gebhart/patrepeval huggingface dataset:
A New Genetic Algorithm for the Multi-Mode Resource-Constrained Project Scheduling Problem (2002)

In this paper we propose a robust genetic algorithm for the multi-mode resourceconstrained project scheduling problem. We present a new representation for the solutions to this problem, which includes an additional bit indicating the scheduling scheme used to construct the schedule, forward or backward. Moreover, we have developed new genetic operators which operate over this representation, exploiting and combining the information in an efficient way. We have designed a new crossover procedure, the two-point forward-backward crossover, and have adapted a mechanism used in a simulated annealing algorithm as a mutation operator in genetic algorithms. Computational results on the standard sets of PSPLIB show the good performance of our algorithm.
Transcriptional regulation of secondary metabolism (2003)

Plants produce secondary metabolites during development and in response to environmental stimuli such as light or pathogen attack. Transcriptional regulation provides the most important control point for the secondary metabolic pathways studied to date. In this article we review the data on the transcription factors that modulate this regulation. For the phenylpropanoid pathway, much is understood about both the specific sequences in the target genes (cis-elements) that are involved in responses to environmental and developmental stimuli, and the transcription factors involved. Most information is available for the light induction of the genes for hydroxycinnamic acid production, the production of anthocyanins in leaves and floral tissues, and the production of proanthocyanidins in seeds. Some of the functional interactions between the different types of transcription factor are now being elucidated, and upstream regulators of the genes encoding the transcription factors identified. For other secondary metabolic pathways much less is known, although good progress has been made on identifying transcription factors involved in controlling terpenoid indole alkaloid production. The identification of defined transcription factor genes provides tools for modulating both the amount and distribution of secondary metabolites in plants, and the validity of this approach has been well established by transgenic plants with modified flavonoid accumulation patterns.
Efficient Nonnegative Matrix Factorization with Random Projections (2010)

The recent years have witnessed a surge of interests in Nonnegative Matrix Factorization (NMF) in data mining and machine learning fields. Despite its elegant theory and empirical success, one of the limitations of NMF based algorithms is that it needs to store the whole data matrix in the entire process, which requires expensive storage and computation costs when the data set is large and high-dimensional. In this paper, we propose to apply the random projection techniques to accelerate the NMF process. Both theoretical analysis and experimental validations will be presented to demonstrate the effectiveness of the proposed strategy.
Development of a bulgur‐like product using extrusion cooking (2003)

Abstract In this study we (1) developed a new bulgur‐like foodstuff using a durum wheat cultivar and an extrusion technique, (2) investigated the physicochemical properties of the extrudates produced and (3) sensorially evaluated the end‐product after cooking. Durum wheat was processed in a laboratory‐scale co‐rotating twin‐screw extruder with different levels of moisture content of the feed (367, 417 and 455 g kg −1 ), screw speed (150 and 200 rpm) and feed rate (2.4 and 2.9 kg h −1 ) to develop the bulgur‐like product. The effects of extrusion conditions on system variables (die pressure and specific mechanical energy (SME)), physical properties (die swell and bulk density), pasting properties (peak, trough and final viscosities) and cooking and sensory properties of the bulgur‐like products were determined. The results indicated that increased feed moisture content resulted in significant decreases in the die pressure and SME values of the extruded durum wheat products. As the moisture content and screw speed increased, the changes in die swell values were not significant. The lowest die swell and highest bulk density values were obtained at the highest feed moisture content. The extrusion variables also affected the pasting properties of the extrudates. Significant increases in each of the pasting properties occurred when the moisture content of the feed was increased. Some of the sensory properties (bulkiness, firmness, stickiness and taste–aroma) improved significantly as the feed moisture content increased, indicating better quality. Increased feed moisture content significantly improved cooking quality as determined by a decrease in colorimetric test results. Extrusion seems to be promising for the production of dry, relatively inexpensive bulgur‐like products with acceptable sensory properties. © 2003 Society of Chemical Industry
Resistin is associated with biomarkers of inflammation while total and high-molecular weight adiponectin are associated with biomarkers of inflammation, insulin resistance, and endothelial function (2009)

Total and HMW adiponectin are inversely associated with markers of insulin secretion/insulinemia, endothelial function, and inflammation. Resistin is positively associated only with markers of inflammation.
The Drosha-DGCR8 complex in primary microRNA processing (2004)

RNase III proteins play key roles in microRNA (miRNA) biogenesis. The nuclear RNase III Drosha cleaves primary miRNAs (pri-miRNAs) to release hairpin-shaped pre-miRNAs that are subsequently cut by the cytoplasmic RNase III Dicer to generate mature miRNAs. While Dicer (class III) and other simple RNase III proteins (class I) have been studied intensively, the class II enzyme Drosha remains to be characterized. Here we dissected the action mechanism of human Drosha by generating mutants and by characterizing its new interacting partner, DGCR8. The basic action mechanism of Drosha was found to be similar to that of human Dicer; the RNase III domains A and B form an intramolecular dimer and cleave the 3' and 5' strands of the stem, respectively. Human Drosha fractionates at approximately 650 kDa, indicating that Drosha functions as a large complex. In this complex, Drosha interacts with DGCR8, which contains two double-stranded RNA (dsRNA)-binding domains. By RNAi and biochemical reconstitution, we show that DGCR8 may be an essential component of the pri-miRNA processing complex, along with Drosha. Based on these results, we propose a model for the action mechanism of class II RNase III proteins.
Diagnosis of Mycoplasma hyopneumoniae (2004)

Mycoplasma hyopneumoniae, the cause of enzootic pneumonia, remains an important pathogen in the swine industry. This small, complex organism colonizes the ciliated cells of the respiratory tract, resulting in little exposure to the immune system. Confirming the presence of M. hyopneumoniae, as well as identifying its role in respiratory disease and pneumonia, remains challenging to the veterinary profession. While culture of the organism remains the gold standard for identification, the use of serology, the polymerase chain reaction and various assays to detect the presence of M. hyopneumoniae in tissue is common in diagnostic laboratories. Because of the role M. hyopneumoniae plays in increasing the severity of pneumonia associated with concurrent bacterial and viral infections, understanding the pathogenesis and diagnostic assays available is critical for developing effective intervention strategies to control respiratory disease on a herd basis.
Molecular cloning, DNA sequencing, and biochemical analyses of Escherichia coli glyoxylate carboligase. An enzyme of the acetohydroxy acid synthase-pyruvate oxidase family. (1993)

Glyoxylate carboligase (Gcl) (EC 4.1.1.47) of Escherichia coli catalyzes the condensation of two molecules of glyoxylate to give tartronic semialdehyde, a key intermediate in glyoxylate catabolism. We report the cloning, genomic location, and DNA sequence of the gene (called gcl) encoding E. coli Gcl and isolation of mutants lacking the enzyme. Gcl is a protein of 593 amino acid residues (64,738 Da) that has a high level (30%) of sequence similarity to the acetohydroxy acid synthases (AHAS) of branched chain amino acid synthetic pathway. Significant sequence identity (26%) was also observed with E. coli pyruvate oxidase, a redox flavoprotein, previously shown to be related to the AHAS enzymes (Chang, Y.-Y., and Cronan, J. E., Jr. (1988) J. Bacteriol. 170, 3937-3945). Consistent with a grouping of Gcl with the AHAS and pyruvate oxidase enzymes. Gcl contains a quinone binding site as well as binding site for thiamine pyrophosphate and FAD. We also found that a gene (orf258) immediately downstream of the gcl gene encoded a protein (Orf258) of 258 residues. Although the gene organization of gcl and orf258 is analogous to that of the ilv gene operons which encode the E. coli AHAS isozyme large and small subunits, Orf258 does not function as a Gcl subunit. Moreover, disruption of the chromosomal copy of orf258 did not affect growth on glyoxylate or glycolate.
Survival of seaward-migrating PIT and acoustic-tagged juvenile Chinook salmon in the Snake and Columbia Rivers: an evaluation of length-specific tagging effects (2013)

Acoustic telemetry is a widely used tool for evaluating the behavior and survival of juvenile salmonids in the Columbia River basin. Thus, it is important to understand how the surgical tagging process and the presence of a transmitter affect survival. This study evaluated the effect of fish length on the survival of yearling and subyearling Chinook salmon during their seaward migrations through the Snake and Columbia Rivers during 2006, 2007, and 2008. Fish were collected at Lower Granite Dam on the Snake River (695 river km from the mouth of the Columbia) and implanted with either only a passive integrated transponder (PIT) tag (PIT fish) or both a PIT tag and an acoustic transmitter (AT fish). Across the 3 years, a total of 157,000 yearling and subyearling fish were tagged and designated as PIT fish and 18,500 as AT fish. Survival was estimated from release at Lower Granite Dam to multiple downstream dams using the Cormack–Jolly–Seber single release model, and analysis of variance was used to test for differences among length classes for both tag types. No length-specific tag effect was detected between PIT and AT fish (that is, length affected the survival of PIT fish and AT fish in a similar manner). Fish length was positively correlated with the survival of both PIT and AT fish. Survival was markedly low among the smallest length class (that is, 80 mm to 89 mm) of both PIT and AT subyearling Chinook salmon and the survival of PIT fish was generally greater than that of AT fish. The lack of a length-specific tag effect suggests that under the conditions used in this study, differences in survival between PIT and AT fish may be due to the process of surgically implanting the transmitter rather than the presence of the transmitter.
An Alternative to SH2 Domains for Binding Tyrosine-Phosphorylated Proteins (1994)

Src homology 2 (SH2) domains bind specifically to tyrosine-phosphorylated proteins that participate in signaling by growth factors and oncogenes. A protein domain was identified that bound specifically to the tyrosine-phosphorylated form of its target protein but differs from known SH2 sequences. Phosphotyrosine-binding (PTB) domains were found in two proteins: SHC, a protein implicated in signaling through Ras; and SCK, encoded by a previously uncharacterized gene. The PTB domain of SHC specifically bound to a tyrosine-phosphorylated 145-kilodalton protein. PTB domains are an alternative to SH2 domains for specifically recruiting tyrosine-phosphorylated proteins into signaling complexes and are likely to take part in signaling by many growth factors.
Liver–Associated Lymphocytes Expressing Nk1.1 Are Essential for Oral Immune Tolerance Induction in A Murine Model (1999)

Oral tolerance is the induction of immunological hyporesponsiveness towards orally administered antigens. Tolerance initiation involves induction of anti-inflammatory (Th2) lymphocytes, with downregulation of pro-inflammatory (Th1) lymphocytes. The liver was previously shown to play a critical role in oral tolerance induction. The aim of the present study was to test whether liver-associated-lymphocytes expressing the NK1.1 marker (NK1.1+ LAL) are substantial for induction of oral tolerance in an experimental colitis model. Colitis was induced in C57 mice by intracolonic instillation of trinitrobenzensulfonic acid (TNBS). Mice received five oral doses of colonic proteins extracted from TNBS-colitis colonic wall. Anti-NK1.1 monoclonal antibodies were injected before tolerance induction. Colitis was assessed by standard clinical, macroscopic, and microscopic scores. Serum IFN-gamma, TGF-beta1, and IL4 levels were measured by enzyme-linked immunosorbent assay. To evaluate the role of NK1.1+ LAL in keeping the balance between immunogenic and tolerogenic subsets of cells, we tested whether peripheral lymphocytes harvested from tolerized and NK1.1-depleted nontolerized mice can adoptively transfer the tolerance into naive irradiated rats. Depletion of NK1.1+ LAL prevented immune tolerance induction in the experimental colitis model. NK1.1+ LAL-depleted nontolerized mice, disclosed severe clinical, macroscopic, and microscopic parameters of colitis. These mice had significantly lower TGF-beta1, IL4, and higher IFN-gamma serum levels, and their lymphocytes failed to transfer the tolerance into naive animals. In contrast, the feeding of colitis-extracted proteins, without NK1.1+ LAL depletion, markedly alleviated the disease. Tolerized mice had higher IL4 and TGF-beta1 and lower IFN-gamma serum levels, and adoptive transfer of their suppressor splenocytes markedly alleviated colitis in naive recipients. NK1.1+ LAL plays a critical role in oral tolerance induction. Depletion of this subset of LAL prevents a shift from Th1 to a Th2 type of immune response, hindering the ability to induce immune tolerance.
Kynurenic Acid Derivatives Inhibit the Binding of Nerve Growth Factor (NGF) to the Low-Affinity p75 NGF Receptor (1995)

The ability of a series of substituted kynurenic acids, thienopyridinonecarboxylic acids, and related compounds to inhibit the binding of nerve growth factor (NGF) to the p75 NGF receptor (NGFR) was evaluated in a radioligand binding assay that utilized a biotinylated derivative of the extracellular domain of p75 NGFR (p75ext) fixed to streptavidin-coated plastic wells. Two compounds, 6-aminokynurenic acid (5h) and the 3-methyl ester of 4,7-dihydro-2-methyl-7-oxothieno[3,2-b]pyridine-3,5-dicarboxylic acid (16), were found to inhibit the binding of [125I]NGF to p75ext with IC50 values in the low micromolar range. Other amino-substituted kynurenic acids also possessed activity at slightly higher concentrations. Several structural features seem to be essential, including the carboxylic acid, a polar group on the benzene ring (or thiophene ring, in the case of analogues of 16), and the C-4 carbonyl group in the pyridinone ring. These compounds were also found to inhibit the binding of [125I]NGF to its receptors in membranes from PC12 cells (which express p75 as well as trka receptors for NGF) and DG44-CHO cells (transfected with full length p75 NGFR). The available data for 5h and 16 do not allow the determination of whether the effects of these compounds are mediated by their interaction with NGF or the NGF receptors.
Novel approaches to hemophilia therapy: successes and challenges (2017)

New therapies for hemophilia A and hemophilia B will likely continue to change clinical practice. Ranging from extended half-life to nonfactor products and gene therapy, these innovative approaches have the potential to enhance the standard of care by decreasing infusion frequency to increase compliance, promoting prophylaxis, offering alternatives to inhibitor patients, and easing route of administration. Each category has intrinsic challenges that may limit the broader application of these promising therapies. To date, none specifically address the challenge of dispersing treatment to the developing world.
High‐cell‐density fermentation for production of L‐N‐carbamoylase using an expression system based on the Escherichia coli rhaBAD promoter (2001)

A high-cell-density fed-batch fermentation for the production of heterologous proteins in Escherichia coli was developed using the positively regulated Escherichia coli rhaBAD promoter. The expression system was improved by reducing of the amount of expensive L-rhamnose necessary for induction of the rhamnose promoter and by increasing the vector stability. Consumption of the inducer L-rhamnose was inhibited by inactivation of L-rhamnulose kinase encoding gene rhaB of Escherichia coli W3110, responsible for the first irreversible step in rhamnose catabolism. Plasmid instability caused by multimerization of the expression vector in the recombination-proficient W3110 was prevented by insertion of the multimer resolution site cer from the ColE1 plasmid into the vector. Fermentation experiments with the optimized system resulted in the production of 100 g x L(-1) cell dry weight and 3.8 g x L(-1) of recombinant L-N-carbamoylase, an enzyme, which is needed for the production of enantiomeric pure amino acids in a two-step reaction from hydantoins.
Strategies for Teaching Reading in the Content Areas (1993)

(1993). Strategies for Teaching Reading in the Content Areas. The Clearing House: A Journal of Educational Strategies, Issues and Ideas: Vol. 67, No. 2, pp. 121-122.
Discovery of five conserved β-defensin gene clusters using a computational search strategy (2002)

The innate immune system includes antimicrobial peptides that protect multicellular organisms from a diverse spectrum of microorganisms. beta-Defensins comprise one important family of mammalian antimicrobial peptides. The annotation of the human genome fails to reveal the expected diversity, and a recent query of the draft sequence with the blast search engine found only one new beta-defensin gene (DEFB3). To define better the beta-defensin gene family, we adopted a genomics approach that uses hmmer, a computational search tool based on hidden Markov models, in combination with blast. This strategy identified 28 new human and 43 new mouse beta-defensin genes in five syntenic chromosomal regions. Within each syntenic cluster, the gene sequences and organization were similar, suggesting each cluster pair arose from a common ancestor and was retained because of conserved functions. Preliminary analysis indicates that at least 26 of the predicted genes are transcribed. These results demonstrate the value of a genomewide search strategy to identify genes with conserved structural motifs. Discovery of these genes represents a new starting point for exploring the role of beta-defensins in innate immunity.
Abstract P4-01-02: Early detection of residual breast cancer through a robust, scalable and personalized analysis of circulating tumour DNA (ctDNA) antedates overt metastatic recurrence (2019)

Abstract Background: Many breast cancer patients relapse after primary treatment but there are no reliable tests to detect distant metastases before they become overt. Here we show earlier identification of recurring patients through a scalable personalised ctDNA analysis. The method is applicable to all patients, and not limited to hot-spot mutations typically detected by gene panels. Methods: Forty-nine non-metastatic breast cancer patients were recruited following surgery and adjuvant therapy. Plasma samples (n=208) were serially collected semi-annually. Using the analytically validated SignateraTM workflow, we determined mutational signatures from primary tumour whole exome data and designed personalised assays targeting 16 variants with high sensitivity by ultra-deep sequencing (average &amp;gt;100,000X). The patient-specific assay was used to detect the presence of the mutational signature in the plasma. Results: In 16 of 18 (89%) clinically-relapsing patients, ctDNA was detected ahead of metastatic relapse being diagnosed by clinical examination, radiological and biochemical (CA15-3) measurements, and remained ctDNA-positive through follow-up. Of the 2 patients not detected by ctDNA, one had a small local recurrence only (now resected) and the other had three primary tumours. None of the 31 non-relapsing patients were ctDNA-positive at any time point (n=142). Metastatic relapse was predicted by Signatera with high accuracy and a lead time of up to 2 years (median=9.5 months). Conclusions: The use of a scalable patient-specific ctDNA-based validated workflow detects breast cancer recurrence ahead of clinical detection. Accurate and earlier prediction by ctDNA analysis could provide a means of monitoring breast cancer patients in need of second-line salvage adjuvant therapy in order to prevent overt life-threatening metastatic progression. Citation Format: Coombes RC, Armstrong A, Ahmed S, Page K, Hastings RK, Salari R, Sethi H, Boydell A-R, Shchegrova SV, Fernandez-Garcia D, Gleason KL, Goddard K, Guttery DS, Assaf ZJ, Balcioglu M, Moore DA, Primrose L, Navarro SL, Aleshin A, Rehman F, Toghill BJ, Louie MC, Zimmermann BG, Lin C-HJ, Shaw JA. Early detection of residual breast cancer through a robust, scalable and personalized analysis of circulating tumour DNA (ctDNA) antedates overt metastatic recurrence [abstract]. In: Proceedings of the 2018 San Antonio Breast Cancer Symposium; 2018 Dec 4-8; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2019;79(4 Suppl):Abstract nr P4-01-02.
Acute lung injury: the role of cytokines in the elicitation of neutrophils. (1994)

Cytokine networks between immune and nonimmune cells of the alveolar-capillary membrane are necessary for cellular communication during pulmonary inflammation. The subsequent events of these cellular/humoral interactions are pivotal to the initiation and propagation of the inflammatory response leading to pulmonary injury. The studies cited in this paper underscore the interrelationship of early response cytokines, adhesion molecules, and the chemokine IL-8 that orchestrate the recruitment of neutrophils into the lung. The paradigm for neutrophil extravasation is likely operative in the microvasculature of the lung, and consists of four or more steps (Figure 3). First, acute lung injury results in the activation of microvascular endothelium in response to the local generation of TNF or IL-1, leading to expression of endothelial cell-derived E- and P-selectins and ICAM-1. The constitutive presence of neutrophil-derived L-selectin allows for the initial adhesive interaction of neutrophils with endothelial cell selectins leading to the "rolling" effect. Second, generation of IL-8 leads to the activation of neutrophils in the vascular compartment and expression of beta 2 integrins, while L-selectin is concomitantly shed. Third, the interaction of the neutrophil beta 2 integrin with its receptor/ligand, ICAM-1, results in the rapid arrest of neutrophils on the endothelium. Fourth, the subsequent events leading to neutrophil extravasation beyond the vascular compartment are dependent upon a combination of haplotaxis (migration in response to an insoluble gradient), the continued expression of beta 2 integrins on neutrophils and ICAM-1 on nonimmune cells, and the maintenance of a neutrophil specific (IL-8) chemotactic gradient. The participation of IL-8 and potentially other C-X-C chemokines in the inflammatory response appears to be critical for the orchestration of the directed migration of inflammatory leukocytes into the lung. After arriving in the lung, these activated leukocytes can respond to noxious stimuli or induce pulmonary injury through the release of reactive oxygen metabolites, proteolytic enzymes, and additional cytokines. Our current knowledge and future investigations regarding the mechanisms involved in neutrophil elicitation may allow us to employ clinical interventional strategies that will attenuate neutrophil-dependent acute lung injury, such as ARDS.