gebhart/patrepeval huggingface dataset:
Fitting photosynthetic carbon dioxide response curves for C3 leaves (2007)

Photosynthetic responses to carbon dioxide concentration can provide data on a number of important parameters related to leaf physiology. Methods for fitting a model to such data are briefly described. The method will fit the following parameters: V(cmax), J, TPU, R(d) and g(m)[maximum carboxylation rate allowed by ribulose 1.5-bisphosphate carboxylase/oxygenase (Rubisco), rate of photosynthetic electron transport (based on NADPH requirement), triose phosphate use, day respiration and mesophyll conductance, respectively]. The method requires at least five data pairs of net CO(2) assimilation (A) and [CO(2)] in the intercellular airspaces of the leaf (C(i)) and requires users to indicate the presumed limiting factor. The output is (1) calculated CO(2) partial pressure at the sites of carboxylation, C(c), (2) values for the five parameters at the measurement temperature and (3) values adjusted to 25 degrees C to facilitate comparisons. Fitting this model is a way of exploring leaf level photosynthesis. However, interpreting leaf level photosynthesis in terms of underlying biochemistry and biophysics is subject to assumptions that hold to a greater or lesser degree, a major assumption being that all parts of the leaf are behaving in the same way at each instant.
Optimal Integration and Characteristics of Vertical Array Devices for Ultra-High Density, Bit-Cost Scalable Flash Memory (2007)

Optimal process integration for array devices of bit-cost scalable (BiCS) flash memory is successfully developed. We adopt SiN-based gate dielectrics for the consistency with the 'gate-first' process which is unique to BiCS flash technology, and 'macaroni' body FETs for better controllability over the sub-threshold characteristics of depletion-mode poly-silicon transistors. With these technologies and newly devised 4F <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sup> cell array, BiCS flash becomes a promising candidate for future ultra-high density memory.
Rapid analysis of rearranged kappa light chain genes of circulating polysaccharide-specific B lymphocytes by means of immunomagnetic beads and the polymerase chain reaction. (1993)

Analysis of rearranged immunoglobulin genes used by B lymphocytes of known specificity is an important tool for the study of diversity and selection of B lymphocytes. Usually hybridoma cell lines are used for such analyses, but they are difficult to obtain from humans and may not be representative of the B lymphocytes activated in vivo. Here, we present a method for rapid analysis of the rearranged kappa light chain genes used by human circulating antigen-specific B lymphocytes. After vaccination with Haemophilus influenzae type b capsular polysaccharide (HibCP) conjugated with protein, the HibCP-specific B lymphocytes were isolated by antigen-coated immunomagnetic beads. After the purification, at least 98% of the immunoglobulin-secreting recovered cells were HibCP specific. The RNA was isolated and amplified by cDNA synthesis using a kappa constant region primer followed by polymerase chain reaction (PCR) using in addition a degenerate kappa light chain signal peptide region primer. The PCR product was cloned into the M13mp18 phage. The cloning efficiency was 100-600 clones/ml of blood. Of the 86 clones sequenced, 90% represented rearranged kappa light chain genes from different antibody-secreting cells. Examples of rearranged kappa genes used by HibCP-specific antibody-secreting cells from 4 adult vaccinees are given, representing the 3 largest of the 4 kappa variable region families. This method is a new tool for the investigation of vaccine-induced antibody responses with special reference to immunoglobulin gene usage and variability.
New kits on the blot—can we microarray the future of atherosclerosis? (2003)

See article by Martinet et al. [19] in this issue .

Cardiovascular diseases (CVDs) have a long track record, reaching pandemic proportions with the industrialization of the world. Current estimates of the World Health Organization project that, in less than 7 years from now, CVD will become the leading cause of death in developing countries and that, in less than 13 years from now, 25 million people will die from CVD on a global scale each year [1]. A major proportion of these CVD deaths will be related to atherosclerotic CVD (ASCVD) and, particularly, to its complication stage [2]. Hence, there is a strong call to the cardiovascular research community to identify pivotal mediators of atherosclerotic lesion formation and complication which at some point may turn into therapeutic targets.

What may be considered as searching for a needle in a haystack has been tremendously facilitated by the availability of the microarray technique. This technique, which allows the detection of labeled RNA hybridizing to DNA molecules attached to a solid surface, evolved in a number of steps in the 1960s and 1970s and was finally moved to high capacity in the 1990s [3,4]. Microarray plates with a density of >250,000 oligonucleotides or >10,000 cDNA per cm2 currently serve as a versatile screening probe in genomics research, and it will not be long until arrays become available that allow the screening of the entire genome on one chip for less than one cell and 1 μg of tissue [5,6]. With regard to cardiovascular medicine, DNA microarray assays have already identified a three-digit number of genes potentially involved in atherosclerosis [7–16].

As marvelous as these assays are, they are not without concern. Indeed, a number of potential pitfalls to these kinds of genomic studies have been reported, … 

*Tel.: +1-507-255-1296; fax: +1-507-255-1824. Email address: herrmann.joerg{at}mayo.edu
COMPARISON OF SKIN ALLOGRAFT REJECTION AND CYTOTOXIC ANTIBODY PRODUCTION IN TWO LINES OF MICE GENETICALLY SELECTED FOR ???HIGH??? AND ???LOW??? ANTIBODY SYNTHESIS (1972)

SUMMARY High (Ab/H) and low (Ab/L) responder lines of mice have been separated by selective breeding for their ability to synthesize humoral antibodies against many unrelated antigens. By contrast, no interline difference has been found so far in cell-mediated immunity. In the present article, the immune responsiveness of the two lines against histocompatibility antigens is studied. Interline skin grafts were rejected in 10.4 days by Ab/L mice and in 12.6 days by Ab/H mice. This difference is significant P<0.01. The survival of intraline skin grafts was more prolonged and showed a wide range of rejection times. Cytotoxic antibody production was markedly higher in Ab/H than in Ab/L mice after immunization with spleen cells or following rejection of first- or second-set skin grafts. A clear-cut interline separation between the humoral and cellular immune responses against histocompatibility antigens has therefore been produced by the selective breeding.
A synthetic approach to poly(.gamma.-glutamyl) conjugates of methotrexate (1983)

Methotrexate poly(gamma-L-glutamate)s bearing two and three glutamate units above that present in methotrexate have been synthesized by extension of a previously described route used to synthesize the lower conjugate bearing one added glutamate unit. Key steps in the sequence are the peptide coupling of N-[4-[[(benzyloxy)carbonyl]-methylamino]benzoyl]-L-glutamic acid alpha-benzyl ester (5) with oligo(gamma-L-glutamate) benzyl esters, removal of blocking groups by catalytic hydrogenolysis, and introduction of the (2,4-diamino-6-pteridinyl)methyl grouping by alkylation with 6-(bromomethyl)-2,4-pteridinediamine hydrobromide. Elaboration of the required oligo(gamma-L-glutamate) chain was achieved one unit at a time, beginning with the coupling of L-glutamic acid dibenzyl ester with [(tert-butyloxy)carbonyl]-L-glutamic acid alpha-benzyl ester (7), followed by selective removal of the tert-butyloxycarbonyl grouping and another coupling step with 5 or 7 as required. Diphenylphosphoryl azide was used as the coupling reagent in each conversion producing a peptide linkage.
The inhibition by 6‐diazo‐5‐oxo‐L‐norleucine of glutamine catabolism of the cultured human lymphoblast (1977)

Abstract The rapid catabolism of glutamine by the cultured human lymphoblast line WI‐L2 can be inhibited greater than 95% by incubation of cell suspensions with 6‐diazo‐5‐oxo‐L‐norleucine (DON). The inhibition persists for at least four hours after removal of DON from the cell suspension. The exposure of cells to DON inhibits over 95% of the glutaminase activity measured in lysates in the presence of either phosphate or maleate. Similarly, γ‐glutamyl transpeptidase, assayed with γ‐glutamyl‐p‐nitroanilide as substrate and glycylglycine as acceptor, is inhibited over 90%. DON‐treated and control cells accumulated radioactive material from suspensions containing [ 14 C]‐L‐glutamine at similar initial rates; the radioactive material accumulated by the DON‐treated cells is all recoverable as glutamine while the radioactive material accumulated by untreated cells is principally recovered as glutamate.
Degradation of phytate in the gut of pigs ‐ pathway of gastrointestinal inositol phosphate hydrolysis and enzymes involved (2001)

The present study gives an overview on the whole mechanism of phytate degradation in the gut and the enzymes involved. Based on the similarity of the human and pigs gut, the study was carried out in pigs as model for humans. To differentiate between intrinsic feed phytases and endogenous phytases hydrolysing phytate in the gut, two diets, one high (control diet) and the other one very low in intrinsic feed phytases (phytase inactivated diet) were applied. In the chyme of stomach, small intestine and colon inositol phosphate isomers and activities of phytases and alkaline phosphatases were determined. In parallel total tract phytate degradation and apparent phosphorus digestibility were assessed. In the stomach chyme of pigs fed the control diet, comparable high phytase activity and strong phytate degradation were observed. The predominant phytate hydrolysis products were inositol phosphates, typically formed by plant phytases. For the phytase inactivated diet, comparable very low phytase activity and almost no phytate degradation in the stomach were determined. In the small intestine and colon, high activity of alkaline phosphatases and low activity of phytases were observed, irrespective of the diet fed. In the colon, stronger phytate degradation for the phytase inactivated diet than for the control diet was detected. Phytate degradation throughout the whole gut was nearly complete and very similar for both diets while the apparent availability of total phosphorus was significantly higher for the pigs fed the control diet than the phytase inactivated diet. The pathway of inositol phosphate hydrolysis in the gut has been elucidated.
Amplification protocols introduce systematic but reproducible errors into gene expression studies (2004)

The desire to perform microarray experiments with small starting amounts of RNA has led to the development of a variety of protocols for preparing and amplifying mRNA. This has consequences not only for the standardization of experimental design, but also for reproducibility and comparability between experiments. Here we investigate the differences between the Affymetrix standard and small sample protocols and address the data analysis issues that arise when comparing samples and experiments that have been processed in different ways. We show that data generated on the same platform using different protocols are not directly comparable. Further, protocols introduce systematic biases that can be largely accounted for by using the correct data analysis techniques.
In Vitro Cell Culture Systems as the Basis for an Extracorporeal Blood Purification Strategy In Multiorgan Failure Treatment (1999)

Multiorgan failure (MOF) based on septic processes is very common but prognostically an extremely severe disease that has to be treated exclusively under intensive care conditions. Extracorporeal blood purification (ECBP) using specific and efficient systems such as the microspheres based detoxification system (MDS) (Artif Organs 1996;20:420) could improve significantly the situation of MOF in terms of the efficient removal of endotoxins as well as key mediators such as tumor necrosis factor alpha (TNF alpha). The purpose of the study was to test the effectiveness of endotoxin and cytokine removal to blunt cellular response. In terms of the in vitro principle methodology, isolated peripheral blood mononuclear cells (PBMC) were incubated with endotoxins and a selective endotoxin adsorbent, which was added at various times (immediately or 30, 60, 120, 240, or 360 min) after the onset of incubation. TNF alpha release of monocytes was measured following a standard procedure after 20 h. Human TNF alpha was incubated with cultured human endothelial cells with and without a specific TNF alpha adsorbent (polyclonal antibodies coated on polystyrene particles). The results showed that after the initial addition of endotoxins, the activation of monocytes can be stopped within 120 min by addition of endotoxin adsorbents. In addition, specific TNF alpha adsorbents are able to prevent intercellular adhesion molecule 1 (ICAM-1) expression of endothelial cells, therefore avoiding activation of endothelial cells. In conclusion, cell culture models are suitable to simulate cell interaction in MOF. Specific adsorbents are able to reduce or block pathophysiologically relevant cell interactions, and the time frame for effective ECBP seems to be very short, and therefore, efficiency must be high.
Factors regulating the activities of the low density lipoprotein receptor and the scavenger receptor on human monocyte-macrophages. (1981)

Improved techniques of cell isolation resulted in 90 to 100 million monocytes from a single donor. Addition of low density lipoprotein (LDL) to to cultures of these cells resulted in the down regulation of LDL receptor activity. Addition of malondialdehyde-altered LDL. which enters the cell through a receptor for negatively charged proteins (the scavenger receptor), produced an even greater down regulation of the LDL receptor, indicating that both receptors are present on the same cell. Within hours of adherence of the cells, there was a dramatic decrease in the activity of both receptors. LDL receptor activity was highest during the first week in culture and then declined, despite the maintenance of a constant LDL concentration in the medium. Scavenger receptor activity surpassed LDL receptor activity by the 6th day and was maximally expressed during the second week. Increasing cell density resulted in a slight increase in the activity of the LDL receptor and a dramatic increase in scavenger receptor activity. Insulin had no significant effect on either receptor. Removing serum from the culture medium for 48 hr resulted in a 3.5-fold increase in LDL receptor activity and a 2-fold decrease in scavenger receptor activity. Twenty-four hr after the cells were re-exposed to serum, the activities of both receptors essentially returned to base line. Heat-inactivation of serum was associated with an increased cholesteryl ester content of the cells and depressed receptor activities. Scavenger receptor activity appears related to the maturation of monocytes into macrophages and is promoted by increasing cell density and serum factors that are heat labile.
Differential receivers with highly -uniform MSM Germanium photodetectors capped by SiGe layer (2013)

Waveguide integrated MSM (metal-semiconductor-metal) Germanium (Ge) photodetectors (PDs) with a SiGe capping layer were exploited for silicon photonics integration. Under optimized epitaxial growth conditions, the capping layer passivated the Ge surface, resulting in sufficiently low dark current of the PDs. In addition, the PDs exhibited a narrower distribution of the dark current than PDs with a Si capping layer, probably due to the lower surface leakage current. Low-noise differential receivers with uniform MSM Ge PDs exhibiting 10 Gbps data transmission were realized.
The Impact of Pediatric Vision Disorders in Adulthood (2011)

In addition to refractive errors such as myopia and astigmatism, ocular disorders that occur in infants, toddlers, and children may present lifelong problems for the child. Conditions such as strabismus, amblyopia, and retinopathy of prematurity may require adaptations in adulthood. In addition, vision disorders that occur in childhood may manifest as problems well into adulthood. When visual impairment is present, there may be further effects on overall health, self-perception, educational attainment, job choices, and a number of other social factors.
THE CONTROL OF ELECTROENCEPHALOGRAPHIC ALPHA RHYTHMS THROUGH AUDITORY FEEDBACK AND THE ASSOCIATED MENTAL ACTIVITY (1970)

ABSTRACT Twenty‐six subjects were given baseline tests for electroencephalographic (EEG) alpha rhythm presence, and then a period of fifteen minutes to gain insight into mental activity associated with alpha presence and absence, while provided with an auditory feedback loop keyed to the presence of alpha. Sixteen of the subjects worked with eyes closed, and ten, with very high initial alpha baseline scores, worked with eyes open. After the fifteen minute practice period permitting control of alpha through feedback, the subjects were given a trial during which they attempted to produce as much alpha as possible and a trial in which they tried to produce as little as possible. The results indicated significant appropriate change for both the generation and suppression trials. Those who were able to control alpha spontaneously reported mental states reflecting relaxation, “letting go,” and pleasant affect associated with maintaining alpha.
The NIH Somatic Cell Genome Editing program (2021)

The move from reading to writing the human genome offers new opportunities to improve human health. The United States National Institutes of Health (NIH) Somatic Cell Genome Editing (SCGE) Consortium aims to accelerate the development of safer and more-effective methods to edit the genomes of disease-relevant somatic cells in patients, even in tissues that are difficult to reach. Here we discuss the consortium's plans to develop and benchmark approaches to induce and measure genome modifications, and to define downstream functional consequences of genome editing within human cells. Central to this effort is a rigorous and innovative approach that requires validation of the technology through third-party testing in small and large animals. New genome editors, delivery technologies and methods for tracking edited cells in vivo, as well as newly developed animal models and human biological systems, will be assembled-along with validated datasets-into an SCGE Toolkit, which will be disseminated widely to the biomedical research community. We visualize this toolkit-and the knowledge generated by its applications-as a means to accelerate the clinical development of new therapies for a wide range of conditions.
The LHRH antagonist Cetrorelix: a review (2000)

In those clinical situations in which an immediate and profound suppression of gonadotrophins is desired, LHRH agonists have the disadvantage of producing an initial stimulatory effect on hormone secretion. Therefore, the use of GnRH antagonists which cause an immediate and dose-related inhibition of LH and FSH by competitive blockade of the receptors is much more advantageous. One of the most advanced antagonist produced to date is Cetrorelix, a decapeptide which has been shown to be safe and effective in inhibiting LH and sex-steroid secretion in a variety of animal species and in clinical studies as well. Clinical trials in patients suffering from advanced carcinoma of the prostate, benign prostate hyperplasia, and ovarian cancer are currently in progress and have already shown the usefulness of this new treatment modality. In particular, the concept that a complete suppression of sex-steroids may not be necessary in indications such as uterine fibroma, endometriosis and benign prostatic hyperplasia represents a promising novel perspective for treatment of these diseases. Following completion of phase III trials in controlled ovarian stimulation for IVF regimens, Cetrorelix was given marketing approval and, thus, became the first LHRH antagonist available clinically.
Object-preserving class transformations (1991)

article Object-preserving class transformations Share on Author: Paul L. Bergstein Northeastern University, College of Computer Science, Cullinane Hall, 360 Huntington Ave., Boston, MA Northeastern University, College of Computer Science, Cullinane Hall, 360 Huntington Ave., Boston, MAView Profile Authors Info & Claims ACM SIGPLAN NoticesVolume 26Issue 11Nov. 1991 pp 299–313https://doi.org/10.1145/118014.117977Published:01 November 1991 33citation366DownloadsMetricsTotal Citations33Total Downloads366Last 12 Months3Last 6 weeks0 Get Citation AlertsNew Citation Alert added!This alert has been successfully added and will be sent to:You will be notified whenever a record that you have chosen has been cited.To manage your alert preferences, click on the button below.Manage my AlertsNew Citation Alert!Please log in to your account Save to BinderSave to BinderCreate a New BinderNameCancelCreateExport CitationPublisher SiteGet Access
Molecular cloning of a defective hepatitis C virus genome from the ascitic fluid of a patient with hepatocellular carcinoma. (1997)

A defective hepatitis C virus (HCV) genome in the ascitic fluid of a patient with hepatocellular carcinoma was cloned and sequenced up to the 3' poly(U) stretch. When compared with the published Taiwanese HCV sequence, this defective genome contained deletions of single nucleotides at eight sites, double nucleotides at two sites, triple nucleotides at four sites, quadruple nucleotides at one site and replacement of a short stretch of sequence at one site. For comparison, the corresponding regions containing these mutations were also cloned from a serum sample from this patient. Except for deletions of two triple nucleotides in the hypervariable region, the reading frames of all serum-derived clones were intact. The defective HCV genome encoded a truncated core protein with 90 amino acid residues (the last 20 amino acid residues came from a different reading frame), whereas the serum-derived genome encoded a full-length core protein. When expressed in Huh-7 cells, these two proteins were localized to the nucleus and cytoplasm, respectively. Using specific primer-sets, ascites- and serum-derived genomes were each detected alone in ascitic fluid and serum samples, respectively, whereas both sequences were present in ascitic mononuclear cells. The defective sequence thus constituted the major virus population in the ascitic fluid whereas a putative helper genome coexisted with it inside the ascitic mononuclear cells. This sequence is possibly a defective and interfering genome.
Modeling, simulation and measurements of queuing delay under long-tail internet traffic (2003)

In this paper we describe an analytical approach for estimating the queuing delay distribution on an Internet link carrying realistic TCP traffic, such as that produced by a large number of finite-size connections transferring files whose sizes are taken from a long-tail distribution. The analytical predictions are validated against detailed simulation experiments and real network measurements. Despite its simplicity, our model proves to be accurate and robust under a variety of operating conditions, and offers novel insights into the impact on the network of long-tail flow length distributions. Our contribution is a performance evaluation methodology that could be usefully employed in network dimensioning and engineering.