gebhart/patrepeval huggingface dataset:
Selecting high-confidence predictions from ordinary differential equation models of biological networks (2008)

Many cellular processes are governed by large and highly-complex networks of chemical interactions and are therefore difficult to intuit. Computational modeling provides a means of encapsulating information about these interactions and can serve as a platform for gaining understanding of the biology and making predictions about cellular response to perturbation. In particular, there has been considerable interest in ordinary differential equation (ODE) models, which have several attractive features: ODEs can describe molecular interactions with mechanistic detail, it is relatively straightforward to implement perturbations, and, in theory, they can predict the concentration and activity of every species as a function of time. However, both the topology and parameters in such models are subject to considerable uncertainty. We explore the ramifications of these sources of uncertainty for making accurate predictions and develop methods of selecting high confidence predictions from uncertain models. In particular, we promote a shift in emphasis from model selection to prediction selection, and use consensus among model ensembles to identify the predictions most likely to be accurate. By constructing decision trees, this consensus can also be used to partition the space of potential perturbations into regions of high and low confidence. We apply our methods to the Fas signaling pathway in apoptosis to satisfy two goals: first, to design a therapeutic cocktail to reduce cell death in the presence of high levels of stimulus, and second, to design experiments that may lead to a better understanding of the biological network. (Copies available exclusively from MIT Libraries, Rm. 14-0551, Cambridge, MA 02139-4307. Ph. 617-253-5668; Fax 617-253-1690.)
The Security of the Extended Codebook (XCB) Mode of Operation. (2007)

The XCB mode of operation was outlined in 2004 as a contribution to the IEEE Security in Storage effort, but no security analysis was provided. In this paper, we provide a proof of security for XCB, and show that it is a secure tweakable (super) pseudorandom permutation. Our analysis makes several new contributions: it uses an algebraic property of XCB’s internal universal hash function to simplify the proof, and it defines a nonce mode in which XCB can be securely used even when the plaintext is shorter than twice the width of the underlying block cipher. We also show minor modifications that improve the performance of XCB and make it easier to analyze. XCB is interesting because it is highly efficient in both hardware and software, it has no alignment restrictions on input lengths, it can be used in nonce mode, and it uses the internal functions of the Galois/Counter Mode (GCM) of operation, which facilitates design re-use and admits multi-purpose implementations.
On the impact of the oxide thickness and reset conditions on activation energy of HfO<inf>2</inf> based ReRAM extracted through disturb measurements (2013)

In this paper, the failure acceleration behavior of HfO <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sub> based ReRAM under constant voltage and high temperature stresses is studied. We extract the activation energy from disturb measurements in the High Resistance State (HRS) for different dielectrics. Various Reset conditions are studied and correlated to the failure mechanism. Low activation energy is obtained in thin dielectric oxides. Based on the hypothesis that the activation energy is linked to the number of oxygen vacancies (i.e. residual conductive filament) in the oxide film, we show that an optimal Reset condition (in terms of voltage stop) can reduce the activation energy in thin HfO <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sub> . On the other hand, the activation energy is higher in thick dielectrics films and it is also tunable thanks to the voltage stop of previous Reset operation.
Curve-fitting with piecewise parametric cubics (1983)

Parametric piecewise-cubic functions are used throughout the computer graphics industry to represent curved shapes. For many applications, it would be useful to be able to reliably derive this representation from a closely spaced set of points that approximate the desired curve, such as the input from a digitizing tablet or a scanner. This paper presents a solution to the problem of automatically generating efficient piecewise parametric cubic polynomial approximations to shapes from sampled data. We have developed an algorithm that takes a set of sample points, plus optional endpoint and tangent vector specifications, and iteratively derives a single parametric cubic polynomial that lies close to the data points as defined by an error metric based on least-squares. Combining this algorithm with dynamic programming techniques to determine the knot placement gives good results over a range of shapes and applications.
A comparison of experience-dependent locomotory behaviors and biogenic amine neurons in nematode relatives of Caenorhabditis elegans (2010)

This study demonstrates that behaviors can differ significantly between species that appear morphologically very similar, and therefore it is important to consider factors, such as ecology of a species in the wild, when formulating hypotheses about the adaptive significance of a behavior. Our results suggest that evolutionary changes in locomotory behaviors are less likely to be caused by changes in neurotransmitter expression of neurons. Such changes could be caused either by subtle changes in neural circuitry or in the function of the signal transduction pathways mediating these behaviors.
Erythropoietin protects cerebrocortical neurons from HIV-1/gp120-induced damage (2004)

Infection with human immunodeficiency virus (HIV)-1 can lead to neurological complications that range from mild cognitive and motor impairment to HIV-associated dementia (HAD). The mechanism of brain injury and dementia remains poorly understood. Interestingly, post mortem brain specimen from HAD patients and transgenic mice expressing the viral envelope protein gp120 present with similar neuropathological signs. The cytokine erythropoietin (EPO) is clinically used to treat anemia but has also been found to prevent neuronal death due to inflammation or excitotoxicity. Here we show that EPO protects cerebrocortical neurons against apoptosis induced by HIV-1/gp120.
The selected lymphocyte antibody method : a novel approach for the generation and genetic analysis of human cytomegalovirus (HCMV) neutralizing monoclonal IgG antibodies (2009)

The generation of human monoclonal antibodies that may be clinically useful is hampered by the lack of an efficient, applicable technology. In this thesis I report the development of the Selected Lymphocyte Antibody Method (SLAM) as an alternative approach to generate monoclonal antibodies and to facilitate the analysis of the human humoral immune response. SLAM technology is based upon the molecular cloning and expression of immunoglobulin heavy and light chain variable region cDNAs from single B lymphocytes that have been identified in a modified hemolytic plaque assay as secreting immunoglobulin which is specific for a target antigen. SLAM technology was first developed in a murine model. Immunoglobulin variable region cDNAs were RT-PCR amplified from single murine B lymphocytes that secreted immunoglobulin which is specific for an epitope found in gpll6 of the Human Cytomegalovirus (HCMV) or in gpl20 of HIV-1. These immunoglobulin variable regions were then cloned and expressed in the context of human immunoglobulin constant regions. The resulting chimeric immunoglobulins were shown to reproduce the same specificity as the "parental" immunoglobulin. To generate human monoclonal antibodies that were specific for gpl 16, peripheral blood B lymphocytes from a single HCMV immune donor were cultured at limiting dilution in the "EL4.B5" B-cell culture system. 107 single B lymphocytes, corrresponding to 34 clones that secreted gpll6-specific immunoglobulin, were identified by hemolytic plaque assay and then isolated by micromanipulation. Immunoglobulin variable region cDNAs were successfully RT-PCR amplified from 29 of the 34 clones. Sequence analysis of the V region cDNAs showed a remarkable restriction in the use of heavy chain variable and joining gene segments as well as restriction in the use of kappa light chain variable and joining gene segments in the associated light chains. Two independent B cell clonotypes were identified based on the utilization of different diversity gene segments in the heavy chain variable regions. Two recombinant monoclonal antibodies (mAbs) that represent each clonotype were expressed and were shown to neutralize HCMV in vitro. Thus, SLAM technology facilitated the generation of two potentially clinically useful antibodies and may be used in the future to generate mAbs against a wide variety of pathogens.
Iperkalemia cronica nei pazienti cardio – renali: q & a per il cardionefrologo pratico (2018)

Cosa intendiamo per iperkalemia? Quali sono i livelli critici di potassiemia?
Modeling Of Display Color Parameters And Algorithmic Color Selection (1986)

A complex and difficult problem for the design of color display systems is the selection of a repertoire of display colors. Color selection is the process in which display visual parameters, operational ambient lighting characteristics, and human visual/perceptual functions are integrated for the purposes of specifying an optimized set of display colors. The object of color selection is not necessarily one of establishing an aesthetic repertoire of display colors, but rather the goal is to select a minimum set of colors that maximize the visual utility and information transfer capabilities of the display. The present paper describes a unique, algorithmic approach to color selection which is based upon psychophysical models of color processing. The selection algorithm, currently implemented on a personal computer, seeks to develop color sets of specified numbers in which the minimum color difference between any pair of colors in the set is maximized. In addition, the computer program combines the selection algorithm with internally derived correction factors for color image field size, ambient lighting characteristics, and anomalous red-green color vision deficiencies of display operators. The program and color selection algorithm together provide an extremely powerful tool for color display system design.
Mucolysis of the colonic mucus barrier by faecal proteinases: Inhibition by interacting polyacrylate (1990)

1. Mucolytic (mucus solubilizing) activity in human faeces has been characterized with both purified human and pig colonic mucin and shown to be mediated by proteolysis. 2. Mucolytic activity was demonstrated by: (i) a drop in mucin viscosity; (ii) a substantial reduction in mucin size, from polymer to degraded subunit, as assessed by Sepharose CL-2B gel filtration; (iii) formation of new N-terminal peptides. 3. Mucolytic activity was also followed in faecal extracts by its proteolytic activity using standard succinyl albumin substrate. Proteolysis extended over the pH range 4.5-11.0. Proteolysis was inhibited at pH 7.5 by soybean trypsin inhibitor and phenylmethanesulphonyl fluoride, suggesting the presence of serine proteinases. 4. The polyacrylate carbomer (934P) inhibited both mucolysis of pig colonic mucin and proteolysis of succinyl albumin. 5. Interaction between the polyacrylate (carbomer 934P) and purified human and pig colonic mucin was demonstrated by a marked synergistic increase in solution viscosity (360% above control). 6. The results demonstrate the presence of a mucolytic activity in the human colonic lumen that has the potential to degrade the mucus barrier, and that polyacrylates inhibit this mucolysis and interact to strengthen the colonic mucus barrier. Polyacrylates may therefore have therapeutic potential in inflammatory bowel disease where luminal proteolytic activity can be raised.
Influence of Digoxin Immune Fab Therapy and Renal Dysfunction on the Disposition of Total and Free Digoxin (1993)

Elimination of digoxin following Fab therapy is prolonged in digoxin-toxic patients with renal dysfunction. In addition, rebound of free digoxin is delayed in anephric patients. Monitoring free digoxin following the administration of Fab may be of value in selected patients to guide additional Fab dosing, confirm possible rebound toxicity, or guide the reinitiation of digoxin therapy.
ActiveAxADD: Toward non‐parametric and orientationally invariant axon diameter distribution mapping using PGSE (2019)

Laplacian regularization solves the ill-posedness regarding the intra axonal compartment. ActiveAx<sub>ADD</sub> can potentially provide non-parametric and orientationally invariant ADDs from isolated intra-axonal signals. However, further work is required before ActiveAx<sub>ADD</sub> can be applied to real data containing extra-axonal contributions, as disentangling the 2 compartment appears to be an overlooked challenge that affects microstructure imaging methods in general.
Operation-valency and the cost of coordination (2003)

This paper introduces operation-valency, a generalization of the valency proof technique originated by Fischer, Lynch, and Paterson. By focusing on critical events that influence the return values of individual operations rather then on critical events that influence a protocol's single return value, the new technique allows us to derive a collection of realistic lower bounds for lock-free implementations of concurrent objects such as linearizable queues, stacks, sets, hash tables, shared counters, approximate agreement, and more. By realistic we mean that they follow the real-world model introduced by Dwork, Herlihy, and Waarts, counting both memory-references and memory-stalls due to contention, and that they allow the combined use of read, write, and read-modify-write operations available on current machines.By using the operation-valency technique, we derive an Ω(√n) non-cached shared memory accesses lower bound on the worst-case time complexity of lock-free implementations of objects in Influence(n), a wide class of concurrent objects including all of those mentioned above, in which an individual operation can be influenced by all others.We also prove the existence of a fundamental relationship between the space complexity, latency, contention, and "influence level" of any lock-free object implementation. Our results are broad in that they hold for implementations combining read/write memory and any collection of read-modify-write operations, and in that they apply even if shared memory words have unbounded size.
ChemInform Abstract: Transparent, Conducting, Amorphous Oxides: Effect of Chemical Composition on Electrical and Optical Properties of Cadmium Germanates. (1997)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
Characterization and analysis of multi-hop wireless MIMO network throughput (2007)

Use of multiple antennas or MIMO has great potential for enhancing the throughput of multi-hop wireless networks via spatial reuse and/or spatial division multiplexing. In this paper, we characterize and analyze the maximum achievable throughput in multi-hop wireless MIMO networks under three MIMO protocols, spatial reuse only (SRP), spatial multiplexing only (SMP), and spatial reuse & multiplexing (SRMP), each of which enhances throughput via a different way of exploiting the MIMO's potential. We show via extensive simulation that as the number of antennas increases, the maximum achievable throughput first rises and then flattens out asymptotically under SRP, while it increases almost linearly under SMP or SRMP. We evaluate the effects of several network parameters on this achievable throughput. We also demonstrate how these results can be used by designers to determine the optimal parameters of multi-hop wireless MIMO networks.
Ultrafast All-Optical Switching Based on Inter-Subband Transition in GaN/AlGaN and InGaAs/AlAsSb Multiple Quantum Wells (2000)

Get PDF Email Share Share with Facebook Tweet This Post on reddit Share with LinkedIn Add to CiteULike Add to Mendeley Add to BibSonomy Get Citation Copy Citation Text Osamu Wada, Haruhiko Yoshida, Teruo Mozume, Arup Neogi, Nikolai Gergiev, Tomoyuki Akiyama, Kiyoshi Asakawa, Nobuo Suzuki, Norio Iizuka, Kei Kaneko, Takashi Asano, and Susumu Noda, "Ultrafast All-Optical Switching Based on Inter-Subband Transition in GaN/AlGaN and InGaAs/AlAsSb Multiple Quantum Wells," Optics & Photonics News 11(12), 45-46 (2000) Export Citation BibTex Endnote (RIS) HTML Plain Text Citation alert Save article
CO Sensitive Pt/SnO2 Diode Type Gas Sensor (1987)

Abstract A Pt(sputtered film)/SnO2(disc) diode was found to respond to small amounts of CO in air at lower temperatures below 100 °C, while no response was observed for CH4 and C3H8. The CO sensitivity of the diode gave a maximum at 90 °C, which was about three times as high as the sensitivity to H2. The 50% response time of the sensor to 1000 ppm CO was about 1 min.
Periostin promotes chronic allergic inflammation in response to Th2 cytokines (2012)

Allergic inflammation triggered by exposure of an allergen frequently leads to the onset of chronic inflammatory diseases such as atopic dermatitis (AD) and bronchial asthma. The mechanisms underlying chronicity in allergic inflammation remain unresolved. Periostin, a recently characterized matricellular protein, interacts with several cell surface integrin molecules, providing signals for tissue development and remodeling. Here we show that periostin is a critical mediator for the amplification and persistence of allergic inflammation using a mouse model of skin inflammation. Th2 cytokines IL-4 and IL-13 stimulated fibroblasts to produce periostin, which interacted with αv integrin, a functional periostin receptor on keratinocytes, inducing production of proinflammatory cytokines, which consequently accelerated Th2-type immune responses. Accordingly, inhibition of periostin or αv integrin prevented the development or progression of allergen-induced skin inflammation. Thus, periostin sets up a vicious circle that links Th2-type immune responses to keratinocyte activation and plays a critical role in the amplification and chronicity of allergic skin inflammation.
Event based control of stochastic linear systems (2015)

In this paper, an event based control strategy for linear systems under stochastic disturbances is presented where the control input generator generates a control which tries to mimic a state feedback control between two successive events. The control input is generated in such a way that the error between the state of this system and the continuous state feedback system is bounded. The event generator triggers an event based on this error and the control input generator modifies its control input in such a way that it corroborates that the error generated up to this triggering instance is reduced to zero and thus it does not have any effect on the future states regardless of the stability of the plant. It is also shown that under this event triggering mechanism, the control input generator generates the control in such a way that the error bound could be made arbitrarily small.
The Engineering Implications of Code Maintenance in Practice (2022)

Allowing developers to move fast when evolving and maintaining low-latency, large-scale distributed systems is a challenging problem due to i) sheer system complexity and scale, ii) degrading code quality, and iii) difficulty of performing reliable rapid change management while the system is in production. Addressing these problems has many benefits to increase system developer efficiency, reliability, performance, as well as code maintenance. In this paper, we present a real-world case study of an architectural refactoring project within an industrial setting. The system in scope is our codenamed ItemIndexer delivery system (I2DS), which is responsible for processing and delivering a large number of items at rapid speed to billions of users in real time. I2DS is running in production, refactored live over a period of 9 months, and assessed through impact validation studies that show a 42% improvement in developer efficiency, 87% improvement in reliability, 20% increase in item scoring, a 10% increase in item matching, and 14% CPU savings.
Experimental investigation of time-reversal of photo-acoustic waves (2006)

Ultrasound focusing through complex media can be achieved using time-reversal techniques. These techniques make use of back-propagating ultrasonic waves generated by localized sources. Such sources generally consist of high acoustic contrasts echoing ultrasonic waves generated by an incident ultrasonic field, or directly by point-like transducers inserted at the desired focusing location. In this work, we experimentally investigate time-reversal of acoustic waves generated by photo-acoustic emission. A frequency-doubled Q-switched Nd:YAG laser was used to illuminate phantom with 5-ns laser pulses. A 128-element ultrasonic transducer array, with a center frequency of 1.5 MHz, was used to detect acoustic waves generated by optically absorbing targets suspended in water. A dedicated 32-channel electronics was used to time-reverse and re-emit the detected ultrasonic field. Gel spheres dyed with India ink (diameter approximately 1-2 mm)illuminated by the laser beam were used to generate the photo-acoustic waves. Time-reversal of the detected field was performed to focus ultrasound in the presence of highly defocusing media in front of the transducer array. We demonstrate how this allows correcting for the aberration in order to provide good quality images in the isoplanetic region surrounding the photo-acoustic source.
MMSE Combining Scheme with Subblock Noise Covariance Matrix for Fractional Sampling-OFDM Receivers (2008)

A diversity scheme with fractional sampling (FS) in OFDM receivers is investigated recently. When a sharp filter is employed, the correlation of noise samples among the adjacent subcarriers increases, and the performance of this scheme is deteriorated. Therefore, low-complexity subcarrier based MMSE combining scheme with the subblock of the noise covariance matrix is proposed in this paper. Numerical results through computer simulation show that the MMSE combining scheme proposed in this paper can outperforms a conventional MRC scheme and a subcarrier based MMSE combining scheme, when the sharp filter is employed.
Layer 2 Virtual Private Networks Using BGP for Auto-Discovery and Signaling (2012)

Layer 2 Virtual Private Networks (L2VPNs) based on Frame Relay or ATM
circuits have been around a long time; more recently, Ethernet VPNs,
including Virtual Private LAN Service, have become popular.
Traditional L2VPNs often required a separate Service Provider
infrastructure for each type and yet another for the Internet and IP
VPNs. In addition, L2VPN provisioning was cumbersome. This document
presents a new approach to the problem of offering L2VPN services
where the L2VPN customer's experience is virtually identical to
that offered by traditional L2VPNs, but such that a Service Provider
can maintain a single network for L2VPNs, IP VPNs, and the Internet,
as well as a common provisioning methodology for all services. This
document is not an Internet Standards Track specification; it is
published for informational purposes.
Effect and mechanism of propofol in hepatic ischemia/reperfusion injury of rat. (2017)

Propofol protects hepatic I/R injury partly by reducing apoptosis and reducing the release of pro-inflammatory cytokines, which is possibly involved in the modulation of the PI3K/AKT/mTOR signaling pathway. All these data suggest that propofol may play certain positive roles in protecting the liver from I/R injury.