gebhart/patrepeval huggingface dataset:
Bacterial persistence and bet hedging inSinorhizobium meliloti (2011)

We recently described a novel bet-hedging mechanism in which the bacterium Sinorhizobium meliloti responds to starvation by forming two discrete cell types via cell division. The old-pole daughter cell retains most of the resource, polyhydroxybutyrate (PHB) and is capable of surviving long-term starvation, while the low-PHB, new-pole daughter cell is capable of quickly resuming growth when starvation ends. Here we present additional data showing that the high-PHB, old-pole cells are similar to bacterial persisters, characterized by metabolic dormancy and antibiotic tolerance. Using two independent methods, we generated clonal populations of S. meliloti that varied in the frequency of the high- and low-PHB phenotypes, and then challenged these populations with ampicillin. Populations containing more high-PHB cells were significantly more antibiotic-tolerant. In a separate experiment, we used GFP fluorescence as a marker of overall metabolic activity. After 24 hours of starvation, new-pole cells were 64% brighter than their old-pole sister cells, demonstrating that the divergence in metabolic rate is rapid.
Taenia solium cysticercosis and taeniasis in urban settings: Epidemiological evidence from a health-center based study among people with epilepsy in Dar es Salaam, Tanzania (2019)

In Africa, urbanization is happening faster than ever before which results in new implications for transmission of infectious diseases. For the zoonotic parasite Taenia solium, a major cause of acquired epilepsy in endemic countries, the prevalence in urban settings is unknown. The present study investigated epidemiological, neurological, and radiological characteristics of T. solium cysticercosis and taeniasis (TSCT) in people with epilepsy (PWE) living in Dar es Salaam, Tanzania, one of the fastest growing cities worldwide. A total of 302 PWE were recruited from six health centers in the Kinondoni district of Dar es Salaam. Serological testing for T. solium cysticercosis-antigen (Ag) and -antibodies (Abs) and for T. solium taeniasis-Abs was performed in all PWE. In addition, clinical and radiological examinations that included cranial computed tomography (CT) were performed. With questionnaires, demographic data from study populations were collected, and factors associated with TSCT were assessed. Follow-up examinations were conducted in PWE with TSCT. T. solium cysticercosis-Ag was detected in three (0.99%; 95% CI: 0-2.11%), -Abs in eight (2.65%; 95% CI: 0.84-4.46%), and taeniasis-Abs in five (1.66%; 95% CI: 0.22-3.09%) of 302 PWE. Six PWE (1.99%; 95% CI: 0.41-3.56%) were diagnosed with neurocysticercosis (NCC). This study demonstrates the presence of TSCT in Dar es Salaam, however, NCC was only associated with a few cases of epilepsy. The small fraction of PWE with cysticercosis- and taeniasis-Abs may suggest that active transmission of T. solium plays only a minor role in Dar es Salaam. A sufficiently powered risk analysis was hampered by the small number of PWE with TSCT; therefore, further studies are required to determine the exact routes of infection and risk behavior of affected individuals.
Fair Scheduling in Cellular Systems in the Presence of Noncooperative Mobiles (2010)

We consider the problem of centrally controlled 'fair' scheduling of resources to one of the many mobile stations connected to a base station (BS). The BS is the only entity making decisions in this framework based on truthful information from the mobiles on their radio channel. We study the well-known family of parametric &#945;-fair scheduling problems from a game-theoretic perspective in which some of the mobiles may be noncooperative. We first show that if the BS is unaware of the noncooperative behavior from the mobiles, the noncooperative mobiles become successful in snatching the resources from the other cooperative mobiles, resulting in unfair allocations. If the BS is aware of the noncooperative mobiles, a new game arises with BS as an additional player. It can then do better by neglecting the signals from the noncooperative mobiles. The BS, however, becomes successful in eliciting the truthful signals from the mobiles only when it uses additional information (signal statistics). This new policy along with the truthful signals from mobiles forms a Nash Equilibrium (NE) called a Truth Revealing Equilibrium. Finally, we propose new iterative algorithms to implement fair scheduling policies that robustify the otherwise non-robust (in presence of noncooperation) &#945;-fair scheduling algorithms.
Prediction of permeability of laminate films; new methods for ultra-thin layers and systems with solute-concentration-dependent diffusivity (1999)

Two numerical methods have been developed for the prediction of gas/vapour transmission rates in multilayer laminate films consisting of different polymers with extensive variations in relative thicknesses. The methods developed allow the use of different spatial step lengths for the different layers. The methods have been applied to experimental oxygen transmission rates through laminates based on low-density polyethylene and poly(ethylene terephthalate) and it was found that the predictions agreed with the experimental results within the experimental error limits. The methods were also used to predict the water vapour transmission rates for a three-layer laminate of low-density polyethylene and polyamide-6. Since water vapour diffusivity in polyamide-6 is a function of the water concentration, different and sometimes complex results were obtained depending on the location of the polyamide-6 layer in the laminate. Calculations showed that the only way to predict the optimum positions of different layers, in order to minimize the penetrant transmission rate through a laminate when the penetrant interacts with the material, is by rigorous simulations using these or similar methods. Copyright © 1999 John Wiley & Sons, Ltd.
Hierarchical Graph Pooling with Structure Learning (2019)

Graph Neural Networks (GNNs), which generalize deep neural networks to graph-structured data, have drawn considerable attention and achieved state-of-the-art performance in numerous graph related tasks. However, existing GNN models mainly focus on designing graph convolution operations. The graph pooling (or downsampling) operations, that play an important role in learning hierarchical representations, are usually overlooked. In this paper, we propose a novel graph pooling operator, called Hierarchical Graph Pooling with Structure Learning (HGP-SL), which can be integrated into various graph neural network architectures. HGP-SL incorporates graph pooling and structure learning into a unified module to generate hierarchical representations of graphs. More specifically, the graph pooling operation adaptively selects a subset of nodes to form an induced subgraph for the subsequent layers. To preserve the integrity of graph's topological information, we further introduce a structure learning mechanism to learn a refined graph structure for the pooled graph at each layer. By combining HGP-SL operator with graph neural networks, we perform graph level representation learning with focus on graph classification task. Experimental results on six widely used benchmarks demonstrate the effectiveness of our proposed model.
Coincident Observation of Lightning using Spaceborne Spectrophotometer and Ground-Level Electromagnetic Sensors (2012)

The present study aims at assessing a possible new way to reveal the properties of lightning flash, using spectrophotometric data obtained by FORMOSAT-2/ISUAL which is the first spaceborne multicolor lightning detector. The ISUAL data was analyzed in conjunction with ground ]based electromagnetic data obtained by Duke magnetic field sensors, NLDN, North Alabama Lightning Mapping Array (LMA), and Kennedy Space Center (KSC) electric field antennas. We first classified the observed events into cloud ]to ]ground (CG) and intra ]cloud (IC) lightning based on the Duke and NLDN measurements and analyzed ISUAL data to clarify their optical characteristics. It was found that the ISUAL optical waveform of CG lightning was strongly correlated with the current moment waveform, suggesting that it is possible to evaluate the electrical properties of lightning from satellite optical measurement to some extent. The ISUAL data also indicated that the color of CG lightning turned to red at the time of return stroke while the color of IC pulses remained unchanged. Furthermore, in one CG event which was simultaneously detected by ISUAL and LMA, the observed optical emissions slowly turned red as the altitude of optical source gradually decreased. All of these results indicate that the color of lightning flash depends on the source altitude and suggest that spaceborne optical measurement could be a new tool to discriminate CG and IC lightning. In the presentation, we will also show results on the comparison between the ISUAL and KSC electric field data to clarify characteristics of each lightning process such as preliminary breakdown, return stroke, and subsequent upward illumination.
RNA editing in the Wilms' tumor susceptibility gene, WT1. (1994)

Rat kidney WT1 cDNAs contain either a thymidine or a cytosine residue at position 839. Genomic WT1 DNA contains only T839. To explain these results, we propose the WT1 transcript undergoes RNA editing in which U839 is converted to C, resulting in the replacement of leucine 280 in WT1 by proline. RNA editing at the same nucleotide was observed in WT1 cDNAs from human testis. In functional assays, the WT1-leucine280 polypeptide repressed the EGR-1 promoter in in vitro assays approximately 30% more efficiently than WT1-proline. Edited WT1-C839 mRNA was barely detectable in neonatal kidney, whereas adult rat kidneys contained both U839 and C839-WT1 mRNA, suggesting a role for the two protein isoforms in growth and differentiation.
Colloidal quasicrystals with 12-fold and 18-fold diffraction symmetry (2011)

Micelles are the simplest example of self-assembly found in nature. As many other colloids, they can self-assemble in aqueous solution to form ordered periodic structures. These structures so far all exhibited classical crystallographic symmetries. Here we report that micelles in solution can self-assemble into quasicrystalline phases. We observe phases with 12-fold and 18-fold diffraction symmetry. Colloidal water-based quasicrystals are physically and chemically very simple systems. Macroscopic monodomain samples of centimeter dimension can be easily prepared. Phase transitions between the fcc phase and the two quasicrystalline phases can be easily followed in situ by time-resolved diffraction experiments. The discovery of quasicrystalline colloidal solutions advances the theoretical understanding of quasicrystals considerably, as for these systems the stability of quasicrystalline states has been theoretically predicted for the concentration and temperature range, where they are experimentally observed. Also for the use of quasicrystals in advanced materials this discovery is of particular importance, as it opens the route to quasicrystalline photonic band gap materials via established water-based colloidal self-assembly techniques.
Protective Effects of Syringic Acid against Acetaminophen-Induced Hepatic Damage in Albino Rats (2010)

The protective effect of the phenolic compound syringic acid, one of the major benzoic acid derivatives from edible plants and fruits, was evaluated against acetaminophen (APAP)-induced hepatotoxicity in rats. Toxicity was induced in adult male albino Wistar rats by the administration of APAP (750 mg/kg body weight) intraperitoneally. Rats were treated with syringic acid (25, 50, and 100 mg/kg body weight) by the oral route. We assessed the activity of hepatic markers aspartate aminotransferase, alanine aminotransferase, alkaline phosphatase, gamma-glutamyl transferase, and bilirubin. Lipid peroxidative markers thiobarbituric acid reactive substances (TBARS), lipid hydroperoxides, and a decrease in enzymatic antioxidants superoxide dismutase, catalase, glutathione peroxidase, and non-enzymatic antioxidants vitamin C, vitamin E and reduced glutathione levels. Liver histology also showed convincing evidence regarding their protective nature against fatty changes induced during APAP intoxication. Syringic acid administered at a dose of 50 mg/kg body weight significantly decreased the activities of hepatic and renal function markers to near normal values when compared with the other two doses. The results suggest that syringic acid could afford a significant protective effect against APAP induced hepatic damage in rats.
Design and analysis of the reference cells for STT-MRAM (2013)

STT-MRAM is currently under intense R&D efforts thanks to its high performances such as non-volatility, fast access speed and high density etc. However, it suffers from intrinsic stochastic switching behaviors and high sensitivity to process variations, which make low power reliable reading become a big challenge. This letter presents three designs of reference cell for STT-MRAM sensing. By using an accurate compact model of STT-MRAM cell, we analyze and compare their performances in terms of power, reliability and area.
Advancing the immunoaffinity platform AFFIRM to targeted measurements of proteins in serum in the pg/ml range (2018)

There is a great need for targeted protein assays with the capacity of sensitive measurements in complex samples such as plasma or serum, not the least for clinical purposes. Proteomics keeps generating hundreds of biomarker candidates that need to be transferred towards true clinical application through targeted verification studies and towards clinically applicable analysis formats. The immunoaffinity assay AFFIRM (AFFInity sRM) combines the sensitivity of recombinant single chain antibodies (scFv) for targeted protein enrichment with a specific mass spectrometry readout through selected reaction monitoring (SRM) in an automated workflow. Here we demonstrate a 100 times improved detection capacity of the assay down to pg/ml range through the use of oriented antibody immobilization to magnetic beads. This was achieved using biotin-tagged scFv coupled to streptavidin coated magnetic beads, or utilizing the FLAG tag for coupling to anti-FLAG antibody coated magnetic beads. An improved multiplexing capacity with an 11-plex setup was also demonstrated compared to a previous 3-plex setup, which is of great importance for the analysis of panels of biomarker targets.
A hierarchy of cell death pathways confers layered resistance to shigellosis in mice (2022)

Abstract Bacteria of the genus Shigella cause shigellosis, a severe gastrointestinal disease driven by bacterial colonization of colonic intestinal epithelial cells. Vertebrates have evolved programmed cell death pathways that sense invasive enteric pathogens and eliminate their intracellular niche. Previously we reported that genetic removal of one such pathway, the NAIP–NLRC4 inflammasome, is sufficient to convert mice from resistant to susceptible to oral Shigella flexneri challenge (Mitchell, Roncaioli et al., 2020). Here, we investigate the protective role of additional cell death pathways during oral mouse Shigella infection. We find that the Caspase-11 inflammasome, which senses Shigella LPS, restricts Shigella colonization of the intestinal epithelium in the absence of NAIP–NLRC4. However, this protection is limited when Shigella expresses OspC3, an effector that antagonizes Caspase-11 activity. TNFα, a cytokine that activates Caspase-8-dependent apoptosis, also provides protection from Shigella colonization of the intestinal epithelium, but only in the absence of both NAIP– NLRC4 and Caspase-11. The combined genetic removal of Caspases-1,-11, and -8 renders mice hyper-susceptible to oral Shigella infection. Our findings uncover a layered hierarchy of cell death pathways that limit the ability of an invasive gastrointestinal pathogen to cause disease.
A Study Based on the Helpful tool in the Initial Assessment of Ovarian Masses: Risk of Malignancy Index (2022)

Objective: To evaluate the Risk of Malignancy Index (RMI)for primary evaluation of ovarian masses. Materials and Methods: This was a prospective observational study conducted for period of two years at DHQ hospital Jhang. Study consisted of 141 female patients admitted for surgical exploration of ovarian masses. Pre-operative ultrasound evaluation of ovarian mass, menopausal status and CA125 were carried out for the patients. Based upon these finding RMI was calculated for all the patients. Post-operative histopathology of resected ovarian mass was done in all the cases to confirm the diagnosis. Results: sensitivity and specificity of CA125 alone at cut off value of 35 was 67.64 %, 83.17% respectively. Using RMI at cut off value of 200 sensitivity and specificity was 76.47%, 85.98 % respectively. Receiver operating characteristic curve (ROC)revealed that RMI was a better discriminate than CA125, ultrasound and menopausal status alone. Conclusion: Risk of malignancy index (RMI) is useful tool in primary evaluation of ovarian masses. It can be used to differentiate between benign and malignant ovarian masses with high sensitivity and specificity.
Malware Detection on Mobile Devices (2010)

We present various approaches for mitigating malware on mobile devices which we have implemented and evaluated on Google Android. Our work is divided into the following three segments: a host-based intrusion detection framework; an implementation of SELinux in Android; and static analysis of Android application files.
Directional Couplers for Integrated Optics (1976)

In the field of integrated optics directional couplers will play an important role. These couplers are not only important for providing just a direction dependent means of coupling but they are also important components for the realisation of optical modulators or switches /1,2/. The usual design for such directional couplers is shown in Fig. 1. Two parallel dielectric waveguides are placed in such close proximity that the evanescent fields overlap. In this case energy will be exchanged periodically between the two waveguides. Because the penetration depths are typically of the order of some fraction of an optical wavelength and the coupling strength depends exponentially on the separation of the two guides, the separation of the two waveguides must be very small and the tolerance for it must be kept very tight. For typical values of relative refractive index differences Δn/n between the core and. the cladding of 1 % for n≈1.5 and a separation of 1 μm the required coupling length for complete energy transfer would be ≈ 4 mm and a tolerance of 10 % (i.e. 0.1 μm) in the separation of the coupled waveguides would already require a 20% change in the coupling length /3/. While the relative tolerances are typical also for microwave components the absolute values are extremely small due to the much smaller optical wavelength. In addition to these tolerance problems there is still the problem of phase matching. The above numerical results were calculated under the assumption of two identical i.e. phase matched waveguides.
Generation of High Repetition Rate Picosecond Optical Pulses Using an Electrooptic Phase Modulator and a Fabry-Perot Filter (1988)

Electrooptic methods to generate ultrashort optical pulses have advantage in controllability and are useful for applications in various fields. One of the typical electrooptic methods is the direct pulse generation making use of a broad-band modulator. In the picosecond range, however, this method has the difficulty of the limitation in high-speed electric circuits. Another approach is to synthesize the optical pulses using widely spread optical sidebands produced by deep electrooptic modulation. The authors have succeeded in producing 700GHz-width optical sidebands by the electrooptic phase modulation1, and in generating a few picosecond pulses using a diffraction grating2. Moreover, they are developing a ”Terahertz optical synthesizer” which makes it possible to synthesize arbitrary shaped optical signal in terahertz range3. These pulse generator and synthesizer will be very useful but rather complicated.
Dielectric Constant, Dipole Moment, and Solubility Parameters of Some Cyclic Acid Esters (2006)

Dielectric constant, dipole moment, and solubility parameters are reported for ethylene carbonate (EC), propylene carbonate (PC), butylene carbonate (BC), and glycerin carbonate (GC). Dielectric constants have been determined from capacitance measurements using an auto-balancing bridge at 20, 25, and 40 °C. Values of permanent dipole moment of carbonates have been obtained from dielectric constant measurements on dilute solutions of carbonates in benzene and 1,4-dioxane. Hildebrand and Hansen solubility parameters of carbonates have been calculated using several different techniques.
Rapid high-resolution volumetric imaging via laser ablation delayering and confocal imaging (2022)

Acquiring detailed 3D images of samples is needed for conducting thorough investigations in a wide range of applications. Doing so using nondestructive methods such as X-ray computed tomography (X-ray CT) has resolution limitations. Destructive methods, which work based on consecutive delayering and imaging of the sample, face a tradeoff between throughput and resolution. Using focused ion beam (FIB) for delayering, although high precision, is low throughput. On the other hand, mechanical methods that can offer fast delayering, are low precision and may put the sample integrity at risk. Herein, we propose to use femtosecond laser ablation as a delayering method in combination with optical and confocal microscopy as the imaging technique for performing rapid 3D imaging. The use of confocal microscopy provides several advantages. First, it eliminates the 3D image distortion resulting from non-flat layers, caused by the difference in laser ablation rate of different materials. It further allows layer height variations to be maintained within a small range. Finally, it enables material characterization based on the processing of material ablation rate at different locations. The proposed method is applied on a printed circuit board (PCB), and the results are validated and compared with the X-ray CT image of the PCB part.