gebhart/patrepeval huggingface dataset:
The Response of Murine Macrophages to Infection with Yersinia pestis as Revealed by DNA Microarray Analysis (2006)

Macrophages play a crucial role in recognition and phagocytosis of pathogens and in the induction of response, immunity and immunopathology. A key strategy employed by numerous pathogens such as Yersinia pestis is to circumvent the immune response of the host via actively down-regulating the activation of macrophages. The study on host-pathogen interaction and gene expression is imperative for the development of alternative therapeutics. We have combined Suppression Subtractive Hybridisation (SSH), Microarray techniques, Northern blot analysis and quantitative reverse transcription coupled PCR (RT-PCR) to gain a view of differential host gene expression in response to Y. pestis-26 degrees C infection. In our study, a total of 22 different genes were identified as up-regulated in response to the Y. pestis infection. These genes include unknown EST's, cytokines, enzyme of cytokine, receptors, ligands, transcriptional factors, inhibitor of transcriptional factor, and proteins involved with cytoskeleton. More interestingly, among them are 7 genes that encode for factors known to be associated with cell cycling and cell proliferation, with 3 of them playing a role in apoptosis. Our data also indicate that macrophage cells undergo apoptosis during an infection with Y. pestis-37 degrees C, however an infection with 26 degrees C cultures results in a delayed apoptosis. The correlation between the delayed apoptosis and the up-regulation of anti-apoptotic gene is currently being studied.
Hierarchical Bayesian Inference in Networks of Spiking Neurons (2004)

There is growing evidence from psychophysical and neurophysiological studies that the brain utilizes Bayesian principles for inference and de-cision making. An important open question is how Bayesian inference for arbitrary graphical models can be implemented in networks of spik-ing neurons. In this paper, we show that recurrent networks of noisy integrate-and-fire neurons can perform approximate Bayesian inference for dynamic and hierarchical graphical models. The membrane potential dynamics of neurons is used to implement belief propagation in the log domain. The spiking probability of a neuron is shown to approximate the posterior probability of the preferred state encoded by the neuron, given past inputs. We illustrate the model using two examples: (1) a motion de-tection network in which the spiking probability of a direction-selective neuron becomes proportional to the posterior probability of motion in a preferred direction, and (2) a two-level hierarchical network that pro-duces attentional effects similar to those observed in visual cortical areas V2 and V4. The hierarchical model offers a new Bayesian interpretation of attentional modulation in V2 and V4. 1
Melatonin potentiates the effects of metformin on glucose metabolism and food intake in high‐fat‐fed rats (2018)

Melatonin improves the beneficial effects of metformin on insulin sensitivity and body mass gain in high-fat fed Sprague-Dawley rats. Therefore, the combination of melatonin and metformin could be beneficial to develop dual therapies to treat or delay type 2 diabetes associated with obesity.
Expression and characterization of human and chimeric human-Paracoccus denitrificans electron transfer flavoproteins. (1994)

Electron transfer flavoprotein (ETF) is a heterodimer that contains a single equivalent of FAD and accepts electrons from nine flavoprotein dehydrogenases in the mitochondrial matrix. Human ETF was expressed in Escherichia coli using the expression vector previously employed to express Paracoccus denitrificans ETF (Bedzyk, L. A., Escudero, K. W., Gill, R. E., Griffin, K. J., and Frerman, F. E. (1993) J. Biol. Chem. 268, 20211-20217). cDNAs encoding the beta and alpha subunits of the human protein were inserted into the vector, mimicking the arrangement of the P. denitrificans genes in which coding sequences are joined by overlapping termination and initiation codons. A human ETF containing 30% P. denitrificans sequence at the amino terminus of the beta subunit was also expressed and purified. This chimeric ETF has 64% sequence identity with the human sequence in the substituted region. Kinetic constants of medium chain and short chain acyl-CoA dehydrogenases for the chimeric ETFs were slightly changed from those of human ETF; but, there are marked differences in the kinetic constants of sarcosine dehydrogenase and electron transfer flavoprotein-ubiquinone oxidoreductase with the two ETFs. Absorption spectra of the three redox states of human, chimeric, and P. denitrificans ETF flavins are identical. However, the flavin circular dichroism spectra of the three ETFs are characteristic for each species. The spectrum of the chimeric ETF has both human and P. denitrificans ETF features. The amplitude of the 436 nm band is identical to that of the of the human ETF flavin, but the amplitude of the 375 nm band is identical to that of the P. denitrificans ETF flavin. Thus, flavin in the chimeric ETF appears to be exposed to dipoles in the protein framework provided by human and bacterial sequences. These spectral data indicate that the flavin is located in the vicinity of the amino-terminal region of the beta subunit. The kinetic data suggest that the amino-terminal region of the beta subunit comprises part of the docking site for some primary dehydrogenases and electron transfer flavoprotein-ubiquinone oxidoreductase.
On densifying coding opportunities in instantly decodable network coding graphs (2012)

In this paper, we propose a coding strategy that maximizes the density of the coding opportunities in instantly decodable network coding (IDNC). Using the graph representation of IDNC, we derive the expression for the expected evolutions of coding opportunities after the transmission of any arbitrary coded packet and show that serving the maximum number of receivers, with the largest numbers of missing packets and erasure probabilities, tends to both maximize the expected number of coding opportunities and increase the expected coding density almost monotonically. Simulation results justify our theoretical findings and demonstrate the importance of maintaining high coding density when optimizing long-term parameters.
A systems biology approach to suppress TNF-induced proinflammatory gene expressions (2013)

Our results demonstrate that Nec-1 modulates TNF-induced proinflammatory response, and may potentially be used as a therapeutic target for inflammatory diseases such as rheumatoid arthritis and osteoarthritis.
Wafer-scale silicon photonic switches beyond die size limit (2019)

Fast optical switches have been proposed as a promising alternative to enable continual scaling of data centers with increasing size and data rates. Silicon photonics is a compelling platform for large-scale integrated photonic switches, leveraging advanced manufacturing foundries for electronic integrated circuits. In the past decade, the port counts of silicon photonic switches have increased steadily to 128×128. Further scaling of the switch is constrained by the maximum reticle size (2–3 cm) of lithography tools. Here, we propose to use wafer-scale integration to overcome the die size limit. As a proof of concept demonstration, we fabricated a 240×240 switch by lithographically stitching a 3×3 array of identical 80×80 switch blocks across reticle boundaries. Stitching loss is substantially reduced (0.004 dB) by tapering the waveguide width to 10 μm. The fabricated switch on a 4 cm×4 cm chip exhibits a maximum on-chip loss of 9.8 dB, an ON/OFF ratio of 70 dB, and switching times of less than 400 ns. To our knowledge, this is the largest integrated photonic switch ever reported. The loss-to-port count ratio (0.04 dB/port) is also the lowest.
Prevalence of pathogenic and antibiotics resistant Escherichia coli from effluents of a slaughterhouse and a municipal wastewater treatment plant in Dakar (2017)

The aim of this study was to detect and characterize pathogenic and antibiotic resistant Escherichia coli isolated from slaughterhouse wastewater and the effluents of a municipal wastewater treatment plant (WWTP) in Dakar, Senegal. Genetic markers associated with enterohemorrhagic E. coli (EHEC) and extraintestinal pathogenic E. coli (ExPEC) were screened in 268 E. coli isolates from slaughterhouse and 272 E. coli isolates from WWTP. Concerning antimicrobial resistance, 40 E. coli isolates were studied for each of the two sampling sites. None of the E. coli isolates harboring the genes associated with EHEC was detected in WWTP. Of the 13 tested virulence genes, fuyA and f17 were the most prevalent. The pathogenic and resistant E. coli was found in the raw wastewater and the influent of slaughterhouse. The final rejection used for urban gardening, including the watering of vegetables does not contain E. coli. These results showed that, after treatment, the sanitation risks associated with the reuse water from WWTP were low. Key words: Escherichia coli, wastewater, enterohemorrhagic E. coli (EHEC), extraintestinal pathogenic E. coli (ExPEC), antimicrobial resistance, slaughterhouse.
Thrust Analysis of the Linear Proportional Solenoid for a Hydraulic Control Valve (1994)

The linear proportional solenoid (LPS) is an actuator for a proportional control valve used in hydraulic pressure-control devices. The LPS must have a constant thrust over a designated displacement range, and the thrust must also increase in proportion to the exciting current. This paper deals with the effect of using dither to remove hysteresis phenomena, and describes numerical solutions for the thrust F and displacement x, which are characteristics of the LPS. Dither is a useful small-amplitude oscillation which is introduced to overcome the effect of hysteresis. When dither is applied, the maximum hysteresis of the thrust is decreased from 6% to 3%. The LPS consists of four different magnetic materials, and its F-x characteristic was calculated by the finite element method (FEM). The calculated F-x characteristics approximated the measured results to within an error of 2%. A newly proposed LPS, which maintains constant thrust over a broader range, is also described.
Sensitivity of Escherichia coli (MutT) and human (MTH1) 8-oxo-dGTPases to in vitro inhibition by the carcinogenic metals, nickel(II), copper(II), cobalt(II) and cadmium(II) (1997)

The toxicity of Ni(II), Co(II) and Cu(II) in animals, and that of Cd(II) in cultured cells, has been associated with generation of the promutagenic lesion 8-oxo-7,8-dihydroguanine (8-oxoguanine) in DNA, among other effects. One possible source of this base may be 8-oxo-7,8-dihydro-2'-deoxyguanosine-5'-triphosphate (8-oxo-dGTP), a product of oxidative damage to the nucleotide pool, from which it is incorporated into DNA. To promote such incorporation, the metals would have to inhibit specific cellular 8-oxo-dGTPases that eliminate 8-oxo-dGTP from the nucleotide pool. The present study was designed to test such inhibition in vitro on 8-oxo-dGTPases from two different species, the human MTH1 protein and Escherichia coli MutT protein. In the presence of Mg(II), the natural activator of 8-oxo-dGTPases, all four metals were found to inhibit both enzymes. For MTH1, the IC50 values (+/- SE; n = 3-4) were 17 +/- 2 microM for Cu(II), 30 +/- 8 microM for Cd(II), 376 +/- 71 microM for Co(II) and 801 +/- 97 microM for Ni(II). For MutT, they were 60 +/- 6 microM for Cd(II), 102 +/- 8 microM for Cu(II), 1461 +/- 96 microM for Ni(II) and 8788 +/- 1003 microM for Co(II). Thus, Cu(II) and Cd(II) emerged as much stronger inhibitors than Ni(II) and Co(II), and MTH1 appeared to be generally more sensitive to metal inhibition than MutT. Interestingly, in the absence of Mg(II), the activity of the enzymes could be restored by Co(II) to 73% of that with Mg(II) alone for MutT, and 34% for MTH1, the other metals being much less or non-effective. The difference in sensitivity to metal inhibition between the two enzymes may reflect the differences in the amino acid ligands, especially the cysteine ligand, outside their evolutionarily conserved Mg(II)-binding active sites, which might indicate predominantly non-competitive or uncompetitive mechanism of the inhibition. The overall results suggest that inhibition of 8-oxo-dGTPases may be involved in the mechanisms of induction of the 8-oxoguanine lesion in DNA by the metal ions studied, especially the non-redox-active Cd(II) cation.
A Laboratory Study of the Reduction of Iron Oxides by Hydrogen (2008)

To reduce the emission of greenhouse gases by the steel industry, particularly for ironmaking, the production of DRI (Direct Reduced Iron) using hydrogen as the reducing gas instead of carbon monoxide is being considered. In this context, the reduction of pure hematite by hydrogen was studied at the laboratory scale, varying the experimental conditions and observing the rate and the course of the reaction. All the reduction experiments were performed in a thermobalance and supplementary characterization methods were used like scanning and transmission electron microscopy, X-ray diffraction, and Mössbauer spectrometry. The influence of rising temperature in the range 550-900 degrees C is to accelerate the reaction; no slowing down was observed, contrary to some literature conclusions. A series of experiments consisted in interrupting the runs before complete conversion, thus enabling the characterization of partially reduced samples. Interpretation confirms the occurrence of three successive and rather separate reduction steps, through magnetite and wustite to iron, and illustrates a clear structural evolution of the samples. Finally, the influence of the sample type was revealed comparing a regular powder, a nanopowder and a sintered sample. The regular powder proved to be the most reactive despite its larger grain size, due to a more porous final structure.
Prävention des virologischen Relapse bei HCV Typ 1: Wer profitiert von der Therapieverlängerung auf 72 Wochen? (2009)

Trotz Verlängerung der Therapiedauer auf 72 Wochen erleiden ca. 35% der Patienten mit langsamer virologischer Response einen Relapse. Welche zusätzlichen Faktoren einen Einfluss auf die Relapserate haben ist bisher nicht ausreichend evaluiert. Ziel dieser Studie war es den Effekt der Therapiedauer in Abhängigkeit von der Viruskinetik, der Ausgangsviruslast sowie der Ribavirindosis auf die Relapserate zu untersuchen.
Investigation of the Schottky Conjecture for compound structures modeled with line charges (2019)

Schottky's Conjecture (SC) posits that when a compound conductive structure is formed by placing a protrusion on top of an underlying base, the total field enhancement factor is the product of the field enhancement factors that would be produced by the base and protrusion in isolation. This is a powerful concept, which, in principle, allows separate treatment of the electrostatic effects of geometric features occurring at differing length scales. Recent work suggests that the degree to which the SC holds depends on the shape of the protrusion and base, and, in particular, on their relative sizes and their degree of self-similarity. Here, we use a Line Charge Model (LCM) to study the applicability of the SC to compound, quasiellipsoidal structures. The general features of compound structures produced by the LCM are discussed. The SC consistently overpredicted the computed field enhancement factor but was seen to provide reasonable estimates, correct to within a factor of 2 or better, when the protrusion was sufficiently small compared to the base; a dependence of the threshold protrusion height on the base radius was identified. This range of applicability of the SC is more restrictive than that previously reported in the literature, and potential causes of this are discussed.
ChemInform Abstract: REMOVAL OF P‐TOLYLSULFONYL GROUPS FROM SULFONAMIDES. PART 4. SYNTHESIS OF PHENYLGLYYOXAL IMINE MONOMERS (1981)

Abstract Synthesen und Reaktionen von N‐Tosyl‐phenacylaminen werden untersucht.
Normal variation in the frequency and location of human auditory cortex landmarks. Heschl's gyrus: where is it? (1998)

Interpersonal communication via the auditory modality is fundamental to normal human development. One of the prominent anatomical specializations supporting this communication is the transverse gyrus of Heschl on the superior surface of the temporal lobe. This gyrus frequently appears duplicated, either by a sulcus indenting the crown of an initially single gyrus (common stem), or by a complete posterior duplication. The frequency of these duplications has been reported to be elevated in populations with learning disabilities and genetic anomalies. The significance of this observation is unclear, however, due to conflicting reports of the base rate of duplication and the location of relevant sulcal landmarks. In this study we report the variation in frequency and location of the sulcal boundaries of Heschl's gyrus in volumetric magnetic resonance imaging scans of 105 normal controls aged 5-65. The major results were as follows: (i) duplications were unstable--the frequency of duplication ranged from 20 to 60% depending on distance from the midline; (ii) common stem duplications were more frequent than posterior duplications, particularly in the right hemisphere. Intra- and interindividual instability in sulcal landmarks pose serious obstacles to the attempt to map behavioral function onto the brain. Novel methods for dealing with structural variation are needed to facilitate the development of valid mapping techniques.
VO2 (A) nanostructures with controllable feature sizes and giant aspect ratios: one-step hydrothermal synthesis and lithium-ion battery performance (2012)

In this paper, uniform 1D VO2 (A) nanostructures with controllable morphologies were prepared via an easy one-step hydrothermal method for the first time. Aspect ratios are tunable from 10 : 1 to 1000 : 1 by changing the synthesis parameters such as the concentration of vanadium source and the reaction time. The mechanism of morphology evolution was investigated and discussed based on the nucleation and growth process of VO2 (A) particles. Electrochemical analyses of VO2 (A) nanostructures were performed, and the results showed a capacity of 277 mAh g−1 for a Li-ion battery using these nanostructures as cathode materials. This shows a significant improvement compared with other vanadium oxides such as VO2 (B) (approximately 180 mAh g−1) and V2O5 (approximately 230 mAh g−1). Unfortunately, the VO2 (A) nanostructures exhibit high initial irreversible loss due to the formation of an intermediate layer after electrochemical reactions.
A Model of a Hybrid Power Plant With Wind Turbines and Compressed Air Energy Storage (2005)

After a general overview of Hybrid Power Plants (HPP) and Compressed Air Energy Storage (CAES), the authors present a thermo-economic model for the simulation and optimization of a HPP consisting of a wind turbine coupled with CAES. In the proposed scheme, during periods of excess power production, atmospheric air is compressed in a multistage compressor and cooled; when there is power demand, the compressed air is heated in multiple expansion stages using the stored heat and conventional thermal sources. Such plants can offer significant benefits in terms of flexibility in matching a fluctuating power demand, particularly when renewable sources, characterized by high and often unpredictable variability, are utilized. The possible advantages in terms of energy and cost savings with respect to other solutions must be carefully assessed, critically depending on performance and efficiencies of each sub-system, most of them operating in transient and off-design conditions. To this purpose, a thermodynamic model composed of several sub-systems describing wind turbine, multi-stage compressor, intercooler, aftercooler, heat recovery system, compressed air storage and turbine has been developed in Matlab/Simulink® environment. In the paper, several scenarios are compared by simulation and optimization analysis and a parametric study of the plant performance with respect to the main design variables is presented.
Physical and genetic mapping of the macular corneal dystrophy locus on chromosome 16q and exclusion of TAT and LCAT as candidate genes. (2000)

We established a genomic contig for the MCD region and dramatically narrowed the MCD critical interval. Mapping data show that the TAT and LCAT genes are not the cause of MCD.
Mortality Among Patients With Schizophrenia (1996)

Results from a 40-year followup study of psychotic patients are presented to illustrate some of the major findings and unanswered questions about excess mortality in schizophrenia and to suggest analytical approaches that take full account of the potential effects of sample heterogeneity. In this study, hospital-diagnosed schizophrenia patients were at increased mortality risk whether or not they met research criteria for schizophrenia. In addition, mortality outcomes of several major diagnostic groups were similar despite substantial clinical and demographic differences between the groups at baseline. These results suggest that both diagnosis-specific and nondiagnostic factors are needed to account for excess mortality in patients with major psychiatric disorders. The issue of heterogeneity is also crucial for the clinical purposes of predicting and ultimately reducing the mortality risk of psychiatric patients, for example, in delineating profiles of high-risk patients who are not necessarily typical of other patients with the same diagnosis.
Measurement and analysis of advanced field emitting cold cathodes (2009)

We report the experimental study of field emission from cold cathodes having a raised ridge or knife-edge structure and analyses using a Transfer Matrix Method (TMM) model used to extract the cathode parameters. Local emission current measurements were done on a copper cathode, which was fabricated using electric discharge machining (EDM) and chemical etching yielding ridges of thickness 15 mum. Measurements of total cathode currents and lateral scans of the localized field emission current distribution with a 40-micron resolution are reported and analyzed.
Using FTC for a 7-Leg Inverter to Ensure Operational Continuity of Two Machines in Case of Fault (2019)

In this paper, a new configuration of the inverter is proposed to feed two machines with independent techniques. that is controlled by a new control, called Fault Tolerant Control (FTC), is implemented to prevent oscillations and operational interruption when a fault occurs in the inverter. The FTC allows continuous operation in case of a fault with the same performances as in the pre-fault condition. Furthermore, by reducing power switches in the inverter, weight, size, and cost are optimized. Simulation results show that with the FTC, the performance of the machines in the fault case is similar to the pre-fault case.
hichipper: A preprocessing pipeline for assessing library quality and DNA loops from HiChIP data (2017)

Mumbach et al. recently described HiChIP, a novel protein-mediated chromatin conformation assay that lowers cellular input requirements while simultaneously increasing the yield of informative reads compared to previous methods. To facilitate the dissemination and adoption of this assay, we introduce hichipper (http://aryeelab.org/hichipper), an open-source HiChIP data preprocessing tool, with features that include bias-corrected peak calling, library quality control, DNA loop calling, and output of processed data for downstream analysis and visualization.