gebhart/patrepeval huggingface dataset:
Deguelin exerts potent nematocidal activity via the mitochondrial respiratory chain (2017)

As a result of limited classes of anthelmintics and an over-reliance on chemical control, there is a great need to discover new compounds to combat drug resistance in parasitic nematodes. Here, we show that deguelin, a plant-derived rotenoid, selectively and potently inhibits the motility and development of nematodes, which supports its potential as a lead candidate for drug development. Furthermore, we demonstrate that deguelin treatment significantly increases gene transcription that is associated with energy metabolism, particularly oxidative phosphorylation and mitoribosomal protein production before inhibiting motility. Mitochondrial tracking confirmed enhanced oxidative phosphorylation. In accordance, real-time measurements of oxidative phosphorylation in response to deguelin treatment demonstrated an immediate decrease in oxygen consumption in both parasitic (<i>Haemonchus contortus</i>) and free-living (<i>Caenorhabditis elegans</i>) nematodes. Consequently, we hypothesize that deguelin is exerting its toxic effect on nematodes as a modulator of oxidative phosphorylation. This study highlights the dynamic biologic response of multicellular organisms to deguelin perturbation.-Preston, S., Korhonen, P. K., Mouchiroud, L., Cornaglia, M., McGee, S. L., Young, N. D., Davis, R. A., Crawford, S., Nowell, C., Ansell, B. R. E., Fisher, G. M., Andrews, K. T., Chang, B. C. H., Gijs, M. A. M., Sternberg, P. W., Auwerx, J., Baell, J., Hofmann, A., Jabbar, A., Gasser, R. B. Deguelin exerts potent nematocidal activity <i>via</i> the mitochondrial respiratory chain.
Dynamic obstacle avoidance for bacteria-powered microrobots (2015)

As microscale robots are becoming increasingly popular due to their potential for medical and industrial applications, various designs of microscale robotic system have been developed. However, there has not been much work on autonomous control algorithms for microscale robots in microfluidic environments. In this paper, we introduce an autonomous navigation algorithm for the bacteria-powered microrobots (BPMs) in a workspace with moving obstacles. A BPM consists of a rigid inorganic body with bacteria attached on the surface. The attached bacteria provide propulsive force and are controllable using electric fields, which had been demonstrated in previous work. We take the controllability of BPMs and the unpredictable motion of dynamic obstacles into account to develop a dynamic obstacle avoidance approach. Moreover, we use finite element simulation to observe an electric field around a moving obstacle to model the field's deformation. Demonstration of dynamic obstacle avoidance approach through simulation results and experimental data are presented in the paper.
Adoptive cytotoxic T lymphocyte therapy triggers a counter-regulatory immunosuppressive mechanismviarecruitment of myeloid-derived suppressor cells (2013)

Complex interactions among multiple cell types contribute to the immunosuppressive milieu of the tumor microenvironment. Using a murine model of adoptive T-cell immunotherapy (ACT) for B16 melanoma, we investigated the impact of tumor infiltrating cells on this complex regulatory network in the tumor. Transgenic pmel-1-specific cytotoxic T lymphocytes (CTLs) were injected intravenously into tumor-bearing mice and could be detected in the tumor as early as on day 1, peaking on day 3. They produced IFN-γ, exerted anti-tumor activity and inhibited tumor growth. However, CTL infiltration into the tumor was accompanied by the accumulation of large numbers of cells, the majority of which were CD11b(+) Gr1(+) myeloid-derived suppressor cells (MDSCs). Notably, CD11b(+) Gr1(int) Ly6G(-) Ly6C(+) monocytic MDSCs outnumbered the CTLs by day 5. They produced nitric oxide, arginase I and reactive oxygen species, and inhibited the proliferation of antigen-specific CD8(+) T cells. The anti-tumor activity of the adoptively-transferred CTLs and the accumulation of MDSCs both depended on IFN-γ production on recognition of tumor antigens by the former. In CCR2(-/-) mice, monocytic MDSCs did not accumulate in the tumor, and inhibition of tumor growth by ACT was improved. Thus, ACT triggered counter-regulatory immunosuppressive mechanism via recruitment of MDSCs. Our results suggest that strategies to regulate the treatment-induced recruitment of these MDSCs would improve the efficacy of immunotherapy.
ProxiTrak (2020)

In the wake of recent COVID-19 pandemic, contact tracing has turned out to be an indispensable technique to help administrative authorities contain localized infections efficiently. In the absence of a definitive and an official vaccine for the infection, practicing social distancing has proved to be an effective norm to prevent the risk of infection. In this paper, we present 'ProxiTrak', a smartphone based solution for an enterprise scenario capable of not only tracing the chain of possible infection transmission among a set of population, but also guiding the users towards following social distancing norms by alerting them in real-time about any possible violation of proximity norms on their smartphones. We devise an effective classification model to make proximity decisions on the smartphone itself using Received Signal Strength Indicator (RSSI) data of on-board Bluetooth Low Energy (BLE) module using multiple mobile devices in different environments, with novel addition of using temporal features from BLE data to boost the model's accuracy. We briefly discuss ProxiTrak's corresponding server-side framework for tracing a possible chain of infection and analysing social connectivities graphically. We also propose on-device decision aggregation and server-side pruning of proximity events to lower the false positive events. Our model is capable of making strong proximity decisions to an accuracy of up to 94% on the devices trained with the model.
New synthesis of polyaromatics through oxidative polymerization by using metal complexes with air (1992)

Abstract The oxidative polymerization provides a new synthetic route to polyaromatics. Poly( p ‐phenylene sulfide) (PPS) is produced by oxidative polymerization of thiophenol with a vanadyl complex catalyst. The metal complexes act as an efficient catalyst of oxygen oxidative polymerization. The polymerization to yield PPS is discussed especially focusing on the catalytic mechanism of the complexes.
Comparison of spatially smoothed weighted subspace methods (2002)

The performances of spatially smoothed weighted MUSIC and weighted state space methods/ESPRIT are analyzed, and compared for the direction of arrival (DOA) estimation problem. A key outcome of the analysis is the observation that, when a forward-backward spatially smoothed approach is used, optimally weighted MUSIC and optimally weighted state space methods/ESPRIT have identical asymptotic behavior. It is also shown that the forward-backward covariance matrix is better conditioned than the forward-only covariance matrix, providing additional justification for the use of the forward-backward approach. The analysis is shown to be extendable to the time-series frequency estimation problem, thereby providing a unified framework for dealing with DOA estimation and time-series frequency estimation.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Impact of carbon source and COD/N on the concurrent operation of partial denitrification and anammox (2019)

Abstract In this study, concurrent operation of anammox and partial denitrification within a nonacclimated mixed culture system was proposed. The impact of carbon sources (acetate, glycerol, methanol, and ethanol) and COD / NO 3 − ‐N ratio on partial denitrification selection under both short‐ and long‐term operations was investigated. Results from short‐term testing showed that all carbon sources supported partial denitrification. However, acetate and glycerol were preferred due to their display of efficient partial denitrification selection, which may be related to their different electron transport pathways in comparison with methanol. Long‐term operation confirmed results of batch tests by showing the contribution of partial denitrification to nitrate removal above 90% after acclimation in both acetate and glycerol reactors. In contrast, methanol showed challenges of maintaining efficient partial denitrification. COD / NO 3 − ‐N ratio mainly controlled the rate of nitrate reduction and not directly partial denitrification selection; thus, it should be used to balance between denitrification rate and anammox rate. Practitioner points The authors aimed to investigate the impact of carbon sources and COD/NO3‐N ratio on partial denitrification selection. All the carbon sources supported partial denitrification as long as the nitrite sink was available. 90% partial denitrification could be achieved with both acetate and glycerol in long‐term operations. COD/NO3‐N ratio did not directly control partial denitrification but can be used to balance between denitrification rate and anammox rate.
Spatial beam reshaping and large-band nonlinear conversion in rectangular-core phosphate glass fibers (2022)

Here we present the ability of Nd<sup>3+</sup>-doped zinc-phosphate glasses to be shaped into rectangular core fibers. At first, the physico-chemical properties of the developed P<sub>2</sub>O<sub>5</sub>-based materials are investigated for different concentrations of neodymium oxide and core and cladding glass compositions are selected for further fiber development. A modified stack-and-draw technique is used to produce multimode large rectangular-core optical fibers. Self-guided nonlinear effects acting as spatial beam reshaping processes occurring in these newly-developed photonic structures lead to the generation of spectral broadenings in the visible and near-infrared spectral domains.
Large-Scale Language Model Rescoring on Long-Form Data (2023)

In this work, we study the impact of Large-scale Language Models (LLM) on Automated Speech Recognition (ASR) of YouTube videos, which we use as a source for long-form ASR. We demonstrate up to 8% relative reduction in Word Error Eate (WER) on US English (en-us) and code-switched Indian English (en-in) long-form ASR test sets and a reduction of up to 30% relative on Salient Term Error Rate (STER) over a strong first-pass baseline that uses a maximum-entropy based language model. Improved lattice processing that results in a lattice with a proper (non-tree) digraph topology and carrying context from the 1-best hypothesis of the previous segment(s) results in significant wins in rescoring with LLMs. We also find that the gains in performance from the combination of LLMs trained on vast quantities of available data (such as C4 [1]) and conventional neural LMs is additive and significantly outperforms a strong first-pass baseline with a maximum entropy LM.
Evaluation of a Competitive Exclusion Culture and Megan Vac 1 on Salmonella Typhimurium Colonization in Neonatal Broiler Chickens (2007)

The present study was designed to evaluate the effect of individual or simultaneous application of 2 products, a competitive exclusion culture (CEC) or Megan Vac 1 (MV), for bioefficacy in reducing Salmonella Typhimurium (ST) cecal colonization in broiler chicks following experimental challenge. In experiment 1, CEC and MV were applied to day-of-hatch broiler chicks, and chicks were experimentally challenged with ST approximately 48 h later. In control chicks, ST was recovered at a level of 3.84 log10 cfu/g following direct plating of cecal contents, and 12 of 19 (63.15%) cultured individual ceca were positive following selective enrichment. In chicks receiving CEC by spray application on day of hatch, a numerical reduction in ST recovered from cecal contents (2.63 log10 cfu/g) and a significant reduction (P < 0.05) in recovery of ST from cultured ceca following selective enrichment (4 of 18, or 22.2%) was observed when compared with controls. Significant reductions in ST cecal colonization in chicks treated with MV alone were not observed in experiment 1. In experiment 2, chicks received day-of-hatch spray application of CEC alone, MV alone, or CEC and MV as a combined application immediately prior to or within 24 h of chick placement. When chicks were experimentally challenged with ST 48 h posthatch, significant reductions (P < 0.05) in cecal colonization by ST were observed with each experimental group when compared with nontreated controls. These data suggest that both commercially available products, alone or in combination, are efficacious in reducing cecal colonization in broiler chicks challenged with ST.
Online learning of load elasticity for electric vehicle charging (2013)

While electric vehicles (EVs) are expected to provide environmental and economical benefits, judicious coordination of EV charging may be necessary to prevent overloading of the distribution grid. Leveraging the smart grid infrastructure, the utility company can adjust the electricity price intelligently for individual customers to elicit desirable load curves. In this context, the present paper addresses the problem of predicting the EV charging behavior of the consumers at different prices, which is a prerequisite for the price adjustment. The dependencies on price responsiveness among neighbouring consumers are captured by adopting a conditional random field (CRF) model. To account for temporal dynamics even in an adversarial setting, the framework of online convex optimization is adopted to develop an efficient online algorithm for estimating the CRF parameters. Numerical tests verify the proposed approach.
Mapping Post-Translational Modifications of de Novo Purine Biosynthetic Enzymes: Implications for Pathway Regulation (2019)

Purines represent a class of essential metabolites produced by the cell to maintain cellular homeostasis and facilitate cell proliferation. In times of high purine demand, the de novo purine biosynthetic pathway is activated; however, the mechanisms that facilitate this process are largely unknown. One plausible mechanism is through intracellular signaling, which results in enzymes within the pathway becoming post-translationally modified to enhance their individual enzyme activities and the overall pathway metabolic flux. Here, we employ a proteomic strategy to investigate the extent to which de novo purine biosynthetic pathway enzymes are post-translationally modified in 293T cells. We identified 7 post-translational modifications on 135 residues across the 6 human pathway enzymes. We further asked whether there were differences in the post-translational modification state of each pathway enzyme isolated from cells cultured in the presence or absence of purines. Of the 174 assigned modifications, 67% of them were only detected in one experimental growth condition in which a significant number of serine and threonine phosphorylations were noted. A survey of the most-probable kinases responsible for these phosphorylation events uncovered a likely AKT phosphorylation site at residue Thr397 of PPAT, which was only detected in cells under purine-supplemented growth conditions. These data suggest that this modification might alter enzyme activity or modulate its interaction(s) with downstream pathway enzymes. Together, these findings propose a role for post-translational modifications in pathway regulation and activation to meet intracellular purine demand.
Diseases of shrimps and natural methods to protect their health (2018)

Shrimp farming is an economically important part of aquaculture. Shrimps constitute the largest portion of shellfish intended for human consumption. According to the World Organization for Animal Health (OIE), viral diseases pose the most serious threat to shrimp farming. There are currently six viral and two bacterial diseases on the OIE list. The most serious viral diseases are white spot disease (WSD), Taura syndrome (TS), infection with yellow head virus genotype 1 (YHV), infectious hypodermal and haematopoietic necrosis (IHHN), infectious myonecrosis (IMN) and white tail disease (WTD), whereas the most dangerous bacterial diseases are acute hepatopancreatic necrosis disease (AHPND) and necrotizing hepatopancreatitis (NHP). All these diseases result in high mortality, thus limiting shrimp production and causing large economic losses. Therefore, effective preparations are constantly sought to control infectious diseases in shrimps. Probiotics and immunostimulants, thanks to their demonstrated antibacterial and antiviral effects, as well their positive impact on the immune system, may play a crucial role in protecting the health of shrimps.
DIFFUSION COATINGS FOR CORROSION RESISTANT COMPONENTS IN COAL GASIFICATION SYSTEMS (2004)

Advanced electric power generation systems use a coal gasifier to convert coal to a gas rich in fuels such as H{sub 2} and CO. The gas stream contains impurities such as H{sub 2}S and HCl, which attack metal components of the coal gas train, causing plant downtime and increasing the cost of power generation. Corrosion-resistant coatings would improve plant availability and decrease maintenance costs, thus allowing the environmentally superior integrated gasification combined cycle plants to be more competitive with standard power-generation technologies. A startup meeting was held at the National Energy Technology Center, Pittsburgh, PA site on July 28, 2003. SRI staff described the technical approach of the project.
Where Did We Come From - The Ribosome (2010)

Loren Williams (director of the NASA-funded Center for Ribosomal Evolution at Georgia Tech) and Nick Hud (director of NSF-funded Origins Project at Georgia Tech) discuss the molecular origin of life on this planet and how this research is relevant to our lives today.
Induction of apoptosis by aqueous extract of Cordyceps militaris through activation of caspases and inactivation of Akt in human breast cancer MDA-MB-231 Cells. (2008)

Cordyceps militaris is well known as a traditional medicinal mushroom and has been shown to exhibit immunostimulatory and anticancer activities. In this study, we investigated the apoptosis induced by an aqueous extract of C. militaris (AECM) via the activation of caspases and altered mitochondrial membrane permeability in human breast cancer MDA-MB-231 cells. Exposure to AECM induced apoptosis, as demonstrated by a quantitative analysis of nuclear morphological change and a flow cytometric analysis. AECM increased hyperpolarization of mitochondrial membrane potential and promoted the activation of caspases. Both the cytotoxic effect and apoptotic characteristics induced by AECM treatment were significantly inhibited by z-DEVD-fmk, a caspase-3 inhibitor, which demonstrates the important role of caspase-3 in the observed cytotoxic effect. AECM-induced apoptosis was associated with the inhibition of Akt activation in a time-dependent manner, and pretreatment with LY294002, a PI3K/Akt inhibitor, significantly increased AECM-induced apoptosis. The results indicated that AECM-induced apoptosis may relate to the activation of caspase-3 and mitochondria dysfunctions that correlate with the inactivation of Akt.
Pectic arabinan side chains are essential for pollen cell wall integrity during pollen development (2014)

Pectin is a complex polysaccharide and an integral part of the primary plant cell wall and middle lamella, contributing to cell wall mechanical strength and cell adhesion. To understand the structure-function relationships of pectin in the cell wall, a set of transgenic potato lines with altered pectin composition was analysed. The expression of genes encoding enzymes involved in pectin acetylation, degradation of the rhamnogalacturonan backbone and type and length of neutral side chains, arabinan and galactan in particular, has been altered. Upon crossing of different transgenic lines, some transgenes were not transmitted to the next generation when these lines were used as a pollen donor, suggesting male sterility. Viability of mature pollen was severely decreased in potato lines with reduced pectic arabinan, but not in lines with altered galactan side chains. Anthers and pollen of different developmental stages were microscopically examined to study the phenotype in more detail. Scanning electron microscopy of flowers showed collapsed pollen grains in mature anthers and in earlier stages cytoplasmic protrusions at the site of the of kin pore, eventually leading to bursting of the pollen grain and leaking of the cytoplasm. This phenomenon is only observed after the microspores are released and the tapetum starts to degenerate. Timing of the phenotype indicates a role for pectic arabinan side chains during remodelling of the cell wall when the pollen grain is maturing and dehydrating.
The Confounding Effects of Particle Size and Substrate Bulk Density on Phanerochaete chrysosporium Pretreatment of Panicum virgatum (2016)

Phanerochaete chrysosporium treatment is less effective as a biological pretreatment on feedstock with larger particle sizes. We hypothesized that the improved effectiveness of the pretreatment when smaller particle sizes are used may be due to the inherently higher bulk density with smaller particle sizes. The effects of substrate bulk density and particle size on the efficacy of P. chrysosporium pretreatment of switchgrass (Panicum virgatum) was tested experimentally. Phanerochaete chrysosporium was grown on senesced switchgrass (2 different particle sizes) with various bulk densities. In all treatments, the fungal-pretreated samples released more glucose during enzymatic saccharification than the control sample. Substrate bulk density was a statistically significant factor in explaining the variation in the amount of glucose released per gram of substrate used. However, the particle size was not found to be a significant factor. On-farm switchgrass pretreatment may not require particle size reduction if the switchgrass is supplied in high-density bales.
Crystallization and preliminary X-ray analysis of arabinofuranosidase C from Aspergillus niger strain 3M43 (1997)

Crystals of arabinofuranosidase C purified from Aspergillus niger strain 3M43 have been obtained by vapour diffusion. The crystal belongs to the space group P2(1) with cell parameters a = 44.28, b = 71.99, c = 45.27 A and beta = 105.98 degrees with one molecule in the asymmetric unit. The X-ray diffraction pattern of these crystals extends to at least 2.20 A resolution with the use of synchrotron radiation. These crystals are stable on exposure to radiation and are suitable for structure determination.
Markov Reliability Modeling for Induction Motor Drives Under Field-Oriented Control (2011)

This paper presents a Markov reliability model of induction motor drives operating under field-oriented control. The model includes faults in the power electronics, machine, speed encoder, and current sensors. The procedure can be extended for more detail, to other machines and to other drive topologies. To develop the model, faults are first identified, and then, a simulation model of the setup is developed and experimentally verified. Faults are injected into the model in sequential levels and the system performance is assessed after each fault. Fault coverage-the probability that the system survives given a fault has occurred-is studied. A complete Markov reliability model is developed to assess the mean time to failure of the system and other reliability factors. This analysis is shown to be simple and useful for assessing the reliability of motor drives and is expected to help in designing fault-tolerance mechanisms for specific drives, where reliability can be evaluated after every design.