gebhart/patrepeval huggingface dataset:
Delivery of antimicrobials into parasites (2003)

To eliminate apicomplexan parasites, inhibitory compounds must cross host cell, parasitophorous vacuole, and parasite membranes and cyst walls, making delivery challenging. Here, we show that short oligomers of arginine enter Toxoplasma gondii tachyzoites and encysted bradyzoites. Triclosan, which inhibits enoyl-ACP reductase (ENR), conjugated to arginine oligomers enters extracellular tachyzoites, host cells, tachyzoites inside parasitophorous vacuoles within host cells, extracellular bradyzoites, and bradyzoites within cysts. We identify, clone, and sequence T. gondii enr and produce and characterize enzymatically active, recombinant ENR. This enzyme has the requisite amino acids to bind triclosan. Triclosan released after conjugation to octaarginine via a readily hydrolyzable ester linkage inhibits ENR activity, tachyzoites in vitro, and tachyzoites in mice. Delivery of an inhibitor to a microorganism via conjugation to octaarginine provides an approach to transporting antimicrobials and other small molecules to sequestered parasites, a model system to characterize transport across multiple membrane barriers and structures, a widely applicable paradigm for treatment of active and encysted apicomplexan and other infections, and a generic proof of principle for a mechanism of medicine delivery.
Cobra Probes Containing Replaceable Thermocouples (2007)

A modification of the basic design of cobra probes provides for relatively easy replacement of broken thermocouples. Cobra probes are standard tube-type pressure probes that may also contain thermocouples and that are routinely used in wind tunnels and aeronautical hardware. They are so named because in side views, they resemble a cobra poised to attack. Heretofore, there has been no easy way to replace a broken thermocouple in a cobra probe: instead, it has been necessary to break the probe apart and then rebuild it, typically at a cost between $2,000 and $4,000 (2004 prices). The modified design makes it possible to replace the thermocouple, in minimal time and at relatively low cost, by inserting new thermocouple wire in a tube.
Optimal pairwise correlating transforms for multiple description coding (2002)

Multiple description coding (MDC) addresses the problem of encoding a source into two (or more) bitstreams such that a high-quality reconstruction is decodable from the two bitstreams together, while a lower, but still acceptable, quality reconstruction is decodable if either of the two bitstreams is lost. Recent research has proposed using transforms to introduce a controlled amount of correlation between the two bitstreams in order to achieve MDC objectives. This paper considers several optimality issues related to such transform based MDC methods. Redundancy rate-distortion (RRD) performance of a general class of transforms is derived and used to identify the optimal transform for achieving any given amount of redundancy. Then, the paper introduces a more general transform-based MDC framework incorporating both the transform mode of redundancy and a second mode of redundancy. The optimal allocation of redundancy among these two modes is analyzed.
Data from Genome-Wide Gene Expression Changes in the Normal-Appearing Airway during the Evolution of Smoking-Associated Lung Adenocarcinoma (2023)

&lt;div&gt;Abstract&lt;p&gt;Smoking perpetuates in cytologically normal airways a molecular “field of injury” that is pertinent to lung cancer and early detection. The evolution of airway field changes prior to lung oncogenesis is poorly understood largely due to the long latency of lung cancer in smokers. Here, we studied airway expression changes prior to lung cancer onset in mice with knockout of the &lt;i&gt;Gprc5a&lt;/i&gt; gene (&lt;i&gt;Gprc5a&lt;/i&gt;&lt;sup&gt;−/−&lt;/sup&gt;) and tobacco carcinogen (NNK) exposure and that develop the most common type of lung cancer, lung adenocarcinoma, within 6 months following exposure. Airway epithelial brushings were collected from &lt;i&gt;Gprc5a&lt;/i&gt;&lt;sup&gt;−/−&lt;/sup&gt; mice before exposure and at multiple times post-NNK until time of lung adenocarcinoma development and then analyzed by RNA sequencing. Temporal airway profiles were identified by linear models and analyzed by comparative genomics in normal airways of human smokers with and without lung cancer. We identified significantly altered profiles (&lt;i&gt;n&lt;/i&gt; = 926) in the NNK-exposed mouse normal airways relative to baseline epithelia, a subset of which were concordantly modulated with smoking status in the human airway. Among airway profiles that were significantly modulated following NNK, we found that expression changes (&lt;i&gt;n&lt;/i&gt; = 22) occurring as early as 2 months following exposure were significantly associated with lung cancer status when examined in airways of human smokers. Furthermore, a subset of a recently reported human bronchial gene classifier (Percepta; &lt;i&gt;n&lt;/i&gt; = 56) was enriched in the temporal mouse airway profiles. We underscore evolutionarily conserved profiles in the normal-appearing airway that develop prior to lung oncogenesis and that comprise viable markers for early lung cancer detection in suspect smokers. &lt;i&gt;Cancer Prev Res; 11(4); 237–48. ©2018 AACR&lt;/i&gt;.&lt;/p&gt;&lt;/div&gt;
A Theory for the Time Arrow (2019)

Physical laws for elementary particles can be described by the quantum dynamics equation given a Hamiltonian. The solution are probability amplitudes in Hilbert space that evolve over time. A probability density function over position and time is given as the magnitude square of such probability amplitude. An entropy can be associated with these probability densities characterizing the position information of a particle. Coherent states are localized wave packets and may describe the spatial distribution for some particle states. We show that due to a dispersion property of Hamiltonians in quantum physics, the entropy of coherent states increases over time. We investigate a partition of the Hilbert space into four sets based on whether the entropy is (i) increasing but not a constant, (ii) decreasing but not a constant, (iii) a constant, (iv) oscillating. We propose a law that entropy (weakly) increases in time in quantum physics. Thus, states in set (ii) are disallowed, and the states in set (iii) cannot complete an oscillation period. Then, according to this law, quantum theory is not time-reversible unless the state is in set (iii), i.e., it is a stationary state (an eigenstate of the Hamiltonian.). This additional law in quantum theory limits physical scenarios beyond conservation laws, providing causality reasoning by defining an arrow of time.
Butyrate differentiates permissiveness to Clostridioides difficile infection and influences growth of diverse C. difficile isolates (2022)

ABSTRACT A disrupted “dysbiotic” gut microbiome engenders susceptibility to the diarrheal pathogen Clostridioides difficile by impacting the metabolic milieu of the gut. Diet, in particular the microbiota accessible carbohydrates (MACs) found in dietary fiber, is one of the most powerful ways to affect the composition and metabolic output of the gut microbiome. As such, diet is a powerful tool for understanding the biology of C. difficile and for developing alternative approaches for coping with this pathogen. One prominent class of metabolites produced by the gut microbiome are short chain fatty acids (SCFAs), the major metabolic end products of MAC metabolism. SCFAs are known decrease the fitness of C. difficile in vitro and that high intestinal SCFA concentrations are associated with reduced fitness of C. difficile in animal models of C. difficile infection (CDI). Here, we use controlled dietary conditions (8 diets that differ only by MAC composition) to show that C. difficile fitness is most consistently impacted by butyrate, rather than the other two prominent SCFAs (acetate and propionate), during murine model CDI. We similarly show that butyrate concentrations are lower in fecal samples from humans with CDI relative to healthy controls. Finally, we demonstrate that butyrate impacts growth in diverse C. difficile isolates. These findings provide a foundation for future work which will dissect how butyrate directly impacts C. difficile fitness and will lead to the development of diverse approaches distinct from antibiotics or fecal transplant, such as dietary interventions, for mitigating CDI in at-risk human populations. IMPORTANCE Clostridioides difficile is a leading cause of infectious diarrhea in humans and it imposes a tremendous burden on the healthcare system. Current treatments for C. difficile infection (CDI) include antibiotics and fecal microbiota transplant, which contribute to recurrent CDIs and face major regulatory hurdles, respectively. Therefore, there is an ongoing need to develop new ways to cope with CDI. Notably, a disrupted “dysbiotic” gut microbiota is the primary risk factor for CDI but we incompletely understand how a healthy microbiota resists CDI. Here, we show that a specific molecule produced by the gut microbiota, butyrate, is negatively associated with C. difficile burdens in humans and in a mouse model of CDI and that butyrate impedes the growth of diverse C. difficile strains in pure culture. These findings help to build a foundation for designing alternative, possibly diet-based, strategies for mitigating CDI in humans.
Module-Integrated GMR-Based Current Sensing for Closed-Loop Control of a Motor Drive (2016)

Current sensor integration in commercial power semiconductor modules is generally based on shunt resistance methods. The resulting losses and lack of galvanic isolation present opportunities for improvement. This paper describes the integration of submillimeter-sized giant magnetoresistive (GMR) point field detectors (PFDs) into commercial IGBT modules to provide nearly lossless galvanically isolated current-sensing capabilities. The IGBT modules are installed into a three-phase inverter motor drive, and the GMR-based integrated current sensors are used for closed-loop current control in a field-oriented induction motor drive. Finite-element analysis of the module interconnect structures is used to determine detector locations offering the highest possible bandwidth current measurements. Additional PFDs are used to decouple rotating magnetic field disturbances or bias fields from permanent magnets. The same GMR PFDs are also used to provide temperature measurements that are used to decouple the effects of changing temperature.
Improvement of photodiode responsivity using the InAs quantum dot family for monolithic integration (2014)

We report a photodiode (PD) hybrid sub-system using a 1.5μm quantum dot (QD) semiconductor optical amplifier (SOA) and a QD-PD for a high-speed and high-sensitivity photoreceiver, and we characterize its responsivity.
On the Delay of Network Coding over Line Networks (2009)

We analyze a simple network where a source and a receiver are connected by a line of erasure channels of different reliabilities. Recent prior work has shown that random linear network coding can achieve the min-cut capacity and therefore the asymptotic rate is determined by the worst link of the line network. In this paper we investigate the delay for transmitting a batch of packets, which is a function of all the erasure probabilities and the number of packets in the batch. We show a monotonicity result on the delay function and derive simple expressions which characterize the expected delay behavior of line networks. Further, we use a martingale bounded differences argument to show that the actual delay is tightly concentrated around its expectation.
Electrosynthesised Metal (Ni, Fe, Co) Oxide Films on Single-Walled Carbon Nanotube Platforms and Their Supercapacitance in Acidic and Neutral pH Media (2016)

The need for alternative energy sources has led to renewed research interests in electrochemical energy storage systems, especially supercapacitors [1]. Carbon materials such as carbon blacks, carbon fibres, cloths and nanotubes [2], have been used as electrode supports in supercapacitors. Carbon nanotubes (CNTs) have attracted attention due to their unique properties such as high surface area and high porosity that lead to high power densities of supercapacitors [2]. In the quest for an alternative sources, researchers have explored the charge storage properties of different metal oxide systems such as anhydrous Co-Ni oxides in alkaline medium, MnO 2 in neutral and acidic conditions, NiO in an acidic conditions [3], Co 3 O 4 in an alkaline medium [4], and Fe 3 O 4 in neutral solution (Na 2 SO 4 ) and in both neutral and alkaline media [5], as an inexpensive alternatives to RuO 2 . In addition to good supercapacitive behaviour, metal oxides also have the advantage that they can be readily made into thin films. Although, supercapacitive properties of metal oxides on different substrates have been reported, this work represents the first time a comparative study of the supercapacitive properties of three metal (Ni, Fe, Co) oxide nanoparticles electrochemically deposited onto SWCNTs was carried out. In this work, Supercapacitive properties of single-walled carbon nanotubes/metal oxides nanocomposites (SWCNT-MO where M=Ni, Fe, Co) is described. The SWCNT-MO nanocomposites were confirmed with SEM, EDX and XPS techniques. Supercapacitive properties of the modified electrodes in H 2 SO 4 and Na 2 SO 4 electrolytes was investigated using cyclic voltammetry (CV), galvanostatic constant current charge-discharge (CD) and the electrochemical impedance spectroscopy (EIS) techniques. Electrodecorating acid-functionalised SWCNTs with metal (Ni, Fe, Co) oxide nanoparticles leads to significant enhancements on the supercapacitive properties of these materials in acidic and neutral media compared to many other literature reports. SWCNT-NiO nanocomposite modified electrodes gave better supercapacitive performance with a specific capacitance of 186 mFcm -2 (or 928 Fg -1 ). This value compared quite favourably and even higher than values hitherto reported in several literature. References 1. M. Winter, R. J. Brodd, Chem. Rev. 2004, 104, 4245. 2. A. T. Chidembo, K. I. Ozoemena, B. O. Agboola, V. Gupta, G. G. Wildgoose, R. G. Compton, Energy Environ. Sci. 2010, 3, 228. 3. Q. Wang, Z. Wen, J. Li, Adv. Funct. Mater. 2006, 16, 2141. 4. L. Cao, M. Lu, H. L. Li, J. Electrochem. Soc. 2005, 152, A871. 5. S. Y. Wang, K. C. Ho, S. L. Kuo, N. L. Wu, J. Electrochem. Soc. 2006, 153, A75.
Maskless Nanopatterning Using a Spatial Light Modulator and Absorbance Modulation (2012)

This paper reports the application of absorbance modulation optical lithography (AMOL) in maskless photon-based patterning of non-periodic two-dimensional arbitrary patterns by using a micromechanical-mirror array-based optical system and absorbance modulation.
Functional Analysis of Bone-Biomaterial Interface (2000)

Abstract Proper function and long-term stability of orthopaedic implants depend on the intimate association between bone cells and the implant biomaterial, a process known as osseointegration. Understanding the processes responsible for the establishment and maintenance of a functional bone-biomaterial interface and how these processes may be enhanced is crucial to the rational design and optimization of prosthetic devices. We have utilized cellular, molecular, and high-resolution imaging approaches to analyze the mechanistic basis of bone-biomaterial interactions. Specifically, we have characterized the initial adhesion of osteoblasts in terms of kinetics and relationship to the surface topography and chemistry of the biomaterials, particularly the cobalt-chrome and titanium alloys commonly used to fabricate orthopaedic prostheses. Results from these studies indicate that the long-term performance of osteoblasts adherent to biomaterials is crucially dependent on the characteristics of the initial adhesion step. Furthermore, osteoactive factors such as members of the transforming growth factor-β superfamily, including TGF-β1 and BMP-2, significantly enhance osteoblast cell adhesion. The molecular components responsible for the adhesion process include extracellular matrix proteins (e.g. fibronectin and collagen type I) and their cognate membrane receptors, the integrins. Our recent studies reveal that specific downstream, intracellular signaling events are also activated as a result of osteoblast adhesion, and that these signaling events are coupled to signal transduction mechanisms mediating growth factor activity. These events in combination regulate the continued expression and maintenance of the osteoblastic phenotype of the adherent cells, resulting in matrix maturation and mineralization, hallmarks of the bony tissue. Our current efforts focus on defining the target molecular pathways responsible for bone cell functioning on biomaterials, and the identification of critical biological and material parameters to optimize long-term osteoblast function and interaction with orthopaedically relevant biomaterials. The information gathered from these studies should provide a rational basis for the design of optimal implant biomaterials. (Supported in part by the NIH and the Annenberg Foundation)
HIGH TEMPERATURE CARBONATION OF LIME IN EXPANSIVE ADDITIVES FOR CONCRETE (2016)

エトリンガイト─石灰複合型膨張材の遊離石灰と、単独合成した遊離石灰の高温炭酸化反応を比較した。膨張材の遊離石灰は処理直後にCO2量が増加したが、その後の炭酸化は緩やかとなった。一方、単独合成した遊離石灰はCO2量が継続的に増加した。膨張材の遊離石灰は緻密な組織を有し、一部が炭酸化しない無水石膏で被覆されていた。このため膨張材表面に露出した遊離石灰のみ反応が進行し、過度な炭酸化が抑制されたと考えられる。遊離石灰の高温炭酸化反応を友澤理論でモデル化し、風化抵抗性や膨張性能の向上に必要な反応率の前後において実測値に近い解析値が得られ、最適な炭酸化処理条件を提案できることが確認された。
The Post 9/11 Partnership: Transatlantic Cooperation against Terrorism (2005)

On the afternoon of September 11, 2001, many Europeans watched their televisions in horror as the second plane flew into the World Trade Center in New York, and then, a few minutes later, another plane flew into the Pentagon in Washington. By the time casualty lists were finalized, between 80–90 Europeans would be among the dead. Many Europeans recognized very quickly that this was an assault not simply on the United States, but on the West and non-Islamic world, including themselves. Although several European countries already had extensive experience with terrorism, it was clear that this attack was of another magnitude, not only in terms of damage and casualties, but also in terms of the network and resources of the perpetrators. The sense of European involvement would be heightened as investigators learned that many of the September 11 hijackers had spent considerable time in Europe, especially in Germany. Clearly, this new type of terrorism could not be defeated or even controlled by the law enforcement resources of any single nation. An effective response would require new levels of cooperation both within the European Union and across the Atlantic — and, indeed, on a global level.
Operation and performance of the ATLAS semiconductor tracker in LHC Run 2 (2022)

Abstract The semiconductor tracker (SCT) is one of the tracking systems for charged particles in the ATLAS detector. It consists of 4088 silicon strip sensor modules. During Run 2 (2015–2018) the Large Hadron Collider delivered an integrated luminosity of 156 fb -1 to the ATLAS experiment at a centre-of-mass proton-proton collision energy of 13 TeV. The instantaneous luminosity and pile-up conditions were far in excess of those assumed in the original design of the SCT detector. Due to improvements to the data acquisition system, the SCT operated stably throughout Run 2. It was available for 99.9% of the integrated luminosity and achieved a data-quality efficiency of 99.85%. Detailed studies have been made of the leakage current in SCT modules and the evolution of the full depletion voltage, which are used to study the impact of radiation damage to the modules.
Hepatoprotective activity of polysaccharopeptides from Pleurotus ostreatus mycelium on thioacetamide-intoxicated mice (2010)

"The present study was undertaken to investigate the hepato-preventive and therapeutic activities of hot-water polysaccharopeptides from the culture broth of Pleurotus ostreatus mycelium. The therapeutic regimen represented by intraperitoneal administration of polysaccharopeptides (25 mg/kg, 3 times per week, for 5 consecutive weeks) to mice after thioacetamide intoxication (200 mg/kg, 3 times per week, for 5 consecutive weeks) was more effective than before thioacetamide intoxication (preventive regimen). The preventive regimen caused less leakage of alkaline phosphatase, less pronounced increase in hepatic malondialdehyde concentration, less notable reduction in hepatic total protein, RNA and DNA contents, and in contrast increased hepatic superoxide dismutase, glutathione peroxidase and glutathione reductase activities. Amelioration of serum levels of alanine and aspartate aminotransferase activities, total protein, as well as hepatic levels of triglycerides, and catalase activities was observed. Post-treatment of liver-injured mice with polysaccharopeptides normalized all the studied parameters, whereas signifimedicantly elevated serum total protein and -globulin levels, as well as hepatic antioxidant enzymes activity. Histological examination of the liver tissues showed that polysaccharopeptides alleviated the thioacetamide-induced alterations, notably inflammation, steatosis, necrosis and fibrosis, especially in the therapeutic regimen."
Vaccine Inoculation Route Modulates Early Immunity and Consequently Antigen-Specific Immune Response (2021)

Vaccination is one of the most efficient public healthcare measures to fight infectious diseases. Nevertheless, the immune mechanisms induced <i>in vivo</i> by vaccination are still unclear. The route of administration, an important vaccination parameter, can substantially modify the quality of the response. How the route of administration affects the generation and profile of immune responses is of major interest. Here, we aimed to extensively characterize the profiles of the innate and adaptive response to vaccination induced after intradermal, subcutaneous, or intramuscular administration with a modified vaccinia virus Ankara model vaccine in non-human primates. The adaptive response following subcutaneous immunization was clearly different from that following intradermal or intramuscular immunization. The subcutaneous route induced a higher level of neutralizing antibodies than the intradermal and intramuscular vaccination routes. In contrast, polyfunctional CD8<sup>+</sup> T-cell responses were preferentially induced after intradermal or intramuscular injection. We observed the same dichotomy when analyzing the early molecular and cellular immune events, highlighting the recruitment of cell populations, such as CD8<sup>+</sup> T lymphocytes and myeloid-derived suppressive cells, and the activation of key immunomodulatory gene pathways. These results demonstrate that the quality of the vaccine response induced by an attenuated vaccine is shaped by early and subtle modifications of the innate immune response. In this immunization context, the route of administration must be tailored to the desired type of protective immune response. This will be achieved through systems vaccinology and mathematical modeling, which will be critical for predicting the efficacy of the vaccination route for personalized medicine.
ChemInform Abstract: SYNTHESIS AND CHARACTERIZATION OF TRANSITION METAL COMPLEXES CONTAINING A PENTADENTATE MACROCYCLIC LIGAND (1975)

Abstract Die Übergangsmetallkomplexe (I)‐(III) werden durch Umsetzung entsprechender Metallsalze mit dem fünfzähnigen cyclischen N‐Liganden in freier Form oder als salpetersaures Ammoniumsalz und metathetische Reaktionen dargestellt.