gebhart/patrepeval huggingface dataset:
Solubility of CaHPO4 2H2O in the system Ca(OH)2-H3PO4-H2O at 5, 15, 25, and 37.5 C (1970)

Solubility isotherms for CaHPO<sub>4</sub> · 2H<sub>2</sub>O, dicalcium phosphate dihydrate, DCPD, in the ternary system Ca(OH)<sub>2</sub> - H<sub>3</sub>PO<sub>4</sub> - H<sub>2</sub>O were determined at 5, 15, 25, and 37.5 °C in the pH range 3.5 - 7; the relative positions of the isotherms indicate that DCPD has a negative thermal coefficient of solubility. The solubility product, <i>K</i> <sub><i>s</i></sub> , of DCPD and the stability constants <i>K</i> <sub><i>x</i></sub> and <i>K</i> <sub><i>y</i></sub> for the ion pairs <mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML"><mml:mrow><mml:mo>[</mml:mo> <mml:msubsup><mml:mrow><mml:mtext>CaHPO</mml:mtext></mml:mrow> <mml:mn>4</mml:mn> <mml:mn>0</mml:mn></mml:msubsup> <mml:mo>]</mml:mo></mml:mrow> </mml:math> and <mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML"> <mml:mrow><mml:mrow><mml:mo>[</mml:mo> <mml:mrow> <mml:msub><mml:mrow><mml:mtext>CaH</mml:mtext></mml:mrow> <mml:mn>2</mml:mn></mml:msub> <mml:msubsup><mml:mrow><mml:mtext>PO</mml:mtext></mml:mrow> <mml:mn>4</mml:mn> <mml:mo>+</mml:mo></mml:msubsup> </mml:mrow> <mml:mo>]</mml:mo></mml:mrow> </mml:mrow> </mml:math> , respectively, were obtained as functions of temperature by the use of a generalized least squares procedure subject to three condition functions - constancy of the solubility product, electrical neutrality in the solution, and congruent dissolution of the solid. The equations obtained are <DispFormula> <mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML"> <mml:mtable> <mml:mtr><mml:mtd><mml:mtext>ln </mml:mtext> <mml:msub><mml:mi>K</mml:mi> <mml:mi>s</mml:mi></mml:msub> <mml:mo>=</mml:mo> <mml:mo>-</mml:mo> <mml:mtext>8403</mml:mtext> <mml:mn>.5</mml:mn> <mml:mo>/</mml:mo> <mml:mi>T</mml:mi> <mml:mo>+</mml:mo> <mml:mtext>41</mml:mtext> <mml:mo>.</mml:mo> <mml:mtext>863</mml:mtext> <mml:mo>-</mml:mo> <mml:mtext>0</mml:mtext> <mml:mo>.</mml:mo> <mml:mtext>09678</mml:mtext> <mml:mi>T</mml:mi></mml:mtd> </mml:mtr> <mml:mtr><mml:mtd><mml:mtext>​ln </mml:mtext> <mml:msub><mml:mi>K</mml:mi> <mml:mi>x</mml:mi></mml:msub> <mml:mo>=</mml:mo> <mml:mo>-</mml:mo> <mml:mtext>51090</mml:mtext> <mml:mo>/</mml:mo> <mml:mi>T</mml:mi> <mml:mo>-</mml:mo> <mml:mn>341.14</mml:mn> <mml:mo>+</mml:mo> <mml:mtext>0</mml:mtext> <mml:mo>.</mml:mo> <mml:mtext>5880</mml:mtext> <mml:mi>T</mml:mi></mml:mtd> </mml:mtr> <mml:mtr><mml:mtd><mml:mtext>​ln </mml:mtext> <mml:msub><mml:mi>K</mml:mi> <mml:mi>y</mml:mi></mml:msub> <mml:mo>=</mml:mo> <mml:mo>-</mml:mo> <mml:mtext>19373</mml:mtext> <mml:mo>/</mml:mo> <mml:mi>T</mml:mi> <mml:mo>-</mml:mo> <mml:mn>122.81</mml:mn> <mml:mo>+</mml:mo> <mml:mtext>0</mml:mtext> <mml:mo>.</mml:mo> <mml:mtext>1994</mml:mtext> <mml:mi>T</mml:mi></mml:mtd> </mml:mtr> </mml:mtable> </mml:math> </DispFormula> The existence of a maximum in <i>K</i> <sub><i>s</i></sub> in the neighborhood of 25 °C is plausible on the basis of available thermodynamic data for DCPD. Thermodynamic functions are reported for the solution of DCPD and for the association of the ion pairs.
Self-nonself discrimination in a computer (2002)

The problem of protecting computer systems can be viewed generally as the problem of learning to distinguish self from other. The authors describe a method for change detection which is based on the generation of T cells in the immune system. Mathematical analysis reveals computational costs of the system, and preliminary experiments illustrate how the method might be applied to the problem of computer viruses.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
A Gateway-Compatible Yeast One-Hybrid System (2004)

Since the advent of microarrays, vast amounts of gene expression data have been generated. However, these microarray data fail to reveal the transcription regulatory mechanisms that underlie differential gene expression, because the identity of the responsible transcription factors (TFs) often cannot be directly inferred from such data sets. Regulatory TFs activate or repress transcription of their target genes by binding to cis-regulatory elements that are frequently located in a gene's promoter. To understand the mechanisms underlying differential gene expression, it is necessary to identify physical interactions between regulatory TFs and their target genes. We developed a Gateway-compatible yeast one-hybrid (Y1H) system that enables the rapid, large-scale identification of protein-DNA interactions using both small (i.e., DNA elements of interest) and large (i.e., gene promoters) DNA fragments. We used four well-characterized Caenorhabditis elegans promoters as DNA baits to test the functionality of this Y1H system. We could detect approximately 40% of previously reported TF-promoter interactions. By performing screens using two complementary libraries, we found novel potentially interacting TFs for each promoter. We recapitulated several of the Y1H-based protein-DNA interactions using luciferase reporter assays in mammalian cells. Taken together, the Gateway-compatible Y1H system will allow the high-throughput identification of protein-DNA interactions and may be a valuable tool to decipher transcription regulatory networks.
Coordinate up-regulation of low-density lipoprotein receptor and cyclo-oxygenase-2 gene expression in human colorectal cells and in colorectal adenocarcinoma biopsies (1999)

Many colorectal cancers have high levels of cyclo-oxygenase 2 (COX-2), an enzyme that metabolizes the essential fatty acids into prostaglandins. Since the low-density lipoprotein receptor (LDLr) is involved in the uptake of essential fatty acids, we studied the effect of LDL on growth and gene regulation in colorectal cancer cells. DiFi cells grown in lipoprotein-deficient sera (LPDS) grew more slowly than cells with LDL. LDLr antibody caused significant inhibition of tumor cell growth but did not affect controls. In addition, LDL uptake did not change in the presence of excess LDL, suggesting that ldlr mRNA lacks normal feedback regulation in some colorectal cancers. Analysis of the ldlr mRNA showed that excess LDL in the medium did not cause down-regulation of the message even after 24 hr. The second portion of the study examined the mRNA expression of ldlr and its co-regulation with cox-2 in normal and tumor specimens from patients with colorectal adenocarcinomas. The ratio of tumor:paired normal mucosa of mRNA expression of ldlr and of cox-2 was measured in specimens taken during colonoscopy. ldlr and cox-2 transcripts were apparent in 11 of 11 carcinomas. There was significant coordinate up-regulation both of ldlr and of cox-2 in 6 of 11 (55%) tumors compared with normal colonic mucosa. There was no up-regulation of cox-2 without concomitant up-regulation of ldlr. These data suggest that the LDLr is abnormally regulated in some colorectal tumors and may play a role in the up-regulation of cox-2.
A new biological contribution of cyclo(His-Pro) to the peripheral inhibition of pancreatic secretion (1997)

The tripeptide pyro-Glu-His-Pro-NH2[thyrotropin-releasing hormone (TRH)] was isolated from the hypothalamus as a thyrotropin-releasing factor. It has a broad spectrum of central nervous system-mediated actions, including the stimulation of exocrine pancreatic secretion. TRH is also synthesized in the endocrine pancreas and found in the systemic circulation. Enzymatic degradation of TRH in vivo produces other bioactive peptides such as cyclo(His-Pro). Because of the short half-life of TRH and the stability of cyclo(His-Pro) in vivo, we postulated that at least part of the peripheral TRH effects on the exocrine pancreatic secretion may be attributed to cyclo(His-Pro), which has been shown to have other biological activities. This study determines in parallel the peripheral effects of TRH and cyclo(His-Pro) as well as the putative contribution of other TRH-related peptides on exocrine pancreatic secretion in rats. TRH and its metabolite cyclo(His-Pro) dose dependently inhibited 2-deoxy-D-glucose (2-DG)-stimulated pancreatic secretion. TRH and all the related peptides tested had no effect on the basal and cholecystokinin-stimulated amylase release from pancreatic acinar cells in vitro. These data indicate that cyclo(His-Pro) mimics the peripheral inhibitory effect of TRH on 2-DG-stimulated exocrine pancreatic secretion. This effect is not detected on isolated pancreatic acini. Our findings provide a new biological contribution for cyclo(His-Pro) with potential experimental and clinical applications.
Accurate interpolation with high-resolution time-variant Radon transforms (2002)

Abstract It is well known that a sparse hyperbolic Radon transform (RT) can be used to extend the aperture of aperture limited data, filter noise, and fill gaps. In the same manner, an elliptical RT can achieve similar results when applied to slant stack sections. A problem with these transformations is that they have a time-variant kernel that results in slow implementation. By defining a model space in terms of an irregularly sampled velocity space to minimize the number of unknowns during the inversion and using sparse matrices, however, the computation time can be kept low enough for practical application. We implement hyperbolic and elliptical time domain RTs by using inversion via weighted conjugate gradient methods with a sparseness constraint. The hyperbolic RT performs accurate interpolation in common-midpoint (CMP) gathers, while the elliptical RT attenuates sampling artifacts in slant stack sections obtained from CMP gathers with poor sampling and gaps.
Platelet Concentrates Stored at 22°C Need Oxygen The Significance of Plastics in Platelet Preservation (1983)

Platelet concentrates prepared by platelet apheresis were stored in plastic blood bags with different gas permeability properties. Inadequate oxygen supply gave an insufficient adenosine triphosphate (ATP) regeneration and a compensatory increase in glycolysis and lactic acid production, giving a rapidly falling pH. At pH below 6.0 the glycolysis was inhibited, oxygen consumption ceased, and ATP dropped towards depletion. Adequate oxygen supply kept the lactic acid production low with small pH changes only, and allowed a sufficient ATP regeneration. The release of alpha-granular platelet Factor 4 (PF4) was almost total at pH below 6.0, while at intact metabolic function there was a slow release of PF4. Platelet preservation is enhanced by the use of blood bags with adequate gas exchange properties. In our study one polyvinyl chloride plastic (PVC) bag gave poor results, while another PVC bag and a polyolefin bag showed intact metabolism for 5 days and a moderate release of PF4.
Analysis of antigenic reactivity of synthetic monosaccharide lipid A analogues with monoclonal antibodies (1987)

In vitro antigenic reactivity of chemically synthesized monosaccharide analogues of nonreducing sugar moiety of lipid A with 4 monoclonal antibodies against Salmonella minnesota R595 lipid A was studied by the inhibition test of enzyme-linked immunosorbent assay (ELISA). In the assays with 2 monoclonal antibodies (mAb 5G and mAb36G), which have been suggested to recognize the Salmonella type lipid A structure, no antigenic reactivity of the tested analogues was observed. However, several monosaccharide analogues exhibited antigenic reactivities with other monoclonal antibodies (mAb161M and mAb19M), especially some structural differences of hydrophobic and/or hydrophilic parts among monosaccharide analogues were recognized by mAb161M.
Expression of the heparan sulfate proteoglycan glypican-1 in the developing rodent (1998)

The glypicans are a family of glycosylphosphatidylinositol (GPI)-anchored proteoglycans that, by virtue of their cell-surface localization and possession of heparan sulfate chains, may regulate the responses of cells to numerous heparin-binding growth factors, cell adhesion molecules, and extracellular matrix components. Mutations in one glypican cause a syndrome of human birth defects, suggesting important roles for these proteoglycans in development. Glypican-1, the first-discovered member of this family, was originally found in cultured fibroblasts, and later shown to be a major proteoglycan of the mature and developing brain. Here we examine the pattern of glypican-1 mRNA and protein expression more widely in the developing rodent, concentrating on late embryonic and early postnatal stages. High levels of glypican-1 expression were found throughout the brain and skeletal system. In the brain, glypican-1 mRNA was widely, and sometimes only transiently, expressed by zones of neurons and neuroepithelia. Glypican-1 protein localized strongly to axons and, in the adult, to synaptic terminal fields as well. In the developing skeletal system, glypican-1 was found in the periosteum and bony trabeculae in a pattern consistent with expression by osteoblasts, as well as in the bone marrow. Glypican-1 was also observed in skeletal and smooth muscle, epidermis, and in the developing tubules and glomeruli of the kidney. Little or no expression was observed in the developing heart, lung, liver, dermis, or vascular endothelium at the stages examined. The tissue-, cell type-, and in some cases stage-specific expression of glypican-1 revealed in this study are likely to provide insight into the functions of this proteoglycan in development.
Imaging with microstructured polymer fibre (2004)

The imaging capabilities of a multicore microstructured polymer optical fibre with a square array of 112 air holes are demonstrated. Coherent imaging is achieved either by guiding light in polymer cores between air holes, or by guiding light in the air channels themselves. This potentially provides a miniaturised endoscope for medical applications, or a two-dimensional parallel optical data link for high-bandwidth interconnects.
THE CYSTEINYL LEUKOTRIENE D4 RECEPTOR ANTAGONIST MONTELUKAST FOR THE TREATMENT OF INTERSTITIAL CYSTITIS (2001)

Montelukast treatment resulted in significant improvement in urinary frequency and pain. Its efficacy for decreasing urinary frequency and pain imply a role of leukotriene receptor antagonists for managing interstitial cystitis but further placebo controlled clinical studies are needed.
Convolutional Matrix Factorization for Document Context-Aware Recommendation (2016)

Sparseness of user-to-item rating data is one of the major factors that deteriorate the quality of recommender system. To handle the sparsity problem, several recommendation techniques have been proposed that additionally consider auxiliary information to improve rating prediction accuracy. In particular, when rating data is sparse, document modeling-based approaches have improved the accuracy by additionally utilizing textual data such as reviews, abstracts, or synopses. However, due to the inherent limitation of the bag-of-words model, they have difficulties in effectively utilizing contextual information of the documents, which leads to shallow understanding of the documents. This paper proposes a novel context-aware recommendation model, convolutional matrix factorization (ConvMF) that integrates convolutional neural network (CNN) into probabilistic matrix factorization (PMF). Consequently, ConvMF captures contextual information of documents and further enhances the rating prediction accuracy. Our extensive evaluations on three real-world datasets show that ConvMF significantly outperforms the state-of-the-art recommendation models even when the rating data is extremely sparse. We also demonstrate that ConvMF successfully captures subtle contextual difference of a word in a document. Our implementation and datasets are available at http://dm.postech.ac.kr/ConvMF.
Identification of a Clinically Relevant Androgen-Dependent Gene Signature in Prostate Cancer (2011)

The androgen receptor (AR) is the principal target for treatment of non-organ-confined prostate cancer (PCa). Androgen deprivation therapies (ADT) directed against the AR ligand-binding domain do not fully inhibit androgen-dependent signaling critical for PCa progression. Thus, information that could direct the development of more effective ADTs is desired. Systems and bioinformatics approaches suggest that considerable variation exists in the mechanisms by which AR regulates expression of effector genes, pointing to a role for secondary transcription factors. A combination of microarray and in silico analyses led us to identify a 158-gene signature that relies on AR along with the transcription factor SRF (serum response factor), representing less than 6% of androgen-dependent genes. This AR-SRF signature is sufficient to distinguish microdissected benign and malignant prostate samples, and it correlates with the presence of aggressive disease and poor outcome. The AR-SRF signature described here associates more strongly with biochemical failure than other AR target gene signatures of similar size. Furthermore, it is enriched in malignant versus benign prostate tissues, compared with other signatures. To our knowledge, this profile represents the first demonstration of a distinct mechanism of androgen action with clinical relevance in PCa, offering a possible rationale to develop novel and more effective forms of ADT.
Design-for-debug for post-silicon validation: Can high-level descriptions help? (2009)

Post-silicon validation is an essential step in the design flow, which is needed to demonstrate that the implemented circuit meets its intended behavior. Due to lack of in-system controllability and observability, design-for-debug hardware is employed to aid post-silicon validation. A number of solutions have been proposed to implement the design-for-debug hardware, as well as to analyze the debug data that is acquired. Although the design entry is done at the register-transfer level, the existing approaches to aid post-silicon validation rely primarily on the information extracted from the gate level circuit descriptions. We anticipate that, as the design complexity continues to grow, extracting and processing circuit information at this level will become increasingly difficult. In this paper, we briefly summarize the known art and discuss some possible directions of investigation that can utilize high-level circuit descriptions to augment the existing solutions.
Clinical Signs of Infection in Diabetic Foot Ulcers With High Microbial Load (2009)

Individual signs of infection do not perform well nor does the IDSA combination of signs. However, a composite predictor based on all signs provides a moderate level of discrimination, suggesting clinical use. Larger sample sizes and alternate reference standards are recommended.
Channel-independent synchronization of orthogonal frequency division multiple access systems (2002)

We develop synchronization algorithms for both the downlink and the uplink of quasi-synchronous and asynchronous orthogonal frequency division multiple access systems. Unlike existing alternatives, the proposed time- and carrier-offset estimators do not require the transmission of known sequences and exhibit performance independent of the underlying channel zero locations. The only necessary assumption is that there are virtual subcarriers which are not occupied by any user. We derive a closed-form variance expression for the carrier-offset estimator at high signal-to-noise ratio (SNR), as a function of the number of active users and the SNR. We compare our method with alternative ones and validate our theoretical derivations with simulation results.
Monoclonal antibodies: will they become an integral part of the evaluation and treatment of prostate cancer - focus on prostate-specific membrane antigen? (1999)

Over the past two decades, monoclonal antibody technology has had an increasing impact on clinical diagnostic and therapeutic options, and this is true in the realm of managing prostate cancer. Several targets such as prostate-specific antigen and prostatic acid phosphatase as well as, more recently, angiogenic antigens such as vascular endothelial growth factor have been examined for therapy. Prostate-specific membrane antigen, a type II integral membrane glycoprotein initially characterized by the monoclonal antibody 7E11, has shown promise. Recent evidence suggests that prostate-specific membrane antigen is also expressed in tumor-associated neovasculature of a wide variety of malignant neoplasms. With its expression in prostate secretory-acinar epithelium and the prostate and in the neovasculature associated with tumors, prostate-specific membrane antigen represents an excellent antigenic target for monoclonal antibody diagnostic and therapeutic options. As research continues, the role of monoclonal antibody imaging and therapy will become increasingly important in the management of prostate cancer.
Automatic synthesis of asynchronous circuits from high-level specifications (1989)

The authors construct a processor design approach that does not require the distribution of a clocking signal. To facilitate design of processors that use fully asynchronous components, the first step is to design hazard-free asynchronous interconnection circuits. To this end, a deterministic algorithm was developed to synthesize asynchronous interconnection circuits from high-level specifications. This approach systematically designs correct asynchronous interconnection circuits with the weakest possible constraints and minimal overhead. The authors are primarily concerned with the synthesis of nonmetastable circuits, even though the procedure is also valid of metastable circuit synthesis. The synthesized logic is hazard-free and guaranteed to have the fastest operation according to a behavioral specification. A high-level description is used to specify circuit behavior, not only for a simpler input format, but also as a basis for determining the final optimum designs. Automatic synthesis and the ability to localize the timing considerations reduce design effort when systems become complex.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Preclinical Evaluation of Novel Glutamate-Urea-Lysine Analogues That Target Prostate-Specific Membrane Antigen as Molecular Imaging Pharmaceuticals for Prostate Cancer (2009)

Prostate-specific membrane antigen (PSMA) is expressed in normal human prostate epithelium and is highly up-regulated in prostate cancer. We previously reported a series of novel small molecule inhibitors targeting PSMA. Two compounds, MIP-1072, (S)-2-(3-((S)-1-carboxy-5-(4-iodobenzylamino)pentyl)ureido)pentanedioic acid, and MIP-1095, (S)-2-(3-((S)-1carboxy-5-(3-(4-iodophenyl)ureido)pentyl)ureido)pentanedioic acid, were selected for further evaluation. MIP-1072 and MIP-1095 potently inhibited the glutamate carboxypeptidase activity of PSMA (K(i) = 4.6 +/- 1.6 nmol/L and 0.24 +/- 0.14 nmol/L, respectively) and, when radiolabeled with (123)I, exhibited high affinity for PSMA on human prostate cancer LNCaP cells (K(d) = 3.8 +/- 1.3 nmol/L and 0.81 +/- 0.39 nmol/L, respectively). The association of [(123)I]MIP-1072 and [(123)I]MIP-1095 with PSMA was specific; there was no binding to human prostate cancer PC3 cells, which lack PSMA, and binding was abolished by coincubation with a structurally unrelated NAALADase inhibitor, 2-(phosphonomethyl)pentanedioic acid (PMPA). [(123)I]MIP-1072 and [(123)I]MIP-1095 internalized into LNCaP cells at 37 degrees C. Tissue distribution studies in mice showed 17.3 +/- 6.3% (at 1 hour) and 34.3 +/- 12.7% (at 4 hours) injected dose per gram of LNCaP xenograft tissue, for [(123)I]MIP-1072 and [(123)I]MIP-1095, respectively. [(123)I]MIP-1095 exhibited greater tumor uptake but slower washout from blood and nontarget tissues compared with [(123)I]MIP-1072. Specific binding to PSMA in vivo was shown by competition with PMPA in LNCaP xenografts, and the absence of uptake in PC3 xenografts. The uptake of [(123)I]MIP-1072 and [(123)I]MIP-1095 in tumor-bearing mice was corroborated by single-photon emission computed tomography/computed tomography (SPECT/CT) imaging. PSMA-specific radiopharmaceuticals should provide a novel molecular targeting option for the detection and staging of prostate cancer.