gebhart/patrepeval huggingface dataset:
Homofermentative Lactate Production Cannot Sustain Anaerobic Growth of Engineered Saccharomyces cerevisiae : Possible Consequence of Energy-Dependent Lactate Export (2004)

Due to a growing market for the biodegradable and renewable polymer polylactic acid, the world demand for lactic acid is rapidly increasing. The tolerance of yeasts to low pH can benefit the process economy of lactic acid production by minimizing the need for neutralizing agents. Saccharomyces cerevisiae (CEN.PK background) was engineered to a homofermentative lactate-producing yeast via deletion of the three genes encoding pyruvate decarboxylase and the introduction of a heterologous lactate dehydrogenase (EC 1.1.1.27). Like all pyruvate decarboxylase-negative S. cerevisiae strains, the engineered strain required small amounts of acetate for the synthesis of cytosolic acetyl-coenzyme A. Exposure of aerobic glucose-limited chemostat cultures to excess glucose resulted in the immediate appearance of lactate as the major fermentation product. Ethanol formation was absent. However, the engineered strain could not grow anaerobically, and lactate production was strongly stimulated by oxygen. In addition, under all conditions examined, lactate production by the engineered strain was slower than alcoholic fermentation by the wild type. Despite the equivalence of alcoholic fermentation and lactate fermentation with respect to redox balance and ATP generation, studies on oxygen-limited chemostat cultures showed that lactate production does not contribute to the ATP economy of the engineered yeast. This absence of net ATP production is probably due to a metabolic energy requirement (directly or indirectly in the form of ATP) for lactate export.
Electroporation: A general phenomenon for manipulating cells and tissues (1993)

Electroporation is a fascinating cell membrane phenomenon with several existing biological applications and others likely. Although DNA introduction is the most common use, electroporation of isolated cells has also been used for: (1) introduction of enzymes, antibodies, and other biochemical reagents for intracellular assays; (2) selective biochemical loading of one size cell in the presence of many smaller cells; (3) introduction of virus and other particles; (4) cell killing under nontoxic conditions; and (5) insertion of membrane macromolecules into the cell membrane. More recently, tissue electroporation has begun to be explored, with potential applications including: (1) enhanced cancer tumor chemotherapy, (2) gene therapy, (3) transdermal drug delivery, and (4) noninvasive sampling for biochemical measurement. As presently understood, electroporation is an essentially universal membrane phenomenon that occurs in cell and artificial planar bilayer membranes. For short pulses (microsecond to ms), electroporation occurs if the transmembrane voltage, U(t), reaches 0.5-1.5 V. In the case of isolated cells, the pulse magnitude is 10(3)-10(4) V/cm. These pulses cause reversible electrical breakdown (REB), accompanied by a tremendous increase molecular transport across the membrane. REB results in a rapid membrane discharge, with the elevated U(t) returning to low values within a few microseconds of the pulse. However, membrane recovery can be orders of magnitude slower. An associated cell stress commonly occurs, probably because of chemical influxes and effluxes leading to chemical imbalances, which also contribute to eventual survival or death. Basic phenomena, present understanding of mechanism, and the existing and potential applications are briefly reviewed.
Mapping epitopes of neutralizing monoclonal antibodies using phage random peptide libraries (1997)

Identification of protective determinants from microbial proteins is a necessary step in the rational design of subunit vaccines. We have previously used a synthetic peptide scan (Pepscan) assay to map a panel of eight neutralizing monoclonal antibodies (mAb; designated as C1.1 to C1.8) to a common motif sequence from Chlamydia trachomatis. In the present study, five of the eight mAbs were used to screen phage random peptide libraries. mAbs C1.1 and C1.3 selected a motif sequence of G-L-X-N-D from a pIII-based phage random peptide library and a motif sequence of G-X-X-N-D from a pVIII-based random peptide library while mAbs C1.6 to C1.8 failed to select recognizable motifs from either of the phage libraries. However, C1.6 to C1.8 bound to the same motif sequence displayed on phage when the appropriate conformational constraints were imposed onto the motif sequence. Thus the specificity of the mAbs identified on Pepscan assays correlates with the mAbs' dependence on local epitope constraints displayed on the phage surface.
Instructive Role of Wnt/ß-Catenin in Sensory Fate Specification in Neural Crest Stem Cells (2004)

Wnt signaling has recently emerged as a key factor in controlling stem cell expansion. In contrast, we show here that Wnt/beta-catenin signal activation in emigrating neural crest stem cells (NCSCs) has little effect on the population size and instead regulates fate decisions. Sustained beta-catenin activity in neural crest cells promotes the formation of sensory neural cells in vivo at the expense of virtually all other neural crest derivatives. Moreover, Wnt1 is able to instruct early NCSCs (eNCSCs) to adopt a sensory neuronal fate in a beta-catenin-dependent manner. Thus, the role of Wnt/beta-catenin in stem cells is cell-type dependent.
Antagonism of Central Melanocortin Receptors in Vitro and in Vivo by Agouti-Related Protein (1997)

Expression of Agouti protein is normally limited to the skin where it affects pigmentation, but ubiquitous expression causes obesity. An expressed sequence tag was identified that encodes Agouti-related protein, whose RNA is normally expressed in the hypothalamus and whose levels were increased eightfold in ob/ob mice. Recombinant Agouti-related protein was a potent, selective antagonist of Mc3r and Mc4r, melanocortin receptor subtypes implicated in weight regulation. Ubiquitous expression of human AGRP complementary DNA in transgenic mice caused obesity without altering pigmentation. Thus, Agouti-related protein is a neuropeptide implicated in the normal control of body weight downstream of leptin signaling.
Interactive Cell Segmentation Based on Active and Semi-Supervised Learning (2015)

Automatic cell segmentation can hardly be flawless due to the complexity of image data particularly when time-lapse experiments last for a long time without biomarkers. To address this issue, we propose an interactive cell segmentation method by classifying feature-homogeneous superpixels into specific classes, which is guided by human interventions. Specifically, we propose to actively select the most informative superpixels by minimizing the expected prediction error which is upper bounded by the transductive Rademacher complexity, and then query for human annotations. After propagating the user-specified labels to the remaining unlabeled superpixels via an affinity graph, the error-prone superpixels are selected automatically and request for human verification on them; once erroneous segmentation is detected and subsequently corrected, the information is propagated efficiently over a gradually-augmented graph to un-labeled superpixels such that the analogous errors are fixed meanwhile. The correction propagation step is efficiently conducted by introducing a verification propagation matrix rather than rebuilding the affinity graph and re-performing the label propagation from the beginning. We repeat this procedure until most superpixels are classified into a specific category with high confidence. Experimental results performed on three types of cell populations validate that our interactive cell segmentation algorithm quickly reaches high quality results with minimal human interventions and is significantly more efficient than alternative methods, since the most informative samples are selected for human annotation/verification early.
PPS RAIM Algorithms and Their Performance* (1995)

This paper describes several receiver autonomous integrity monitoring (RAIM)-type algorithms that are candidates for use in military Precise Positioning Service (PPS) GPS receivers. Although these PPS RAIM-type algorithms are based on the Standard Positioning Service (SPS) RAIM and RAIM-type algorithms described in RTCA/DO-208, TSO-C129, and elsewhere, a number of interesting modifications are necessary to adapt those SPS algorithms for use in a PPS receiver. Among these modifications are not having to deal with selective availability (SA) effects and needing to operate in a “fewer-than-all-in-view” mode. The performance of the PPS RAIM-type algorithms is presented with respect to both TSO-C-129 requirements and global detection availability for en route, terminal, and nonprecision approach operation. The performance of the algorithms is compared against the evolving required navigation performance (RNP) standards for primary-means navigation, and a preliminary evaluation is offered.
Incremental and Decremental Support Vector Machine Learning (2000)

An on-line recursive algorithm for training support vector machines, one vector at a time, is presented. Adiabatic increments retain the KuhnTucker conditions on all previously seen training data, in a number of steps each computed analytically. The incremental procedure is reversible, and decremental &amp;quot;unlearning&amp;quot; offers an efficient method to exactly evaluate leave-one-out generalization performance. Interpretation of decremental unlearning in feature space sheds light on the relationship between generalization and geometry of the data. 1
Glucose and fat metabolism in adipose tissue of acetyl-CoA carboxylase 2 knockout mice (2005)

Acc2-/- mutant mice, when fed a high-fat/high-carbohydrate (HF/HC) diet, were protected against diet-induced obesity and diabetes. To investigate the role of acetyl-CoA carboxylase 2 (ACC2) in the regulation of energy metabolism in adipose tissues, we studied fatty acid and glucose oxidation in primary cultures of adipocytes isolated from wild-type and Acc2-/- mutant mice fed either normal chow or a HF/HC diet. When fed normal chow, oxidation of [14C]palmitate in adipocytes of Acc2-/- mutant mice was approximately 80% higher than in adipocytes of WT mice, and it remained significantly higher in the presence of insulin. Interestingly, in addition to increased fatty acid oxidation, we also observed increased glucose oxidation in adipocytes of Acc2-/- mutant mice compared with that of WT mice. When fed a HF/HC diet for 4-5 months, adipocytes of Acc2-/- mutant mice maintained a 25% higher palmitate oxidation and a 2-fold higher glucose oxidation than WT mice. The mRNA level of glucose transporter 4 (GLUT4) decreased several fold in the adipose tissue of WT mice fed a HF/HC diet; however, in the adipose tissue of Acc2-/- mutant mice, it was 7-fold higher. Moreover, lipolysis activity was higher in adipocytes of Acc2-/- mutant mice compared with that in WT mice. These findings suggest that continuous fatty acid oxidation in the adipocytes of Acc2-/- mutant mice, combined with a higher level of glucose oxidation and a higher rate of lipolysis, are major factors leading to efficient maintenance of insulin sensitivity and leaner Acc2-/- mutant mice.
Stimuli‐Responsive Controlled Drug Release from a Hollow Mesoporous Silica Sphere/Polyelectrolyte Multilayer Core–Shell Structure (2005)

Keeping drugs under control: Hydrothermally stable, hollow mesoporous silica spheres have a high drug storage capacity, and polyelectrolyte multilayers coated on the spheres act as a switch for drug release which is controlled by the pH or ionic strength of the release medium. The picture shows the release of ibuprofen (IBU) from spheres with and without coatings of sodium polystyrene sulfonate (PSS) and poly(allylamine hydrochloride) (PAH). Supporting information for this article is available on the WWW under http://www.wiley-vch.de/contents/jc_2002/2005/z501500_s.pdf or from the author. Please note: The publisher is not responsible for the content or functionality of any supporting information supplied by the authors. Any queries (other than missing content) should be directed to the corresponding author for the article.
Improved Glycemic Control and Enhanced Insulin Sensitivity in Type 2 Diabetic Subjects Treated With Pioglitazone (2001)

These results suggest that pioglitazone therapy in type 2 diabetic patients decreases lasting and postprandial plasma glucose levels by improving hepatic and peripheral (muscle) tissue sensitivity to insulin.
Recombinant Adeno-Associated Virus Utilizes Cell-Specific Infectious Entry Mechanisms (2014)

There is a recognized need for improved rAAV vector targeting strategies that result in delivery of fewer total particles, averting untoward toxicity and/or an immune response against the vector. A critical step in rAAV transduction is entry and early trafficking through the host cellular machinery, the mechanisms of which are under continued study. However, should the early entry and trafficking mechanisms of rAAV differ across virus serotype or be dependent on host cell environment, this could expand our ability to target particular cells and tissue for selective transduction. Thus, the observation that inhibiting macropinocytosis leads to cell-specific enhancement or inhibition of rAAV transduction that extends to the organismic level exposes a new means of modulating vector targeting.
Hydration behavior of porcine cornea crosslinked with riboflavin and ultraviolet A (2007)

Collagen crosslinking using riboflavin and UVA led to a significant change in the swelling behavior of the anterior stroma, confirming prior findings that the crosslinking effect is strongest in the anterior half of the stroma. Crosslinked cornea did not induce a specific signal on OCT, and OCT is therefore not suited for clinical controls of the crosslinking effect.
Mannose Binding Lectin Is Required for Alphavirus-Induced Arthritis/Myositis (2012)

Mosquito-borne alphaviruses such as chikungunya virus and Ross River virus (RRV) are emerging pathogens capable of causing large-scale epidemics of virus-induced arthritis and myositis. The pathology of RRV-induced disease in both humans and mice is associated with induction of the host inflammatory response within the muscle and joints, and prior studies have demonstrated that the host complement system contributes to development of disease. In this study, we have used a mouse model of RRV-induced disease to identify and characterize which complement activation pathways mediate disease progression after infection, and we have identified the mannose binding lectin (MBL) pathway, but not the classical or alternative complement activation pathways, as essential for development of RRV-induced disease. MBL deposition was enhanced in RRV infected muscle tissue from wild type mice and RRV infected MBL deficient mice exhibited reduced disease, tissue damage, and complement deposition compared to wild-type mice. In contrast, mice deficient for key components of the classical or alternative complement activation pathways still developed severe RRV-induced disease. Further characterization of MBL deficient mice demonstrated that similar to C3(-/-) mice, viral replication and inflammatory cell recruitment were equivalent to wild type animals, suggesting that RRV-mediated induction of complement dependent immune pathology is largely MBL dependent. Consistent with these findings, human patients diagnosed with RRV disease had elevated serum MBL levels compared to healthy controls, and MBL levels in the serum and synovial fluid correlated with severity of disease. These findings demonstrate a role for MBL in promoting RRV-induced disease in both mice and humans and suggest that the MBL pathway of complement activation may be an effective target for therapeutic intervention for humans suffering from RRV-induced arthritis and myositis.
Modulation of Host Innate Immune Response in the Bladder by UropathogenicEscherichia coli (2007)

Uropathogenic Escherichia coli (UPEC), the most frequent cause of urinary tract infection (UTI), is associated with an inflammatory response which includes the induction of cytokine/chemokine secretion by urothelial cells and neutrophil recruitment to the bladder. Recent studies indicate, however, that UPEC can evade the early activation of urothelial innate immune response in vitro. In this study, we report that infection with the prototypic UPEC strain NU14 suppresses tumor necrosis factor alpha (TNF-alpha)-mediated interleukin-8 (CXCL-8) and interleukin-6 (CXCL-6) secretion from urothelial cell cultures compared to infection with a type 1 piliated E. coli K-12 strain. Furthermore, examination of a panel of clinical E. coli isolates revealed that 15 of 17 strains also possessed the ability to suppress cytokine secretion. In a murine model of UTI, NU14 infection resulted in diminished levels of mRNAs encoding keratinocyte-derived chemokine, macrophage inflammatory peptide 2, and CXCL-6 in the bladder relative to infection with an E. coli K-12 strain. Furthermore, reduced stimulation of inflammatory chemokine production during NU14 infection correlated with decreased levels of bladder and urine myeloperoxidase and increased bacterial colonization. These data indicate that a broad phylogenetic range of clinical E. coli isolates, including UPEC, may evade the activation of innate immune response in the urinary tract, thereby providing a pathogenic advantage.
Use of 5′-γ-Ferrocenyl Adenosine Triphosphate (Fc-ATP) Bioconjugates Having Poly(ethylene glycol) Spacers in Kinase-Catalyzed Phosphorylations (2011)

The 5'-γ-ferrocenyl adenosine triphosphate (Fc-ATP) bioconjugates (3 and 4), containing the poly(ethylene glycol) spacers, were synthesized and compared to a hydrophobic analogue as co-substrates for the following protein kinases: sarcoma related kinase (Src), cyclin-dependent kinase (CDK), casein kinase II (CK2α), and protein kinase A (PKA). Electrochemical kinase assays indicate that the hydrophobic Fc-ATP analogue was an optimal co-substrate for which K(M) values were determined to be in the 30-200 μM range, depending on the particular protein kinase. The luminescence kinase assay demonstrated the kinase utility for all Fc-ATP conjugates, which is in line with the electrochemical data. Moreover, Fc-ATP bioconjugates exhibit competitive behavior with respect to ATP. Relatively poor performance of the polar Fc-ATP bioconjugates as co-substrates for protein kinases was presumably due to the additional H-bonding and electrostatic interactions of the poly(ethylene glycol) linkers of Fc-ATP with the kinase catalytic site and the target peptides. Phosphorylation of the full-length protein, His-tagged pro-caspase-3, was demonstrated through Fc-phosphoamide transfer to the Ser residues of the surface-bound protein by electrochemical means. These results suggest that electrochemical detection of the peptide and protein Fc-phosphorylation via tailored Fc-ATP co-substrates may be useful for probing protein-protein interactions.
Simultaneous heart rate-motion sensor technique to estimate energy expenditure (2001)

The simultaneous HR-motion sensor technique is a good predictor of EE during selected lifestyle activities, and allows researchers to more accurately quantify free-living PA.
Employing Human Performance Optimization Initiatives from Historically Black Colleges and Universities: The Case of the U.S. Military (2011)

Abstract To preemptively respond to the ever changing battlefield and in light of growing threats to national security, the U.S. Department of Defense (DoD) and by extension the U.S. military, have developed human performance optimization (HPO) initiatives to improve warfighter performance for increasing mission readiness. African American officers, by way of the Reserve Officer Training Corps (ROTC) at Historically Black Colleges and Universities (HBCUs), have long been and continue to be an important constituency for this strategy. Using the results of an online search via the Internet of HPO-like academic offerings at HBCUs, this paper proposes that the U.S. military could enhance its war fighting capability, and specifically that of its African American officers, for increased preparedness, increased performance and sustained and increased readiness by modeling HPO like programs at HBCUs. The authors examine similar efforts around the world, offer the potential benefits to be derived from expanded collaborations between the U.S. military and HBCUs and discuss the implications for the U.S. military and militaries within international communities, HBCUs and future research.
Determination of secondary ion mass spectrometry relative sensitivity factors for polar and non-polar ZnO (2011)

Zinc oxide (ZnO) is regarded as a promising material for optoelectronic devices, due to its electronic properties. Solely, the difficulty in obtaining p-type ZnO impedes further progress. In this connection, the identification and quantification of impurities is a major demand. For quantitative information using secondary ion mass spectrometry (SIMS), so-called relative sensitivity factors (RSF) are mandatory. Such conversion factors did not yet exist for ZnO. In this work, we present the determined RSF values for ZnO using primary (ion implanted) as well as secondary (bulk doped) standards. These RSFs have been applied to commercially available ZnO substrates of different surface termination (a-plane, Zn-face, and O-face) to quantify the contained impurities. Although these ZnO substrates originate from the same single-crystal, we observe discrepancies in the impurity concentrations. These results cannot be attributed to surface termination dependent RSF values for ZnO.
A Comparative Study on the Acidic Properties and Catalytic Activities of TiO2, SiO2, Al2O3, SiO2–Al2O3, SiO2–TiO2, Al2O3–TiO2, and TiO2–SiO2–Al2O3 (1991)

Abstract Investigations are carried out to have a systematic comparison of the acidic properties and catalytic activities of single oxide TiO2, SiO2, Al2O3, their binary oxides and the ternary oxide TiO2–SiO2–Al2O3. The acidity distributions are measured by using butylamine titration technique and the test reactions selected for the catalytic activity measurements are alkylation of toluene with 2-propanol and the dehydration of 2-propanol. The single oxides have only low acid strength and are not at all active in catalyzing the alkylation reaction, but are marginally active in the dehydration of 2-propanol. However the binary oxides SiO2–TiO2 and Al2O3–TiO2 of 10% by weight of TiO2 are found to contain very strong acid sites Ho≤−8.2 and are highly active catalysts in both the test reactions. But TiO2–SiO2–Al2O3 of 10% by weight of TiO2 showed the highest acid amount and the highest activity in the aikylation and dehydration reactions compared to the binary oxides. The acid amount and the catalytic activity of the ternary oxide increased with the increase of TiO2 content upto 50 mol% of TiO2 and then decreased. The ternary oxide containing 80 mol% of TiO2 is rich in weak acid sites. The increase of TiO2 content does not affect the selectivity.
Putting rigor back in RAD (1994)

Nurses' social intelligence is widely used in clinical practice and is shown to have a significant direct and indirect impact on clinical nursing. To effectively apply social intelligence in the clinical context, individual and organizational efforts are required to share and transfer knowledge and capacity-building methods through collective intelligence and education.