gebhart/patrepeval huggingface dataset:
Whole-Herd Optimization with the Cornell Net Carbohydrate and Protein System. I. Predicting Feed Biological Values for Diet Optimization with Linear Programming (2000)

We developed a diet optimizer for least-cost diet formulation with the Cornell Net Carbohydrate and Protein System (CNCPS) using linear programming. The CNCPS model is intrinsically nonlinear, and feed biological values vary with animal and feed characteristics. To allow linear diet optimization, we first used the CNCPS model to generate biological values to characterize the energy and protein content of each feed for the specific group for which the diet was being formulated. The biological values used were metabolizable energy (Mcal/kg), metabolizable protein [(% dry matter (DM)], passage rate (%/h), bacteria yield efficiencies (g/g), and degradation rate of the carbohydrate B2 fraction (%/h). In addition, the ruminal balances for nitrogen and peptides were included in the optimizer to optimize ruminal degradation of fiber. The objective function was to minimize diet cost subject to animal requirement and feed availability constraints. The animal constraints were set by requirements for DM intake (kg/d), metabolizable energy (Mcal/kg), metabolizable protein (%DM), and effective neutral detergent fiber (%DM) for a given level of production. Data from a dairy farm were used to evaluate this linear diet optimizer. Across all classes of dairy cattle, the CNCPS 4.0 model typically obtained a solution in less than six iterations that met the requirements with nearly 100% accuracy. We conclude this linear optimizer can be used to accurately formulate least-cost diets with the CNCPS model.
Catalase Is Differentially Expressed in Dividing and Nondividing Protoplasts (1994)

Based on our previous results that peroxidase is induced in dividing tobacco protoplasts but it is not expressed in the nondividing grapevine (Vitis vinifera L.) protoplasts during culture (C.I. Siminis, A.K. Kanellis, K.A. Roubelakis-Angelakis [1993] Physiol Plant 87: 263-270), we further tested the hypothesis that oxidative stress may be implicated in the recalcitrance of plant protoplasts. The expression of catalase, a major defense enzyme against cell oxidation, was studied during isolation and culture of mesophyll protoplasts from the recalcitrant grapevine and regenerating tobacco (Nicotiana tabacum L.). Incubation of tobacco leaf strips with cell wall-degrading enzymes resulted in a burst of catalase activity and an increase in its immunoreactive protein; in contrast, no such increases were found in grapevine. The cathodic and anodic catalase isoforms consisted exclusively of subunits [alpha] and [beta], respectively, in tobacco, and of subunits [beta] and [alpha], respectively, in grapevine. The catalase specific activity increased only in grapevine protoplasts during culture. The ratio of the enzymatic activities to the catalase immunoreactive protein declined in dividing tobacco protoplasts and remained fairly constant in nondividing tobacco and grapevine protoplasts during culture. Also, in dividing tobacco protoplasts the de novo accumulation of the catalase [beta] subunit gave rise to the acidic isoenzymes, whereas in nondividing tobacco and grapevine protoplasts, after 8 d in culture, only the basic isoenzymes remained due to de novo accumulation of the [alpha] subunit. The pattern of catalase expression in proliferating tobacco leaf cells during callogenesis was similar to that in dividing protoplasts. The different responses of catalase expression in dividing and nondividing tobacco and grapevine mesophyll protoplasts may indicate a specificity of catalase related to induction of totipotency.
Preventive Effects ofEscherichia coliStrain Nissle 1917 on Acute and Chronic Intestinal Inflammation in Two Different Murine Models of Colitis (2004)

Escherichia coli strain Nissle 1917 (EcN) is as effective in maintaining remission in ulcerative colitis as is treatment with mesalazine. This study aims to evaluate murine models of acute and chronic intestinal inflammation to study the antiinflammatory effect of EcN in vivo. Acute colitis was induced in mice with 2% dextran-sodium sulfate (DSS) in drinking water. EcN was administered from day -2 to day +7. Chronic colitis was induced by transfer of CD4(+) CD62L(+) T lymphocytes from BALB/c mice in SCID mice. EcN was administered three times/week from week 1 to week 8 after cell transfer. Mesenteric lymph node (MLN) cytokine secretion (of gamma interferon [IFN-gamma], interleukin 5 [IL-5], IL-6, and IL-10) was measured by enzyme-linked immunosorbent assay. Histologic sections of the colon were analyzed by using a score system ranging from 0 to 4. Intestinal contents and homogenized MLN were cultured, and the number of E. coli-like colonies was determined. EcN was identified by repetitive extragenic palindromic (REP) PCR. EcN administration to DSS-treated mice reduced the secretion of proinflammatory cytokines (IFN-gamma, 32,477 +/- 6,377 versus 9,734 +/- 1,717 [P = 0.004]; IL-6, 231 +/- 35 versus 121 +/- 17 [P = 0.02]) but had no effect on the mucosal inflammation. In the chronic experimental colitis of the transfer model, EcN ameliorated the intestinal inflammation (histology score, 2.7 +/- 0.2 versus 1.9 +/- 0.3 [P = 0.02]) and reduced the secretion of proinflammatory cytokines. Translocation of EcN and resident E. coli into MLN was observed in the chronic colitis model but not in healthy controls. Administration of EcN ameliorated acute and chronic experimental colitis by modifying proinflammatory cytokine secretion but had no influence on the acute DSS-induced colitis. In this model, preexisting colitis was necessary for translocation of EcN and resident E. coli into MLN.
Epothilone B and its Analogs - A New Family of Anticancer Agents (2003)

Epothilones are naturally occurring 16-membered macrolides with the ability to promote tubulin polymerization in vitro and to stabilize preformed microtubules against Ca(2+)- or cold-induced depolymerization. In contrast to paclitaxel (Taxol((R))) epothilones are also active in vitro against multidrug-resistant cancer cell lines as well as cell lines whose paclitaxel-resistance is derived from specific beta-tubulin mutations. Based on their attractive in vitro biological profile epothilones have turned into important lead structures in anticancer drug discovery and hundreds of analogs and derivatives of epothilone A and B have been prepared and biologically characterized over the past four years. A number of compounds, including natural epothilone B, deoxyepothilone B, and epothilone B lactam (BMS-247550) have also been reported to exhibit profound in vivo antitumor activity in animal models. Apart from providing a brief summary of the SAR that has emerged from the above in vitro studies, this minireview will largely focus on the biology and chemistry of those analogs for which in vivo antitumor activity has been reported in the literature. Two of these compounds, natural epothilone B and epothilone B lactam (BMS-247550) have advanced to clinical studies in humans.
Monitoring of complement activation biomarkers and eculizumab in complement-mediated renal disorders (2016)

Various complement-mediated renal disorders are treated currently with the complement inhibitor eculizumab. By blocking the cleavage of C5, this monoclonal antibody prevents cell damage caused by complement-mediated inflammation. We included 23 patients with atypical haemolytic uraemic syndrome (aHUS, n = 12), C3 glomerulopathies (C3G, n = 9) and acute antibody-mediated renal graft rejection (AMR, n = 2), treated with eculizumab in 12 hospitals in Germany. We explored the course of complement activation biomarkers and the benefit of therapeutic drug monitoring of eculizumab. Complement activation was assessed by analysing the haemolytic complement function of the classical (CH50) and the alternative pathway (APH50), C3 and the activation products C3d, C5a and sC5b-9 prior to, 3 and 6 months after eculizumab treatment. Eculizumab concentrations were determined by a newly established specific enzyme-linked immunosorbent assay (ELISA). Serum eculizumab concentrations up to 1082 μg/ml point to drug accumulation, especially in paediatric patients. Loss of the therapeutic antibody via urine with concentrations up to 56 μg/ml correlated with proteinuria. In aHUS patients, effective complement inhibition was demonstrated by significant reductions of CH50, APH50, C3d and sC5b-9 levels, whereas C5a levels were only reduced significantly after 6 months' treatment. C3G patients presented increased C3d and consistently low C3 levels, reflecting ongoing complement activation and consumption at the C3 level, despite eculizumab treatment. A comprehensive complement analysis together with drug monitoring is required to distinguish mode of complement activation and efficacy of eculizumab treatment in distinct renal disorders. Accumulation of the anti-C5 antibody points to the need for a patient-orientated tailored therapy.
Great Expectations: Expectation Based Reasoning in Medical Diagnosis. (1988)

Several different approaches to knowledge representation for medical expert systems have been explored. We suggest that a modified version of the script formalism, which we term “expectation-based reasoning”, may offer an additional knowledge representation for medical information, addressing certain shortcomings of previous approaches. This representation can drive expert system analysis for diagnosis and workup advice. The script formalism structures the knowledge base around a set of temporally sequenced event frames, each containing a list of default expectations. This model, we believe, allows straightforward knowledge generation from a domain expert, since it may closely parallel a central aspect of human clinical decision-making: that of projecting assumptions for a “hypothesize-and-test” inference mechanism. A prototype expectation-based expert system, OSCAR, is under development to explore this approach.
Mature Adipocytes Inhibit In Vitro Differentiation of Human Preadipocytes via Angiotensin Type 1 Receptors (2002)

Recent studies suggest that angiotensin II (Ang II) plays a role in the adipogenesis of murine preadipocytes. Here, we examined the role of Ang II for the differentiation of primary cultured human preadipocytes. Preadipocytes were isolated from human adipose tissue and stimulated to differentiate. Quantitation of gene expression during adipogenesis was performed for renin-angiotensin system (RAS) genes. The influence of the RAS on adipogenic differentiation was investigated by addition of either angiotensinogen (AGT), Ang II, or angiotensin receptor antagonists to the differentiation medium. We also examined the influence of adipocytes on adipogenesis by co-culture experiments. Expression of the RAS genes AGT, renin, angiotensin-converting enzyme, and Ang II type 1 receptor increased during adipogenesis. Stimulation of the Ang II type 1 receptor by Ang II reduced adipose conversion, whereas blockade of this receptor markedly enhanced adipogenesis. Adipocytes were able to inhibit preadipocyte differentiation in the co-culture, and this effect was abolished by blockade of the Ang II type 1 receptor. This finding points to a functional role of the RAS in the differentiation of human adipose tissue. Because AGT secretion and Ang II generation are characteristic features of adipogenesis, we postulate a paracrine negative-feedback loop that inhibits further recruitment of preadipocytes by maturing adipocytes.
Promoting neuron adhesion and growth (2008)

During nervous system development, the extracellular matrix (ECM) plays a pivotal role offering anchorage points to maturing neurons and neurites, as well as a permissive environment for tissue formation. Thus enhancement of cell adhesion is often an important criterion when designing biomaterials for neural tissue engineering. In addition to functionalizing biomaterials with ECM-derived cell adhesive molecules, there is emerging evidence that indicates the surface topography, stiffness, and electrical properties play an important role in neuron adhesion and neurite outgrowth. We describe recent developments in biomaterials modification for simulating the microenvironment in order to promote neuron adhesion and growth, as well as to encourage nerve regeneration after injury or disease.
The Salivary Apyrase of the Blood-Sucking Sand Fly Phlebotomus Papatasi Belongs to the Novel Cimex Family of Apyrases (2001)

Apyrases are enzymes that hydrolyze nucleotide di- and triphosphates to orthophosphate and mononucleotides. At least two families of enzymes, belonging to the 5'-nucleotidase and to the actin/heat shock 70/sugar kinase superfamily, have evolved independently to serve the apyrase reaction. Both families require either Ca(2+) or Mg(2+) for their action. A novel apyrase enzyme sequence, with no homology to any other known protein sequence, was found recently in the salivary glands of the hematophagous bed bug Cimex lectularius. This enzyme functions exclusively with Ca(2+). Here, we report the finding of a cDNA similar to that of the C. lectularius salivary apyrase isolated from a salivary gland cDNA library of Phlebotomus papatasi. Transfection of insect cells with the P. papatasi salivary gland apyrase cDNA resulted in the secretion of a Ca(2+)-dependent apyrase whose activity was indistinguishable from that in salivary homogenates of P. papatasi. Homologous sequences were found in humans, in another sand fly (Lutzomyia longipalpis), in the fruit fly Drosophila melanogaster, in the nematode Caenorhabditis elegans and in the protozoan Cryptosporidium parvum, indicating that this family of enzymes is widespread among animal species.
Engineering Soluble Monomeric Streptavidin with Reversible Biotin Binding Capability (2005)

Monomeric streptavidin with reversible biotin binding capability has many potential applications. Because a complete biotin binding site in each streptavidin subunit requires the contribution of tryptophan 120 from a neighboring subunit, monomerization of the natural tetrameric streptavidin can generate streptavidin with reduced biotin binding affinity. Three residues, valine 55, threonine 76, and valine 125, were changed to either arginine or threonine to create electrostatic repulsion and steric hindrance at the interfaces. The double mutation (T76R,V125R) was highly effective to monomerize streptavidin. Because interfacial hydrophobic residues are exposed to solvent once tetrameric streptavidin is converted to the monomeric state, a quadruple mutein (T76R,V125R,V55T,L109T) was developed. The first two mutations are for monomerization, whereas the last two mutations aim to improve hydrophilicity at the interface to minimize aggregation. Monomerization was confirmed by four different approaches including gel filtration, dynamic light scattering, sensitivity to proteinase K, and chemical cross-linking. The quadruple mutein remained in the monomeric state at a concentration greater than 2 mg/ml. Its kinetic parameters for interaction with biotin suggest excellent reversible biotin binding capability, which enables the mutein to be easily purified on the biotin-agarose matrix. Another mutein (D61A,W120K) was developed based on two mutations that have been shown to be effective in monomerizing avidin. This streptavidin mutein was oligomeric in nature. This illustrates the importance in selecting the appropriate residues and approaches for effective monomerization of streptavidin.
Nonlinear circuit analysis using the method of harmonic balance—a review of the art. II. Advanced concepts (1991)

Abstract The harmonic balance method is a technique for the numerical solution of nonlinear analog circuits operating in a periodic, or quasi‐periodic, steady‐state regime. The method can be used to efficiently derive the continuous‐wave response of numerous nonlinear microwave components including amplifiers, mixers, and oscillators. Its efficiency derives from imposing a predetermined steady‐state form for the circuit response onto the nonlinear equations representing the network, and solving for the set of unknown coefficients in the response equation. Its attractiveness for nonlinear microwave applications results from its speed and ability to simply represent the dispersive, distributed elements that are common at high frequencies. The last decade has seen the development and application of harmonic balance techniques to model analog circuits, particularly microwave circuits. The first part of this article reviewed the fundamental achievements made during this time. In this part, the extension of the method to quasi‐periodic regimes, optimization analysis, oscillator analysis, studies of various convergence strategies, and practical applications are discussed. A critical assessment of the various types of harmonic balance techniques is given. Examples of designs which have been modeled using the harmonic balance technique and built both in hybrid and MMIC form are presented.
Peripheral Blood Mononuclear Cell Gene Expression in Chronic Obstructive Pulmonary Disease (2013)

Although most cases of chronic obstructive pulmonary disease (COPD) occur in smokers, only a fraction of smokers develop the disease. We hypothesized distinct molecular signatures for COPD and emphysema in the peripheral blood mononuclear cells (PBMCs) of current and former smokers. To test this hypothesis, we identified and validated PBMC gene expression profiles in smokers with and without COPD. We generated expression data on 136 subjects from the COPDGene study, using Affymetrix U133 2.0 microarrays (Affymetrix, Santa Clara, CA). Multiple linear regression with adjustment for covariates (gender, age, body mass index, family history, smoking status, and pack-years) was used to identify candidate genes, and ingenuity pathway analysis was used to identify candidate pathways. Candidate genes were validated in 149 subjects according to multiplex quantitative real-time polymerase chain reaction, which included 75 subjects not previously profiled. Pathways that were differentially expressed in subjects with COPD and emphysema included those that play a role in the immune system, inflammatory responses, and sphingolipid (ceramide) metabolism. Twenty-six of the 46 candidate genes (e.g., FOXP1, TCF7, and ASAH1) were validated in the independent cohort. Plasma metabolomics was used to identify a novel glycoceramide (galabiosylceramide) as a biomarker of emphysema, supporting the genomic association between acid ceramidase (ASAH1) and emphysema. COPD is a systemic disease whose gene expression signatures in PBMCs could serve as novel diagnostic or therapeutic targets.
Nanobiotechnology applications of reconstituted high density lipoprotein (2010)

High-density lipoprotein (HDL) plays a fundamental role in the Reverse Cholesterol Transport pathway. Prior to maturation, nascent HDL exist as disk-shaped phospholipid bilayers whose perimeter is stabilized by amphipathic apolipoproteins. Methods have been developed to generate reconstituted (rHDL) in vitro and these particles have been used in a variety of novel ways. To differentiate between physiological HDL particles and non-natural rHDL that have been engineered to possess additional components/functions, the term nanodisk (ND) is used. In this review, various applications of ND technology are described, such as their use as miniature membranes for solubilization and characterization of integral membrane proteins in a native like conformation. In other work, ND harboring hydrophobic biomolecules/drugs have been generated and used as transport/delivery vehicles. In vitro and in vivo studies show that drug loaded ND are stable and possess potent biological activity. A third application of ND is their use as a platform for incorporation of amphiphilic chelators of contrast agents, such as gadolinium, used in magnetic resonance imaging. Thus, it is demonstrated that the basic building block of plasma HDL can be repurposed for alternate functions.
Rearrangement of immunoglobulin gamma 1-chain gene and mechanism for heavy-chain class switch. (1980)

Cloning and nucleotide sequence determination suggest that the rearranged gamma 1-chain gene in a gamma 1-chain-producing myeloma a-pears to be formed by the recombination between the 5' flanking regions of the gamma 1- and mu-chain genes of undifferentiated cells. The recombination site is distinct from the putative J region and is a novel region that we call the S region. We have extended our previous model that explains the heavy-chain class switching by two or more successive recombination events.
Diagnostic Inaccuracy of Smartphone Applications for Melanoma Detection (2013)

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Fog Computing: An Overview of Big IoT Data Analytics (2018)

A huge amount of data, generated by Internet of Things (IoT), is growing up exponentially based on nonstop operational states. Those IoT devices are generating an avalanche of information that is disruptive for predictable data processing and analytics functionality, which is perfectly handled by the cloud before explosion growth of IoT. Fog computing structure confronts those disruptions, with powerful complement functionality of cloud framework, based on deployment of micro clouds (fog nodes) at proximity edge of data sources. Particularly big IoT data analytics by fog computing structure is on emerging phase and requires extensive research to produce more proficient knowledge and smart decisions. This survey summarizes the fog challenges and opportunities in the context of big IoT data analytics on fog networking. In addition, it emphasizes that the key characteristics in some proposed research works make the fog computing a suitable platform for new proliferating IoT devices, services, and applications. Most significant fog applications (e.g., health care monitoring, smart cities, connected vehicles, and smart grid) will be discussed here to create a well‐organized green computing paradigm to support the next generation of IoT applications.