gebhart/patrepeval huggingface dataset:
Probing the Structural Determinants of Type II‘ β-Turn Formation in Peptides and Proteins (2002)

The structural determinants of type II' beta-turns were probed through a comprehensive CD, NMR, and molecular dynamics analysis of 10 specially designed beta-hairpin peptides. The peptide model used in this study is a synthetic, water-soluble, 14-residue cyclic analogue of gramicidin S which contains two well-defined type II' beta-turns connected by a highly stable, amphipathic, antiparallel beta-sheet. A variety of coded and noncoded amino acids were systematically substituted in one of the two type II' turns to analyze the effects of backbone chirality, side-chain steric restriction, and side-chain/side-chain interactions. beta-Sheet content (as measured through a variety of experimental methods), molecular dynamics, and 3D structural analysis of the turn regions were used to assess the effects of each amino acid substitution on type II' beta-turn stabilization. Our results demonstrate that backbone heterochirality, which determines equatorial and axial side-chain orientation at the i+1 and i+2 residues of type II' turns, may account for up to 60% of type II' beta-turn stabilization. Steric restriction through side-chain N-alkylation appears to enhance type II' beta-turn propensity and may account for up to 20% of type II' beta-turn stabilization. Finally, aromatic/proline side-chain interactions appear to account for approximately 10% of type II' beta-turn stabilization. We believe this information could be particularly useful for the prediction of beta-turn propensity, the development of peptide-based drugs, and the de novo design of peptides, proteins, and peptidyl mimetics.
Renewal of the terminal bronchiolar epithelium in the rat following exposure to NO2 or O3. (1976)

Rats were exposed to either NO2 or O3 to determine whether nonciliated cells (Clara cells) could divide and differentiate into ciliated cells in the terminal bronchioles. Dividing cells were labeled with tritiated thymidine, visualized in the light and electron microscopes using autoradiographic techniques, and studied for up to 15 days after labeling. Electron microscopic autoradiography 1 hour after injection of tritiated thymidine showed that all labeled cells in the terminal bronchioles were nonciliated. However, 4 days after injection of tritiated thymidine, 67.8 per cent of the labeled cells were nonciliated and 32.2 per cent were ciliated. Light microscopic autoradiography showed that the new labeled ciliated cell population was stable for up to 15 days. These results indicate that nonciliated cells divide and the sister cells may form new ciliated and nonciliated cells. Thus, nonciliated cells can act as progenitor cells for the terminal bronchiolar epithelium.
Lgr5 is a potential marker of colorectal carcinoma stem cells that correlates with patient survival (2012)

These findings suggest that Lgr5 may play an important role in the progression and prognosis of colorectal carcinoma, and may be a potential new therapeutic target for the treatment of colorectal cancer patients. It may also be considered as a potential marker for colorectal cancer stem cells (CSCs).
Multiple Reflections in Acoustic Surface Wave Reflective Arrays (1975)

The effects of multiple reflections in two-dimensional acoustic surface wave reflective arrays are examined via a computa- tional model which accounts for all multiple reflections. A weak re- flection unit cell scattering matrix is developed in detail for scattering on an anisotropic surface. Several reflecting geometries are solved for the weak reflection case providing a comparative basis against which the distortions of frequency responses and spatial beam pro- files induced by multiple reflections are compared. By comparing computed frequency responses and beam profiles to experiment, it is found that single reflector scattering coefficients can be deduced. I. INTRODUCTIOK
Obstacle Avoidance System in Autonomous Ground Vehicle Using Ground Plane Image Processing and Omnidirectional Drive (2015)

Today one of the major concerns for any industry is availability of workspace and adequate intratransport systems. This paper suggests the possible and probably cheap solution for both of above incapacities by implying sensor controlled motion of Omni-directional wheels. We have synchronized the image processing capability of Raspberry Pie processor with the sensitivity of motor driver circuit to obtain a precise and accurate motion of platform mounted with mecanum wheel that do not require any turning radius. As an image sensor we have used the simple CCD camera. The set of Image transformations are applied on the image to detect the obstacle precisely. We designed mecanum wheel with main constraint kept as shortage of space and load carrying capacity, hence we were able to report design of the wheel with specific dimensions. The image processing and simulation is done in the MATLAB environment. This choice has added the possibilities of the inclusion of advance control strategies and the use of image processing toolbox.
A multiple coil solenoid to provide an axial magnetic field with near-linear gradient (1988)

A model is presented for a multiple coil solenoid capable of providing an axial magnetic field with an increasing magnitude which varies in a near-linear manner over a specified length of the axis. A design programme has been developed and a coil arrangement constructed and tested. Its performance is in fair agreement with predictions.
On the occurrence of the S<sub>N</sub>(ANRORC)‐mechanism in the reaction of 2‐bromo‐4‐phenylpyrimidine with potassium amide in liquid ammonia (1973)

Abstract On amination of 2‐bromo‐4‐phenylpyrimidine with potassium amide, 2‐amino‐4‐phenylpyrimidine, β‐amino‐β‐phenylacrylonitrile and 4‐amino‐l‐cyano‐2‐phenyl‐l‐aza‐1,3‐butadiene are formed. 2‐Bromo‐4‐phenyl‐[l,3‐ 15 N]‐pyrimidine has been prepared and found to give on amination 2‐amino‐4‐phenylpyrimidine. which contains the original 15 N mainly in the exocyclic amino group. This is explained by a mechanism, involving an initial Addition of the Nucleophile to position 6, a subsequent Ring‐Opening by fission of the N(1)‐C(6) bond and Ring‐Closure (S N (ANRORC)‐mechanism).
Biodistribution of p-Boronophenylalanine in Patients with Glioblastoma Multiforme for Use in Boron Neutron Capture Therapy (1998)

Intravenous BPA administration up to a dose of 250 mg/kg is safe and well tolerated. BPA uptake in surgical samples of glioblastoma tissue is variable and may depend on the fraction of viable tumor cells in the individual sample. Further clinical studies using BPA as a boron delivery agent for boron neutron capture therapy of glioblastoma multiforme appear warranted.
High Quality Factor Lamb Wave Resonators (2014)

High Quality Factor Lamb Wave Resonators by Jie Zou Master of Science in Electrical Engineering and Computer Sciences University of California, Berkeley Professor Albert P. Pisano, Chair The small-in-size and CMOS compatible micro-electromechanical system (MEMS) resonators are likely to be the driving core of a new generation of devices such as radio frequency (RF) filters and timing references. Thanks to the CMOS compatibility, ability of high frequencies, low motional impedances (Rm), small frequency-induced drifts, and capability of multiple frequencies operation on a single chip, the aluminum nitride (AlN) Lamb wave resonators have attracted attention among various micromechanical resonator technologies. The lowest-order symmetric (S0) Lamb wave mode in an AlN thin plate is particularly preferred because it exhibits high acoustic phase velocity, a low dispersive phase velocity characteristic, and a moderate electromechanical coupling coefficient. In this report, basic analysis of the Lamb waves propagating in AlN and the device design techniques are presented in detail. Then, a novel technique to enhance the quality factor (Q) of Lamb wave resonator by utilizing an AlN plate formed in a butterfly shape is investigated in this paper. In the conventional design, the Q’s of the micromachined Lamb wave resonators are largely harmed by the energy dissipation through the support tethers. The finite element analysis (FEA) simulation results show that the butterflyshaped topology can efficiently change the displacement field in the AlN plate and reduce the vibration in the support tethers. The unloaded Q of the resonator is raised from 3,360 to 4,758 by simply using of the butterfly-shaped AlN plate with a tether-to-plate angle α = 59o, representing a 1.42× increase. The experimental Q’s are also in good agreement with the anchor loss Q’s computed using the PML-based FEA method. __________________________________________ Professor Albert P. Pisano, Chair Date
À la Recherche d’un Dieu Perdu: Recreating Religion in La Tentation de Saint Antoine (2007)

La Tentation de Saint Antoine is "un livre qui fait peur," according to Flaubert scholar Jeanne Bem (13). Indeed, it is a monstrous text that presents us with multiple characters and an amalgam of heresies and temptations. Confusion further stems from the difference in versions: one version of the text was written in 1848, a second version was partially published in 1856, and the final version appeared in 1874. The monstrosity resides lastly in the form of the text: we wonder how to define the genre of La Tentation. Flaubert first conceived of it as a play, perhaps even a puppet play, but the didascalies read more like descriptions in a novel and are impossible to act out.[1]
Human iPSC-Derived Endothelial Cells and Microengineered Organ-Chip Enhance Neuronal Development (2018)

Human stem cell-derived models of development and neurodegenerative diseases are challenged by cellular immaturity in vitro. Microengineered organ-on-chip (or Organ-Chip) systems are designed to emulate microvolume cytoarchitecture and enable co-culture of distinct cell types. Brain microvascular endothelial cells (BMECs) share common signaling pathways with neurons early in development, but their contribution to human neuronal maturation is largely unknown. To study this interaction and influence of microculture, we derived both spinal motor neurons and BMECs from human induced pluripotent stem cells and observed increased calcium transient function and Chip-specific gene expression in Organ-Chips compared with 96-well plates. Seeding BMECs in the Organ-Chip led to vascular-neural interaction and specific gene activation that further enhanced neuronal function and in vivo-like signatures. The results show that the vascular system has specific maturation effects on spinal cord neural tissue, and the use of Organ-Chips can move stem cell models closer to an in vivo condition.
The New Principal (2006)

This case focuses on some of the considerations and activities involved in human resource management that confront a principal at the beginning of the school year. The principal, who was an assistant principal in a neighboring district last year, is faced with a number of questions and unfamiliar procedures that accompany the new work context. By identifying and addressing the challenges faced by this novice principal, aspiring educational leaders can model her skills in prioritizing, communicating, and strategically implementing human resource responsibilities in a school setting.
Release of bovine serum albumin from a hydrogel‐cored biodegradable polymer fiber (2006)

We have developed a novel biodegradable, polymeric fiber construct that is coextruded using a wet-spinning process into a core-sheath format with a polysaccharide pre-hydrogel solution as the core fluid and poly(L-lactic acid) (PLLA) as the sheath. The biodegradable, biocompatible fibers were extruded from polymeric emulsions comprised of solutions of various molecular weights of PLLA dissolved in chloroform and containing dispersed, protein-free aqueous phases comprising up to 10% of the emulsion volume. Biologically sensitive agents can be loaded via a dispersed aqueous phase in the polymer, and/or directly into the polysaccharide. We show that this core-sheath fiber format will load a model protein that can be delivered for extended periods in vitro. Bovine serum albumin (BSA) was loaded into the fiber core as a model protein. We have shown that the greater the volume of the protein-free aqueous phase dispersed into the polymeric continuous-phase emulsion, the greater the total release of BSA encapsulated by a core gel comprised of 1% sodium alginate solution. We conclude this fiber format provides a promising vehicle for in vivo delivery of biological molecules. Its biocompatibility and biodegradability also allow for its use as a possible substrate for tissue engineering applications.
Novel coupled-cavity TWT structure using two-step LIGA fabrication (2003)

In order to make millimeter-wave sources practical, improved fabrication methods are required. The use of Lithographie, Galvanoformung, Abformung; German acronym (LIGA) to fabricate a coupled-cavity traveling-wave tube (TWT) is presented. The proposed circuit design will focus on two-step LIGA fabrication and dual in-line ladder structure with a rectangular beam tunnel. The fabrication sequence of two-step LIGA is illustrated and the advantages and tradeoff of this approach are described. Three electromagnetic codes-HFSS, GdfidL, and MAGIC3D-are employed to analyze the circuit characteristics in cold and hot test simulations. Finally, the results from small and large signal analyses are presented to verify the validity of the circuit design.
Organic corrosion inhibitors for mild steel in aerated near neutral chloride solutions (1990)

Over 120 organic compounds have been investigated as potential corrosion inhibitors for mild steel in simulated engine coolants. A relationship has been found between the corrosion potential (Ecorr) and inhibitor performance (Rp). With straight chain alkyl carboxylates, maximum inhibition was found for C6- C10 monocarboxylates and C7- C12 dicarboxylates. Polarization curves for selected inhibitors and the Ecorr- Rp relationship suggest these compounds affect only the anodic dissolution. The inhibitor effectiveness of sebacate was found to be unaffected by stirring or the presence of corrosion products.
Strictly Localized Sensor Self-Deployment for Optimal Focused Coverage (2011)

We consider sensor self-deployment problem, constructing FOCUSED coverage (F-coverage) around a Point of Interest (POI), with novel evaluation metric, coverage radius. We propose to deploy sensors in polygon layers over a locally computable equilateral triangle tessellation (TT) for optimal F-coverage formation, and introduce two types of deployment polygon, H-polygon and C-polygon. We propose two strictly localized solution algorithms, Greedy Advance (GA), and Greedy-Rotation-Greedy (GRG). The two algorithms drive sensors to move along the TT graph to surround POI. In GA, nodes greedily proceed as close to POI as they can; in GRG, when their greedy advance is blocked, nodes rotate around POI along locally computed H- or C-polygon to a vertex where greedy advance can resume. We prove that they both yield a connected network with maximized hole-free area coverage. To our knowledge, they are the first localized sensor self-deployment algorithms that provide such coverage guarantee. We further analyze their coverage radius property. Our study shows that GRG guarantees optimal or near optimal coverage radius. Through extensive simulation we as well evaluate their performance on convergence time, energy consumption, and node collision.
Profile-based pretenuring (2007)

Pretenuring can reduce copying costs in garbage collectors by allocating long-lived objects into regions that the garbage collector will rarely, if ever, collect. We extend previous work on pretenuring as follows: (1) We produce pretenuring advice that is neutral with respect to the garbage collector algorithm and configuration. We thus can and do combine advice from different applications. We find for our benchmarks that predictions using object lifetimes at each allocation site in Java programs are accurate, which simplifies the pretenuring implementation. (2) We gather and apply advice to both applications and Jikes RVM, a compiler and runtime system for Java written in Java. Our results demonstrate that building combined advice into Jikes RVM from different application executions improves performance, regardless of the application Jikes RVM is compiling and executing. This build-time advice thus gives user applications some benefits of pretenuring, without any application profiling. No previous work uses profile feedback to pretenure in the runtime system. (3) We find that application-only advice also consistently improves performance, but that the combination of build-time and application-specific advice is almost always noticeably better. (4) Our same advice improves the performance of generational, Older First, and Beltway collectors, illustrating that it is collector neutral . (5) We include an immortal allocation space in addition to a nursery and older generation, and show that pretenuring to immortal space has substantial benefit.
Interaction of HLA‐DR and CD74 at the cell surface of antigen‐presenting cells by single particle image analysis (2012)

Major histocompatibility complex (MHC) class II-associated antigen presentation involves an array of interacting molecules. CD74, the cell surface isoform of the MHC class II-associated invariant chain, is one such molecule; its role remains poorly defined. To address this, we have employed a high-resolution single-particle imaging method for quantifying the colocalization of CD74 with human leukocyte antigen (HLA)-DR molecules on human fibroblast cells known for their capacity to function as antigen-presenting cells. We have also examined whether the colocalization induces internalization of HLA-DR using HA(307-319), a "universal" peptide that binds specifically to the peptide-binding groove of all HLA-DR molecules, irrespective of their alleles. We have determined that 25 ± 1.3% of CD74 and 17 ± 0.3% of HLA-DR are colocalized, and the association of CD74 with HLA-DR and the internalization of HLA-DR are both inhibited by HA(307-319). A similar inhibition of HLA-DR internalization was observed in freshly isolated monocyte-derived dendritic cells. A key role of CD74 is to translocate HLA-DR molecules to early endosomes for reloading with peptides prior to recycling to the cell surface. We conclude that CD74 regulates the balance of peptide-occupied and peptide-free forms of MHC class II at the cell surface.
Simulation and comparison of Albrecht's function point and DeMarco's function bang metrics in a CASE environment (1993)

Software size estimates provide a basis for software cost estimation during software development. Hence, it is important to measure the system size reliably as early as possible. Two of the best known specification level metrics, Albrecht's function points (A.J. Albrecht, 1979) and DeMarco's function bang metrics (T. DeMarco, 1982) are compared by a simulation study in which automatically generated randomized dataflow diagrams (DFDs) were used as a statistical sample to automatically count function points and function bang in a built CASE environment. These value counts were correlated statistically using correlation coefficients and regression analysis. The simulation study permits sufficient variation in the base material to cover most types of system specifications. Moreover, it allows sufficient sampling sizes to make statistical analysis of data. The obtained results show that in certain cases there is a relatively good statistical correlation between these metrics.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Components of a highly integrated DBF terminal antenna for mobile Ka-band satellite communications (2003)

In this paper several components for a highly integrated digital beamforming (DBF) antenna array for Ka-band satellite systems are presented. The general concept of array construction based on a modular approach is introduced and the construction of a constituent array module discussed. Following this outline, different components, designed and tested to later be incorporated into the array module, are treated with the focus set on the Ka-band receiver and transmitter frontends.
Automatic Adjustment of Transfer Functions for 3D Volume Visualization. (2000)

In most volume rendering scenarios implicit classification is performed manually by specification data values to visual attributes. An appropriate classification requires both specialized knowledge of the interesting structures within the data set as well as the technical knowhow of the computer scientist. Recent automatic data-driven techniques are verywell capable of separating different regions in the data set. However, their applicability in practice is limited, since they do not contain any information about the critical structures which are of interest. In this scenario we propose an efficient and reproducible way to automatically assign transfer function templates, which include individual knowledge as well as personal taste. The presented approach is based on dynamic programming and was successfully applied in medical environment. 1
Doppler radar respiration measurement for gated lung cancer radiotherapy (2011)

Respiration-gated radiation therapy is a promising treatment modality that precisely delivers prescribed radiation dose to the lung tumor while minimizing the incidence and severity of normal tissue complications. Conventional gating techniques either rely on implanted fiducial markers or external surrogates such as markers placed on patients' abdomen. They are either invasive to the patients or do not have sufficient accuracy. In this paper, we present a non-contact Doppler radar method to non-invasively measure the respiration signals, from which, accurate gating signals can be derived to control the linac. No marker is needed in our method, which makes it very convenient in use. We measured the respiration using a 5.8 GHz quadrature radar. Analysis of the measured signal is presented. It has been shown that the non-contact means of respiration measurement is able to supply reliable breathing motions and accurate gating signals for radiotherapy of mobile tumors.
Analog circuit reliability in sub-32 nanometer CMOS: Analysis and mitigation (2011)

The paper discusses reliability threats and opportunities for analog circuit design in high-k sub-32 nanometer technologies. Compared to older SiO <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sub> or SiON based technologies, transistor reliability is found to be worse in high-k nodes due to larger oxide electric fields, the severely aggravated PBTI effect and increased time-dependent variability. Conventional reliability margins, based on accelerated stress measurements on individual transistors, are no longer sufficient nor adequate for analog circuit design. As a means to find more accurate, circuit-dependent reliability margins, advanced degradation effect models are reviewed and an efficient method for stochastic circuit reliability simulation is discussed. Also, an example 6-bit 32nm current-steering digital-to-analog converter is studied. Experiments demonstrate how the proposed simulation tool, combined with novel design techniques, can provide an up to 89% better area-power product of the analog part of the circuit under study, while still guaranteeing a 99.7% yield over a lifetime of 5 years.