gebhart/patrepeval huggingface dataset:
Fabrication of Extracellular Matrix-derived Foams and Microcarriers as Tissue-specific Cell Culture and Delivery Platforms (2017)

Cell function is mediated by interactions with the extracellular matrix (ECM), which has complex tissue-specific composition and architecture. The focus of this article is on the methods for fabricating ECM-derived porous foams and microcarriers for use as biologically-relevant substrates in advanced 3D in vitro cell culture models or as pro-regenerative scaffolds and cell delivery systems for tissue engineering and regenerative medicine. Using decellularized tissues or purified insoluble collagen as a starting material, the techniques can be applied to synthesize a broad array of tissue-specific bioscaffolds with customizable geometries. The approach involves mechanical processing and mild enzymatic digestion to yield an ECM suspension that is used to fabricate the three-dimensional foams or microcarriers through controlled freezing and lyophilization procedures. These pure ECM-derived scaffolds are highly porous, yet stable without the need for chemical crosslinking agents or other additives that may negatively impact cell function. The scaffold properties can be tuned to some extent by varying factors such as the ECM suspension concentration, mechanical processing methods, or synthesis conditions. In general, the scaffolds are robust and easy to handle, and can be processed as tissues for most standard biological assays, providing a versatile and user-friendly 3D cell culture platform that mimics the native ECM composition. Overall, these straightforward methods for fabricating customized ECM-derived foams and microcarriers may be of interest to both biologists and biomedical engineers as tissue-specific cell-instructive platforms for in vitro and in vivo applications.
An Optimal Key Distribution Scheme for Secure Multicast Group Communication (2010)

Many IP multicast-based applications, such as multimedia conferencing, multiplayer games, require controlling the group memberships of senders and receivers. One common solution is to encrypt the data with a session key shared with all authorized senders/receivers. To efficiently update the session key in the event of member removal, many rooted-tree based group key distribution schemes have been proposed. However, most of the existing rooted-tree based schemes are not optimal. In other words, given the O(log N) storage overhead, the communication overhead is not minimized. On the other hand, although Flat Table scheme achieves optimality, it is rather dismissed due to the vulnerability to collusion attacks. In this paper, we propose a key distribution scheme - EGK that attains the same optimality as Flat Table without collusion vulnerability. Additionally, EGK provides constant message size and requires O(log N) storage overhead at the group controller, which makes EGK suitable for applications containing a large number of multicasting group members. Moreover, adding members in EGK requires just one multicasting message. EGK is the first work with such features and out- performs all existing schemes.
Detecting anomalous latent classes in a batch of network traffic flows (2014)

We focus on detecting samples from anomalous latent classes, “buried” within a collected batch of known (“normal”) class samples. In our setting, the number of features for each sample is high. We posit and observe to be true that careful “feature selection” within unsupervised anomaly detection may be needed to achieve the most accurate results. Our approach effectively selects features (tests), even though there are no labeled anomalous examples available to form a basis for standard (supervised) feature selection. We form pairwise feature tests based on bivariate Gaussian mixture null models, with one test for every pair of features. The mixtures are estimated using known class samples (null “training set”). Then, we obtain p-values on the test batch samples under the null hypothesis. Subsequently, we calculate approximate joint p-values for candidate anomalous clusters, defined by (sample subset, test subset) pairs. Our approach sequentially detects the most significant clusters of samples in a networking context. We compare our “p-value clustering algorithm”, using ROC curves, with alternative p-value based methods and with the one-class SVM. All the competing methods make sample-wise detections, i.e. they do not jointly detect anomalous clusters. The anomalous class was either an HTTP bot (Zeus) or peer-to-peer (P2P) traffic. Our p-value clustering approach gives promising results for detecting the Zeus bot and P2P traffic amongst Web.
Industrialized high-sensitivity fiber optic near-IR diode-laser-based gas analysis system (1994)

An industrialized computer-controlled fiber optic laser diode gas analysis system is described. A unique signal processing scheme completely eliminates both non-gas-related transmission variation and long-term drift. Sensitivities better than 1 ppm(DOT)m and 200 ppm(DOT)m is routinely achieved for field-installed systems for ammonia and oxygen, respectively. due to the superior selectivity of laser diodes, interference effects from coexisting gases, such as water vapor in ammonia measurements, are easily avoided.
Compositional-tailoring of optical properties in IR transparent chalcogenide glasses for precision glass molding (2013)

The structural and optical properties of AsSe chalcogenide glass, starting with As40Se60, were studied as a function of Ge or Se additions. These elements provide broad glass forming options when combined with the host matrix to allow for compositional tuning of properties. Optimization of glass composition has been shown to produce bulk glasses with a thermoptic coefficient (dn/dT) equal to zero, as well as a composition which could demonstrate a net zero change in index after precision glass molding (PGM). The bulk glass density, coefficient of thermal expansion (CTE), refractive index, and dn/dT were measured for all bulk compositions, as was the refractive index after PGM. For the bulk glasses examined, both the refractive index (measured at discrete laser wavelengths from 3.4 to10.6 μm) and dn/dT were observed to decrease as the molecular percentage of either Ge or Se is increased. Compared to the starting glass’ network, additions of either Ge or Se lead to a deviation from the “optimally constrained” binary glass’ average coordination number <r> = 2.4. Additions of Se or Ge serve to decrease or increase the average coordination number (CN) of the glass, respectively, while also changing the network’s polarizability. After a representative PGM process, glasses exhibited an “index drop” consistent with that seen for oxide glasses.<sup>1</sup> Based on our evaluation, both the Gecontaining and Ge-free tielines show potential for developing unique compositions with either a zero dn/dT for the unmolded, bulk glass, as well as the potential for a glass that demonstrates a net zero “index drop” after molding. Such correlation of glass chemistry, network, physical and optical properties will enable the tailoring of novel compositions suitable for prototyping towards targeted molding behavior and final properties.
Understanding generator stator ground faults and their protection schemes (2016)

Because of stator winding construction, an insulation failure is more likely to result in a winding-to-ground fault than in a phase-to-phase fault. Other failures, such as a broken conductor or turn-to-turn fault, may not be detected until the fault develops into a winding-to-ground fault. Consequently, stator ground fault protection is one of the indispensable schemes for protecting a generator stator winding. Dedicated stator ground fault protection is required for high-impedance-grounded machines. Neutral overvoltage protection is the simplest method for detecting a stator winding-to-ground fault, but this method does not detect faults over the entire winding. Therefore, additional protection is required in the form of third-harmonic undervoltage, third-harmonic voltage balance, or subharmonic injection. Each of these protection schemes is available in several alternatives.
Power efficient mobile video streaming using HTTP/2 server push (2015)

This paper proposes a power efficient video streaming mechanism on mobile devices over cellular networks. We first develop an analytical model to identify and quantify the power inefficiency in mobile video streaming, due to the mismatch between HTTP request schedule and the radio resource control schedule. Based on the analytical model, we develop a low power video streaming mechanism by employing the server push technology available in the HTTP/2 protocol. We implemented the server push-based low power streaming mechanism in an HTTP DASH video streaming prototype involving mobile devices and the 4G/LTE cellular network. Our experiments show significant battery power savings on mobile devices using our server push strategy.
High Level Design Space Exploration of Shared Bus Communication Architectures (2004)

System-on-Chip (SoC) designs are increasingly becoming more complex. Efficient on-chip communication architectures are critical for achieving desired performance in these systems. System designers typically use Bus Cycle Accurate (BCA) models written in high level languages such as C/C++ to explore the communication design space. These models capture all of the bus signals and strictly maintain cycle accuracy, which is useful for reliable performance exploration but results in slow simulation speeds for complex designs, even when they are modeled using high level languages. Recently there have been several efforts to use the Transaction Level Modeling (TLM) paradigm for improving simulation performance in BCA models. However these BCA models capture a lot of details that can be eliminated when exploring communication architectures.
An innovative Steiner tree based approach for polygon partitioning (2008)

As device technology continues to scale past 65 nm, the heavy application of resolution enhancement techniques (RET) makes the complexity, run time and quality issues in mask data preparation (MDP) grow severely. As one major and core step in MDP, polygon partitioning converts the complex layout shapes into trapezoids suitable for mask writing. The partitioning run time and quality of the resulting polygon partitions directly impacts the cost, integrity, and quality of the written mask. In this work, we introduce an innovative approach to solve the polygon partition problem by constructing a variant Steiner minimal tree: minimal partition tree (MPT). We prove the equivalence between MPT and the optimal polygon partition. Also, the solution search space for MPT is further reduced for the efficiency of the MPT algorithms. Finally, a generic MPT algorithm flow and a linear-time heuristic algorithm based on it are proposed. Experiments show that MPT solves the polygon partitioning with very promising and high quality results.
Prevalence of the Genes Encoding Propionicin T1 andProtease-Activated Antimicrobial Peptide and Their Expressionin ClassicalPropionibacteria (2004)

The purpose of this study was to investigate the frequency of production of the bacteriocin propionicin T1 and the protease-activated antimicrobial peptide (PAMP) and their corresponding genes in 64 isolates of classical propionibacteria. This study revealed that these genes are widespread in Propionibacterium jensenii and Propionibacterium thoenii but absent from the remaining species of classical propionibacteria that were studied. The pro-PAMP-encoding gene (pamA) was found in 63% of the P. jensenii strains and 61% of the P. thoenii strains, and all of these strains displayed PAMP activity. The propionicin T1-encoding gene (pctA) was present in 89% of the P. thoenii strains and 54% of the P. jensenii strains. All P. thoenii strains containing the pctA gene exhibited antimicrobial activity corresponding to propionicin T1 activity, whereas only 38% of the pctA-containing P. jensenii strains displayed this activity. Sequencing of the pctA genes revealed the existence of two allelic variants that differed in a single nucleotide in six strains of P. jensenii; in these strains the glycine at position 55 of propionicin T1 was replaced by an aspartate residue (A variant). No strains harboring the A variant showed any antimicrobial activity against propionicin T1-sensitive bacteria. An open reading frame (orf2) located immediately downstream from the pctA gene was absent in three strains containing the G variant of propionicin T1. Two of these strains showed low antimicrobial activity, while the third strain showed no antimicrobial activity at all. The protein encoded by orf2 showed strong homology to ABC transporters, and it has been proposed previously that this protein is involved in the producer immunity against propionicin T1. The limited antimicrobial activity exhibited by the strains lacking orf2 further suggests that this putative ABC transporter plays an important role in propionicin T1 activity.
Gaucher disease as a paradigm of current issues regarding single gene mutations of humans. (1993)

Gaucher disease is a glycolytic storage disease caused by a deficiency in activity of the catabolic enzyme glucocerebrosidase. Over 35 different mutations have been documented, including missense and nonsense point mutations, splicing mutations, deletions and insertions, a fusion gene, and examples of gene conversion. Gaucher disease is most common in the Ashkenazi Jewish population, in which just five of the mutations in this population account for 98% of the disease-producing alleles. Each of these mutations is found in the context of a single haplotype, a finding consistent with a single origin of each mutation. Although it is clear that these mutations provide a selective advantage in the Jewish population and thus constitute a balanced polymorphism, the nature of the advantage is unknown. Gaucher disease can be treated symptomatically, by administration of the missing enzyme, by allogeneic bone marrow transplantation, and potentially by gene transfer into hematopoietic stem cells. Increasing understanding of this disease has, as in other genetic disorders, created a host of social and ethical dilemmas regarding matters such as the cost of treatment for rare diseases and the advantages and disadvantages of population-targeted genetic screening.
Surface Micromachined Combined Magnetometer/Accelerometer for Above-IC Integration (2014)

This paper presents a combined magnetometer/accelerometer sharing a single surface micromachined structure. The device utilizes electrical current switching between two perpendicular directions on the structure to achieve a 2-D in-plane magnetic field measurement based on the Lorentz force. The device can concurrently serve as a 1-D accelerometer for out-of-plane acceleration, when the current is switched off. Accordingly, the proposed design is capable of separating magnetic and inertial force measurements, achieving higher accuracy through a single compact device. The sensor supports static operation at atmospheric pressure, precluding the need for complex vacuum packaging. It can alternatively operate at resonance under vacuum for enhanced sensitivity. The device is fabricated using a low-temperature surface micromachining technology, which is fully adapted for above-IC integration on standard CMOS substrates. The resonance frequency of one of the fabricated structures is measured to be 6.53 kHz with a quality factor of ~30 at a 10-mTorr ambient vacuum level. The magnetic field and acceleration sensitivities of the device are measured using discrete electronics to be 1.57 pF/T and 1.02 fF/g, respectively, under static operation.
<i>Vo-Norvana</i> : Versatile Framework for Efficient Segmentation of Large Point Cloud Data Sets (2023)

Dense three-dimensional (3D) point clouds collected from rapidly evolving data acquisition techniques such as light detection and ranging (lidar) and structure from motion (SfM) multiview stereo (MVS) photogrammetry contain detailed geometric information of a scene suitable for a wide variety of applications. Among the many processes within a typical point cloud processing workflow, segmentation is often a crucial step to group points with similar attributes to support more advanced modeling and analysis. Segmenting large point cloud data sets (i.e., hundreds of millions to billions of points) can be extremely time consuming and tedious with current tools, which primarily rely on significant manual effort. While many automated methods have been proposed, the practicality, scalability, and versatility of these approaches remain a bottleneck stifling processing of large data sets. To overcome these challenges, this paper introduces a novel, generalized segmentation framework called Vo-Norvana, which incorporates a new voxelization technique, a normal variation analysis considering the positioning uncertainty of the point cloud, and a custom region growing process for clustering. The proposed framework was tested with several large-volume data sets collected in diverse scene types using several data acquisition platforms including terrestrial lidar, mobile lidar, airborne lidar, and drone-based SfM-MVS photogrammetry. In evaluating the accuracy of models generated from Vo-Norvana against manual segmentation, the average error of the position, orientation, and dimensions are 2.7 mm, 0.083°, and 0.9 mm, respectively. Over 0.2 million points per second and 36 thousand voxels per second can be achieved when segmenting an airborne lidar data set containing over 639 million points to about 1 million segments.
Synthesis and biological evaluation of synthetic viridins derived from C(20)-heteroalkylation of the steroidal PI-3-kinase inhibitor wortmannin (2004)

A series of viridin analogs was prepared from wortmannin by nucleophilic ring opening at C(20) and evaluated against the signaling kinases PI-3-kinase and mTOR. Several subnanomolar enzyme inhibitors with orders of magnitude selectivity for PI-3-kinase and strong cytotoxic activity against four cancer cell lines were identified. Among the ten most promising derivatives, six demonstrated lower liver toxicity and greater promise for inhibition of tumor cell growth than the lead structure wortmannin.
Antibodies directed against synthetic peptides distinguish between GTP-binding proteins in neutrophil and brain. (1987)

Antisera AS/6 and 7, raised against a synthetic peptide KENLKDCGLF corresponding to the carboxyl-terminal decapeptide of transducin-alpha, react on immunoblots with purified transducin-alpha and with proteins of 40-41 kDa in all tissues tested. The latter represent one or more forms of Gi alpha but not Go alpha, since a synthetic peptide, KNNLKDCGLF, corresponding to the carboxyl-terminal decapeptide of two forms of Gi alpha blocks AS/6 and 7 reactivity with transducin-alpha and Gi alpha on immunoblots, whereas the corresponding Go-related peptide, ANNLRGCGLY, does not. Antisera LE/2 and 3, raised against the synthetic peptide LERIAQSDYI, corresponding to an internal sequence predicted by one form of Gi alpha cDNA (Gi alpha-2) and differing by 3 residues from the sequence of another form, Gi alpha-1, react strongly with a 40-kDa protein abundant in neutrophil membranes and with the major pertussis toxin substrate purified from bovine neutrophils. LE/2 and 3 reveal a relatively faint 40-kDa band on immunoblots of crude brain membranes or of purified brain Gi/Go. LE/2 and 3 do not react with transducin-alpha or Go alpha nor with the 41-kDa form of pertussis toxin substrate in brain, Gi alpha-1. These antisera distinguish between the major pertussis toxin substrates of brain and neutrophil and tentatively identify the latter as Gi alpha-2.
<i>Vibrio cholerae</i> ACE stimulates Ca<sup>2+</sup>-dependent Cl<sup>−</sup>/HCO<sub>3</sub> <sup>−</sup>secretion in T84 cells in vitro (2000)

ACE, accessory cholera enterotoxin, the third enterotoxin in Vibrio cholerae, has been reported to increase short-circuit current (I(sc)) in rabbit ileum and to cause fluid secretion in ligated rabbit ileal loops. We studied the ACE-induced change in I(sc) and potential difference (PD) in T84 monolayers mounted in modified Ussing chambers, an in vitro model of a Cl(-) secretory cell. ACE added to the apical surface alone stimulated a rapid increase in I(sc) and PD that was concentration dependent and immediately reversed when the toxin was removed. Ion replacement studies established that the current was dependent on Cl(-) and HCO(3)(-). ACE acted synergistically with the Ca(2+)-dependent acetylcholine analog, carbachol, to stimulate secretion in T84 monolayers. In contrast, the secretory response to cAMP or cGMP agonists was not enhanced by ACE. The ACE-stimulated secretion was dependent on extracellular and intracellular Ca(2+) but was not associated with an increase in intracellular cyclic nucleotides. We conclude that the mechanism of secretion by ACE involves Ca(2+) as a second messenger and that this toxin stimulates a novel Ca(2+)-dependent synergy.
Manufacturing Capability of Micro-Transfer Printing (2019)

Micro-Transfer printing is a mass transfer process that provides fast and precise assembly of micro-components onto non-native substrates. The process was originally conceived at the University of Illinois [1, 2], and has been developed at X-Celeprint. The process involves the fabrication of retrievable micro-components, elastomer stamp retrieval and transfer-printing of the micro-components to a non-native substrate and finally the interconnection [3]. With this process a large array of micro-components can be transferred at one time with an accuracy of +/- 1.5um 3 sigma and transfer yields exceeding 99%.
Estimation of Quartz Resonator Q and other Figures of Merit by an Energy Sink Method (2007)

An important determinant of the quality factor Q of a quartz resonator is the loss of energy from the electrode area to the base via the mountings. The acoustical characteristics of the plate resonator are changed when the plate is mounted onto a base substrate. The base substrate affects the frequency spectra of the plate resonator. A resonator with a high Q may not have a similarly high Q when mounted on a base. Hence, the base is an energy sink and the Q will be affected by the shape and size of this base. A lower bound Q will be obtained if the base is a semi-infinite base since it will absorb all acoustical energies radiated from the resonator. A scaled boundary finite element method is employed to model a semi-infinite base. The frequency spectra of the quartz resonator with and without the base are presented. In addition to the loss of energy via the base, there are other factors which affect the resonator Q, such as, for example, material dissipation, and damping at the interfaces of quartz and electrodes. The energy dissipation due to material damping increases with the resonant frequency and the reduction of resonator size; hence material damping becomes important in the current and future miniaturized resonators operating at very high frequencies. An energy sink model along with material dissipation would provide realistic Q, motional capacitance, motional resistance, and other figures of merit useful for designing resonators. The model could be used for evaluating resonator and mountings designs of microelectromechanical systems and miniaturized devices. The effect of the mountings, and plate and electrode geometries on the resonator Q and other electrical parameters are presented for AT-cut quartz resonators. Model results from the energy sink method were compared with experimental results and were found to be good.