmolality based, in part, on the tissue gain of Na, Cl, and K. This study evaluates the contribution of bulk flow of cerebrospinal fluid (CSF) into brain to the volume regulatory gain of electrolytes. Artificial CSF containing radiolabeled albumin and diethylenetriamine penta-acetic acid (DTPA) was perfused for 60 min through the ventricles and/or subarachnoid space of anesthetized rats, and tracer clearances from CSF to brain were measured as a function of plasma osmolality. Osmolality was elevated after 30 min of perfusion by intraperitoneal injection of hypertonic NaCl or mannitol. Albumin and DTPA clearances increased with osmolality at the same rate, despite a sevenfold difference in diffusion coefficient, consistent with osmotic stimulation of a bulk flow component of tracer influx into brain. The volume shift estimated on the basis of this data is 114 microliters CSF/g dry wt brain for a 60-mosmol/kg increase in osmolality. Results indicate that CSF is a major source of the volume regulatory gain of Na and Cl, but not of K.
ANTIBIOTIC USE IN PLANT AGRICULTURE (2002)

▪ Abstract Antibiotics have been used since the 1950s to control certain bacterial diseases of high-value fruit, vegetable, and ornamental plants. Today, the antibiotics most commonly used on plants are oxytetracycline and streptomycin. In the USA, antibiotics applied to plants account for less than 0.5% of total antibiotic use. Resistance of plant pathogens to oxytetracycline is rare, but the emergence of streptomycin-resistant strains of Erwinia amylovora, Pseudomonas spp., and Xanthomonas campestris has impeded the control of several important diseases. A fraction of streptomycin-resistance genes in plant-associated bacteria are similar to those found in bacteria isolated from humans, animals, and soil, and are associated with transfer-proficient elements. However, the most common vehicles of streptomycin-resistance genes in human and plant pathogens are genetically distinct. Nonetheless, the role of antibiotic use on plants in the antibiotic-resistance crisis in human medicine is the subject of debate.
Protein oxidative damage in the stratum corneum: evidence for a link between environmental oxidants and the changing prevalence and nature of atopic dermatitis in Japan (2003)

This study has found an association between AD severity and markers of ROS-associated damage, adding weight to the hypothesis that environmentally generated ROS may induce oxidative protein damage in the stratum corneum, leading to the disruption of barrier function and exacerbation of AD.