gebhart/patrepeval huggingface dataset:
Medium optimization for lipid production through co‐fermentation of glucose and xylose by the oleaginous yeast Lipomyces starkeyi (2008)

Abstract Co‐fermentation of lignocellulose‐based carbohydrates is a potential solution to improve the economics of microbial lipid production. In the present paper, experiments were performed to optimize the media composition for lipid production by the oleaginous yeast Lipomyces starkeyi AS 2.1560 through co‐fermentation of glucose and xylose (2 : 1 wt/wt). Statistical screening of nine media variables was performed by a Plackett–Burman design. Three factors, namely mixed sugar, yeast extract and FeSO 4 , were found as significant components influencing cellular lipid accumulation. Further optimization was carried out using a Box–Behnken factorial design to study the effects of these three variables on lipid production. A mathematical model with the R 2 value at 96.66% was developed to show the effect of each medium composition and their interactions on the lipid production. The model estimated that a maximal lipid content of 61.0 wt‐% could be obtained when the concentrations of mixed sugar, yeast extract and FeSO 4 were at 73.3 g/L (glucose 48.9 g/L, xylose 24.4 g/L), 7.9 g/L and 4.0 mg/L, respectively. The predicted value was in good accordance with the experimental data of 61.5%. Compared with the initial media, the optimized media gave 1.59‐fold and 2.03‐fold increases for lipid content and lipid productivity, respectively.
Identification of the Transactivation Domain of the Transcription Factor Sox-2 and an Associated Co-activator (2000)

The importance of interactions between Sox and POU transcription factors in the regulation of gene expression is becoming increasingly apparent. Recently, many examples of the involvement of Sox-POU partnerships in transcription have been discovered, including a partnership between Sox-2 and Oct-3. Little is known about the mechanisms by which these factors modulate transcription. To better understand the molecular interactions involved, we mapped the location of the transactivation domain of Sox-2. This was done in the context of its interaction with Oct-3, as well as its ability to transactivate as a fusion protein linked to the DNA-binding domain of Gal4. Both approaches demonstrated that Sox-2 contains a transactivation domain in its C-terminal half, containing a serine-rich region and the C terminus. We also determined that the viral oncoprotein E1a inhibits the ability of the Gal4/Sox-2 fusion protein to transactivate, as well as the transcriptional activation mediated by the combined action of Sox-2 and Oct-3. In contrast, a mutant form of E1a, unable to bind p300, lacks both of these effects. Importantly, we determined that p300 overcomes the inhibitory effects of E1a in both assays. Together, these findings suggest that Sox-2 mediates its effects, at least in part, through the co-activator p300.
Analyzing the Puzzle of the Japanese Labor Market (1993)

Economic analysis of labor markets would be much easier were it not for the great success of the Japanese economy. If Japan were an economic basket-case, we would all argue over whether Japan’s problems stemmed from the horrendous job security practice of ‘lifetime employment’; absence of employment flexibility and low job mobility; management’s concern for employees instead of profits; and such peculiar institutions as extensive seniority wage payments, the Shunto Offensive, mandatory retirement, and the like. Labor relations specialists would decry the presence of enterprise level unionism that includes relatively high level white-collar workers (company unions in the US context), of labor disputes where workers strike by wearing a black band saying ‘On Strike’ while continuing to work, and of sharp differentiation between primary and secondary labor markets. Management specialists would denounce the long consultations and discussions with lower-level employees to reach consensus, as opposed to Western-style hierarchical decision-making; and would have called for greater division of labor in the production process.
Supporting flexible communication in heterogeneous multi-user environments (2002)

A flexible communication model for multi-user interfaces is presented. It allows for coupling arbitrary user interface objects between heterogeneous applications dynamically. When coupled, UI objects are synchronized by broadcasting events and re-executing the corresponding actions in the different application environments. To be coupled, objects have to be compatible, but not necessarily identical. The communication mechanism is based on a centralized server. In addition to multiplexing callbacks, it also handles arbitrary remote procedure calls in a standardized way, thus allowing the transfer of internal state information between applications. Our communication mechanism is implemented as a set of primitives that extend an OSF/Motif-based UI toolbox library. It can be easily used to develop multi-user interfaces in very much the same way as single-user applications, or to extend single-user applications to multi-user ones.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Single-Molecule Fluorescence Observed with Mercury Lamp Illumination (1999)

We demonstrate that it is possible to observe single fluorescent molecules using a standard fluorescence microscope with mercury lamp excitation and an inexpensive cooled charge-coupled device (CCD) camera. With this equipment, we have been able to observe single molecules of tetramethyl-rhodamine, rhodamine 6G, fluorescein isothiocyanate and green fluorescent protein. Immobilized molecules were observed both in air and in aqueous solution.
Self-Assembly of Cobalt Nanoparticle Rings (2002)

Weakly ferromagnetic cobalt nanoparticles can assemble spontaneously into nanosized "bracelets" when dispersed in organic solvents containing resorcinarenes as surfactants. Bracelet self-assembly occurs in solution and is directed by magnetic dipolar interactions, whereas nanoparticle rings with larger diameters are produced by evaporation-driven flow on wetted surfaces.
Changes in Collagen Cross-Linking in Degenerative Disc Disease and Scoliosis (1998)

These changes in the cross-link profile of the intervertebral disc in degenerative disc disease and scoliosis are indicative of increased matrix turnover and tissue remodeling and likely to have implications for the progression of these disorders.
A Tale of Two Targets: Differential RNA Selectivity of Nucleobase–Aminoglycoside Conjugates (2006)

Aminoglycoside antibiotics are RNA-binding polyamines that can bind with similar affinities to structurally diverse RNA targets. To design new semisynthetic aminoglycosides with improved target selectivity, it is important to understand the energetic and structural basis by which diverse RNA targets recognize similar ligands. It is also imperative to discover how novel aminoglycosides could be rationally designed to have enhanced selectivity for a given target. Two RNA drug targets, the prokaryotic ribosomal A-site and the HIV-1 TAR, provide an excellent model system in which to dissect the issue of target selectivity, in that they each have distinctive interactions with aminoglycosides. We report herein the design, synthesis, and binding activity of novel nucleobase-aminoglycoside conjugates that were engineered to be more selective for the A-site binding pocket. Contrary to the structural design, the conjugates bind the A-site more weakly than does the parent compound and bind the TAR more tightly than the parent compound. This result implies that the two RNA targets differ in their ability to adapt to structurally diverse ligands and thus have inherently different selectivities. This work emphasizes the importance of considering the inherent selectivity traits of the RNA target when engineering new ligands.
Aortic Distensibility in Patients with Cerebrovascular Disease (1995)

1. Non-invasive aortic compliance measurements have been used previously to assess the distensibility of the aorta in several pathological conditions associated with increased cardiovascular risk. We set out to establish whether aortic compliance is abnormal in patients with stroke. 2. Pulse wave velocity measurements of thoraco-abdominal aortic compliance were made in 20 stroke patients and 25 age- and sex-matched hospitalized, non-stroke control subjects putatively free of cardiovascular disease. Since compliance varies with non-chronic changes in blood pressure, a blood pressure corrected index of aortic distensibility, Cp, was calculated. 3. Aortic compliance was significantly reduced in patients with stroke compared with non-stroke control subjects (0.46 +/- 0.27 versus 0.86 +/- 0.34%/10 mmHg, P < 0.0002), corresponding with higher values for pulse wave velocity. Stroke patients also had significantly higher systolic and diastolic blood pressures (P < 0.02 and P < 0.002 respectively) and total cholesterol levels (P < 0.004) than the control subjects. Calculation of Cp did not alter the observation of stiffer aortas in the stroke cohort (P < 0.0007). 4. In both stroke patient and control cohorts, as expected, inverse trends were observed between aortic compliance and blood pressure. Also as expected, in the control group Cp values did not show a relationship with blood pressure (r = 0.02, P = 0.092, not significant). However, in the stroke cohort a marked dependence of Cp on blood pressure was observed (r = -0.48, P = 0.03). 5. Transoesophageal echocardiographic studies have recently identified advanced atherosclerosis in the ascending aorta as a possible source of cerebral emboli and an independent risk factor for ischaemic stroke.(ABSTRACT TRUNCATED AT 250 WORDS)
Identification of major cell classes in the developing mammalian nervous system (1985)

A major difficulty in studying early developmental processes and testing hypotheses of possible cellular mechanisms of development has been the inability to reproducibly identify specific cell types. We have generated monoclonal antibodies that distinguish among major cell types present during mammalian neurogenesis. These antibodies have been used to analyze the development of cellular organization in the early nervous system. Monoclonal antibody Rat-401 identifies a transient radial glial cell in the embryonic rat central nervous system (CNS) that is temporally and spatially suited to guide neuronal migration. Rat-401 also identifies a peripheral non-neuronal cell that may establish axon routes from the CNS to the periphery. Monoclonal antibody Rat-202 recognizes an antigen present in early axons, their growth cones, and filopodia, and has allowed us to follow early axons and observe the structures they contact. Two other antibodies that recognize axons demonstrate antigenically distinct phases in axon development. In addition, we report a marker for another cell class present in the developing nervous system, the endothelial cells that give rise to the CNS vasculature.
Non-Hodgkin's lymphoma time trends: United States and international data. (1992)

Incidence data from the Surveillance, Epidemiology, and End Results Program of the National Cancer Institute, earlier incidence surveys, and the International Agency for Research on Cancer, mortality data from the National Center for Health Statistics, and population data from the Census Bureau were used to assess rates of non-Hodgkin's lymphoma. Mortality and incidence rates have been increasing for many years. Larger increases among older persons suggest a role for improving diagnosis, particularly during the 1950s and 1960s. Urban/rural and socioeconomic differences have diminished over time. Since the early 1970s, incidence rates increased at 3-4%/year, more rapidly than for all other cancers except melanoma of the skin and lung cancer among women. Incidence rates increased over all ages except the very young, among whites and blacks, in geographic areas both in the United States and internationally, and both sexes. During the 1980s, the impact of AIDS is apparent among young and middle-aged men. Differences in non-Hodgkin's lymphoma rates persist between races and sexes. Increases have been more marked for extranodal disease, particularly those arising in the brain, and for high-grade tumors. Explanations accounting for all the increases in rates are not readily available.
Reducing Uncertainty in Undersampled MRI Reconstruction with Active Acquisition (2019)

The goal of MRI reconstruction is to restore a high fidelity image from partially observed measurements. This partial view naturally induces reconstruction uncertainty that can only be reduced by acquiring additional measurements. In this paper, we present a novel method for MRI reconstruction that, at inference time, dynamically selects the measurements to take and iteratively refines the prediction in order to best reduce the reconstruction error and, thus, its uncertainty. We validate our method on a large scale knee MRI dataset, as well as on ImageNet. Results show that (1) our system successfully outperforms active acquisition baselines; (2) our uncertainty estimates correlate with error maps; and (3) our ResNet-based architecture surpasses standard pixel-to-pixel models in the task of MRI reconstruction. The proposed method not only shows high-quality reconstructions but also paves the road towards more applicable solutions for accelerating MRI.
Molecular evolution and diversity in Bacillus anthracis as detected by amplified fragment length polymorphism markers (1997)

Bacillus anthracis causes anthrax and represents one of the most molecularly monomorphic bacteria known. We have used AFLP (amplified fragment length polymorphism) DNA markers to analyze 78 B. anthracis isolates and six related Bacillus species for molecular variation. AFLP markers are extremely sensitive to even small sequence variation, using PCR and high-resolution electrophoresis to examine restriction fragments. Using this approach, we examined ca. 6.3% of the Bacillus genome for length mutations and ca. 0.36% for point mutations. Extensive variation was observed among taxa, and both cladistic and phenetic analyses were used to construct a phylogeny of B. anthracis and its closest relatives. This genome-wide analysis of 357 AFLP characters (polymorphic fragments) indicates that B. cereus and B. thuringiensis are the closest taxa to B. anthracis, with B. mycoides slightly more distant. B. subtilis, B. polymyxa, and B. stearothermophilus shared few AFLP markers with B. anthracis and were used as outgroups to root the analysis. In contrast to the variation among taxa, only rare AFLP marker variation was observed within B. anthracis, which may be the most genetically uniform bacterial species known. However, AFLP markers did establish the presence or absence of the pXO1 and pXO2 plasmids and detected 31 polymorphic chromosomal regions among the 79 B. anthracis isolates. Cluster analysis identified two very distinct genetic lineages among the B. anthracis isolates. The level of variation and its geographic distribution are consistent with a historically recent African origin for this pathogenic organism. Based on AFLP marker similarity, the ongoing anthrax epidemic in Canada and the northern United States is due to a single strain introduction that has remained stable over at least 30 years and a 1,000-mile distribution.
The Effects of Acid Treatment on the Electrochemical Properties of 0.5 Li[sub 2]MnO[sub 3]⋅0.5 LiNi[sub 0.44]Co[sub 0.25]Mn[sub 0.31]O[sub 2] Electrodes in Lithium Cells (2006)

The electrochemical properties of electrodes, when preconditioned and activated with acid for , have been studied in lithium cells. Powder X-ray diffraction data and electrochemical measurements provide supporting evidence for an intergrown, composite electrode structure from which can be leached from the component with acid, thereby mimicking the electrochemical charge process at high potentials . The -rich domains generated by acid treatment are reduced during electrochemical discharge at a lower potential than electrochemically generated -rich domains. With prolonged cycling between 4.6 and , plots of untreated and acid-treated electrodes develop similar, but not identical, character, suggesting a coalescence and redox interaction of the manganese ions in -rich and regions of the structure. Acid treatment eliminates the first-cycle capacity loss of the electrodes, consistent with earlier reports for related systems, but it damages their cycling stability and rate capability.
Role for dipeptidyl peptidase IV in tumor suppression of human non small cell lung carcinoma cells (2004)

Lung cancer is the leading cause of cancer death. Lung cancers produce a variety of mitogenic growth factors that stimulate tumor cell proliferation and migration. The cell surface protease, dipeptidyl peptidase IV (DPPIV), is involved in diverse biologic functions, including peptide-mediated cellular growth and differentiation. DPPIV is expressed in various normal tissues, including lung tissue, and its expression is lost in many types of human cancers. DPPIV expression and its enzymatic activity are detected in normal bronchial and alveolar epithelium but different histologic subtypes of lung carcinomas lose DPPIV expression. To investigate the role of DPPIV in lung carcinoma, we examined the expression of DPPIV at both mRNA and protein levels in non small cell lung cancer (NSCLC) cell lines and normal human bronchial epithelial cells. DPPIV expression was detectable in normal lung epithelial cells, but was absent or markedly reduced in all NSCLC cell lines at both mRNA and protein levels. Restoration of DPPIV expression in NSCLC cells resulted in profound morphologic changes, inhibition of cell proliferation, anchorage-independent growth, in vitro cell migration and tumorigenicity in nude mice. DPPIV reexpression also correlated with increased p21 expression, leading to induction of apoptosis and cell cycle arrest in G1 stage. These effects were accompanied by increased expression of cell surface proteins, fibroblast-activating protein (Fapalpha) and CD44 that are associated with suppression of tumor growth and metastasis. Thus, DPPIV functions as a tumor suppressor, and its downregulation may contribute to the loss of growth control in NSCLC cells.
Definition of the region on NS3 which contains multiple epitopes recognized by dengue virus serotype-cross-reactive and flavivirus-cross-reactive, HLA-DPw2-restricted CD4+ T cell clones. (1998)

The epitopes recognized by six CD4+ CD8- cytotoxic T lymphocyte (CTL) clones established from a dengue-3 virus-immune donor were defined. (i) Three CTL clones, JK10, JK34 and JK39, were cross-reactive for dengue virus types 1-4. (ii) One clone, JK28, was cross-reactive for dengue virus types 1-4 and West Nile virus. (iii) Two clones, JK26 and JK49, were cross-reactive for dengue virus types 1-4, West Nile virus and yellow fever virus. The clones, except for JK49, recognized the same epitope on NS3 in an HLA-DPw2-restricted fashion. The smallest synthetic peptide recognized by the five CTL clones was a 10 aa peptide which comprises aa 255-264 on dengue virus NS3. JK49 recognized the overlapping epitope which comprises aa 257-266 in an HLA-DPw2-restricted fashion. Analysis of T cell receptor (TCR) usage by these T cell clones revealed that (i) JK10 and JK34 use V alpha11, and JK34 and JK28 use V beta23, and (ii) the amino acid sequences of the V(D)J junctional region of the TCR were different among these five CTL clones. There were, however, single amino acid conservations among TCRs of some of these T cell clones. These results indicate that the region on NS3 which comprises aa 255-266 contains multiple epitopes recognized by dengue serotype-cross-reactive and flavivirus-cross-reactive CD4+ CTL in an HLA-DPw2-restricted fashion and that a single epitope can be recognized by T cells which have heterogeneous virus specificities.
Structure of the chicken neuron-glia cell adhesion molecule, Ng-CAM: origin of the polypeptides and relation to the Ig superfamily. (1991)

The neuron-glia cell adhesion molecule (Ng-CAM) mediates both neuron-neuron and neuron-glia adhesion; it is detected on SDS-PAGE as a predominant 135-kD glycoprotein, with minor components of 80, 190, and 210 kD. We have isolated cDNA clones encoding the entire sequence of chicken Ng-CAM. The predicted extracellular region includes six immunoglobulin-like domains followed by five fibronectin-type III repeats, structural features that are characteristic of several neural CAMs of the N-CAM superfamily. The amino acid sequence of chicken Ng-CAM is most similar to that of mouse L1 but the overall identity is only 40% and Ng-CAM contains a short fibronectin-like segment with an RGD sequence that has no counterpart in L1. These findings suggest that Ng-CAM and L1 may not be equivalent molecules in chicken and mouse. The amino-terminal sequences of the 210-, 190-, and 135-kD components of Ng-CAM are all the same as the predicted amino terminus of the molecule, whereas the 80-kD component begins within the third fibronectin repeat. The cDNA sequence is continuous across the junction between the 135- and 80-kD components, and a single 170-kD Ng-CAM polypeptide was isolated from tunicamycin-treated cells. In addition, all cDNA probes hybridized on Northern blots to a 6-kb RNA, and most hybridized to single bands on Southern blots. These results indicate that the Ng-CAM components are derived from a single polypeptide encoded by a single gene, and that the 135- and 80-kD components are generated from the 210/190-kD species by proteolytic cleavage. The 135-kD component contains most of the extracellular region including all of the immunoglobulin-like domains. It has no transmembrane segment, but it is tightly associated with the membrane. The 80-kD component contains two and a half type III repeats plus the RGD-containing segment, as well as the single transmembrane and cytoplasmic domains. These structural features of Ng-CAM provide a framework for understanding its multiple functions in neuron-neuron interactions, neurite fasciculation, and neuron-glia interactions.
Temperature and pressure dependence of resonance in multi-layer microcantilevers (2005)

The resonance frequency of the fundamental and four higher order modes of a silicon dioxide microcantilever is measured. The effect on these modes of depositing a 400 nm gold coating is investigated theoretically and experimentally. We derive an analytical solution to the eigenmodes of a multi-layered cantilever and verify its validity by comparison to finite-element analysis as well as the experimentally obtained results. The temperature and pressure dependence of the resonance frequencies is investigated experimentally and found to be in good agreement with theoretical models. An experimentally obtained value for the temperature dependence of Young's modulus of elasticity for thermally grown SiO2 is presented.