gebhart/patrepeval huggingface dataset:
Construction of a Stable α-Galactosidase-Producing Baker's Yeast Strain (1988)

Molasses is widely used as a substrate for commercial yeast production. The complete hydrolysis of raffinose, which is present in beet molasses, by Saccharomyces strains requires the secretion of alpha-galactosidase, in addition to the secretion of invertase. Raffinose is not completely utilized by commercially available yeast strains used for baking, which are Mel. In this study we integrated the yeast MEL1 gene, which codes for alpha-galactosidase, into a commercial mel baker's yeast strain. The Mel phenotype of the new strain was stable. The MEL1 gene was expressed when the new Mel baker's yeast was grown in molasses medium under conditions similar to those used for baker's yeast production at commercial factories. The alpha-galactosidase produced by this novel baker's yeast strain hydrolyzed all the melibiose that normally accumulates in the growth medium. As a consequence, additional carbohydrate was available to the yeasts for growth. The new strain also produced considerably more alpha-galactosidase than did a wild-type Mel strain and may prove useful for commercial production of alpha-galactosidase.
Material Engineering of GexSbyTez and GaxSby Phase Change Materials for High Performance Phase Change Memory (2012)

Abstract not Available.
Molecular models of multiple sclerosis severity identify heterogeneity of pathogenic mechanisms (2020)

The inability to measure putative pathogenic processes in the central nervous system (CNS) of living subjects precludes the determination of their temporal distribution, intra-individual heterogeneity, and their ability to predict disease course. Using multiple sclerosis (MS) as an example of a complex neurological disorder, we sought to determine if cerebrospinal fluid (CSF) biomarkers can be aggregated to predict future rates of MS progression and provide molecular insight into mechanisms of CNS destruction. 1,305 CSF biomarkers were analyzed blindly in the longitudinal training dataset (N=129) of untreated MS patients, using DNA-aptamer assay. Random forest models, validated in an independent longitudinal cohort (N=64), uncovered signatures of MS severity, measured by clinical scales and volumetric brain imaging. Cluster analysis revealed intra-individual molecular heterogeneity of disease mechanisms that include both CNS- and immune-related pathways and may represent novel targets for inhibiting MS progression.
Selective Development of Myogenic Mesenchymal Cells from Human Embryonic and Induced Pluripotent Stem Cells (2012)

Human embryonic stem (ES) cells and induced pluripotent stem (iPS) cells are promising sources for the cell therapy of muscle diseases and can serve as powerful experimental tools for skeletal muscle research, provided an effective method to induce skeletal muscle cells is established. However, the current methods for myogenic differentiation from human ES cells are still inefficient for clinical use, while myogenic differentiation from human iPS cells remains to be accomplished. Here, we aimed to establish a practical differentiation method to induce skeletal myogenesis from both human ES and iPS cells. To accomplish this goal, we developed a novel stepwise culture method for the selective expansion of mesenchymal cells from cell aggregations called embryoid bodies. These mesenchymal cells, which were obtained by dissociation and re-cultivation of embryoid bodies, uniformly expressed CD56 and the mesenchymal markers CD73, CD105, CD166, and CD29, and finally differentiated into mature myotubes in vitro. Furthermore, these myogenic mesenchymal cells exhibited stable long-term engraftment in injured muscles of immunodeficient mice in vivo and were reactivated upon subsequent muscle damage, increasing in number to reconstruct damaged muscles. Our simple differentiation system facilitates further utilization of ES and iPS cells in both developmental and pathological muscle research and in serving as a practical donor source for cell therapy of muscle diseases.
Development of Porous Sintered-Ceramic Separators for Application in a Li--Al/LiCl--KCl/FeS Battery (1979)

The procedure for fabrication of porous sintered-ceramic separators and the technical feasibility of using such separators in Li-Al/molten LiCl-KCl/FeS battery cells have been investigated. Processing techniques have been developed to fabricate ~1.5-2.5 mm thick, ~35-60% porous, flat, sintered Y{sub 2}O{ sub 3} and MgO separator plates with sufficient strength to allow handling prior to and during cell assembly. These separators performed successfully in laboratory-scale cells for up to ~2000 h and 283 cycles, indicating that the concept of a sintered separator is viable for Li-Al/FeS batteries. The particularly attractive features of these separators are potentially low cost, pre-fabricated form that allows easy cell assembly, and small pore size (average diameter 0.5-1.0 ~m) which provides good particle retention. The test results from the sintered-separator cells indicate that Y{sub 2}O{ sub 3} is probably unsuitable for long-term performance in Li-Al/FeS cells because of its reaction with the positive active material. This is in agreement with the recently reported data on cells with Y{sub 2}O{ sub 3} felt and powder separators. Sintered MgO separators, however, showed good chemical and mechanical stability in the cell environment. (auth)
Non‐native <i>N</i>‐Aroyl <scp>L</scp>‐Homoserine Lactones Are Potent Modulators of the Quorum Sensing Receptor RpaR in <i>Rhodopseudomonas palustris</i> (2013)

Quorum sensing (QS) is a process by which bacteria use low-molecular-weight signaling molecules (or autoinducers) to assess their local population densities and alter gene expression levels at high cell numbers. Many Gram-negative bacteria use N-acyl L-homoserine lactones (AHLs) with aliphatic acyl groups as signaling molecules for QS. However, bacteria that utilize AHLs with aroyl acyl groups have been recently discovered; they include the metabolically versatile soil bacterium Rhodopseudomonas palustris, which uses p-coumaroyl HL (p-cAHL) as its QS signal. This autoinducer is especially unusual because its acyl group is believed to originate from a monolignol (i.e., p-coumarate) produced exogenously by plants in the R. palustris environment, rather than through the endogenous fatty acid biosynthesis pathway like other native AHLs. As such, p-cAHL could signal not only bacterial density, but also the availability of an exogenous plant-derived substrate and might even constitute an interkingdom signal. Like other Gram-negative bacteria, QS in R. palustris is controlled by the p-cAHL signal binding its cognate LuxR-type receptor, RpaR. We sought to determine if non-native aroyl HLs (ArHLs) could potentially activate or inhibit RpaR in R. palustris, and thereby modulate QS in this bacterium. Herein, we report the testing of a set of synthetic ArHLs for RpaR agonism and antagonism by using a R. palustris reporter strain. Several potent non-native RpaR agonists and antagonists were identified. Additionally, the screening data revealed that lower concentrations of ArHL are required to strongly agonize RpaR than to antagonize it. Structure-activity relationship analyses of the active ArHLs indicated that potent RpaR agonists tend to have sterically small substituents on their aryl groups, most notably in the ortho position. In turn, the most potent RpaR antagonists were based on either the phenylpropionyl HL (PPHL) or the phenoxyacetyl HL (POHL) scaffold, and many contained an electron-withdrawing group at either the meta or para positions of the aryl ring. To our knowledge, the compounds reported herein represent the first abiotic chemical modulators of RpaR, and more generally, the first abiotic ligands capable of intercepting QS in bacteria that utilize native ArHL signals. In view of the origins of the p-cAHL signal in R. palustris, the largely unknown role of QS in this bacterium, and R. palustris' unique environmental lifestyles, we anticipate that these compounds could be valuable as chemical probes to study QS in R. palustris in a range of fundamental and applied contexts.
Integral imaging display method based on holographic diffuser and discrete lens array (2020)

To solve the problems of traditional integral imaging, such as poor visual quality, the ray-crosstalk in display, and grainy obvious, a display method based on discrete glued lens array and holographic diffuser is proposed. The proposed method replaces the continuous single lens array in the traditional display method of integral imaging with a discrete glued lens array and a holographic diffuser. In this paper, the structure and imaging quality of single lens and glued lens are designed, analyzed and compared. And the diffusion effect of the holographic diffuser is theoretically analyzed. We have designed two display system based on the ultra-high-density small-pitch LED display plane. The experimental results show that the visual quality of the proposed method is significantly improved compared with the traditional integral imaging display method. Compared with the traditional integral imaging display method based on a continuous single lens array, the proposed method can effectively reduce the influence of ray-crosstalk on the 3D images, smooth the discontinuous light field distribution, and reduce graininess to improve visual quality. In addition, since the traditional continuous single lens array needs to manufacture an abrasive tool with the same size as the display platform during processing, and the discrete glued lens array only needs to process the unit lens and then assemble them. If a large-scale integral imaging display system is to be manufactured, discrete lens array is more suitable, because the discrete glued lens array is cheaper and easier to be manufactured. In order to meet the experimental expectations and improve the display visual quality, we used a glued lens array in the experiment. Compared with aspheric lens that is difficult to process, the glued lens is easier to design and process and has good display visual quality.
Material selection for hybrid floating gate NAND memory applications (2016)

This article discusses the materials aspects involved in the successful integration of hybrid floating gate (HFG) devices for NAND applications. In HFG, a Si(n type)\metal(p type) stack replaces the standard poly‐Si FG. The high work function metal helps to enlarge the program window by limiting the leakage through the high‐ k intergate dielectric (IGD); the use of high‐ k IGD enables to scale the equivalent oxide thickness (EOT) of the HFG cell. Our recent progresses in the understanding of the materials characteristics (IGD crystallinity and HFG‐IGD thermal stability) that influence memory performance have allowed to demonstrate that HFG can be a solution to scale planar flash beyond the 20 nm node with the best preferable hybrid floating gate structure being a Ru‐based HFG and a 3‐layers IGD stack of HfAlO\Al 2 O 3 \HfAlO. Indeed, through the correct selection and combination of materials for process conditions that are relevant in flash memory fabrication flows, we will show that program windows can be suitably engineered. Finally, the materials challenges for keeping acceptable memory retention characteristics are also highlighted.
Rapid determination of hospital-acquired meticillin-resistant Staphylococcus aureus lineages (2007)

Multilocus sequence typing (MLST) and multi-strain microarray analysis have shown that most human Staphylococcus aureus strains belong to ten dominant clonal complexes (CCs) or lineages, each with unique surface architecture. Meticillin-resistant S. aureus (MRSA) strains currently belong to six of these lineages (CC1, CC5, CC8, CC22, CC30 and CC45), each of which has independently acquired mobile genetic elements (MGEs) carrying antibiotic resistance genes. MLST and microarrays are expensive and time consuming methods for routine determination of S. aureus lineage. A restriction-modification (RM) test has now been developed that is rapid, simple, inexpensive and accurately determines lineage of hospital-acquired MRSA. The RM test is based on three PCRs for hsdS gene variants, as hsdS genes likely control the independent evolution of S. aureus lineages. The RM test correctly identified 102 MRSA isolates as belonging to one of the six lineages/CCs. Real-time MRSA typing can be used to identify and track changes in local MRSA outbreaks, and provide support for targeting infection control strategies. Simple and accurate typing methods will also support large scale epidemiological studies, and could lead to greater understanding of the carriage, spread and virulence of different MRSA lineages.
Femtosecond ultraviolet pulse generation in β-BaB2O4 (1988)

Intracavity doubling in β-BaB2 O4 (BBO) of femtosecond pulses into the ultraviolet with high efficiency is reported. Pulse widths down to 43 fs at a 108 Hz repetition rate and outputs as high as 20 mW per arm of the femtosecond laser on a continuous-wave basis can be achieved. The ultraviolet pulse widths were determined through detailed cross-correlation measurements based on sum-frequency mixing to 210 nm in ultrathin BBO crystals.
Long wavelength GaInNAsSb/GaNAsSb multiple quantum well lasers (2002)

The high demand for 1.3–1.55 µm lasers has led to the investigation of GaInNAsSb/GaNAsSb on GaAs. In-plane lasers operating out to 1.49 µm, with threshold current density of 930 A/cm2 per quantum well and pulsed power up to 70 mW, are presented. In addition, photoluminescence out to 1.6 µm from GaInNAsSb quantum wells was observed.
Speech recognition in unseen and noisy channel conditions (2017)

Speech recognition in varying background conditions is a challenging problem. Acoustic condition mismatch between training and evaluation data can significantly reduce recognition performance. For mismatched conditions, data-adaptation techniques are typically found to be useful, as they expose the acoustic model to the new data condition(s). Supervised adaptation techniques usually provide substantial performance improvement, but such gain is contingent on having labeled or transcribed data, which is often unavailable. The alternative is unsupervised adaptation, where feature-transform methods and model-adaptation techniques are typically explored. This work investigates robust features, feature-space maximum likelihood linear regression (fMLLR) transform, and deep convolutional nets to address the problem of unseen channel and noise conditions. In addition, the work investigates bottleneck (BN) features extracted from deep autoencoder (DAE) networks trained by using acoustic features extracted from the speech signal. We demonstrate that such representations not only produce robust systems but also that they can be used to perform data selection for unsupervised model adaptation. Our results indicate that the techniques presented in this paper significantly improve performance of speech recognition systems in unseen channel and noise conditions.
Odorant-sensitive adenylate cyclase: rapid, potent activation and desensitization in primary olfactory neuronal cultures. (1991)

Using primary olfactory neuronal cultures, we have demonstrated rapid, potent increases in cAMP levels and adenylate cyclase [AC; ATP pyrophosphate-lyase (cyclizing), EC 4.6.1.1] activity in response to odorants. Isobutyl-methoxypyrazine is active at 1 nM. Odorant enhancement is dependent on Ca2+ concentration with maximal effects at 10-100 microM. Biphasic temporal and concentration-related effects occur with all odorants. All odorants examined elicit desensitization with AC responses abolished when odorants are reapplied immediately after removal. When reapplied 1 min after removal, odorants elicit an AC response greater than on first exposure, implying a cellular "memory" for odorants.
Specific immunization strategies against oxidized low-density lipoprotein: A novel way to reduce nonalcoholic steatohepatitis in mice (2012)

Antibodies to oxLDL play an important role in the pathogenesis of NASH. Therefore, the potential of phosphorylcholine-based vaccination strategies as a novel tool for the prevention and therapy of NASH should be tested in the future.
Immune response profiling of patients with spondyloarthritis reveals signalling networks mediating TNF-blocker function in vivo (2020)

We show that TNFi target multiple immune cell pathways that cooperate to resolve inflammation. We propose that immune response profiling provides new insight into the biology of TNF-blocker action in patients and can identify signalling pathways associated with therapeutic responses to biological therapies.
Neural-Guided Deductive Search for Real-Time Program Synthesis from Examples (2018)

Synthesizing user-intended programs from a small number of input-output examples is a challenging problem with several important applications like spreadsheet manipulation, data wrangling and code refactoring. Existing synthesis systems either completely rely on deductive logic techniques that are extensively hand-engineered or on purely statistical models that need massive amounts of data, and in general fail to provide real-time synthesis on challenging benchmarks. In this work, we propose Neural Guided Deductive Search (NGDS), a hybrid synthesis technique that combines the best of both symbolic logic techniques and statistical models. Thus, it produces programs that satisfy the provided specifications by construction and generalize well on unseen examples, similar to data-driven systems. Our technique effectively utilizes the deductive search framework to reduce the learning problem of the neural component to a simple supervised learning setup. Further, this allows us to both train on sparingly available real-world data and still leverage powerful recurrent neural network encoders. We demonstrate the effectiveness of our method by evaluating on real-world customer scenarios by synthesizing accurate programs with up to 12x speed-up compared to state-of-the-art systems.
Development of a Human Monoclonal Antibody against Cytomegalovirus with the Aim of a Passive Immunotherapy (1990)

A human monoclonal antibody (Mab) against cytomegalovirus (CMV) has been studied with the aim of applying it as a passive immunotherapeutic agent for CMV infection. The monoclonal antibody, designated Mab C23, was produced by a hybridoma generated by cell fusion of a human lymphocyte and a mouse myeloma cell. This IgG1 Mab was highly purified by four kinds of column chromatography and compared with native human IgG1. No difference in the constant region was detected by either protein nuclear magnetic resonance or immunoreactivity with goat antibodies against human IgG.KeywordsCell FusionHuman Monoclonal AntibodyNormal Human TissueHuman Embryonic LungPassive ImmunotherapyThese keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.
Preparation of solid drug/cyclodextrin complexes of acidic and basic drugs. (2004)

One of the main obstacles in pharmaceutical applications of cyclodextrins is their increase of the formulation bulk. Even at maximum incorporation 500 mg of a solid drug/cyclodextrin complex will only contain between 50 and 125 mg of the drug, assuming a low molecular weight drug (MW 200 to 400 Dalton) and an average molecular weight cyclodextrin (MW about 1500 Dalton). In general, the complexation efficiency is low and consequently the complex powder contains a significant amount of empty cyclodextrin molecules. In the present study the complexation efficiency is increased by ionization of the drug molecule through addition of volatile acid (i.e. acetic acid) or base (i.e. ammonia) to the aqueous complexation media of basic or acidic drugs, respectively. The volatile acid or base was then removed during lyophilization and heating in a vacuum oven resulting in formation of solid cyclodextrin complexes of the unionized drug. Thus, the complexation efficiency was temporary increased by the ionization but then again decreased leading to formation of the thermodynamically unstable solid drug/cyclodextrin complexes. When dissolved the energy of the system was lowered by expelling the drug molecules from the cyclodextrin cavities resulting in formation of supersaturated drug solutions and ultimately precipitation of the drug.
Generalized shape autocorrelation (1990)

This paper presents an efficient and homogeneous paradigm for automatic acquisition and recognition of nonparametric shapes. Acquisition time varies from linear to cubic in the number of object features. Recognition time is linear to cubic in the number of features in the image and grows slowly with the number of stored models. Nonparametric shape representation is achieved by spatial autocorrelation transforms. Both acquisition and recognition are two-step processes. In the first phase, spatialautocorrelationoperators are applied to the image data to perform local shape analysis. Then, spatial autocorrelation operators are applied to the local shape descriptors to either create entries (acquisition) or index (recognition) into a table containing the distributed shape information. The output of the table is used to generate a density function on the space of possible shapes with peaks corresponding to high confidence in the presence of a particular shape instance. The behavior of the system on a set of complex shapes is shown with respect to occlusion, geometric transformation, and cluttered scenes.
Liposomes functionalized to overcome the blood&ndash;brain barrier and to target amyloid-&beta; peptide: the chemical design affects the permeability across an in vitro model (2013)

Our results suggest that RI7217 promotes the in vitro barrier crossing of liposomes containing phosphatidic acid, targeting the Alzheimer's disease amyloid-β peptide. Moreover, for the first time, we prove herein the superior efficiency of covalent coupling of RI7217 versus biotin/streptavidin ligation to facilitate liposomes in overcoming the BBB in vitro.
Urinary cell <scp>mRNA</scp> profiles predictive of human kidney allograft status (2014)

Kidney allograft status is currently characterized using the invasive percutaneous needle core biopsy procedure. The procedure has become safer over the years, but challenges and complications still exist including sampling error, interobserver variability, bleeding, arteriovenous fistula, graft loss, and even death. Because the most common type of acute rejection is distinguished by inflammatory cells exiting the intravascular compartment and gaining access to the renal tubular space, we reasoned that a kidney allograft may function as an in vivo flow cytometer and sort cells involved in rejection into urine. To test this idea, we developed quantitative polymerase chain reaction (PCR) assays for absolute quantification of mRNA and pre-amplification protocols to overcome the low RNA yield from urine. Here, we review our single center urinary cell mRNA profiling studies that led to the multicenter Clinical Trials in Organ Transplantation (CTOT-04) study and the discovery and validation of a 3-gene signature of 18S rRNA-normalized measures of CD3ε mRNA and IP-10 mRNA and 18S rRNA that is diagnostic and predictive of acute cellular rejection in the kidney allograft. We also review our development of a 4-gene signature of mRNAs for vimentin, NKCC2, E-cadherin, and 18S rRNA diagnostic of interstitial fibrosis/tubular atrophy (IF/TA).