gebhart/patrepeval huggingface dataset:
Cytostretch, an Organ-on-Chip Platform (2016)

Organ-on-Chips (OOCs) are micro-fabricated devices which are used to culture cells in order to mimic functional units of human organs. The devices are designed to simulate the physiological environment of tissues in vivo. Cells in some types of OOCs can be stimulated in situ by electrical and/or mechanical actuators. These actuations can mimic physiological conditions in real tissue and may include fluid or air flow, or cyclic stretch and strain as they occur in the lung and heart. These conditions similarly affect cultured cells and may influence their ability to respond appropriately to physiological or pathological stimuli. To date, most focus has been on devices specifically designed to culture just one functional unit of a specific organ: lung alveoli, kidney nephrons or blood vessels, for example. In contrast, the modular Cytostretch membrane platform described here allows OOCs to be customized to different OOC applications. The platform utilizes silicon-based micro-fabrication techniques that allow low-cost, high-volume manufacturing. We describe the platform concept and its modules developed to date. Membrane variants include membranes with (i) through-membrane pores that allow biological signaling molecules to pass between two different tissue compartments; (ii) a stretchable micro-electrode array for electrical monitoring and stimulation; (iii) micro-patterning to promote cell alignment; and (iv) strain gauges to measure changes in substrate stress. This paper presents the fabrication and the proof of functionality for each module of the Cytostretch membrane. The assessment of each additional module demonstrate that a wide range of OOCs can be achieved.
Optimal design and nonlinearities in a z-axis resonant accelerometer (2015)

Micro-Electro-Mechanical Systems (MEMS) accelerometers are micro-sized devices largely used for detecting accelerations in the consumer and automotive market. Both capacitive and resonant sensing have been successfully employed in these devices. In the present work, we focus on a z-axis resonant accelerometer recently proposed in [1] fabricated by the Thelma© surface-micromachining technique developed by STMicroelectronics. After a full non-linear dynamic study, an optimization of the design of the device is carried out. The main goal of the optimization process is to increase the sensitivity of the device together with the reliability and the linearity.
Rational Design of α‐Helical Antimicrobial Peptides to Target Gram‐negative Pathogens, <i>Acinetobacter baumannii</i> and <i>Pseudomonas aeruginosa</i>: Utilization of Charge, ‘Specificity Determinants,’ Total Hydrophobicity, Hydrophobe Type and Location as Design Parameters to Improve the Therapeutic Ratio (2011)

The rapidly growing problem of increased resistance to classical antibiotics makes the development of new classes of antimicrobial agents with lower rates of resistance urgent. Amphipathic cationic α-helical antimicrobial peptides have been proposed as a potential new class of antimicrobial agents. The goal of this study was to take a broad-spectrum, 26-residue, antimicrobial peptide in the all-D conformation, peptide D1 (K13) with excellent biologic properties and address the question of whether a rational design approach could be used to enhance the biologic properties if the focus was on Gram-negative pathogens only. To test this hypothesis, we used 11 and 6 diverse strains of Acinetobacter baumannii and Pseudomonas aeruginosa, respectively. We optimized the number and location of positively charged residues on the polar face, the number, location, and type of hydrophobe on the non-polar face and varied the number of 'specificity determinants' in the center of the non-polar face from 1 to 2 to develop four new antimicrobial peptides. We demonstrated not only improvements in antimicrobial activity, but also dramatic reductions in hemolytic activity and unprecedented improvements in therapeutic indices. Compared to our original starting peptide D1 (V13), peptide D16 had a 746-fold improvement in hemolytic activity (i.e. decrease), maintained antimicrobial activity, and improved the therapeutic indices by 1305-fold and 895-fold against A. baumannii and P. aeruginosa, respectively. The resulting therapeutic indices for D16 were 3355 and 895 for A. baumannii and P. aeruginosa, respectively. D16 is an ideal candidate for commercialization as a clinical therapeutic to treat Gram-negative bacterial infections.
Genetic Diversity and Differentiation of Relict Plant Liriodendron Populations Based on 29 Novel EST-SSR Markers (2019)

Surviving relict populations of species that were more widespread in ancient times can teach us a lot, such as evolution and genetic differentiation. One such relict plant is Liriodendron, of which populations remain in China (L. chinense (Hemsl.) Sarg.) and the USA (L. tulipifera L.). Studying the genetic structure of these populations would give insight into the genetic differentiation and the breeding strategy. In this work, we developed and characterized 29 novel simple sequence repeat (SSR) markers based on expressed sequence tags (ESTs) from hybrid Liriodendron (Liriodendron chinense × tulipifera) callus. In total, 29 SSRs with perfect primer-designed were used to assess genetic diversity and differentiation. The set of polymorphic EST-SSR loci was identified in 48 Liriodendron individuals, represented by 35 individuals sampled from 14 provenances of L. chinense and 13 individuals sampled from 5 provenances of L. tulipifera. Our results indicated that L. chinense populations possess slightly higher genetic diversity than L. tulipifera populations. Based on genetic distances, 48 Liriodendron individuals clustered into three groups (the eastern China L. chinense, the western China L. chinense and L. tulipifera), although the STRUCTURE analysis of the Liriodendron populations revealed just two clear genetic clusters (L. chinense and L. tulipifera). Among these 29 novel markers, ESSR119 showed an obvious species-specific characteristic which can be very useful in marker-assisted selection (MAS). In general, all these EST-SSR markers may have agronomic potential and constitute a basis for future studies on the identification, innovation, and even preservation of Liriodendron germplasms.
High-throughput nanofabrication of plasmonic structures and metamaterials with high resolution nanostencil lithography (2011)

We demonstrate a novel fabrication approach for high-throughput fabrication of engineered plasmonic antenna arrays and metamaterials with Nanostencil Lithography (NSL). NSL technique, relying on deposition of materials through a shadow mask, offers the flexibility and the resolution to fabricate radiatively engineer nanoantenna arrays for excitation of collective plasmonic resonances. We confirmed that the antenna arrays fabricated by NSL shows high optical quality similar to EBL fabricated ones. Furthermore, we show nanostencils can be reused multiple times to fabricate selfsame structures with identical optical responses repeatedly and reliably. This capability is particularly useful when highthroughput replication of the optimized nanoparticle arrays is desired. In addition to its high-throughput capability, NSL permits single step nanofabrication of plasmonic devices on surfaces that are difficult to work with electron/ion beam techniques. Nanostencil lithography is a resist free process thus allows the transfer of the nanopatterns to any planar substrate whether it is conductive, insulating or magnetic. As proof of the versatility of the NSL technique, we show fabrication of plasmonic structures and metamaterials in variety of geometries. In metamaterial and plasmonic devices, unique geometries with small gaps and asymmetries can induce novel electromagnetic responses such as plasmon induced transparency and also giant near-field intensities that are important for enhanced vibrational spectroscopy and non-linear optics applications. This nanofabrication scheme, enabling the reusability of stencil and offering flexibility on the substrate choice and nano-pattern design could significantly enhance wide-use of plasmonics in sensing technologies.1
Overview of multipole-based acoustic infinite elements (1997)

There is a rapidly growing interest in using infinite elements based on multipole expansions for modeling acoustic wave propagation in unbounded domains, either time harmonic or transient. The technology has exhibited many advantages, foremost among them being a very high computational efficiency, convergence and, therefore, unlimited accuracy throughout the entire fluid domain, broadband capability, and a conventional finite-element software implementation. The latter enables these infinite elements, along with conventional finite-size acoustic elements and coupling elements, to be easily added to standard structural element libraries to convert structural codes to structural acoustic codes for fast, accurate modeling of scattering and/or radiation problems in exterior regions. The talk will cover: basic concepts of multipoles, multipole expansions, and the related infinite elements; past contributions to the field; current research, including the author’s; and an assessment of the most promising direction for this technology.
Subtyping lymphocytes in peripheral blood by immunoperoxidase labeling and light scatter/absorption flow cytometry. (1985)

Abstract Lymphocyte subpopulations in a whole-blood sample can be detected by adapting mouse monoclonal antibodies (MAbs) and peroxidase (EC 1.11.1.7) labeling to a flow cytometer equipped with a tungsten-halogen light source and scatter/absorption optics (Technicon H6000). In the optimized cytochemical conditions each cell population generates a distinct, well-separated cluster, for accurate "thresholding" of the surface-antigen negative and positive lymphocyte populations in the presence of other leukocytes. After reaction with MAb, the erythrocytes are lysed, and the lymphocytes and other leukocytes are fixed. Biotinylated anti-mouse IgG, used as a bridge, amplifies the response from the avidin-peroxidase label. Granulocytes and monocytes, which have high endogenous peroxidase activity, and the labeled lymphocytes are stained in a specific amount of hydrogen peroxide plus 4-chloro-1-naphthol in 4-(2-hydroxyethyl)-1-piperazine-ethanesulfonic acid buffer. Accuracy and precision are equivalent to those of flow cytometers that measure immunofluorescence (e.g., Ortho Spectrum III), as demonstrated with OKT3, OKT4, OKT8, OKT11, and Leu 12 MAbs.
Production Data Analysis and Forecasting Using a Comprehensive Analysis System (1999)

Abstract Analysis of production data to obtain estimates of the intrinsic properties of a reservoir and of the current well condition can be performed using a number of available analysis procedures. Each of these analyses were developed using differing assumptions and often result in poor agreement between the parameter estimates obtained with each analysis when performed separately. A logical and comprehensive analysis system has been developed and used for field applications which enables the engineer to rapidly perform each of these production data analyses on the same set of production data and obtain a "best-indicated" set of parameter estimates of the reservoir and well properties. The analyses that can be performed on the production data include water control diagnostics, material balance analyses, empirical and advanced decline curve analyses using integral and derivative functions, automated history matching using analytic pressure or rate-transient solutions, and commingled reservoir production forecasting and economic evaluations. The systematic analysis of production data in this manner can be used to obtain estimates of the reservoir and well parameters for cases where other means of obtaining these values are often not available.
<i>Hahb‐4</i>, a homeobox‐leucine zipper gene potentially involved in abscisic acid‐dependent responses to water stress in sunflower* (2002)

Abstract Homeodomain‐leucine zipper proteins constitute a family of transcription factors found only in plants. We have characterized a full‐length cDNA encoding the sunflower homeobox‐leucine zipper protein Hahb‐4 ( Helianthus annuus h omeo b ox‐4). The complete cDNA is 674 base pairs long and contains an open reading frame of 177 amino acids that belongs to the Hd‐Zip I subfamily. Northern blot and RNAse A protection analysis show that the expression of Hahb‐4 is rapidly, strongly and reversibly induced by water deficit in whole seedlings, roots, stems and leaves. A similar fast induction of Hahb‐4 expression is observed when seedlings are subjected to a treatment with the hormone abscisic acid (ABA). Nuclei prepared from seedlings treated with ABA or subjected to water stress show a significant increase of protein(s) that specifically bind the sequence 5′‐CAAT(A/T)ATTG‐3′, recognized in vitro by Hahb‐4, suggesting that an active protein is synthesized in response to these treatments. The promoter region of the Hahb‐4 gene contains sequences that fit the consensus for a G‐box present in some AB A r esponsive e lements (ABREs). We propose that Hahb‐4 may function in signalling cascade(s) that control(s) a subset of the ABA‐mediated responses of sunflower to water stress.
Design of high-intensity focused ultrasound transmitters based on optoacoustic generation (2011)

We design focused ultrasound transmitters based on optoacoustic generation. Focused ultrasound is generated from a thin layer of light-absorbing source which is excited by pulsed laser beam. When compared to piezoelectric transducer, our new approach has advantages of high frequency generation and high geometrical gain. Material and geometrical considerations are discussed.
Intragastric ketone ester administration prevents CNS oxygen toxicity (CNS‐OT) and modulates tidal volume and respiratory frequency in rats (2013)

In clinical and military operations, hyperbaric oxygen (HBO) can generate central nervous system oxygen toxicity (seizures). In a previous study, we demonstrated that the intragastric administration of ketone ester (KE), a non‐ionized ketone bodies precursor, has a prominent anti‐seizure effect. In this follow‐up study, we tested the anticonvulsant properties of multiple KEs, and their effects on cardio‐respiration. 60 male rats were implanted with radio‐telemetry devices to record EEG, diaphragmatic electromyogram (dEMG) and ECG. Rats were orally administered with one of four KEs: beta hydroxybutyrate , R,S‐1,3‐butanediol , acetoacetate monoester (AcAc), and acetoacetate diester (AcAc 2 ). 30 min later, rats were exposed to HBO at 5 atmosphere absolute, until the onset of CN‐SOT, and the latency to seizure (LS) was measured. Our results showed that: a) AcAc 2 was found to be the most potent anticonvulsant ester, as it increased the LS of 574%, compared to controls; b) AcAc and AcAc 2 administration caused a significant increase in tidal volume (V T ) and thus minute ventilation c) while stabilizing respiratory frequency (f resp ) between 15 min before and after seizure, compared to controls. We report that 1) KEs (notably AcAc and AcAc 2 ) increase the animal's resistance to seizures, and 2) ventilation (V T and f resp ) was significantly stimulated by the oral administration of KEs.
Electronic synthesis of light (2017)

We report on bidirectional frequency conversion between the microwave and optical domains using electro-optics. Advances in communications, time keeping, and quantum sensing have all come to depend upon the coherent interoperation of light wave and microwave signals. To connect these domains, which are separated by a factor of 10,000 in frequency, requires specialized technology that has until now only been achieved by ultrafast mode-locked lasers. In contrast, electro-optic modulation (EOM) combs arise deterministically by imposing microwave-rate oscillations on a continuous-wave laser. Here we demonstrate electro-optic generation of a 160 THz bandwidth supercontinuum and realize f-2f self-referencing. Coherence of the supercontinuum is achieved through optical filtering of electronic noise on the seed EOM comb. The mode frequencies of the supercontinuum are derived from the electronic oscillator and they achieve <5×10−14 fractional accuracy and stability, which opens a novel regime for tunable combs with wide mode spacing apart from the requirements of mode locking.
Scalable Anti-Censorship Framework Using Moving Target Defense for Web Servers (2017)

Although the Internet has become a hub around which every aspect of our lives-from commerce to leisurely activities-is centered, many around the world are not able to freely access information over the Internet. Some governments censor what the people can and cannot see. In this paper, regardless of the socio-political view points, we focus on the design of anti-censorship technology that can be implemented on the side of the information purveyors. The primary objective is to develop a framework for combating censorship. Our approach aims to make it too expensive and impractical for the adversary to censor Web sites. In particular, we propose the use of Mobile IPv6 to form a moving target defense strategy, where the Web servers logically behave as if they are the mobile nodes (without actually moving). The potential efficacy of this framework is modeled analytically. Probabilistic models are used to derive important metrics and parameters. One key factor termed swarming ratio enables hosting sites to reason about the amount of resources needed to force the adversary's costs over practical limits. This model is used to guide the performance goals and architectural setup of the prototype implementation (modifications are made on the server-side software and Kernel without changing the standard Mobile IPv6 protocol). Hence, the solution can be utilized without any changes to the existing network infrastructure. Furthermore, we introduce a novel, credit-based accounting strategy for grouping of users to drastically shift resource requirements in our favor. Lab-based tests are used to measure performance overheads, and based on the findings, targeted optimizations are performed to consider practical deployment scenarios. The end result is a solution that may also be combined with existing anti-censorship methods (that are end-user-based and/or assisted by friendly network assets) to form a robust anti-censorship solution.
SNR performance of an adaptive sigma delta modulator (2001)

In a previous study, we proposed an adaptive sigma delta modulator with improved dynamic range. The modulator adapts the step size of the quantizer from estimates of the quantizer input instead of the modulator input. In this study, we conduct an error variance analysis of the new modulator and derive expression for the SNR. The derived expression shows that the SNR is independent of the input signal strength, which supports the simulation results
Progress toward the commercial realization of high performance holographic data storage (2005)

The promise of using volume holography to deliver high performance optical storage systems is at hand. The possibility of extremely large storage capacities and fast transfer rates make holographic storage ideal for high performance video applications. An overview of advances at InPhase Technologies is presented. Progress toward high-density implementations as well as the development of a functional prototype is presented. These systems are the first fully functional holographic recordable drives developed. Their development paves the way for the commercialization of this technology.
Poly(TEMPO)/Zinc Hybrid‐Flow Battery: A Novel, “Green,” High Voltage, and Safe Energy Storage System (2016)

The combination of a polymer-based 2,2,6,6-tetramethylpiperidinyl-N-oxyl (TEMPO) catholyte and a zinc anode, together with a cost-efficient size-exclusion membrane, builds a new type of semi-organic, "green," hybrid-flow battery, which features a high potential range of up to 2 V, high efficiencies, and a long life time.
Electrodialytic Capillary Suppressor for Open Tubular Ion Chromatography (2016)

We describe an electrodialytic capillary suppressor for suppressed conductometric open tubular ion chromatography (SC-OTIC). For practical eluent concentrations, suppressor active lengths less than ∼1 mm are adequate. In its preferred embodiment, the suppressor consists of a solid polymer ion exchanger block. Two 0.45-mm-diameter parallel cylindrical passages are provided: these provide for passage of regenerant water and placement of platinum wire electrodes. The suppression channel is made by making a crack in the soft polymer block, using a needle 0.3 mm in diameter. The suppression channel runs parallel to and is flanked by the two aforementioned electrode channels through which water is pumped. The suppressor ends of the separation and the detection capillaries are tapered. The tapered ends of the capillaries are inserted into the suppression channel with the tips 0.4-1.1 mm apart. Using a suppression length of 1 mm, we were able to suppress 100 mM hydroxide @ 100 nL/min (10 neq/min). With such a suppressor coupled to an AS18 latex-coated surface-sulfonated cyclo-olefin polymer (COP) capillary column with an inner diameter (i.d.) of 28 μm and using an on-capillary admittance detector (AD), the feasibility of both isocratic and gradient SC-OTIC was demonstrated. At 170 nL/min (substantially above the Van Deemter optimum), the plate count for fluoride exceeded 70 000 plates/m under isocratic conditions. The dispersion induced by the suppressor could not be determined, because the peak half-widths after suppression were paradoxically less than those without suppression; this apparent negative dispersion is likely an artifact of the detector.
Organization and regulation of the <i>Corynebacterium glutamicum hom‐thrB</i> and <i>thrC</i> loci (1988)

The genes encoding the three terminal enzymes in the threonine biosynthetic pathway, homoserine dehydrogenase (hom), homoserine kinase (thrB) and threonine synthase (thrC) have been isolated from Corynebacterium glutamicum. The C. glutamicum hom and thrB genes were subcloned on a 3.6 kb SalI-generated chromosomal fragment. The C. glutamicum thrC gene was shown not to be linked to the hom-thrB locus. L-methionine represses the cloned homoserine dehydrogenase and homoserine kinase similar to that of the chromosomally encoded hom and thrB gene products. Northern hybridization analysis demonstrates that this repression is mediated at the level of transcription and that hom-thrB represents an operon in C. glutamicum.
Space-time-multipath coding using digital phase sweeping or circular delay diversity (2005)

We design novel space-time multipath (STM) coded multi-antenna transmissions over frequency-selective Rayleigh fading channels. We develop STM coded systems that guarantee the maximum possible space-multipath diversity, along with large coding gains, and high bandwidth efficiency for any number of transmit-receive antennas. By incorporating subchannel grouping, we also enable desirable tradeoffs between performance and complexity. Our designs rely on digital phase sweeping or block circular delay operations and apply to both single- and multi-carrier systems. Their merits are confirmed by corroborating simulations and comparisons with existing approaches.
S-band GaAs FET Reconfigurable Reflectarray for Passive Communications (2020)

A reflectarray operating at 3.5 GHz is created with individual control of unit element reconfigurability for beamsteering in both azimuth and elevation. The unit element has been co-designed with a gallium arsenide (GaAs) FET on the back side of the reflector to allow the reflected phase to change between 0° and 180°. The phase control can be used to both beamform the reflected signal in a desired direction and modulate data onto a signal of opportunity for short range communications. The simplicity of the unit element and control routing enables the elements to be electrically small (~λ/6 spacing). Over-the-air laboratory measurements indicate the ability to modulate the reflected signal at 10 kbps with a path forward towards higher data rates.