gebhart/patrepeval huggingface dataset:
Scaling deterministic lateral displacement arrays for high throughput and dilution-free enrichment of leukocytes (2011)

A disposable device for fractionation of blood into its components that is simple to operate and provides throughput of greater than 1 mL min−1 is highly sought after in medical diagnostics and therapies. This paper describes a device with parallel deterministic lateral displacement devices for enrichment of leukocytes from blood. We show capture of 98% and approximately ten-fold enrichment of leukocytes in whole blood. We demonstrate scaling up through the integration of six parallel devices to achieve a flow rate of 115 µL of undiluted blood per minute per atmosphere of applied pressure.
Epidermal Cells on Stubs Used for Detection of GSR with SEM-EDX: Analysis of DNA Polymorphisms (1996)

DNA from epidermal cells attached to the adhesive tape of stubs employed to collect and identify gunshot residue (GSR) with scanning electron microscope (SEM) was extracted, amplified with PCR and typed. The method allowed identification of specimens when attribution to a definite person was uncertain. These results also suggest that adhesive tape could be used as a non invasive method for obtaining biological material suitable for DNA analysis from the skin surface.
Review: L'amour Fou (1973)

Book Review| July 01 1973 Review: L'amour Fou L'amour Fou Lawrence Shaffer Lawrence Shaffer Search for other works by this author on: This Site PubMed Google Scholar Film Quarterly (1973) 26 (4): 52–57. https://doi.org/10.2307/1211503 Views Icon Views Article contents Figures & tables Video Audio Supplementary Data Peer Review Share Icon Share Twitter LinkedIn Tools Icon Tools Get Permissions Cite Icon Cite Search Site Citation Lawrence Shaffer; Review: L'amour Fou. Film Quarterly 1 July 1973; 26 (4): 52–57. doi: https://doi.org/10.2307/1211503 Download citation file: Ris (Zotero) Reference Manager EasyBib Bookends Mendeley Papers EndNote RefWorks BibTex toolbar search Search nav search search input Search input auto suggest search filter All ContentFilm Quarterly Search This content is only available via PDF. Copyright 1973 The Regents of the University of California Article PDF first page preview Close Modal You do not currently have access to this content.
Heterogeneity of Fracture Syndromes in Postmenopausal Women* (1985)

Studies were performed on 32 women with vertebral crush fractures (mean age, 65.1 yr) and 27 patients with recent hip fractures (mean age, 83.6 yr). Histomorphometric analysis of undecalcified transiliac crest biopsies revealed significant differences between the two fracture groups. Trabecular bone volume (TBV) was significantly lower in vertebral fracture than in hip fracture patients (12.0 +/- 4.4% (+/- SD) vs. 14.8 +/- 3.6%; P = 0.014), while thickness of cortices was significantly lower for hip fracture than for vertebral fracture patients (436 +/- 231 vs. 823 +/- 465 microns; P less than 0.001). The TBV and radial bone mass (measured by absorptiometry on the shaft) for the vertebral fracture group were significantly lower than age-expected values. For the patients with hip fractures, the TBV was significantly above the expected value, and radial bone mass was not significantly different from the expected value. Other quantitative histological measurements did not generally differ between the two fracture groups and were compatible with normal or increased bone remodeling. The serum PTH in the hip fracture group was significantly increased above that expected in normal women of similar age. These data demonstrate the anatomical heterogeneity of osteoporotic fracture syndromes. Patients with vertebral fractures have an early deficit of trabecular bone for their age, while those with hip fractures have a deficit of both cortical and trabecular bone compared to women of age 50 yr, but the deficit is not excessive compared to others of similar age without fractures.
Mariner mutagenesis of Brucella melitensis reveals genes with previously uncharacterized roles in virulence and survival (2006)

The identification of novel genes within previously described groups was expected, and nearly two-thirds of the 95 genes had not been previously reported as contributing to survival and virulence using random Tn5-based mutagenesis. The results of this work provide added insight with regard to the regulatory elements, nutritional demands and mechanisms required for efficient intracellular growth and survival of the organism.
Genomically encoded analog memory with precise in vivo DNA writing in living cell populations (2014)

Cellular memory is crucial to many natural biological processes and sophisticated synthetic biology applications. Existing cellular memories rely on epigenetic switches or recombinases, which are limited in scalability and recording capacity. In this work, we use the DNA of living cell populations as genomic "tape recorders" for the analog and distributed recording of long-term event histories. We describe a platform for generating single-stranded DNA (ssDNA) in vivo in response to arbitrary transcriptional signals. When coexpressed with a recombinase, these intracellularly expressed ssDNAs target specific genomic DNA addresses, resulting in precise mutations that accumulate in cell populations as a function of the magnitude and duration of the inputs. This platform could enable long-term cellular recorders for environmental and biomedical applications, biological state machines, and enhanced genome engineering strategies.
Energetics of overall metabolic reactions of thermophilic and hyperthermophilic Archaea and Bacteria (2001)

Thermophilic and hyperthermophilic Archaea and Bacteria have been isolated from marine hydrothermal systems, heated sediments, continental solfataras, hot springs, water heaters, and industrial waste. They catalyze a tremendous array of widely varying metabolic processes. As determined in the laboratory, electron donors in thermophilic and hyperthermophilic microbial redox reactions include H2, Fe(2+), H2S, S, S2O3(2-), S4O6(2-), sulfide minerals, CH4, various mono-, di-, and hydroxy-carboxylic acids, alcohols, amino acids, and complex organic substrates; electron acceptors include O2, Fe(3+), CO2, CO, NO3(-), NO2(-), NO, N2O, SO4(2-), SO3(2-), S2O3(2-), and S. Although many assimilatory and dissimilatory metabolic reactions have been identified for these groups of microorganisms, little attention has been paid to the energetics of these reactions. In this review, standard molal Gibbs free energies (DeltaGr(0)) as a function of temperature to 200 degrees C are tabulated for 370 organic and inorganic redox, disproportionation, dissociation, hydrolysis, and solubility reactions directly or indirectly involved in microbial metabolism. To calculate values of DeltaGr(0) for these and countless other reactions, the apparent standard molal Gibbs free energies of formation (DeltaG(0)) at temperatures to 200 degrees C are given for 307 solids, liquids, gases, and aqueous solutes. It is shown that values of DeltaGr(0) for many microbially mediated reactions are highly temperature dependent, and that adopting values determined at 25 degrees C for systems at elevated temperatures introduces significant and unnecessary errors. The metabolic processes considered here involve compounds that belong to the following chemical systems: H-O, H-O-N, H-O-S, H-O-N-S, H-O-C(inorganic), H-O-C, H-O-N-C, H-O-S-C, H-O-N-S-C(amino acids), H-O-S-C-metals/minerals, and H-O-P. For four metabolic reactions of particular interest in thermophily and hyperthermophily (knallgas reaction, anaerobic sulfur and nitrate reduction, and autotrophic methanogenesis), values of the overall Gibbs free energy (DeltaGr) as a function of temperature are calculated for a wide range of chemical compositions likely to be present in near-surface and deep hydrothermal and geothermal systems.
Highly Porous and Stable Metal−Organic Frameworks:  Structure Design and Sorption Properties (2000)

Gas sorption isotherm measurements performed on the evacuated derivatives of four porous metal−organic frameworks (MOF-n), Zn(BDC)·(DMF)(H2O) (DMF = N,N‘-dimethylformamide, BDC = 1,4-benzenedicarboxylate) (MOF-2), Zn3(BDC)3·6CH3OH (MOF-3), Zn2(BTC)NO3·(C2H5OH)5H2O (BTC = 1,3,5-benzenetricarboxylate) (MOF-4), and Zn4O(BDC)3·(DMF)8C6H5Cl (MOF-5), reveal type I isotherms for n = 2, 3, and 5, which is evidence of microporous and accessible channels having high structural integrity and organization. Although gas sorption into MOF-4 was not observed, careful examination of its ethanol sorption isotherms at 22 and 32 °C point to the presence of coordinatively unsaturated zinc centers within its pores, which upon ethanol sorption undergo coordination transitions from 3- to 4-, 4- to 5-, and 5- to 6-coordination. MOF-n materials were produced by building the extended analogues of molecular metal carboxylate clustersa strategy that has allowed the realization of the most porous and thermally stable framework yet reported: the evacuated form of MOF-5 is especially stable in air at 300 °C and has a free pore volume representing 55−60% of its crystal as determined by gas sorption and single-crystal diffraction studies.
<title>Adaptive distributed multimedia streaming server in Internet settings</title> (2003)

We present an adaptive distributed multimedia server architecture (ADMS) that builds upon the idea of offensive adaptivity, where the server proactively controls its layout through replication or migration of server components to recommended hosts. Proactive actions are taken when network or server resources become critical when fulfilling client demands. Recommendations are provided by a so-called "host recommender" which represents an integral part of Vagabond2 -- the middleware used for component distribution. Recommendations are based on measured or estimated server and network resource availabilities. Network distance and host resource metrics -- obtained from network and host resource services respectively -- may be communicated as MPEG-21 DIA descriptors. Finally we evaluate our architecture in a real-world streaming scenario.
Nano- and Microengineering: 3-D Colloidal Photonic Crystals Prepared from Sub-μm-sized Polystyrene Latex Spheres Pre-Coated with Luminescent Polyelectrolyte/Nanocrystal Shells (2000)

Colloidal photonic crystals doped with luminescent semiconductor nanocrystals are prepared here by a layer-by-layer deposition technique. This method, which involves the consecutive electrostatic adsorption of polyelectrolyte and nanocrystals such as CdTe onto submicrometer-sized polystyrene latex globules (see Figure), is described as being very versatile and can be extended to the fabrication of either optically active or passive shells of different thickness.
Atomic Layer Etching at the Tipping Point: An Overview (2015)

The ability to achieve near-atomic precision in etching different materials when transferring lithographically defined templates is a requirement of increasing importance for nanoscale structure fabrication in the semiconductor and related industries. The use of ultra-thin gate dielectrics, ultra thin channels, and sub-20 nm film thicknesses in field effect transistors and other devices requires near-atomic scale etching control and selectivity. There is an emerging consensus that as critical dimensions approach the sub-10 nm scale, the need for an etching method corresponding to <i>Atomic Layer Deposition</i> (ALD), i.e. <i>Atomic Layer Etching</i> (ALE), has become essential, and that the more than 30-year quest to complement/replace continuous directional plasma etching (PE) methods for critical applications by a sequence of individual, self-limited surface reaction steps has reached a crucial stage. A key advantage of this approach relative to continuous PE is that it enables optimization of the individual steps with regard to reactant adsorption, self-limited etching, selectivity relative to other materials, and damage of critical surface layers. In this overview we present basic approaches to ALE of materials, discuss similarities/crucial differences relative to thermal and plasma-enhanced ALD, and then review selected results on ALE of materials aimed at pattern transfer. Furthermore, the overview concludes with a discussion of opportunities and challenges ahead.
Effects of Chromium Picolinate Supplementation on Body Composition, Strength, and Urinary Chromium Loss in Football Players (1994)

The effects of 9 weeks of daily chromium supplementation (200 microgram Cr as picolinate) were investigated in a double-blind design in football players during spring training. Testing was done pre-, mid-, and postsupplementation on the following criterion measures: urinary chromium excretion, girth and skinfold measures, percent body fat and lean body mass, and isometric and dynamic strength. With the exception of 2 variables (of 65 variables analyzed), no significant group by trials interactions were found (based on a repeated measures ANOVA). The two exceptions were unrelated and inconsequential. For 27 of the 38 subjects, average urinary chromium loss at pre was 0.36 microgram/24 hr, whereas it was undetectable (<0.1 microgram/24 hr) for 10 subjects and excessive in 1 subject (2.4 micrograms/24 hr). Subjects receiving chromium supplements demonstrated urinary chromium losses five times greater than those in the placebo group at mid and post. Chromium picolinate supplementation was ineffective in bringing about changes in body composition or strength during a program of intensive weight-lifting training.
Total Synthesis of (±)-Perophoramidine (2004)

The first total synthesis of racemic perophoramidine is described. The key step features the highly stereoselective introduction of the vicinial quaternary centers via base-promoted carbon-carbon bond formation between a 3-alkylindole and a 3-bromo-3-alkylindolin-2-one. This transformation presumably proceeds through a conjugate addition or Diels-Alder cycloaddition of the 3-alkylindole with a 3-alkylindol-2-one intermediate.
A comparative study of single hop WDM interconnections for multiprocessors (1995)

Article Free Access Share on A comparative study of single hop WDM interconnections for multiprocessors Authors: Kiran R. Desai Department of Computer Science, State University of New York, Binghamton, NY Department of Computer Science, State University of New York, Binghamton, NYView Profile , Kanad Ghose Department of Computer Science, State University of New York, Binghamton, NY Department of Computer Science, State University of New York, Binghamton, NYView Profile Authors Info & Claims ICS '95: Proceedings of the 9th international conference on SupercomputingJuly 1995 Pages 154–163https://doi.org/10.1145/224538.224555Published:03 July 1995Publication History 1citation309DownloadsMetricsTotal Citations1Total Downloads309Last 12 Months10Last 6 weeks6 Get Citation AlertsNew Citation Alert added!This alert has been successfully added and will be sent to:You will be notified whenever a record that you have chosen has been cited.To manage your alert preferences, click on the button below.Manage my AlertsNew Citation Alert!Please log in to your account Save to BinderSave to BinderCreate a New BinderNameCancelCreateExport CitationPublisher SiteeReaderPDF
G Protein–Coupled Receptors Revisited: Therapeutic Applications Inspired by Synthetic Biology (2013)

G protein-coupled receptors (GPCRs) mediate the majority of cellular responses to hormones and neurotransmitters within the human body. They have much potential in the emerging field of synthetic biology, which is the rational, systematic design of biological systems with desired functionality. The responsiveness of GPCRs to a plethora of endogenous and exogenous ligands and stimuli make them ideal sensory receptor modules of synthetic gene networks. Such networks can activate target gene expression in response to a specific stimulus. Additionally, because GPCRs are important pharmacological targets of various human diseases, genes encoding their protein/peptide ligands can also be incorporated as target genes of the response output elements of synthetic gene networks. This review aims to critically examine the potential role of GPCRs in constructing therapeutic synthetic gene networks and to discuss various challenges in utilizing GPCRs for synthetic biology applications.
Challenges in building large-scale information retrieval systems (2009)

Building and operating large-scale information retrieval systems used by hundreds of millions of people around the world provides a number of interesting challenges. Designing such systems requires making complex design tradeoffs in a number of dimensions, including (a) the number of user queries that must be handled per second and the response latency to these requests, (b) the number and size of various corpora that are searched, (c) the latency and frequency with which documents are updated or added to the corpora, and (d) the quality and cost of the ranking algorithms that are used for retrieval. In this talk I will discuss the evolution of Google's hardware infrastructure and information retrieval systems and some of the design challenges that arise from ever-increasing demands in all of these dimensions. I will also describe how we use various pieces of distributed systems infrastructure when building these retrieval systems. Finally, I will describe some future challenges and open research problems in this area.
Identification, Cloning, Expression, and Biochemical Characterization of the Testis-specific RNA Polymerase II Elongation Factor ELL3 (2000)

The human ELL gene, which is a frequent target for translocation in acute myeloid leukemia, was initially isolated from rat liver nuclei and found to be an RNA polymerase II elongation factor. Based on homology to ELL, we later cloned ELL2 and demonstrated that it can also increase the catalytic rate of transcription elongation by RNA polymerase II. To better understand the role of ELL proteins in the regulation of transcription by RNA polymerase II, we have initiated a search for proteins related to ELLs. In this report, we describe the molecular cloning, expression, and characterization of ELL3, a novel RNA polymerase II elongation factor approximately 50% similar to both ELL and ELL2. Our transcriptional studies have demonstrated that ELL3 can also increase the catalytic rate of transcription elongation by RNA polymerase II. The C-terminal domain of ELL, which we recently demonstrated to be required and sufficient for the immortalization of myeloid progenitor cells, shares strong similarities to the C-terminal domain of ELL3. ELL3 was localized by immunofluorescence to the nucleus of cells, and Northern analysis indicated that ELL3 is a testis-specific RNA polymerase II elongation factor.
Cost effective traffic grooming in WDM rings (2002)

We provide network designs for optical wavelength division multiplexed (OWDM) rings that minimize overall network cost, rather than just the number of wavelengths needed. The network cost includes the cost of the transceivers required at the nodes as well as the number of wavelengths. The transceiver cost includes the cost of terminating equipment as well as higher-layer electronic processing equipment, and in practice, can dominate over the cost of the number of wavelengths in the network. The networks support dynamic (time varying) traffic streams that are at lower rates (e.g., OC-3, 155 Mb/s) than the lightpath capacities (e.g., OC-48, 2.5 Gb/s). A simple OWDM ring is the point-to-point ring, where traffic is transported on WDM links optically, but switched through nodes electronically. Although the network is efficient in using link bandwidth, it has high electronic and opto-electronic processing costs. Two OWDM ring networks are given that have similar performance but are less expensive. Two other OWDM ring networks are considered that are nonblocking, where one has a wide sense nonblocking property and the other has a rearrangeably nonblocking property. All the networks are compared using the cost criteria of number of wavelengths and number of transceivers.
A combination of roxithromycin and imipenem as an antimicrobial strategy against biofilms formed by Staphylococcus aureus (2001)

We examined the effects of a combination of roxithromycin and imipenem on a biofilm model of Staphylococcus aureus. Treatment with roxithromycin alone and imipenem alone did not decrease the number of viable bacterial cells compared with the control. However, a combination treatment of roxithromycin and imipenem significantly decreased the number of viable bacterial cells on day 8 after inoculation in the in vivo model (P < 0.01). On days 5 and 8 after inoculation, numerous polymorphonuclear leucocytes and macrophages invaded the bacterial clusters in the roxithromycin- and roxithromycin/imipenem-treated groups, but did not invade the control or imipenem-treated groups. The present study indicated that a combination of roxithromycin and imipenem is a potentially effective treatment for S. aureus biofilm-associated skin infections as it can induce the invasion of polymorphonuclear leucocytes into the biofilm.
Dielectrophoresis in Microchips Containing Arrays of Insulating Posts:  Theoretical and Experimental Results (2003)

Dielectrophoresis (DEP), a nonlinear electrokinetic transport mechanism, can be used to concentrate and sort cells, viruses, and particles. To date, microfabricated DEP-based devices have typically used embedded metal electrodes to apply spatially nonuniform, time-varying (AC) electric fields. We have developed an alternative method in which arrays of insulating posts in a channel of a microchip produce the spatially nonuniform fields needed for DEP. Electrodes may be located remotely, allowing operation of the device down to zero frequency (DC) without excessive problems of electrolysis. Applying a sufficiently large electric field across an insulating-post array produces two flow regimes through a competition between electrokinetic flow (combined electrophoresis and electroosmosis) and dielectrophoresis. "Streaming DEP" is observed when DEP dominates diffusion but is overcome by electrokinetic flow. Particles concentrated by DEP forces in areas of electric field extrema travel electrokinetically down the array in flowing streams. In an array of posts, dielectrophoretic forcing within repeated rows adds coherently to produce flowing streams of highly concentrated and rarefied particles. We demonstrate that this reinforcement is a strong function of alignment of the array with respect to the applied electric field and that the particle concentrations can be "enhanced" or "depleted" along columns of posts, enabling a novel class of continuous-flow, selective particle filter/concentrator devices. To our knowledge, this is the first observation of streaming dielectrophoresis. The second regime is "trapping DEP," in which DEP forces dominate over both diffusion and electrokinetic flow, reversibly immobilizing particles on the insulating posts, enabling inexpensive and embedded batch filter/concentrator devices. Devices can be biased electrically to manipulate particles selectively by varying the field strength to vary the relative magnitudes of electrokinetic flow and DEP. Post shapes are contoured easily to control electric field gradients and, hence, DEP behavior. Simple simulations based on similitude of fluid flow and electric field that solve the Laplace equation to obtain fluid velocity have also been developed to predict the dielectrophoretic behavior in an array of posts. These simulations are in excellent agreement with the experimental observations and provide insight into electrokinetic behavior to enable design of dielectrophoretic concentrators and sorters.