gebhart/patrepeval huggingface dataset:
Bayesian Compressive Sensing (2008)

The data of interest are assumed to be represented as N-dimensional real vectors, and these vectors are compressible in some linear basis B, implying that the signal can be reconstructed accurately using only a small number M Lt N of basis-function coefficients associated with B. Compressive sensing is a framework whereby one does not measure one of the aforementioned N-dimensional signals directly, but rather a set of related measurements, with the new measurements a linear combination of the original underlying N-dimensional signal. The number of required compressive-sensing measurements is typically much smaller than N, offering the potential to simplify the sensing system. Let f denote the unknown underlying N-dimensional signal, and g a vector of compressive-sensing measurements, then one may approximate f accurately by utilizing knowledge of the (under-determined) linear relationship between f and g, in addition to knowledge of the fact that f is compressible in B. In this paper we employ a Bayesian formalism for estimating the underlying signal f based on compressive-sensing measurements g. The proposed framework has the following properties: i) in addition to estimating the underlying signal f, "error bars" are also estimated, these giving a measure of confidence in the inverted signal; ii) using knowledge of the error bars, a principled means is provided for determining when a sufficient number of compressive-sensing measurements have been performed; iii) this setting lends itself naturally to a framework whereby the compressive sensing measurements are optimized adaptively and hence not determined randomly; and iv) the framework accounts for additive noise in the compressive-sensing measurements and provides an estimate of the noise variance. In this paper we present the underlying theory, an associated algorithm, example results, and provide comparisons to other compressive-sensing inversion algorithms in the literature.
Diagnostic and Prognostic Value of Plasma Tumor M2 Pyruvate Kinase in Periampullary Cancer (2007)

An elevated Tu-M2-PK more than 27 U/mL measured on admission in suspected periampullary cancer is a predictor of adverse prognosis in periampullary cancer.
Quantitative technologies establish a novel microRNA profile of chronic lymphocytic leukemia (2007)

MicroRNAs (miRNAs) are a novel class of small noncoding RNAs that modulate the expression of genes at the posttranscriptional level. These small molecules have been shown to be involved in cancer, apoptosis, and cell metabolism. In the present study we provide an informative profile of the expression of miRNAs in primary chronic lymphocytic leukemia (CLL) cells using 2 independent and quantitative methods: miRNA cloning and quantitative real-time-polymerase chain reaction (qRT-PCR) of mature miRNAs. Both approaches show that miR-21 and miR-155 are dramatically overexpressed in patients with CLL, although the corresponding genomic loci are not amplified. miR-150 and miR-92 are also significantly deregulated in patients with CLL. In addition, we detected a marked miR-15a and miR-16 decrease in about 11% of cases. Finally, we identified a set of miRNAs whose expression correlates with biologic parameters of prognostic relevance, particularly with the mutational status of the IgV(H) genes. In summary, the results of this study offer for the first time a comprehensive and quantitative profile of miRNA expression in CLL and their healthy counterpart, suggesting that miRNAs could play a primary role in the disease itself.
Efficacy of esterified glucomannan to counteract mycotoxicosis in naturally contaminated feed on performance and serum biochemical and hematological parameters in broilers (2003)

A study was conducted to determine the efficacy of esterified glucomannan in counteracting the toxic effects of mycotoxins in naturally contaminated diet (aflatoxin 168 ppb, ochratoxin 8.4 ppb, zearalenone 54 ppb, and T-2 toxin 32 ppb) fed to commercial broilers. One-day-old broiler chicks were randomly assigned to one of the four dietary treatments with five replicates of 14 chicks each. Four dietary treatments were 1) control; 2) esterified glucomannan, an adsorbent, tested at 0.05% of diet; 3) naturally contaminated diet; and 4) esterified glucomannan (0.05%) plus naturally contaminated diet. Body weight, feed consumption, feed efficiency, hematology, and serum biochemical and enzyme activities were evaluated. Compared with the control, the naturally contaminated diet significantly decreased body weight and feed consumption and resulted in poor feed efficiency. Esterified glucomannan effectively alleviated the growth depression caused by the naturally contaminated diet. Increased relative weights of liver and gizzard were observed in chicks fed the naturally contaminated diet. Further, feeding a naturally contaminated diet was associated with significant decreases in urea nitrogen and hematocrit values along with altered gamma-glutamyl transferase activity; however, urea nitrogen concentration was improved with addition of esterified glucomannan. These findings suggest that addition of dietary esterified glucomannan is effective in counteracting the toxic effects of naturally contaminated feed with mycotoxins.
Structural analysis of recombinant von Willebrand factor: Identification of hetero‐ and homo‐dimers (1994)

Wild-type full-length cDNA of von Willebrand factor (vWF) was expressed in CHO cells. Recombinant vWF (rvWF) was obtained and its molecular composition investigated by two-dimensional electrophoresis. Results of first dimension electrophoresis under non-reducing conditions showed that rvWF-dimer represents a mixture of three different species. Second dimension electrophoresis under reducing conditions revealed, that these protein species represent (i) homo-dimers of either two unprocessed or two fully processed, mature vWF polypeptides, and (ii) the hetero-dimer of unprocessed and mature rvWF monomers. Compared with vWF-dimers from human plasma, which contained predominantly proteolytically degraded polypeptides, recombinant vWF-dimers were shown to consist of non-proteolyzed subunits only.
Richardson–Lucy algorithm with total variation regularization for 3D confocal microscope deconvolution (2006)

Confocal laser scanning microscopy is a powerful and popular technique for 3D imaging of biological specimens. Although confocal microscopy images are much sharper than standard epifluorescence ones, they are still degraded by residual out-of-focus light and by Poisson noise due to photon-limited detection. Several deconvolution methods have been proposed to reduce these degradations, including the Richardson-Lucy iterative algorithm, which computes maximum likelihood estimation adapted to Poisson statistics. As this algorithm tends to amplify noise, regularization constraints based on some prior knowledge on the data have to be applied to stabilize the solution. Here, we propose to combine the Richardson-Lucy algorithm with a regularization constraint based on Total Variation, which suppresses unstable oscillations while preserving object edges. We show on simulated and real images that this constraint improves the deconvolution results as compared with the unregularized Richardson-Lucy algorithm, both visually and quantitatively.
Binding of the 97 kDa glucocorticoid receptor to the 5' upstream flanking region of the mouse c-Ha-ras oncogene. (1989)

Glucocorticoids regulate transcription of specific genes through the interaction of glucocorticoid hormone receptor complexes with DNA binding sites called glucocorticoid response elements (GREs). The GRE consensus sequence has been defined to be the imperfect palindromic sequence 5'-GGTACANNNTGTTCT-3', the most highly conserved portion being the 5'-TGTTCT-3' hexamer. We have identified 5 potential GREs in the 5' upstream noncoding region of the mouse c-Ha-ras oncogene, two with the same hexanucleotide sequence and three with a similar sequence. When subcloned fragments of the mouse c-Ha-ras 5' upstream region (containing the 2 hexamer GREs of exact homology) were fused to the chloramphenicol acetyltransferase (CAT) reporter gene and transfected into HeLa cells, CAT expression driven from the ras promoter was induced up to 3-fold in the presence of dexamethasone. To determine whether the 5' upstream region of the mouse Ha-ras gene was capable of specifically interacting with the glucocorticoid receptor complex, we performed Southwestern blot analysis showing that cloned DNA fragments from the 5' upstream region of the mouse c-Ha-ras gene were able to bind a 97 kDa protein in whole cell extracts from both primary SENCAR mouse epidermal cells and HeLa G cells. Immunodepletion of the epidermal cell extract with a monoclonal antibody to the glucocorticoid receptor verified that the 97 kDa protein bound by the Ha-ras 5' region was indeed the glucocorticoid receptor protein. Our results demonstrate that the upstream noncoding region of the mouse c-Ha-ras gene binds the glucocorticoid receptor. Furthermore, the presence of glucocorticoids enhances the transcription of the mouse Ha-ras promoter region in a transient gene expression assay.
Infection of macaque monkeys with a chimeric human and simian immunodeficiency virus (1992)

Two macaque monkeys were inoculated with a chimeric human and simian immunodeficiency virus carrying the tat, rev, vpu and env genes of human immunodeficiency virus type 1. Infectious virus was recovered from one of the monkeys at 2 and 6 weeks post-infection. The hybrid nature of the isolated viruses was verified by Southern and Western blotting analyses. Both of the monkeys infected with the chimera elicited a humoral antibody response against the virus.
19 Early Events in Human Herpesvirus Infection of Cells (1994)

Herpesviruses are large, highly complex enveloped viruses containing linear double-stranded DNA. Following primary infection, which is frequently inapparent, the intact viral genome persists in host cells for the life of the individual. Since the presence of the viral genome does not significantly impair normal cellular functions, herpesvirus latent infections are largely asymptomatic. Latently infected cells also escape destruction by the immune system, in part because few viral proteins that can be recognized and targeted by the immune system are produced during latency. In addition, some herpesviruses have evolved specific strategies that interfere with immune recognition. Many, if not all, latent herpesvirus infections are interrupted by periods of reactivation induced by trauma, stress, infection, immunosuppression, or other processes. With reactivation, herpesviruses enter the productive phase of the viral life cycle, and viral particles are produced. Virus production leads to death of the host cell. Furthermore, virus-producing cells are targeted for destruction by the immune system. Destruction of cells and immune processes lead to inflammation with its associated symptomatology. Most of the herpesviruses are ubiquitous pathogens. For example, more than 90% of individuals worldwide have been exposed to herpes simplex virus type 1 (HSV-1) and Epstein-Barr virus (EBV) by adulthood. The other human herpesviruses, which include cytomegalovirus (HCMV), varicella zoster virus (VZV), herpes simplex virus type 2 (HSV-2), and herpesviruses 6, 7, and 8 (or 6A, 7, and 6B) are also quite prevalent in most populations. Herpesviruses have been found in many species. Marek’s disease in chickens, Aujeszky’s disease in pigs, and...
Nonthoracotomy Implantable Cardioverter Defibrillator Placement in Children: Use of Subcutaneous Array Leads and Abdominally Placed Implantable Cardioverter Defibrillators in Children (2001)

In children in whom endocardial, right ventricular placement of a defibrillation lead is precluded, defibrillation is possible and safe between an abdominally placed "active can" ICD device and a subcutaneous array lead. This approach may avoid a thoracotomy in children with no possibility for transvenous ICD placement.
Functional basis of protection against age-related macular degeneration conferred by a common polymorphism in complement factor B (2009)

Mutations and polymorphisms in complement genes have been linked with numerous rare and prevalent disorders, implicating dysregulation of complement in pathogenesis. The 3 common alleles of factor B (fB) encode Arg (fB(32R)), Gln (fB(32Q)), or Trp (fB(32W)) at position 32 in the Ba domain. The fB(32Q) allele is protective for age-related macular degeneration, the commonest cause of blindness in developed countries. Factor B variants were purified from plasma of homozygous individuals and were tested in hemolysis assays. The protective variant fB(32Q) had decreased activity compared with fB(32R). Biacore comparison revealed markedly different proenzyme formation; fB(32R) bound C3b with 4-fold higher affinity, and formation of activated convertase was enhanced. Binding and functional differences were confirmed with recombinant fB(32R) and fB(32Q); an intermediate affinity was revealed for fB(32W). To confirm contribution of Ba to binding, affinity of Ba for C3b was determined. Ba-fB(32R) had 3-fold higher affinity compared with Ba-fB(32Q). We demonstrate that the disease-protective effect of fB(32Q) is consequent on decreased potential to form convertase and amplify complement activation. Knowledge of the functional consequences of polymorphisms in complement activators and regulators will aid disease prediction and inform targeting of diagnostics and therapeutics.
Identification of Markers for Newly Formed β-Cells in the Perinatal Period: A Time of Recognized β-Cell Immaturity (2010)

Markers of beta-cell maturity would be useful in staging the differentiation of stem/progenitor cells to beta-cells whether in vivo or in vitro. We previously identified markers for newly formed beta-cells in regenerating rat pancreases after 90% partial pancreatectomy. To test the generality of these markers of newly formed beta-cells, we examined their expression during the perinatal period, a time of recognized beta-cell immaturity. We show by semiquantitative RT-PCR and immunostaining over the time course from embryonic day 18/20 to birth, 1 day, 2 days, 3 days, 7 days, and adult that MMP-2, CK-19, and SPD are truly markers of new and immature beta-cells and that their expression transiently peaks in the perinatal period and is not entirely synchronous. The shared expression of these markers among fetal, newborn, and newly regenerated beta-cells, but not adult, strongly supports their use as potential markers for new beta-cells in the assessment of both the maturity of stem cell-derived insulin-producing cells and the presence of newly formed islets (neogenesis) in the adult pancreas.
repairing a double-strand break (2000)

roken chromosomes pose a serious threat to cell sur-vival. The presence of an unrepaired double-strandbreak (DSB) will trigger the DNA-damage response sys-tems of a cell to arrest its progression through the cellcycle and, sometimes, to cause apoptotic cell death. Buteven if a cell with an unrepaired DSB continues to divide,the broken chromosome fragments will mis-segregate andbe degraded, producing aneuploidy.In response to this threat, cells have elaborated animpressive arsenal of DNA-repair pathways. There aretwo general types of repair: homologous recombination(HR) and nonhomologous end-joining (NHEJ). These twoprocesses are in competition with each other and onefocus of this review is to examine the way that this compe-tition is regulated. But the cell’s options are far more com-plex than simply electing to employ HR or NHEJ. Thereare several types of homologous repair: gene conversion,break-induced replication and single-strand annealing(reviewed in Ref. 1). Similarly, there are also several alter-native end-joining mechanisms
Quadratic state-space modeling technique for analysis and simulation of power electronic converters (2002)

This paper presents a quadratic state-space modeling technique for analysis and simulation of power electronic converters. The methodology is based on using least-square-error fitting to derive a quadratic state-space representation for each topology, together with automatic determinations of switching topology. The algorithm integrates the advantages of calculating circuit responses at circuit level and determining switching instants at device level. Several key features of the new model that leads to significant improvements in computational efficiency include: (1) its simplicity of using quadratic polynomial representation for each circuit topology; (2) its directness of calculating the switching instants; and (3) its generality of determining valid topology without prior understanding of the switching relationships. Several examples illustrating the generality and simulation speed of the proposed approach are presented. The accuracy of the new approach is verified with the exact method. The computational efficiency is demonstrated by comparing its simulation time with the commercial software using a stepwise integration algorithm.
Two murine homologues of the human chemokine receptor CXCR4 mediating stromal cell‐derived factor 1α activation of Gi2 are differentially expressed in vivo (1997)

Previous results have shown that pertussis toxin-sensitive Gi proteins are likely to be involved in regulating the emigration of mature thymocytes from the thymus. In this study, a low stringency polymerase chain reaction (PCR) approach was used to identify Gi protein-coupled cell surface receptors expressed in mouse thymocytes. Among the ten G protein-coupled receptor cDNA isolated, the most prevalent cDNA encoded a polypeptide highly homologous to the human leukocyte-expressed seven-transmembrane-domain receptor LESTR, also referred to as HIV entry cofactor, fusin, or CXCR4. Isolation of full-length cDNA revealed that alternative RNA splicing produces transcripts encoding two isoforms of the murine LESTR, differing by the presence of two amino acids in the N-terminal portion of the longer protein. Functional reconstitution of recombinant murine LESTR with recombinant heterotrimeric G proteins in baculovirus-infected insect cells showed that both receptor variants mediate stromal cell-derived factor 1alpha activation of the pertussis toxin-sensitive G protein Gi2. Receptor subtype-specific reverse transcriptase-PCR analysis revealed differential expression of the two receptor mRNA in lymphoid tissues and brain, indicating that distinct functions are mediated by the two receptor isoforms in these tissues. The presence of LESTR mRNA in very early thymocytes as well as in immature (CD4+ CD8+) thymocytes suggests that both CD4 and LESTR are co-expressed and render developing human thymocytes susceptible for HIV entry, which may affect generation of both CD4+ CD8- and CD4- CD8+ mature lineages.
Role of N-linked glycans of envelope glycoproteins in infectivity of human immunodeficiency virus type 1 (1990)

We have shown that enzymatic removal of N-linked glycans from human immunodeficiency virus type 1 (HIV-1) recombinant envelope glycoproteins gp160 and gp120 produced in BHK-21 cells did not significantly reduce their ability to bind to CD4, the cellular receptor for the virus. Because recombinant proteins may behave differently from proteins present on virions, we investigated whether such viral envelope glycoproteins either in a purified form or present on viral particles could be deglycosylated by treatment with an endoglycosidase F-N-glycanase mixture which cleaves all accessible glycan moieties. Endoglycosidase analysis of the carbohydrate composition of purified viral gp120 (vgp120) indicated a glycosylation pattern similar to that for recombinant gp120 (rgp120), and treatment with endoglycosidase F-N-glycanase resulted in comparable molecular weight (MW) reduction for both molecules. Similarly, after immunoblotting of the deglycosylated viral preparation, the characteristic 160- and 120-kilodalton (kDa) bands were replaced by 90- and 60-kDa bands, respectively. The apparent MW of gp41 shifted to 35 kDa. These results are consistent with complete deglycosylation. The immunoreactive conformation of envelope glycoproteins remained unaltered after deglycosylation: they were recognized to the same extent by specific human polyclonal or mouse monoclonal antibodies, and no proteolysis of viral proteins occurred during enzymatic treatment. Deglycosylation of vgp120 resulted in a less than 10-fold reduction of the ability to bind to CD4, presented either in a soluble form or at the cell membrane. In addition, deglycosylation significantly reduced, but did not abolish, HIV-1 binding to and infectivity of CD4+ cells as determined, respectively, by an indirect immunofluorescence assay and a quantitative dose-response infection assay. Taken together, these results indicate that removal of glycans present on mature envelope glycoproteins of HIV-1 diminishes but does not abolish either virus binding to CD4 or its capacity to infect CD4+ cells.
Primary Structure of an Allergenic Peptide Occurring in the Chymotryptic Hydrolysate of Gluten (1995)

An allergenic peptide was isolated from the chymotryptic hydrolysate of gluten by gel filtration and HPLC. The primary structure of the peptide was determined as Ser-Gln-Gln-Gln-Gln- Pro-Pro-Phe-Ser-Gln-Gln-Gln-Pro-Pro-Phe-Ser-Gln-Gln-Gln-Gln-Pro-Pro-Phe- Ser- Gln-Gln-Gln-Gln-Pro-Pro-Phe-Ser-Gln-Gln-Gln-Pro-Pro-Phe. The amino acid sequence similarity shows that the peptide originated from a low-molecular-weight glutenin chain.
Mechanism of the Reductive Half-reaction in Cellobiose Dehydrogenase (2003)

The extracellular flavocytochrome cellobiose dehydrogenase (CDH; EC ) participates in lignocellulose degradation by white-rot fungi with a proposed role in the early events of wood degradation. The complete hemoflavoenzyme consists of a catalytically active dehydrogenase fragment (DH(cdh)) connected to a b-type cytochrome domain via a linker peptide. In the reductive half-reaction, DH(cdh) catalyzes the oxidation of cellobiose to yield cellobiono-1,5-lactone. The active site of DH(cdh) is structurally similar to that of glucose oxidase and cholesterol oxidase, with a conserved histidine residue positioned at the re face of the flavin ring close to the N5 atom. The mechanisms of oxidation in glucose oxidase and cholesterol oxidase are still poorly understood, partly because of lack of experimental structure data or difficulties in interpreting existing data for enzyme-ligand complexes. Here we report the crystal structure of the Phanerochaete chrysosporium DH(cdh) with a bound inhibitor, cellobiono-1,5-lactam, at 1.8-A resolution. The distance between the lactam C1 and the flavin N5 is only 2.9 A, implying that in an approximately planar transition state, the maximum distance for the axial 1-hydrogen to travel for covalent addition to N5 is 0.8-0.9 A. The lactam O1 interacts intimately with the side chains of His-689 and Asn-732. Our data lend substantial structural support to a reaction mechanism where His-689 acts as a general base by abstracting the O1 hydroxyl proton in concert with transfer of the C1 hydrogen as hydride to the re face of the flavin N5.
Preparing for Trial (1988)

This is the first practical chapter in the book. We shall take a look at the nuts and bolts of preparing for trial, giving and taking instructions, and gathering the evidence. This is where we start to put legal theory into practice. While it may be possible to scrape through the court process by looking out of one's depth and obtaining the sympathy of the court, there is no way that anyone, be they social worker, litigant in person, or even advocate, can be successful in court without first making adequate preparation.