gebhart/patrepeval huggingface dataset:
Olfactory receptors affect inflammatory processes of lung epithelial cells (2023)

Background Lung epithelial cells are centrally involved in the development of non-type 2 inflammation, e.g. in COPD and cystic fibrosis, for which therapeutic options are needed. Olfactory receptors (ORs) belong to the group of pharmacologically used G-protein coupled receptors and are expressed in almost every cell type where they influence numerous cellular processes.
Sensors and Systems for In Situ Observations of Marine Carbon Dioxide System Variables (2010)

Autonomous chemical sensors are required to document the marine carbon dioxide system's evolving response to anthropogenic CO 2 inputs, as well as impacts on shortand long-term carbon cycling. Observations will be required over a wide range of spatial and temporal scales, and measurements will likely need to be maintained for decades. Measurable CO 2 system variables currently include total dissolved inorganic carbon (DIC), total alkalinity (A T ), CO 2 fugacity (f CO2 ), and pH, with comprehensive characterization requiring measurement of at least two variables. These four parameters are amenable to in situ analysis, but sustained deployment remains a challenge. Available methods encompass a broad range of analytical techniques, including potentiometry, spectrophotometry, conductimetry, and mass spectrometry. Instrument capabilities (precision, accuracy, endurance, reliability, etc.) are diverse and will evolve substantially over the time that the marine CO 2 system undergoes dramatic changes. Different suites of measurements/parameters will be appropriate for different sampling platforms and measurement objectives.
The SARS-CoV-2 RNA–protein interactome in infected human cells (2020)

Characterizing the interactions that SARS-CoV-2 viral RNAs make with host cell proteins during infection can improve our understanding of viral RNA functions and the host innate immune response. Using RNA antisense purification and mass spectrometry, we identified up to 104 human proteins that directly and specifically bind to SARS-CoV-2 RNAs in infected human cells. We integrated the SARS-CoV-2 RNA interactome with changes in proteome abundance induced by viral infection and linked interactome proteins to cellular pathways relevant to SARS-CoV-2 infections. We demonstrated by genetic perturbation that cellular nucleic acid-binding protein (CNBP) and La-related protein 1 (LARP1), two of the most strongly enriched viral RNA binders, restrict SARS-CoV-2 replication in infected cells and provide a global map of their direct RNA contact sites. Pharmacological inhibition of three other RNA interactome members, PPIA, ATP1A1, and the ARP2/3 complex, reduced viral replication in two human cell lines. The identification of host dependency factors and defence strategies as presented in this work will improve the design of targeted therapeutics against SARS-CoV-2.
Negative effective permeability in polaritonic photonic crystals (2004)

We find that a two-dimensional photonic crystal composed of polaritonic materials behaves as an effective medium with negative permeability in the micron wavelength range. The resonance in μeff is due to the large values of ε(ω) attained near the transverse phonon frequency ωT. The minimal wavelength for achieving an effective permeability less than −1 in a LiTaO3 crystal, obtained by optimizing the rod size and the lattice constant, is around 12μm, a range previously inaccessible using dielectric metamaterials. For certain dissipation levels, we find that other polaritonic media also exhibit a resonant effect with μeff&amp;lt;−1 for wavelengths ranging from 2 to ∼100μm.
A new framework for characterization of halftone textures (2006)

Characterization of halftone texture is important for quantitative assessment of halftone quality. In this paper, we develop a new framework based on directional local sequency analysis and a filter bank structure. We decompose a halftone image into subband images, from which we can easily reconstruct the original halftone. Based on these subband images, we define the directional sequency spectrum which is analogous to the two-dimensional Fourier spectrum, and formulate several texture measures. Two test image sets are used to justify these measures.
Bianisotropic Effective Parameters of Optical Metamagnetics and Negative-Index Materials (2011)

Approaches to the adequate homogenization of optical metamaterials are becoming more and more complex, primarily due to an increased understanding of the role of asymmetric electrical and magnetic responses, in addition to the nonlocal effects of the surrounding medium, even in the simplest case of plane-wave illumination. The current trend in developing such advanced homogenization descriptions often relies on utilizing bianisotropic models as a base on top of which novel optical characterization techniques can be built. In this paper, we first briefly review general principles for developing a bianisotropic homogenization approach. Second, we present several examples validating and illustrating our approach using single-period passive and active optical metamaterials. We also show that the substrate may have a significant effect on the bianisotropic characteristics of otherwise symmetric passive and active metamaterials.
Engineering Hydrogels beyond a Hydrated Network (2019)

In recent years, many mechanical, physical, chemical, and biochemical features of biomatrices have emerged as important properties to dictate the fates of cells. To construct chemically defined biomaterials to recapitulate various biological niches for both cell biology research and therapeutic utilities, it has become increasingly clear that a simple hydrated polymer network would not be able to provide the complex cues and signaling required for many types of cells. The researchers are facing a growing list of mechanophysical and biochemical properties, while each of them could be an important cellular trigger. To include all these design parameters in screening and synthesis is practically difficult, if not impossible. Developing novel high throughput screening technology by combining assay miniaturization, computer simulations, and modeling can help researchers to tackle the challenge to identify the most relevant parameters to tailor materials for specific applications.
Metabolic syndrome independently predicts future diabetes in women with a history of gestational diabetes mellitus (2016)

Metabolic syndrome (MetS) is an established predisposing condition for type 2 diabetes mellitus (T2DM). However, it is not thoroughly evaluated whether MetS increases the risk of T2DM in women with a previous history of gestational diabetes mellitus (GDM) who already at high risk of T2DM compared with the general population. We investigated the impact of MetS on the development of postpartum diabetes in women with a history of GDM.This was a multicenter, prospective cohort study of women diagnosed with GDM. The follow-up evaluations, including the oral glucose tolerance test, were completed at 6 weeks postpartum and annually thereafter. MetS was diagnosed at the initial postpartum evaluation according to the revised criteria of the National Cholesterol Education Program-Adult Treatment Panel III. The risk of developing type 2 diabetes (T2DM) in the follow-up period was analyzed based on the presence of MetS, and the adjusted risk was calculated using a Cox proportional hazards model.A total of 412 women without diabetes at the initial postpartum evaluation participated in the annual follow-up for median 3.8 years. MetS was prevalent in 66 (19.2%) women at the initial postpartum evaluation. The incidences of diabetes in women with and without MetS were 825 and 227 per 10,000 person-years, respectively (P < 0.001). The presence of MetS was an independent risk factor for T2DM, with a hazard ratio (HR) of 2.23 (95% confidence interval 1.04-5.08) in multivariate analysis after adjustment for clinical and metabolic parameters. When we considered MetS and impaired fasting glucose (IFG) separately, women with MetS, IFG, or both had an increased risk of T2DM, with HRs of 4.17, 4.36, and 6.98, respectively.The presence of MetS during the early postpartum period is an independent risk factor for the development of T2DM in women with a previous history of GDM.
Code transformations for low power caching in embedded multimedia processors (2002)

In this paper, we present several novel strategies to improve software controlled cache utilization, so as to achieve lower power requirements for multi-media and signal processing applications. Our methodology is targeted towards embedded multi-media and DSP processors. This methodology rakes into account many program parameters like the locality of data, size of data structures, access structures of large array variables, regularity of loop nests and the size and type of cache with the objective of improving the cache performance for lower power. We also take into account the potential overhead due to the different transformations on the instruction count and the number of execution cycles to meet the real time constraints and code size limitations. Experiments on a real life demonstrator illustrate the fact that our methodology is able to achieve significant gain in power requirements while meeting all other system constraints.
Multiplex sensors and the constant radiance theorem (2002)

Coherent mode representation of the cross-spectral density is used to derive a modal analog of the constant radiance theorem with general applicability to linear optical systems. The theorem is used to consider the relationship between spatial detector geometry and multiplexing capacity.
A Computer Scientist with a Biologist's Ambition (2022)

No abstract available.
Strain at Fracture Data for Use in Polysilicon Microsystem Design (2002)

This paper presents research on the strain at fracture of polysilicon at the micro scale. Compliant mechanisms and cantilever beams were tested to failure, the deflection measured, and the strain calculated. The results of three studies are given and the culmination of all three is presented in this paper. The information on the fracture strain and the associated uncertainty can be used to provide conservative strength estimates that can be used in design of compliant mechanisms in MEMS.
Identification of CD163 as an anti-inflammatory receptor for HMGB1-haptoglobin complexes. (2016)

Abstract Secreted by activated cells or passively released by damaged cells, extracellular HMGB1 functions as a pro-inflammatory mediator of infection or injury. It was previously unknown whether HMGB1 can be partner with other endogenous proteins to tilt the balance towards anti-inflammatory activities. Here we demonstrated that an acute phase protein, haptoglobin, effectively binds HMGB1, and triggers anti-inflammatory programs in a CD163-dependent fashion. Specifically, the HMGB1 and haptoglobin complexes elicit the production of anti-inflammatory enzymes (heme oxygenase-1) and cytokines (e.g., IL-10) in wild type, but not in CD163-deficient macrophages. Genetic disruption of haptoglobin or CD163 expression renders animals more susceptible to lethal sepsis, whereas administration of haptoglobin to wild type or to haptoglobin-gene deficient animals confers significant protection. These findings reveal a novel mechanism by which an acute phase protein modulates extracellular HMGB1 activities, and provides a novel strategy for treatment of HMGB1-dependent inflammatory diseases.
Design and Deployment of Visible-Thermal Biometric Surveillance Systems (2007)

Automatic video surveillance in uncontrolled outdoor settings is a very challenging computer vision task. Nearly infinite variability of the environmental factors and the open-ended goals of many surveillance problems conspire to create situations where even the most advanced detection, tracking and recognition algorithms falter. While the common academic response to such challenges is to develop new, more powerful algorithms capable of handling a broader range of conditions with acceptable performance, this course of action is sometimes not appropriate from the industrial-commercial point of view. Sometimes systems must be deployed sooner than would allow for the development cycle of complex new algorithms, and must be more robust than most such algorithms can be expected to be on short notice. Under those circumstances, one may look toward better data quality as one means of improving performance while remaining close to the existing state-of-the-art in algorithmic technology. This is often the motivation for deployment of multimodal surveillance systems in the real world. This presentation constitutes a brief foray into design issues for visible-thermal systems, with emphasis on biometric surveillance.
Synthesis and Catalytic Characteristics of Novel Constrained-Geometry Organoactinide Catalysts. The First Example of Actinide-Mediated Intramolecular Hydroamination (2003)

The synthesis, characterization, and reactivity of a series of organoactinide constrained-geometry complexes, (CGC)An(NRR‘)2 (CGC = Me2Si(η5-Me4C5)(tBuN); An = Th, 1; An = U, 2; R = R‘ = Me, a; R = Et, R‘ = Me, b; R = R‘ = Et, c), are reported. These complexes are effective precatalysts for intramolecular catalytic hydroamination/cyclization of aminoalkenes and aminoalkynes. Comparisons of structure and reactivity are drawn with previously reported trivalent organolanthanide CGC catalytic systems.
6‐(1‐Oxobutyl)‐5,8‐dimethoxy‐1,4‐naphthoquinone inhibits lewis lung cancer by antiangiogenesis and apoptosis (2007)

Lung cancer is a leading cause of cancer mortality worldwide. Novel and nontoxic agents targeting angiogenesis and tumor cell proliferation and survival are desirable for lung cancer chemoprevention and treatment. Previously we have reported that 6-(1-oxobutyl)-5,8-dimethoxy-1,4-naphthoquinone (OXO) exhibits anti-tumor activity against S-180 sarcoma in vitro and in vivo. Here we studied the anti-angiogenic and apoptogenic attributes of OXO in vitro and in vivo targeting lung cancer. In human umbilical vein endothelial cells (HUVECs), we show that OXO more potently inhibited VEGF-stimulated than basic bFGF-stimulated HUVEC proliferation and capillary differentiation. In Lewis lung carcinoma (LLC) cells, OXO not only induces S-phase arrest and mitochondria/caspase-9 pathway mediated apoptosis, but also effectively down-regulated the hypoxia-induced expression of HIF-1alpha and VEGF at mRNA and protein levels in LLC and decreased VEGF secretion into conditioned culture media. OXO significantly reduced in vivo functional angiogenesis in the mouse Matrigel plug assay. Furthermore, OXO potently inhibited the growth of LLC cells inoculated on the flank of syngenic mice at dosages that did not affect their body weight. The in vivo anti-cancer effect was associated with decreased HIF-1alpha and VEGF expression, decreased microvessel density as well as a reduction of tumor cell proliferation and increased tumor cell apoptosis. Taken together, these results demonstrate that OXO exerts anti-cancer activity through anti-angiogenesis and tumor cell cycle arrest and apoptosis. These findings warrant additional studies of OXO as a novel agent for the chemoprevention and treatment of lung cancer.
Automated Diffraction Tomography: A New Era for Electron Crystallography (2011)

Extended abstract of a paper presented at Microscopy and Microanalysis 2011 in Nashville, Tennessee, USA, August 7–August 11, 2011.
A feedback implosion suppression algorithm for satellite reliable multicast (2004)

We propose a knapsack-based feedback suppression algorithm for reliable multicast transport protocols operating over a satellite network. A reliable transport protocol needs to identify the packets which failed to reach a given destination. This is achieved through feedback packets returned to the source. For multicast services, receiver feedback has been shown to lead to the feedback implosion problem. Feedback implosion is a well-studied problem and various solutions exist in the literature. However, these solutions mainly focus on terrestrial networks and do not take into account the inherent characteristics of the satellite channel and the architecture of the deployed network. Therefore, we need to revisit the problem and provide a new set of solutions for efficient integration to next generation satellite systems. We introduce a feedback implosion suppression algorithm, which effectively suppresses the amount of feedback relayed through the satellite channel, while ensuring that critical information is conveyed in a timely fashion. The performance of the algorithm is evaluated through simulations.
Comparison of parametric and linear mass detection in the presence of detection noise (2011)

We experimentally investigate the performance of a nonlinear parametrically driven mass sensor in the presence of detection noise. Mass detection is achieved by measuring the amount of methanol vapor adsorption on the sensor. To demonstrate the advantage of parametric sensing in counteracting the influence of detection noise, we operate the sensor in both the parametric and harmonic resonance mode. Comparison of the results shows that in contrast to conventional linear harmonic sensing, the detection sensitivity does not deteriorate for the parametric case when a tenfold increase in detection noise is introduced. Furthermore, we demonstrate additional functionality of the parametric sensor by utilizing it as a threshold detector, whose performance remains the same despite the added detection noise. Taken together, these results suggest that for mass detection in the presence of detection noise, a parametrically operated sensor may offer better performance over one operated harmonically in the linear regime.
Vitamin D receptor agonist EB1089 is a potent regulator of prostatic “intracrine” metabolism (2013)

These data highlight a potential application of VDR-based therapies for the reduction of growth-promoting androgens within the tumor micro-environment.
39.4: Invited Paper : Liquid Crystals for Ophthalmic Lenses and Biosensing Applications (2014)

Abstract We introduce two bio‐photonic applications of liquid crystals. One is the ophthalmic lenses with large aperture size. The challenge and the solutions are discussed. The other is the biosensing devices based on a switchable surface of a liquid crystal and polymer composite film, such as a sperm testing devices and high‐density lipoproteins. Liquid crystals indeed have great potentials beyond displays.
Development of a continuous generation/supply system of highly concentrated ozone gas for low-temperature oxidation process (2004)

A system is described which can continuously generate/supply highly concentrated (HC) ozone gas to satisfy the future need for practical low-temperature oxidation. This system comprises four ozone vessels, each with independent temperature control. The system can supply a constant flow of HC ozone gas by allocating one of four modes of operation, i.e., accumulation/storage, vaporization (supply), evacuation, and cooling, to each of the ozone vessels so that all the modes can be simultaneously addressed. The maximum flow rate is 60 sccm with a flux stability of ±1.1%, and an ozone concentration of over 99.5 vol % can be achieved at the system outlet. The system was applied to the formation of an ultrathin SiO2 film on a 4 in. diameter silicon wafer substrate.
Real-time video fusion using a distributed architecture in robotic surgery (2009)

The use of medical robotics has been increasing in recent years. This increase in popularity can be attributed to the improvement in dexterity robots provide over traditional laparoscopy, as well as the increasing number of applications of robotic surgery. The daVinci from Intuitive Surgical, one of the more commonly used robotic surgery systems, relies on stereo laparoscopic video for guidance, which restricts visualization to only surface anatomy. Oftentimes the localization of subsurface anatomic structures is critical to the success of surgical intervention. The implementation of image guidance in medical robotics adds the ability to see into the surface; however, current implementations are restrictive in terms of flexibility or scalability, especially in the ability to process real-time video data. We present a system architecture which allows for use of multiple computers through a centralized database; which can fuse additional information to the real-time video stream. This architecture is independent of hardware or software and is extensible to a large number of clinical applications.
AN-C2V: An Auto-Nulling Bridge-Based Signal Conditioning Circuit for Leaky Capacitive Sensors (2020)

This paper presents a fully analog auto-nulling bridge based capacitance-to-voltage (AN-C2V) converter circuit for measuring the capacitive component of the leaky capacitive sensors. The circuit utilizes an active bridge based architecture in which the quadrature components of the output are taken. An integrator-controller is used for auto-nulling. A unity gain, frequency-independent quadrature phase shift amplifier is designed for an accurate generation of 90° phase-shifted signal. Experiments conducted on the developed prototype demonstrate that the proposed AN-C2V system is able to estimate the sensor capacitor ranging from 47.2pF to 668.3pF with a maximum error of about ± 0.18% with respect to the commercial LCR meter. The effectiveness of the circuit is tested with the commercial leaky capacitive humidity sensor. The effect of leakage resistor, parasitic capacitor, frequency of excitation signal, and supply voltage is negligible on the final output, which results in a very robust and accurate solution for leaky capacitive sensors.
Concentration of Milataxel (MAC-321, TL-139) and its major metabolite (M-10) in xenograft tumors from mice dosed orally and intravenously (2006)

512 Milataxel is a novel taxane that has shown substantial anti-tumor activity versus taxane-sensitive and taxane-resistant human tumors in mouse xenograft models. Milataxel has entered phase II clinical studies. Mice implanted with human xenograft tumors (SKMES-lung, HCT-15-colon and A-375 melanoma) were treated with oral and a non-cremophor milataxel IV formulation. Concentrations of milataxel and its major metabolite, M-10, were measured using HPLC-UV-βRAM and LC/MS. Levels for parent and metabolite were found to be different when measuring 14 C labeled species in tumor. M-10 levels were typically 50% higher than parent in tumors from non-Pgp cell lines when milataxel was administered either orally or IV. Measurable levels of parent drug and metabolite persisted for 10 days post dosing. In-vitro IC50 evaluation of Milataxel and M-10 show both to be potent cytotoxics, but M-10 was shown to be a substrate for Pgp. Oral Milataxel has completed a phase I study and plasma levels of M-10 and parent were measured.