gebhart/patrepeval huggingface dataset:
Identification of genes negatively regulated by Fis: Fis and RpoS comodulate growth-phase-dependent gene expression in Escherichia coli (1995)

Fis is a nucleoid-associated protein in Escherichia coli that has been shown to regulate recombination, replication, and transcription reactions. It is expressed in a transient manner under batch culturing conditions such that high levels are present during early exponential phase and low levels are present during late exponential phase and stationary phase. We have screened a random collection of transposon-induced lac fusions for those which give decreased expression in the presence of Fis. Thirteen different Fis-repressed genes were identified, including glnQ (glutamine high-affinity transport), mglA (methyl-galactoside transport), xylF (D-xylose-binding protein), sdhA (succinate dehydrogenase flavoprotein subunit), and a newly identified aldehyde dehydrogenase, aldB. The LacZ expression patterns revealed that many of the fusions were maximally expressed at different stages of growth, including early log phase, mid- to late log phase, and stationary phase. The expression of some of the late-exponential- and stationary-phase genes was dependent on the RpoS sigma factor, whereas that of others was affected negatively by RpoS. We conclude that Fis negatively regulates a diverse set of genes and that RpoS can function to both activate and inhibit the expression of specific genes.
Studies on prodrugs. III. A convenient and practical preparation of ampicillin prodrugs. (1984)

In order to prepare ampicillin prodrugs conveniently for practical use, a new synthetic method for 6β-aminopenicillanic acid (6-APA) esters as key intermediates of various ampicillin prodrugs has been developed. Acylation of 6-APA esters to ampicillin esters was achieved in good yields by using phenylglycyl chloride hydrochloride in dichloromethane in the presence of sodium bicarbonate and amide, or ammonium bicarbonate alone. KBT-1585, bacampicillin, talampicillin and pivampicillin have been obtained in good yields by this procedure.
Biodegradable PEO/PLA block copolymers (1988)

Poly(ether ester) block copolymers based on polyethylene oxide (PEO) and polylactic acid (PLA) segments were synthesized and characterized, with the aim of developing a new family of bioadsorbable polymers. The materials developed were tailored to meet various mechanical and degradation requirements, and overcome the limitations of the few existing biodegradable polymers. The copolymeric matrices were characterized by means of infrared spectroscopy, differential scanning calorimetry, and nuclear magnetic resonance spectroscopy. The composition of the copolymers synthesized varied between 20 and 84 mol% lactic acid, with PEO chains in the 600-6000 molecular weight range. The solubility properties of the copolymers in a series of organic solvents are described. The equilibrium water content and the water contact angle of various matrices were determined and related to their composition and structure. The incorporation of PEO into the chain yielded highly hydrophilic materials, with equilibrium water contents higher than 60%. Stress/strain curves are presented.
Tox-boxes, fungal secondary metabolites, and plant disease (2001)

Proceedings of the National Academy of Sciences (PNAS), a peer reviewed journal of the National Academy of Sciences (NAS) - an authoritative source of high-impact, original research that broadly spans the biological, physical, and social sciences.
Retroviral delivery and tetracycline-dependent expression of IL-1beta-converting enzyme (ICE) in a rat glioma model provides controlled induction of apoptotic death in tumor cells. (1996)

Interleukin 1beta-converting enzyme (ICE) is a member of a growing family of cysteine proteases shown to be a crucial component in the activation of a genetic program that leads to autonomous cell death in mammalian cells. In this study, a murine ICE-lacZ fusion gene was introduced into a novel retroviral vector designed to achieve regulated ectopic expression of a foreign gene in mammalian cells. By delivering the ICE-lacZ gene within a retroviral vector and under the control of a tetracycline-regulated promoter, we were able to utilize the intrinsic cell death program of ICE as a means for tumoricidal therapy in a rat brain tumor model. Both in culture and in vivo suppression of ICE-lacZ expression was extremely tight in the presence of tetracycline, as determined by the lack of X-galactosidase-positive tumor cells and by cell viability. When tetracycline was withdrawn, ICE-lacZ gene expression was rapidly turned on and apoptosis-mediated cell death occurred in essentially all tumor cells.
Eosinophilic and Neutrophilic Inflammation in Asthma: Insights from Clinical Studies (2009)

Cellular inflammation of the airways with eosinophils and neutrophils is a characteristic feature of asthma and is considered relevant to the pathogenesis of the disease. Studies of large numbers of subjects with well-characterized asthma in recent years has resulted in new insights about the clinical and pathologic correlates of eosinophilic and neutrophilic inflammation in asthma. For example, eosinophilic asthma is a distinct phenotype of asthma that is associated pathologically by thickening of the basement membrane zone and pharmacologically by corticosteroid responsiveness. In contrast, noneosinophilic asthma, a sizeable subgroup of asthma that includes patients with severe disease, is not characterized by thickening of the basement membrane zone, and it appears to be relatively corticosteroid resistant. Eosinophilic and neutrophilic asthma are not mutually exclusive subtypes of asthma. Rather, neutrophils accumulate in the airways in patients with asthma with more severe airflow obstruction, where eosinophils may also be present in excess. In addition, neutrophils are prominent in airway secretions during acute severe asthma exacerbations, where it is possible that they have roles in both the initiation and resolution of attacks. These insights about the relationships between cellular inflammation and disease phenotypes of asthma support the concept that different subgroups of patients with asthma, despite clinically similar features, can be defined by specific cellular and molecular markers. The promise now is that these markers will ultimately guide personalized treatment programs.
Bimodal Polyethylenes Obtained with a Dual-Site Metallocene Catalyst System. Effect of Trimethylaluminium Addition (2001)

Bimodal polyethylenes were obtained with the dual site Cp*2ZrCl2(1)/Et(IndH4)2ZrCl2(2) metallocene catalyst system with a mixture of methylaluminoxane (MAO) and trimethylaluminium (TMA) as the cocatalyst. Polymer properties can be controlled by the amount of TMA added, monomer pressure, polymerization temperature and the addition of hexene or hydrogen. TMA is suggested to be partly coordinated to the active sites, thereby enhancing termination (1), increasing comonomer incorporation (2), but also partially blocking coordination and chain transfer to hydrogen. For the ansa catalyst, hydrogen probably relieves dormant (β-agostic) sites.
Side effects of retroviral gene transfer into hematopoietic stem cells (2003)

Recent conceptual and technical improvements have resulted in clinically meaningful levels of gene transfer into repopulating hematopoietic stem cells. At the same time, evidence is accumulating that gene therapy may induce several kinds of unexpected side effects, based on preclinical and clinical data. To assess the therapeutic potential of genetic interventions in hematopoietic cells, it will be important to derive a classification of side effects, to obtain insights into their underlying mechanisms, and to use rigorous statistical approaches in comparing data. We here review side effects related to target cell manipulation; vector production; transgene insertion and expression; selection procedures for transgenic cells; and immune surveillance. We also address some inherent differences between hematopoiesis in the most commonly used animal model, the laboratory mouse, and in humans. It is our intention to emphasize the need for a critical and hypothesis-driven analysis of "transgene toxicology," in order to improve safety, efficiency, and prognosis for the yet small but expanding group of patients that could benefit from gene therapy.
Effectiveness of preoperative intranasal dexmedetomidine compared with oral midazolam for the prevention of emergence delirium in pediatric patients undergoing general anesthesia (2016)

There is no scientific evidence identifying the effectiveness of preoperative intranasal dexmedetomidine, compared with oral midazolam, for the prevention of emergence delirium in the pediatric patient population.
Estimating or Propagating Gradients Through Stochastic Neurons for Conditional Computation (2013)

Stochastic neurons and hard non-linearities can be useful for a number of reasons in deep learning models, but in many cases they pose a challenging problem: how to estimate the gradient of a loss function with respect to the input of such stochastic or non-smooth neurons? I.e., can we "back-propagate" through these stochastic neurons? We examine this question, existing approaches, and compare four families of solutions, applicable in different settings. One of them is the minimum variance unbiased gradient estimator for stochatic binary neurons (a special case of the REINFORCE algorithm). A second approach, introduced here, decomposes the operation of a binary stochastic neuron into a stochastic binary part and a smooth differentiable part, which approximates the expected effect of the pure stochatic binary neuron to first order. A third approach involves the injection of additive or multiplicative noise in a computational graph that is otherwise differentiable. A fourth approach heuristically copies the gradient with respect to the stochastic output directly as an estimator of the gradient with respect to the sigmoid argument (we call this the straight-through estimator). To explore a context where these estimators are useful, we consider a small-scale version of {\em conditional computation}, where sparse stochastic units form a distributed representation of gaters that can turn off in combinatorially many ways large chunks of the computation performed in the rest of the neural network. In this case, it is important that the gating units produce an actual 0 most of the time. The resulting sparsity can be potentially be exploited to greatly reduce the computational cost of large deep networks for which conditional computation would be useful.
MspA provides the main hydrophilic pathway through the cell wall of Mycobacterium smegmatis (2001)

MspA is an extremely stable, oligomeric porin from Mycobacterium smegmatis that forms water-filled channels in vitro. Immunogold electron microscopy and an enzyme-linked immunosorbent assay demonstrated that MspA is localized in the cell wall. An mspA deletion mutant did not synthesize detectable amounts of mspA mRNA, as revealed by amplification using mspA-specific primers and reverse-transcribed RNA. Detergent extracts of the DeltamspA mutant exhibited a significantly lower porin activity in lipid bilayer experiments and contained about fourfold less porin than extracts of wild-type M. smegmatis. The chromosome of M. smegmatis encodes three proteins very similar to MspA. Sequence analysis of the purified porin revealed that mspB or mspC or both genes are expressed in the DeltamspA mutant. The properties of this porin, such as single channel conductance, extreme stability against denaturation, molecular mass and composition of 20 kDa subunits, are identical to those of MspA. Deletion of mspA reduced the cell wall permeability towards cephaloridine and glucose nine- and fourfold respectively. These results show that MspA is the main general diffusion pathway for hydrophilic molecules in M. smegmatis and was only partially replaced by fewer porins in the cell wall of the DeltamspA mutant [corrected] This is the first experimental evidence that porins are the major determinants of the exceptionally low permeability of mycobacteria to hydrophilic molecules.
Piezoresistance in Quantized Conduction Bands in Silicon Inversion Layers (1971)

Piezoresistance measurements have been carried out on n-type inversion layers on (100), (110), and (111) silicon at room temperature as a function of the gate voltage (perpendicular electric field). It has been shown that the values of the piezoresistance coefficients depend not only on the surface orientation but also on the magnitude of the gate voltage. The strongest surface field influence was observed in the (100) plane whereas no gate voltage dependence could be detected on (111) surfaces. The data obtained have been interpreted in terms of the quantization of energy levels in inversion layers. This quantization causes generally an occupation anisotropy of the valleys mostly pronounced for an electric field in the [100] direction and disappearing for a [111] direction of the field. Theoretical expressions for the (100) piezoresistance coefficients π11 and π12 have been derived taking into account the field dependences of the population effect and of the intervally scattering contribution, both affected by the valley anisotropy. Experimental data have been fitted to the theory. From this fit numerical values of the occupation anisotropy of the valleys and of the anisotropy of the relaxation times relating to the intervalley scattering have been obtained.
Simulation tests of a lidar-based spacecraft pose determination algorithm (2007)

The autonomous close-in maneuvering necessary for the rendezvous and docking of two spacecraft requires a relative navigation sensor system that can determine the relative position and orientation (pose) of the controlled spacecraft with respect to the target spacecraft. Lidar imaging systems offer the potential for accurately measuring the relative six degree-of-freedom positions and orientations and the associated rates. In this paper, we present simulation results generated using a high fidelity modeling program. A simulated lidar system is used to capture close-proximity range images of a model target spacecraft, producing 3-D point cloud data. The sequentially gathered point-clouds are compared with the previous point-cloud using a real-time point-plane correspondence-less variant of the Iterative Closest Points (ICP) algorithm. The resulting range and pose estimates are used in turn to prime the next time-step iteration of the ICP algorithm. Results from detailed point-plane simulations and will be presented. The implications for real-time implementation are discussed.
Isolation and characterization of viral agents associated with porcine proliferative enteritis (1987)

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Structure and Pathology of Tau Protein in Alzheimer Disease (2012)

Alzheimer's disease (AD) is the most common type of dementia. In connection with the global trend of prolonging human life and the increasing number of elderly in the population, the AD becomes one of the most serious health and socioeconomic problems of the present. Tau protein promotes assembly and stabilizes microtubules, which contributes to the proper function of neuron. Alterations in the amount or the structure of tau protein can affect its role as a stabilizer of microtubules as well as some of the processes in which it is implicated. The molecular mechanisms governing tau aggregation are mainly represented by several posttranslational modifications that alter its structure and conformational state. Hence, abnormal phosphorylation and truncation of tau protein have gained attention as key mechanisms that become tau protein in a pathological entity. Evidences about the clinicopathological significance of phosphorylated and truncated tau have been documented during the progression of AD as well as their capacity to exert cytotoxicity when expressed in cell and animal models. This paper describes the normal structure and function of tau protein and its major alterations during its pathological aggregation in AD.
The Intestinal Microbiota and Obesity (2011)

Obesity has been and continues to be an epidemic in the United States. Obesity has been addressed in multiple health initiatives, including Healthy People 2010, with no state meeting the proposed goal of a prevalence of obesity < 15% of the adult population. In contrast, obesity rates have continued to increase, with the self-reported prevalence of obesity among adults increasing by 1.1% from 2007 to the present. Indeed, since 2009, 33 states reported obesity prevalences of 25% or more with only 1 state reporting prevalence < 20%. There have been multiple approaches for the treatment of obesity, including fad diets, incentive-based exercise programs, and gastric bypass surgery; none of which have been optimal. In a murine model, it was shown that the majority of the intestinal microbiome consists of two bacterial phyla, the Bacteroidetes and the Firmicutes, and that the relative abundance of these two phyla differs among lean and obese mice; the obese mouse had a higher proportion of Firmicutes to Bacteroidetes (50% greater) than the lean mouse. The same results were appreciated in obese humans compared to lean subjects. The postulated explanation for this finding is that Firmicutes produce more complete metabolism of a given energy source than do Bacteroidetes, thus promoting more efficient absorption of calories and subsequent weight gain. Researchers were able to demonstrate that colonizing germ-free mice with the intestinal microbiome from obese mice led to an increased total body fat in the recipient mice despite a lack of change in diet. The converse, that, colonizing germ-free obese mice with the intestinal microbiome of thin mice causing a decreased total body fat in the recipient mice, has not yet been done. Other possible mechanisms by which the intestinal microbiome affects host obesity include induction of low-grade inflammation with lipopolysaccharide, regulation of host genes responsible for energy expenditure and storage, and hormonal communication between the intestinal microbiome and the host. The following review discusses the microbiome-obesity relationship and proposed mechanisms by which the intestinal microbiota is hypothesized to influence weight gain.
Electrodeless direct current dielectrophoresis using reconfigurable field‐shaping oil barriers (2007)

We demonstrate dielectrophoretic (DEP) potential wells using pairs of insulating oil menisci to shape the DC electric field. These oil menisci are arranged in a configuration similar to the quadrupolar electrodes, typically used in DEP, and are shown to produce similar field gradients. While the one-pair well produces a focusing effect on particles in flow, the two-pair well results in creating spatial traps against crossflows. Uncharged polystyrene particles were used to map the DEP force fields and the experimental observations were compared against the field profiles obtained by numerically solving Maxwell's equations. We demonstrate trapping of a single particle due to negative DEP against a pressure-driven crossflow. This can be easily extended to trap and hold cells and other objects against flow for a longer time. We also show the results of particle trapping experiments performed to observe the effect of adjusting the oil menisci and the gap between two pairs of menisci in a four-menisci configuration on the nature of the DEP well formed at the center. A design parameter, Theta, capturing the dimensions of the DEP energy well, is defined and simulations exploring the effects of different geometric features on Theta are presented.
Cluster Analysis Identifies Distinct Pathogenetic Patterns in C3 Glomerulopathies/Immune Complex–Mediated Membranoproliferative GN (2017)

Membranoproliferative GN (MPGN) was recently reclassified as alternative pathway complement-mediated C3 glomerulopathy (C3G) and immune complex-mediated membranoproliferative GN (IC-MPGN). However, genetic and acquired alternative pathway abnormalities are also observed in IC-MPGN. Here, we explored the presence of distinct disease entities characterized by specific pathophysiologic mechanisms. We performed unsupervised hierarchical clustering, a data-driven statistical approach, on histologic, genetic, and clinical data and data regarding serum/plasma complement parameters from 173 patients with C3G/IC-MPGN. This approach divided patients into four clusters, indicating the existence of four different pathogenetic patterns. Specifically, this analysis separated patients with fluid-phase complement activation (clusters 1-3) who had low serum C3 levels and a high prevalence of genetic and acquired alternative pathway abnormalities from patients with solid-phase complement activation (cluster 4) who had normal or mildly altered serum C3, late disease onset, and poor renal survival. In patients with fluid-phase complement activation, those in clusters 1 and 2 had massive activation of the alternative pathway, including activation of the terminal pathway, and the highest prevalence of subendothelial deposits, but those in cluster 2 had additional activation of the classic pathway and the highest prevalence of nephrotic syndrome at disease onset. Patients in cluster 3 had prevalent activation of C3 convertase and highly electron-dense intramembranous deposits. In addition, we provide a simple algorithm to assign patients with C3G/IC-MPGN to specific clusters. These distinct clusters may facilitate clarification of disease etiology, improve risk assessment for ESRD, and pave the way for personalized treatment.
Influence of 8-Methyl-nonenoic Acid on Capsaicin Biosynthesis in In-Vivo and In-Vitro Cell Cultures of Capsicum Spp. (2006)

Capsaicin is a bioactive molecule synthesized by enzymatic (putative capsaicin synthase) condensation of vanillylamine, a phenyl propanoid intermediate with 8-methyl-nonenoic acid, a fatty acid derivative from leucine/valine pathway. Analysis of levels of 8-methyl-nonenoic acid and phenyl propanoid intermediates in high, medium, and low pungent Capsicum genotypes revealed that the 8-methyl-nonenoic acid pool plays a crucial role in determining the efficacy of capsaicin levels. Cerulenin-mediated inhibition of 8-methyl-nonenoic acid synthesis decreased the capsaicin biosynthesis in Capsicum cell suspension cultures. Similarly amino oxy acetate inhibited vanillylamine synthesis but failed to reduce capsaicin production. The mRNA transcript analysis of keto acyl synthase (KAS), a crucial enzyme involved in 8-methyl-nonenoic acid and an amino transferase (AMT), involved in vanillylamine biosynthesis was studied. The mRNA transcript analysis revealed the progressive developmental expression of KAS gene in the placenta during the ontogeny of the fruit, whereas AMT transcripts levels did not show significant differences. Hence, the study demonstrates the influence of 8-methyl-nonenoic acid and its possible regulatory role in capsaicin biosynthesis in Capsicum spp.