gebhart/patrepeval huggingface dataset:
Illuminating the mechanistic roles of enzyme conformational dynamics (2007)

Many enzymes mold their structures to enclose substrates in their active sites such that conformational remodeling may be required during each catalytic cycle. In adenylate kinase (AK), this involves a large-amplitude rearrangement of the enzyme's lid domain. Using our method of high-resolution single-molecule FRET, we directly followed AK's domain movements on its catalytic time scale. To quantitatively measure the enzyme's entire conformational distribution, we have applied maximum entropy-based methods to remove photon-counting noise from single-molecule data. This analysis shows unambiguously that AK is capable of dynamically sampling two distinct states, which correlate well with those observed by x-ray crystallography. Unexpectedly, the equilibrium favors the closed, active-site-forming configurations even in the absence of substrates. Our experiments further showed that interaction with substrates, rather than locking the enzyme into a compact state, restricts the spatial extent of conformational fluctuations and shifts the enzyme's conformational equilibrium toward the closed form by increasing the closing rate of the lid. Integrating these microscopic dynamics into macroscopic kinetics allows us to model lid opening-coupled product release as the enzyme's rate-limiting step.
Towards detection of modified firmware on solid state drives via side channel analysis (2018)

Modern embedded devices are getting cheaper, easier to produce, and smarter. These smarter devices are able to store and process data locally at a scale that would have been infeasible until recent years. Functions that used to be performed on more powerful, dedicated systems and servers with security features are now being pushed to these unsecured commercial embedded devices. In the Internet of Things (IoT) space, this problem is manifesting itself with almost daily reports of compromise of network-connected embedded systems. While IoT device insecurity makes for attention-grabbing headlines, there are entire classes of embedded devices which do not have direct Internet connectivity for which security is still vitally important.
Aminophylline fails to reverse conscious sedation with midazolam in dentistry. (1986)

A double blind, randomized crossover study investigated whether aminophylline reverses the conscious sedation with midazolam in dentistry to result in quicker clinical recovery than when midazolam is used alone. Twenty-five patients between 17-30 years of age (ASA Grade 1) were sedated with midazolam for bilateral third molar extractions, one side being operated on one visit. Aminophylline or normal saline was given at the end of the surgical procedure on one visit and the alternative during the second visit. No significant difference in recovery was noted with either solution, suggesting that aminophylline does not produce significant reversal of sedation to achieve quicker clinical recovery. The majority of patients preferred to be alert following the operation while some (N = 5) wished to be drowsy, indicating the necessity to question the patient as to preference before deciding to administer a reversal agent.
Design and wideband spurious performance prediction for a mixed-resonator combline/TE01-mode DR filter using FDTD (1999)

A four-pole mixed-resonator filter comprised of combline resonators and TE01-mode dielectric resonators (DRs) has been designed using the FDTD method so that only minimal tuning of the prototype is required. Resonant frequencies, interresonator coupling through rectangular slots, and unloaded Q-values are calculated for the DR and the combline resonator, and they compare extremely well with results available in the literature. S-parameters are computed over a large bandwidth to validate the improved spurious performance of the filter, and they give excellent agreement with measured results. ©1999 John Wiley & Sons, Inc. Microwave Opt Technol Lett 23: 266–273, 1999.
Synthesis of crocin, picrocrocin and safranal by saffron stigma-like structures proliferated in vitro. (1987)

Crocin, picrocrocin, and safranal as the major secondary metabolites are important for the high quality of spice saffron. Crocin and picrocrocin were detected in stigma-like structures proliferated in vitro. Safranal appeared after heat treatment. The contents and relative ratio of these substances in the stigma-like structures were similar to those in intact young stigmas, indicating that these stigma-like structures showed not only morphological but also biochemical similarity to the intact stigmas.
Aroma production by cultures of Ceratocystis moniliformis (1976)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTAroma production by cultures of Ceratocystis moniliformisElaine Lanza, Khee Hwee Ko, and James K. PalmerCite this: J. Agric. Food Chem. 1976, 24, 6, 1247–1250Publication Date (Print):November 1, 1976Publication History Published online1 May 2002Published inissue 1 November 1976https://pubs.acs.org/doi/10.1021/jf60208a019https://doi.org/10.1021/jf60208a019research-articleACS PublicationsRequest reuse permissionsArticle Views133Altmetric-Citations53LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-Alertsclose Get e-Alerts
Using A Web-Based Supply Chain Management Simulation As An Experiential Learning Tool Across The Business Curriculum (2005)

A web based version of the common “Beer Distribution Game” that facilitates experiential learning was developed and tested for use across the business curriculum. While the fundamental elements of the original paper based game were preserved, the web-based on-line multiplayer version offers refinements to game play, administration and debriefing that allow more focus on the learning experience and open possible applications beyond the traditional one-time demonstration of the bullwhip effect. The web-based supply chain management simulation was tested and refined in Strategic Management courses and Integrated Business Curriculum courses at two widely separated universities. Students responded favorably to the on-line simulation and were very willing to reflect on what they learned about how they made decisions, how worked under conditions of uncertainty, how they treated information and how they worked in the supply chain environment. The simulation can be used to demonstrate systems thinking and various other concepts throughout the business school curriculum including courses in Operations Management, Strategy, Information Systems, and Marketing.
Multi-modal surface registration for markerless initial patient setup in radiation therapy using microsoft's Kinect sensor (2011)

In radiation therapy, prior to each treatment fraction, the patient must be aligned to computed tomography (CT) data. Patient setup verification systems based on range imaging (RI) can accurately verify the patient position and adjust the treatment table at a fine scale, but require an initial manual setup using lasers and skin markers. We propose a novel markerless solution that enables a fully-automatic initial coarse patient setup. The table transformation that brings template and reference data in congruence is estimated from point correspondences based on matching local surface descriptors. Inherently, this point-based registration approach is capable of coping with gross initial misalignments and partial matching. Facing the challenge of multi-modal surface registration (RI/CT), we have adapted state-of-the-art descriptors to achieve invariance to mesh resolution and robustness to variations in topology. In a case study on real data from a low-cost RI device (Microsoft Kinect), the performance of different descriptors is evaluated on anthropomorphic phantoms. Furthermore, we have investigated the system's resilience to deformations for mono-modal RI/RI registration of data from healthy volunteers. Under gross initial misalignments, our method resulted in an average angular error of 1.5° and an average translational error of 13.4 mm in RI/CT registration. This coarse patient setup provides a feasible initialization for subsequent refinement with verification systems.
Effect of chromium source on tissue concentration of chromium in pigs1,2 (2008)

The concentration of Cr in several tissues in response to high-level, short-term supplementation was used to determine the relative bioavailability among 4 organic Cr sources and to assess the relative safety of high levels of supplementation. Crossbred pigs (n = 40; mean BW = 48.1 +/- 0.9 kg) were allotted to 5 diets: a control diet with no added Cr, or 5,000 microg/kg of Cr from Cr tripicolinate (CrTP), Cr propionate (CrPrp), Cr methionine (CrMet), or Cr yeast (CrY). Twenty gilts were housed individually and barrows were housed in pairs. Average duration of feeding before slaughter was 75 d. For the total experiment, pigs fed the unsupplemented diet had less ADG than pigs fed CrY (P < 0.05). Serum clinical chemistry values, obtained during the final week of the experiment, demonstrated few effects with no responses that would raise concern about metabolic changes in response to the Cr sources. The effects of the forms of Cr fed on carcass measurements and meat quality were also minimal. All Cr sources reduced cooler shrink (P < 0.05) and most resulted in some meat color change on d 1 postslaughter. For tissue Cr content, 4 of 5 tissues (bone, kidney, liver, and ovary) were increased (P < 0.05) in Cr content by supplementation with CrTP and CrMet, whereas only 2 tissues (bone and kidney) were increased (P < 0.05) by CrY, and none were increased by CrPrp. In all tissues of response, CrTP exceeded CrMet and CrMet exceeded CrY. Comparing the relative increase in tissue Cr for all responsive tissues (bone, kidney, liver, and ovary) gave a range of responses, for which the mean bioavailability relative to CrTP across tissues was 13.1% for CrPrp (0.2 to 19.0%), 50.5% for CrMet (36.2 to 79.1%), and 22.8% for CrY (2.5 to 47.9%). In summation, these results show very clear Cr effects on multiple tissues, which is conclusive evidence of absorption and deposition. The lack of a negative response in growth performance, carcass measures, and clinical chemistry at the increased quantities used herein provides assurance that normal quantities of addition are extremely safe.
Impaired regulation of NF-κB and increased susceptibility to colitis-associated tumorigenesis in CYLD-deficient mice (2006)

Cylindromatosis (CYLD) is a deubiquitinating enzyme that is altered in patients with familial cylindromatosis, a condition characterized by numerous benign adnexal tumors. However, the regulatory function of CYLD remains unsettled. Here we show that the development of B cells, T cells, and myeloid cells was unaffected in CYLD-deficient mice, but that the activation of these cells with mediators of innate and adaptive immunity resulted in enhanced NF-kappaB and JNK activity associated with increased TNF receptor-associated factor 2 (TRAF2) and NF-kappaB essential modulator (NEMO) ubiquitination. CYLD-deficient mice were more susceptible to induced colonic inflammation and showed a dramatic increase in the incidence of tumors compared with controls in a colitis-associated cancer model. These results suggest that CYLD limits inflammation and tumorigenesis by regulating ubiquitination in vivo.
Excimer laser enhanced nitridation of silicon substrates (1984)

Silicon direct nitridation has been successfully done using purified ammonia gas and an ArF excimer laser (λ=193 nm). Direct nitride films were grown at a substrate temperature of 400 °C and a laser pulse energy of 15 mJ/pulse cm2. As far as Auger signal intensities are concerned, there is little difference between the excimer laser enhanced nitrided films grown at 400 °C and thermally nitrided films grown at 1000 °C. The maximum film thickness grown is limited to 2.5 nm at 400 °C by diffusion of nitridation species across the grown film. The temperature rise on the substrate surface irradiated by the laser was calculated and found to be around 50 °C. Therefore, the thermal effect of the laser irradiation is of little significance in this experiment. The photochemically dissociated products of ammonia molecules were investigated by a quadrupole mass analyzer. The photochemically generated NH2 radicals seem to enhance the nitridation.
Implementation and testing of an automated EST processing and similarity analysis system (2002)

Expressed sequence tag (EST) sequencing projects are being undertaken in an effort to identify the function of as many genes as possible from entire genomes. Putative function can be determined by analyzing the similarity of the ESTs to sequences in the public databases. We are involved in a long-term project to research and develop database technology to store and analyze ESTs for Arabidopsis thaliana. The massive amounts of ESTs being produced through automated sequencing technologies necessitates the automated processing and similarity analysis of the ESTs. This paper describes a complete software system that takes ESTs from a sequencing machine, analyzes them for quality, and searches in public databases of previously known sequences. Automating the processing and analysis of the several thousand ESTs produced to date by the Michigan State University, Arabidopsis cDNA Sequencing Project has improved the quality of the EST data and the speed at which ESTs can be entered in the public databases.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Differentially private sequential data publication via variable-length n-grams (2012)

Sequential data is being increasingly used in a variety of applications. Publishing sequential data is of vital importance to the advancement of these applications. However, as shown by the re-identification attacks on the AOL and Netflix datasets, releasing sequential data may pose considerable threats to individual privacy. Recent research has indicated the failure of existing sanitization techniques to provide claimed privacy guarantees. It is therefore urgent to respond to this failure by developing new schemes with provable privacy guarantees. Differential privacy is one of the only models that can be used to provide such guarantees. Due to the inherent sequentiality and high-dimensionality, it is challenging to apply differential privacy to sequential data. In this paper, we address this challenge by employing a variable-length n-gram model, which extracts the essential information of a sequential database in terms of a set of variable-length n-grams. Our approach makes use of a carefully designed exploration tree structure and a set of novel techniques based on the Markov assumption in order to lower the magnitude of added noise. The published n-grams are useful for many purposes. Furthermore, we develop a solution for generating a synthetic database, which enables a wider spectrum of data analysis tasks. Extensive experiments on real-life datasets demonstrate that our approach substantially outperforms the state-of-the-art techniques.
Utilization of the t* Partial Switching Properties of Ferroelectrics in Memory Devices (1965)

Some ferroelectric materials exhibit a transition from stable to unstable partial switching at a critical pulsewidth t*. Schemes are proposed for utilizing this t* effect for coincident and successive addressing of a matrix memory, for a nondestructive readout from a matrix and for the simplification of a ferroelectric-electroluminescent display system. The practical limitations on these schemes are considered in terms of measurements made of t* in single crystal triglycine sulphate (TGS). Though the t* effect was observed to be a sharp rather than an absolute transition in the switching properties, the degree of sharpness was, however, sufficiently high to make t* devices feasible. For example, a coincidentally addressed t* TGS matrix can tolerate 105 disturb pulses. By comparison, a conventional matrix designed around the pseudocoercive field of TGS can only tolerate 10 disturbs. Even more impressive is that for the ``nondestructive'' type of readout operation 109 readouts can be made from a t* matrix before the stored information has to be rewritten.
Coordinated beamforming in clustered HetNets: System design and performance evaluation (2014)

In this paper, we consider interference issues arising in HetNets where the small-cells are deployed in closely-spaced clusters. Such dense deployments pose an important challenge for scaling throughput proportional to the number of cells, since inter-cell interference becomes a key bottleneck for achieving high capacity. We examine key design issues around the use of coordinated beamforming (CBF) strategies for mitigating inter-small-cell interference in such clustered layouts. In particular, we show that system planning of the sounding reference signal (SRS), along with multi-user channel estimation approaches, are critical to realize the benefits of CBF. We also develop key notions of beneficiary sets and co-operative clusters for enabling such interference mitigation in cellular networks. Through extensive and detailed system simulations, we showcase the benefits of the proposed system designs for two use cases: (1) a dense urban Micro-cellular deployment, and (2) a clustered small-cell Stadium deployment. System parameter optimization of SRS power control and co-operative cluster size are also developed. Significant capacity gains are observed for both these deployments using the proposed system design in clustered small-cell topologies.
Neural differentiation of human embryonic stem cells (2008)

Availability of human embryonic stem cells (hESC) has enhanced human neural differentiation research. The derivation of neural progenitor (NP) cells from hESC facilitates the interrogation of human embryonic development through the generation of neuronal subtypes and supporting glial cells. These cells will likely lead to novel drug screening and cell therapy uses. This review will discuss the current status of derivation, maintenance and further differentiation of NP cells with special emphasis on the cellular signaling involved in these processes. The derivation process affects the yield and homogeneity of the NP cells. Then when exposed to the correct environmental signaling cues, NP cells can follow a unique and robust temporal cell differentiation process forming numerous phenotypes.
A Microfluidic Platform for Characterization of Protein–Protein Interactions (2009)

Traditionally, expensive and time consuming techniques such as mass spectrometry and Western Blotting have been used for characterization of protein-protein interactions. In this paper, we describe the design, fabrication, and testing of a rapid and inexpensive sensor, involving the use of microelectrodes in a microchannel, which can be used for real-time electrical detection of specific interactions between proteins. We have successfully demonstrated detection of target glycoprotein-glycoprotein interactions, antigen-antibody interactions, and glycoprotein-antigen interactions. We have also demonstrated the ability of this technique to distinguish between strong and weak interactions. Using this approach, it may be possible to multiplex an array of these sensors onto a chip and probe a complex mixture for various types of interactions involving protein molecules.
25-Hydroxyvitamin D <sub>3</sub> 1α-Hydroxylase and Vitamin D Synthesis (1997)

Renal 25-hydroxyvitamin D3 1alpha-hydroxylase [1alpha(OH)ase] catalyzes metabolic activation of 25-hydroxyvitamin D3 into 1alpha, 25-dihydroxyvitamin D3 [1alpha,25(OH)2D3], an active form of vitamin D, and is inhibited by 1alpha,25(OH)2D3. 1alpha(OH)ase, which was cloned from the kidney of mice lacking the vitamin D receptor (VDR-/- mice), is a member of the P450 family of enzymes (P450VD1alpha). Expression of 1alpha(OH)ase was suppressed by 1alpha, 25(OH)2D3 in VDR+/+ and VDR+/- mice but not in VDR-/- mice. These results indicate that the negative feedback regulation of active vitamin D synthesis is mediated by 1alpha(OH)ase through liganded VDR.
High Sensitivity MEMS Ultrasound Arrays by Lateral Ferroelectric Polarization (2000)

This paper discusses the design of advanced micromachined ferroelectric ultrasound transducers for use at 3 MHz. 16 X 16 arrays of resonant monomorph sensors have been constructed, with sol-gel PZT as the active ferroelectric layer deposited on insulating layers of ZrOz and SiOz. A novel in-plane polarization of the PZT is used to maximize sensitivity, while trading off reduced output capacitance to match the CMOS buffer electronics. This results in about 30 dB improved sensitivity compared to conventional polarizing across the thickness of the PZT layer. Fluid-filled through wafer holes are used as an acoustic matching network to achieve resonance at both 1 and 3 MHz. A lumped element equivalent circuit model is presented, as well as Finite Element Analysis results. Performance predictions for projector efficiency and receive response are given. Test results are presented including transmit response, receive sensitivity, and frequency response.
Wideband Circularly Polarized Dielectric Resonator Antenna (2007)

A circularly polarized quadruple strip feed cylindrical dielectric resonator antenna utilizing a pair of 90deg hybrid couplers is investigated experimentally. The antenna is shown to deliver an impedance bandwidth (S <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">11</sub> < -10 dB) of 34.5%, from 1.75 to 2.48 GHz, and an axial-ratio bandwidth (AR < 3 dB) of 25.9%, from 1.65 to 2.14 GHz. The gain and radiation patterns are found to be stable within the passband.
A highly stereoselective synthesis of 3-hydroxy-1-aryltetralin lignans based on the stereoselective hydroxylation of α,β-dibenzyl-γ-butyro-lactones: the first synthesis of (±)-cycloolivil (1996)

Lignans of the 3-hydroxy-1-aryltetralin series 1 and 2 have been synthesised in good yields in a highly diastereoselective manner. The stereochemistry at C-1, C-2 and C-3 of 1 and 2 was completely controlled by an electrophilic addition of oxodiperoxymolybdenum(pyridine)hexamethylphosphoric triamide (MoOPH) to the metal enolates of α,β-disubstituted γ-butyrolactones 4 and the Friedel–Crafts type intramolecular cyclisation of 3. This method was applied to the stereoselective synthesis of (±)-cycloolivil 1e.
Zur Energie‐Ersparnis bei der Chloralkali‐Elektrolyse mit Hilfe einer reversiblen Wasserstoff‐Abscheidungs‐ oder Sauerstof‐Lösungselektrode als Hauptkathode (1962)

Abstract Die Möglichkeiten der Energie‐Ersparnis bei der Chloralkali‐Elektrolyse durch Senkung der Zellspannung werden erläutert. Die in den letzten Jahren entwickelten Wasserstoff‐ und Sauerstoff‐Elektroden großer Reversibilität ermöglichen eine elektrochemische Nutzung der Amalgam‐Energie bzw. eine Herabsetzung der Überspannung beim Diaphragma‐Verfahren. Die technischen Probleme insbesondere bei der Serienschaltung von Primärzelle und der als galvanisches Element wirkenden Sekundärzelle werden diskutiert.