gebhart/patrepeval huggingface dataset:
Global evaluation of biofuel potential from microalgae (2014)

In the current literature, the life cycle, technoeconomic, and resource assessments of microalgae-based biofuel production systems have relied on growth models extrapolated from laboratory-scale data, leading to a large uncertainty in results. This type of simplistic growth modeling overestimates productivity potential and fails to incorporate biological effects, geographical location, or cultivation architecture. This study uses a large-scale, validated, outdoor photobioreactor microalgae growth model based on 21 reactor- and species-specific inputs to model the growth of Nannochloropsis. This model accurately accounts for biological effects such as nutrient uptake, respiration, and temperature and uses hourly historical meteorological data to determine the current global productivity potential. Global maps of the current near-term microalgae lipid and biomass productivity were generated based on the results of annual simulations at 4,388 global locations. Maximum annual average lipid yields between 24 and 27 m(3)·ha(-1)·y(-1), corresponding to biomass yields of 13 to 15 g·m(-2)·d(-1), are possible in Australia, Brazil, Colombia, Egypt, Ethiopia, India, Kenya, and Saudi Arabia. The microalgae lipid productivity results of this study were integrated with geography-specific fuel consumption and land availability data to perform a scalability assessment. Results highlight the promising potential of microalgae-based biofuels compared with traditional terrestrial feedstocks. When water, nutrients, and CO2 are not limiting, many regions can potentially meet significant fractions of their transportation fuel requirements through microalgae production, without land resource restriction. Discussion focuses on sensitivity of monthly variability in lipid production compared with annual average yields, effects of temperature on productivity, and a comparison of results with previous published modeling assumptions.
A novel zoom invariant video object tracking algorithm (ZIVOTA) (2004)

This paper describes a novel zoom-invariant video object-tracking algorithm (ZIVOTA). ZIVOTA extracts the object feature points and construct an affine-based model to predict the size and position of an object during the tracking process. The proposed affine model is zoom invariant, which makes it possible to track object with nonrigid size and shape. Compared to traditional frame difference and optical flow methods, ZIVOTA largely reduces the computational cost because it explores only relevant object feature points and processes smaller number of point instead of the full frame. Moreover, it is more accurate since affine transformation is viewpoint invariant.
Compiler -assisted hardware-based data prefetching for next generation processors (2007)

Prefetching has emerged as one of the most successful techniques to bridge the gap between modern processors and memory systems. On the other hand, as we move to the deep sub-micron era, power consumption has become one of the most important design constraints besides performance. Intensive research efforts have been done on data prefetching focusing on performance improvement, however, as far as we know, the energy aspects of prefetching have not been fully investigated. This dissertation investigates data prefetching techniques for next-generation processors targeting both energy-effciency and performance speedup. We first evaluate a number of state-of-the-art data prefetching techniques from an energy perspective and identify the main energy-consuming components due to prefetching. We then propose a set of compiler-assisted energy-aware techniques to make hardware-based data prefetching more energy-efficient. From our evaluation on a number of data prefetching techniques, we have found that if leakage is optimized with recently proposed circuit-level techniques, most of the energy overhead of hardware data prefetching comes from prefetch hardware related costs and unnecessary L1 data cache lookups related to prefetches that hit in the L1 cache. This energy overhead on the memory system can be as much as 30%. We propose a set of power-aware prefetch filtering techniques to reduce the energy overhead of hardware data prefetching techniques. Our proposed techniques include three compiler-based filtering approaches that make the prefetch predictor more energy efficient. We also propose a hardware-based filtering technique to further reduce the energy overhead due to unnecessary prefetching in the L1 data cache. The energy-aware filtering techniques combined could reduce up to 40% of the energy overhead introduced due to aggressive prefetching with almost no performance degradation. We also develop a location-set driven data prefetching technique to further reduce the energy consumption of prefetching hardware. In this scheme, we use a power-aware prefetch engine with a novel design of an indexed hardware history table. With the help of compiler-based location-set analysis, we show that the proposed prefetching scheme reduces the energy consumed by the prefetch history table by 7-11X with very small impact on performance. Our experiments show that the proposed techniques could overcome the prefetching-related energy overhead in most applications, improving the energy-delay product by 33% on average. For many applications studied, our work has transformed data prefetching into not only a performance improvement mechanism, but an energy saving technique as well.
Cytokines and BMP-4 promote hematopoietic differentiation of human embryonic stem cells (2003)

Human embryonic stem cells (hESCs) randomly differentiate into multiple cell types during embryoid body (EB) development. To date, characterization of specific factors capable of influencing hematopoietic cell fate from hESCs remains elusive. Here, we report that the treatment of hESCs during EB development with a combination of cytokines and bone morphogenetic protein-4 (BMP-4), a ventral mesoderm inducer, strongly promotes hematopoietic differentiation. Hematopoietic progenitors of multiple lineages were generated from EBs and were found to be restricted to the population of progeny expressing cell surface CD45. Addition of BMP-4 had no statistically significant effect on hematopoietic differentiation but enabled significant enhancement in progenitor self-renewal, independent of cytokine treatment. Hematopoietic commitment was characterized as the temporal emergence of single CD45+ cells first detectable after day 10 of culture and was accompanied by expression of hematopoietic transcription factors. Despite the removal of cytokines at day 10, hematopoietic differentiation of hESCs continued, suggesting that cytokines act on hematopoietic precursors as opposed to differentiated hematopoietic cells. Our study establishes the first evidence for the role of cytokines and BMP-4 in promoting hematopoietic differentiation of hESC lines and provides an unprecedented system to study early developmental events that govern the initiation of hematopoiesis in the human.
Preventing postextubation respiratory failure* (2006)

Department of Medicine, Caritas–St. Elizabeth’s Medical Center, Tufts University School of Medicine, Boston, MA The author has no financial interests to disclose.
Identification of a Ca 2+ -Pectate Binding Site on an Apoplastic Peroxidase (2001)

Sabine Carpin, , Mireille de Meyer, Patrice Simon, Hubert Greppin, Claude Penel, Identification of a ${\rm Ca}^{2+}\text{-Pectate}$ Binding Site on an Apoplastic Peroxidase ⁺, The Plant Cell, Vol. 13, No. 3 (Mar., 2001), pp. 511-520
Biochemical Characterization of the Intracellular Domain of the Human Guanylyl Cyclase C Receptor Provides Evidence for a Catalytically Active Homotrimer (2000)

Guanylyl cyclase C (GCC) is the receptor for the family of guanylin peptides and bacterial heat-stable enterotoxins (ST). The receptor is composed of an extracellular, ligand-binding domain and an intracellular domain with a region of homology to protein kinases and a guanylyl cyclase catalytic domain. We have expressed the entire intracellular domain of GCC in insect cells and purified the recombinant protein, GCC-IDbac, to study its catalytic activity and regulation. Kinetic properties of the purified protein were similar to that of full-length GCC, and high activity was observed when MnGTP was used as the substrate. Nonionic detergents, which stimulate the guanylyl cyclase activity of membrane-associated GCC, did not appreciably increase the activity of GCC-IDbac, indicating that activation of the receptor by Lubrol involved conformational changes that required the transmembrane and/or the extracellular domain. The guanylyl cyclase activity of GCC-IDbac was inhibited by Zn(2+), at concentrations shown to inhibit adenylyl cyclase, suggesting a structural homology between the two enzymes. Covalent cross-linking of GCC-IDbac indicated that the protein could associate as a dimer, but a large fraction was present as a trimer. Gel filtration analysis also showed that the major fraction of the protein eluted at a molecular size of a trimer, suggesting that the dimer detected by cross-linking represented subtle differences in the juxtaposition of the individual polypeptide chains. We therefore provide evidence that the trimeric state of GCC is catalytically active, and sequences required to generate the trimer are present in the intracellular domain of GCC.
Electronic-photonic integrated circuits on the CMOS platform (2006)

The optical components industry stands at the threshold of a major expansion that will restructure its business processes and sustain its profitability for the next three decades. This growth will establish a cost effective platform for the partitioning of electronic and photonic functionality to extend the processing power of integrated circuits. BAE Systems, Lucent Technologies, Massachusetts Institute of Technology, and Applied Wave Research are participating in a high payoff research and development program for the Microsystems Technology Office (MTO) of DARPA. The goal of the program is the development of technologies and design tools necessary to fabricate an application-specific, electronicphotonic integrated circuit (AS-EPIC). As part of the development of this demonstration platform we are exploring selected functions normally associated with the front end of mixed signal receivers such as modulation, detection, and filtering. The chip will be fabricated in the BAE Systems CMOS foundry and at MIT's Microphotonics Center. We will present the latest results on the performance of multi-layer deposited High Index Contrast Waveguides, CMOS compatible modulators and detectors, and optical filter slices. These advances will be discussed in the context of the Communications Technology Roadmap that was recently released by the MIT Microphotonics Center Industry Consortium.
Overexpression of either c-myc or c-erbB-2/neu proto-oncogenes in human breast carcinomas: correlation with poor prognosis. (1988)

Tumor specimens from 116 untreated patients with primary breast carcinoma at different clinical stages were analyzed for the structure and/or the expression of c-myc and c-erbB-2/neu proto-oncogenes. An amplification of the c-myc proto-oncogene (3 to greater than 50 fold) was detected only in 6% of carcinomas, with no evidence of locus rearrangement. High c-myc RNA levels detected in 45% of tumors were found significantly (p less than 0.01) correlated with lymph node involvement. Amplification (3 to greater than 30 fold) of the c-erbB-2/neu gene was observed in 20% of cancers. A 5 kb c-erbB-2/neu gene transcript was detected in the 103 cancer specimens analyzed. High levels of transcripts were observed in 36% of tumors. Overexpression did not depend only on amplification since found in 14 tumor samples with a single gene copy. The gene amplification and overexpression were found significantly associated with cancers of poor prognosis. Moreover our data show that both proto-oncogenes are overexpressed only in 12.5% of tumor samples and suggest that each gene might play a different role in tumor progression.
Alternative antibody formats. (2010)

During the past two decades, numerous recombinant antibody formats have been designed and produced by genetic engineering, extending and improving the activities of naturally occurring antibodies. However, while whole IgG molecules, antibody fragments and chemically modified derivatives thereof are being used clinically, alternative antibody formats still await regulatory approval. This review summarizes recent progress in the development of alternative antibody formats for therapeutic applications, with an emphasis on molecules that are in clinical testing.
Engineering poliovirus as a vaccine vector for the expression of diverse antigens (1994)

As a step toward developing poliovirus as a vaccine vector, poliovirus recombinants were constructed by fusing exogenous peptides (up to 400 amino acids) and an artificial cleavage site for viral protease 3Cpro to the amino terminus of the viral polyprotein. Viral replication proceeded normally. An extended polyprotein was produced in infected cells and proteolytically processed into the complete array of viral proteins plus the foreign peptide, which was excluded from mature virions. The recombinants retained exogenous sequences through successive rounds of replication in culture and in vivo. Infection of animals with recombinants elicited a humoral immune response to the foreign peptides.
The use of a microwave oven in the chemical transformation of long chain fatty acid esters (1988)

The use of a microwave oven as an energy source allowed transformation of fatty acid derivatives to be complete in a few minutes. Hydrolysis of triglycerides, esterification of free fatty acids, epoxidation of unsaturated fatty acid esters, cyclization of dioxostearates and oxounsaturated fatty acid esters into furanoid derivatives, conversion of epoxystearate to oxostearate derivatives, and substitution of a tosyl group by an azide all took about five min to complete and were in very high yields. The most sluggish reaction encountered was the acid catalyzed hydrolysis (ring opening) reaction of a furanoid ester to the corresponding 1,4-dioxo derivative, which required three 10-min periods of heating. The use of microwaves not only decreased the reaction time considerably but also allowed smaller volumes of solvent and lower quantities of reagents to be used as compared with the conventional methodologies reported.
Organization and characterization of genes essential for symbiotic nitrogen fixation from Bradyrhizobium japonicum I110 (1986)

A total of 96 independent Tn5 insertions within a 39-kilobase-pair (kbp) segment of chromosomal DNA containing the three structural genes for nitrogenase (nifH, nifD, and nifK) from Bradyhizobium japonicum I110 were obtained in Escherichia coli and transferred to the wild-type strain by marker exchange. Individual transconjugants containing a Tn5 insertion were inoculated onto Glycine max cv. Wilkin (soybeans) and analyzed for their effect on symbiotic nitrogen fixation. In addition to the three structural genes, genes essential for nitrogen fixation (fix genes) were located in three separate regions: 9 kbp upstream of the nifDK operon; 1.5 kbp downstream of the nifDK operon; 4.5 kbp upstream of nifH. All of the fix::Tn5 insertion strains formed nodules which contained low or undetectable levels of nitrogenase activity. Bacteroids isolated from these nodules had approximately the same levels of the nifDK and nifH transcripts as those detectable from nodules formed by the wild-type strain. Western blot analysis of bacteroid proteins from nodules formed by the fix::Tn5 mutants or the wild-type strain showed the presence of similar levels of the nitrogenase protein subunits. The region upstream of nifH was characterized further by DNA sequence analysis and was shown to contain the nifB gene. The coding sequence of the nifB gene consisted of 1,494 nucleotides and was preceded by putative promoter (5' GTGG-10 base pairs [bp] TTGCA 3') and upstream activator (5' TGT-4 bp-T-5 bp-ACA 3') sequences.
Regulatory on/off minimization of metabolic flux changes after genetic perturbations (2005)

Predicting the metabolic state of an organism after a gene knockout is a challenging task, because the regulatory system governs a series of transient metabolic changes that converge to a steady-state condition. Regulatory on/off minimization (ROOM) is a constraint-based algorithm for predicting the metabolic steady state after gene knockouts. It aims to minimize the number of significant flux changes (hence on/off) with respect to the wild type. ROOM is shown to accurately predict steady-state metabolic fluxes that maintain flux linearity, in agreement with experimental flux measurements, and to correctly identify short alternative pathways used for rerouting metabolic flux in response to gene knockouts. ROOM's growth rate and flux predictions are compared with previously suggested algorithms, minimization of metabolic adjustment, and flux balance analysis (FBA). We find that minimization of metabolic adjustment provides accurate predictions for the initial transient growth rates observed during the early postperturbation state, whereas ROOM and FBA more successfully predict final higher steady-state growth rates. Although FBA explicitly maximizes the growth rate, ROOM does not, and only implicitly favors flux distributions having high growth rates. This indicates that, even though the cell has not evolved to cope with specific mutations, regulatory mechanisms aiming to minimize flux changes after genetic perturbations may indeed work to this effect. Further work is needed to identify metrics that characterize the complete trajectory from the initial to the final metabolic steady states after genetic perturbations.
Culturally Relevant Practices and Management of an ELA Teacher: A Tale of Two Classrooms (2014)

A culturally relevant pedagogical stance requires a complex understanding of content and culture. For English Language Arts (ELA) teachers, that complex understanding includes recognizing, valuing, and centering content from diverse authors and realizing the possible impact of that content may have on the lives of students. Teachers with such a stance use culturally relevant teaching consistently and effectively with diverse learners. Additionally, they are able to customize standards, practices, and tools based on the needs of their students—not just at the planning stages of curriculum implementation, but during implicit or explicit instruction and classroom management. Thus, this study utilizes qualitative methodology in order to profile Ms. Steck, a culturally relevant teacher, by examining the ways in which she uses culturally relevant pedagogy to inform her daily instruction and classroom management choices in two diverse learning spaces — Blocks A and D.
Interferon-induced versus chemokine transcripts as lupus biomarkers (2008)

Compelling support for a central role for interferon-alpha in lupus pathogenesis has led to a new focus on the role of innate immune system activation in the generation of pathogenic mediators. These insights have been extended in translational studies of patients with well-characterized disease activity and clinical manifestations in order to identify informative molecular biomarkers. Chemokines are among the interferon-inducible genes, and new data support an association between the expression of chemokines and both lupus disease activity and organ damage. Longitudinal studies that relate molecular biomarkers to disease activity will be needed to validate these promising data and establish a sensitive measure of change for interventional studies and patient care.
Metabolic Engineering of Escherichia coli for l -Tyrosine Production by Expression of Genes Coding for the Chorismate Mutase Domain of the Native Chorismate Mutase-Prephenate Dehydratase and a Cyclohexadienyl Dehydrogenase from Zymomonas mobilis (2008)

The expression of the feedback inhibition-insensitive enzyme cyclohexadienyl dehydrogenase (TyrC) from Zymomonas mobilis and the chorismate mutase domain from native chorismate mutase-prephenate dehydratase (PheA(CM)) from Escherichia coli was compared to the expression of native feedback inhibition-sensitive chorismate mutase-prephenate dehydrogenase (CM-TyrA(p)) with regard to the capacity to produce l-tyrosine in E. coli strains modified to increase the carbon flow to chorismate. Shake flask experiments showed that TyrC increased the yield of l-tyrosine from glucose (Y(l-Tyr/Glc)) by 6.8-fold compared to the yield obtained with CM-TyrA(p). In bioreactor experiments, a strain expressing both TyrC and PheA(CM) produced 3 g/liter of l-tyrosine with a Y(l-Tyr/Glc) of 66 mg/g. These values are 46 and 48% higher than the values for a strain expressing only TyrC. The results show that the feedback inhibition-insensitive enzymes can be employed for strain development as part of a metabolic engineering strategy for l-tyrosine production.
Organization of a cluster of erythromycin genes in Saccharopolyspora erythraea (1990)

We used a series of gene disruptions and gene replacements to mutagenically characterize 30 kilobases of DNA in the erythromycin resistance gene (ermE) region of the Saccharopolyspora erythraea chromosome. Five previously undiscovered loci involved in the biosynthesis of erythromycin were found, eryBI, eryBII, eryCI, eryCII, and eryH; and three known loci, eryAI, eryG, and ermE, were further characterized. The new Ery phenotype, EryH, was marked by (i) the accumulation of the intermediate 6-deoxyerythronolide B (DEB), suggesting a defect in the operation of the C-6 hydroxylase system, and (ii) a block in the synthesis or addition reactions for the first sugar group. Analyses of ermE mutants indicated that ermE is the only gene required for resistance to erythromycin, and that it is not required for production of the intermediate erythronolide B (EB) or for conversion of the intermediate 3-alpha-mycarosyl erythronolide B (MEB) to erythromycin. Mutations in the eryB and eryC loci were similar to previously reported chemically induced eryB and eryC mutations blocking synthesis or attachment of the two erythromycin sugar groups. Insertion mutations in eryAI, the macrolactone synthetase, defined the largest (at least 9-kilobase) transcription unit of the cluster. These mutants help to define the physical organization of the erythromycin gene cluster, and the eryH mutants provide a source for the production of the intermediate DEB.
Sequence-specific modification of genomic DNA by small DNA fragments (2003)

Small DNA fragments have been used to modify endogenous genomic DNA in both human and mouse cells. This strategy for sequence-specific modification or genomic editing, known as small-fragment homologous replacement (SFHR), has yet to be characterized in terms of its underlying mechanisms. Genotypic and phenotypic analyses following SFHR have shown specific modification of disease-causing genetic loci associated with cystic fibrosis, beta-thalassemia, and Duchenne muscular dystrophy, suggesting that SFHR has potential as a therapeutic modality for the treatment of monogenic inherited disease.