gebhart/patrepeval huggingface dataset:
Replacement of a Phenylalanine by a Tyrosine in the Active Site Confers Fructose-6-phosphate Aldolase Activity to the Transaldolase of Escherichia coli and Human Origin (2008)

Based on a structure-assisted sequence alignment we designed 11 focused libraries at residues in the active site of transaldolase B from Escherichia coli and screened them for their ability to synthesize fructose 6-phosphate from dihydroxyacetone and glyceraldehyde 3-phosphate using a newly developed color assay. We found one positive variant exhibiting a replacement of Phe(178) to Tyr. This mutant variant is able not only to transfer a dihydroxyacetone moiety from a ketose donor, fructose 6-phosphate, onto an aldehyde acceptor, erythrose 4-phosphate (14 units/mg), but to use it as a substrate directly in an aldolase reaction (7 units/mg). With a single amino acid replacement the fructose-6-phosphate aldolase activity was increased considerably (>70-fold compared with wild-type). Structural studies of the wild-type and mutant protein suggest that this is due to a different H-bond pattern in the active site leading to a destabilization of the Schiff base intermediate. Furthermore, we show that a homologous replacement has a similar effect in the human transaldolase Taldo1 (aldolase activity, 14 units/mg). We also demonstrate that both enzymes TalB and Taldo1 are recognized by the same polyclonal antibody.
Buffer Management Policies for DTN Applications with Different QoS Requirements (2015)

Delay and Disruption Tolerant Networks (DTNs) have been proposed for challenging environments where the instability or lack of end-to-end paths is the rule rather than the exception. In this context, the principle of store-carry-and forward is used to sustain data sessions under intermittent connectivity, and data replication to increase the probability of on-time delivery. However, these techniques create the need for efficient scheduling and buffer management techniques, as the data load is generally larger than the amount of the available resources (i.e. bandwidth per communication opportunity, and buffer storage). A number of recent schemes have been proposed to make forwarding decisions that improve or even optimize the usage of these resources, in one way or another. Nevertheless, the majority of these schemes consider application sessions (and thus data messages) of equal importance. Furthermore, the few proposals that consider different traffic classes, do so in a somewhat "ad-hoc" manner, failing to provide real QoS guarantees. To this end, in this paper we formulate the problem of maximizing the network performance, in a limited resource network, subject to constraints corresponding to distinct QoS requirements (e.g., delivery probability) for each application class. Based on this formulation, we propose a distributed algorithm which: (i) guarantees that the individual QoS constraints are satisfied, when this is feasible given the amount of available resources, and (ii) allocates any remaining resources optimally, so as to maximize the desired performance metric. Simulation results, based on synthetic and realistic mobility scenarios, support our theoretical claims and further show that our policy outperforms other existing QoS prioritization schemes.
Synthesis and Their Antitumor Activity of 1, 4-Benzoquinone Derivatives (1980)

The 1, 4-benzoquinone derivatives I, II and III (Chart 1) were synthesized. In the synthesis of I (m=0), a new reaction was found, in which 1, 4-benzoquinones reacted with 1-trimethylsilyl-4-substituted-2, 3-dioxopiperazine derivatives to yield 2-(4-substituted-2, 3-dioxo-1-piperazinyl) hydroquinones. In this reaction, the substituent effect was investigated and the reaction mechanism was discussed. Compound II of this series showed antitumor activity against L1210 and S180.
Threshold logic circuit design of parallel adders using resonant tunneling devices (2000)

Resonant tunneling devices and circuit architectures based on monostable-bistable transition logic elements (MOBILEs) are promising candidates for future nanoscale integration. In this paper, the design of clocked MOBILE-type threshold logic gates and their application to arithmetic circuit components is investigated. The gates are composed of monolithically integrated resonant tunneling diodes and heterostructure field-effect transistors. Experimental results are presented for a programmable NAND/NOR gate. Design related aspects such as the impact of lateral device scaling on the circuit performance and a bit-level pipelined operation using a four phase clocking scheme are discussed. The increased computational functionality of threshold logic gates is exploited in two full adder designs having a minimal logic depth of two circuit stages. Due to the self-latching behavior the adder designs are ideally suited for an application in a bit-level pipelined ripple carry adder. To improve the speed a novel pipelined carry lookahead addition scheme for this logic family is proposed.
One-way edge mode in a magneto-optical honeycomb photonic crystal (2009)

We study the edge states in two-dimensional photonic crystals arising from a singular point in $k$ space at which two dispersion surfaces intersect. The zigzag edge states in a honeycomb lattice for TM polarization are analogous to the electronic ones in graphene nanoribbons. Electromagnetic modes at the zigzag edges of such photonic crystals consisting of ferrite rods are allowed to propagate only along one direction. The one-way propagation is insensitive to imperfections on the zigzag edge.
Virtual proteomics of pathology specimens: Mass spectrometric detection of multiple proteins in formalin-fixed paraffin-embedded tissue. (2007)

A9 The goal of personalized medicine is to deliver the best treatment to the patient. In clinical oncology, proteomics can evaluate differential expression and post-translational modifications of proteins in healthy and diseased states. Given that many novel anticancer therapies are designed to target tumor proteins, proteomic analysis of tumor tissue should complement conventional genomic or immunohistochemical (IHC) analyses in delivering information relevant for diagnosis, prognosis and predicting tumor response to treatment.  Formalin fixation and paraffin embedding (FFPE) of diagnostic specimens is the preparation method of choice for pathological assessment. We undertook this study to identify differentially expressed proteins in FFPE specimens from various pathological states of breast tissue and to compare expression of select known tumor biomarkers in normal and diseased states. Tissue was extracted using an improved protocol that results in enhanced protein yields. We examined FFPE archival breast tissue specimens including 23 normal samples from reduction mammoplasties (control group), 21 fibroadenomas, 25 node negative breast cancers, and 22 node positive breast cancers (test group). Histological subtype and the expression status of estrogen and progesterone receptors, HER2, p53, and Ki-67 were evaluated in the breast cancer specimens. Ten micron FFPE sections were microdissected, de-paraffinized, digested with trypsin, and analyzed by liquid chromatography electrospray ionization mass spectrometry (LC-ESI MS).  We developed a novel strategy for MS data mining referred to as “virtual proteomics”, which encompassed diverse mathematical operations on data sets. First, we identified differentially expressed mass/time signals, which were subjected to on- and off-line MS analysis. Data were searched against on-line protein data libraries for the identifications of likely target proteins based on the observed peptide sequences (discovery mode). In parallel, we interrogated the MS data with virtual probes derived from theoretical tryptic digests of known cancer biomarkers (hypothesis testing mode). In the discovery mode, we identified over 5 proteins that were present in >50% specimens in >1 test groups with >10-fold relative differences in expression in comparison with the controls, Mowse scores of >70 (p
Scheme for x-ray tracing in capillary optics (1994)

A set of trigonometric equations is derived for deterministic x-ray tracing in capillaries. A variety of capillary shapes is encompassed by this approach. The resulting reflectivity coefficients, gain factors, and angular beam divergence are determined. The results can also be applied to the case of neutron and proton guiding in narrow pipes.
Recovery of Nonrigid Curvilinear Objects Using Optical Flow (1989)

Abstract The kinetic depth effect which recognizes a 3‐D structure from a 2‐D information is explained from an algorithmic viewpoint among other human vision functions such as binocular vision. This paper proposes an algorithm for reconstructing the structure and motion of a 3‐D nonrigid object using the information of positions and velocities in the time sequence of images. It is assumed that the nonrigid object does not deviate significantly from rigidity. First, the object is analyzed approximately by assuming that it is rigid. Then the first‐order terms of Ct (which is an interval of two adjacent frames) are added to improve the approximation. Models of rigid and nonrigid objects were made, and information of their positions and optical flows were formed. The effectiveness of the proposed algorithm was confirmed by applying this to the data of the models.
Estudio cromosómico en leucemias linfoblásticas agudas (2017)

Se han identificado anormalidades clonales en aproximadamente 65-90% de los ninos con leucemia linfoblastica aguda (LLA). El objetivo de este estudio es identificar las alteraciones que permitan caracterizar LLA en nuestra poblacion. Se aplicaron las tecnicas citogeneticas y moleculares estandar para analizar lascelulas en medula osea. Pseudodiploidias fueron observadas en 43.4% de los casos, hiperdiploidfas en 32.9% e hipodiploidfas en 21%. Los cromosomas #3, #8, #10, #12, #15, #16, #17, #18, #19, #21, #22 y X estuvieron mayormente involucrados en diferentes tipos de cambios. El rearreglo BCR-ABL fue encontradoen el 42.8% de los casos. Algunos de estos resultados son similares a los publicados por otros autores, por lo que pueden considerarse como evidencia de que estos cromosomas estan involucrados en rearreglos no al azar en la LLA. La determination de estas anormalidades es una herramienta util que ayudara a caracterizar la LLA, a disenar un tratamiento adecuado y ayudara en el pronostico del paciente.
Thermal Protective Properties of the Allomyrina dichotoma Beetle Forewing for Thermal Protection Systems (2018)

This paper studies the heat-shielding performance of a beetle forewing to explore how it has excellent thermal protective properties. With an experimental setup of a self-developed heating environment, the heat transfer characteristics of the beetle forewing were tested at 50°C under steady state conditions. Two types of the forewings are considered: cut wing and live wing. The heat transfer results show that the live forewing provides a good heat-shielding performance with the heat-shielding index stabilizing at around 22.1%, which is 60% higher than that of the cut wing. Based on scanning electron microscope images of the microstructure of the cross section of the beetle forewing, a simplified finite element analysis is performed to numerically calculate the heat transfer properties of the forewing. The numerical simulations reveal that the proposed structure of the forewing is good for the design of an effective thermal protection system. In addition, the uncertainty analysis is performed to evaluate the quality of experimental data. These results provide a foundational understanding of the heat transfer characteristics of beetle forewing, which will inspire a promising candidate for an actively cooled thermal protection systems.
Relevance of Community Structure in Assessing Indeterminacy of Ecological Predictions (2002)

The community matrix is potentially a powerful tool for community ecology. While it details direct interactions between community members, it can also be used to quantify all indirect effects that occur in a community, and thereby to make predictions regarding population response to experimental treatments or natural disturbances. These predictions are essentially hypotheses of system behavior that can be rigorously evaluated. Use of the community matrix, however, has been hindered by indeterminacy and ambiguity in response predictions. In this study, we reveal a theoretical source of the problem that arises as a consequence of community structure. Using a qualitative analysis of the community matrix, we detail the complementary feedback cycles that contribute to the response of a population following a sustained or press perturbation. Complementary feedback is the sum of all direct and indirect effects that can contribute to a response. We develop a “weighted-predictions matrix” that assigns a probability scale to sign determinacy of predicted responses. This matrix is formed by the quotient of the net sum of complementary feedback cycles and the absolute number of complementary feedback cycles. A qualitative analysis of system structure provides a theoretical benchmark for understanding a spectrum of behavior in biological systems, and for framing and prioritizing management interventions for whole communities. This advance clarifies much of the uncertainty and ambiguity found in predicting the behavior of large and complex systems. We validate these tools by analyzing published studies of community response.
The Effects of Internal Fixation on Calcium Carbonate (1996)

Internal fixation resulted in histologically and biomechanically superior healing of autologous iliac crest bone graft in this canine model of anterior interbody fusion. Although fixation did not statistically improve the biomechanical properties of ceramic fusion segments, it had a profound effect on the ability of the ceramic to be revascularized and remodeled. Porous ceramic bone graft substitutes appear to depend on a stable environment for incorporation.
Synthetic Studies on d‐Biotin. Part 6. An Expeditious and Enantiocontrolled Approach to the Total Synthesis of d‐Biotin via a Polymer‐Supported Chiral Oxazaborolidine‐Catalyzed Reduction of meso‐Cyclic Imide. (2004)

Abstract For Abstract see ChemInform Abstract in Full Text.
Breakdown of the quantum Hall effect in periodic and aperiodic antidot arrays (1997)

We have studied the breakdown of the quantum Hall effect in GaAs/${\mathrm{Al}}_{\mathrm{x}}$${\mathrm{Ga}}_{1\mathrm{\ensuremath{-}}\mathrm{x}}$As heterostructures with antidot arrays as a function of the density and distribution of antidots. For periodic arrays (lithographic antidot diameter 100 nm) and periods from 400 to 1000 nm, the breakdown current is systematically reduced with increasing antidot density and determined by the peak value of the local current density. In aperiodic arrays, the breakdown current is markedly lower than in periodic arrays of the same antidot density due to higher local current densities at the same total current.
A Temporal Model of Human IgE and IgG Antibody Function (2013)

The diversity of the human antibody repertoire that is generated by V(D)J gene rearrangement is extended by nine constant region genes that give antibodies their complex array of effector functions. The application of high throughput sequencing to the study of V(D)J gene rearrangements has led to significant recent advances in our understanding of the antigen-binding repertoire. In contrast, our understanding of antibody function has changed little, and mystery still surrounds the existence of four distinctive IgG subclasses. Recent observations from murine models and from human studies of VDJ somatic point mutations suggest that the timing of emergence of cells from the germinal center may vary as a consequence of class switching. This should lead to predictable differences in affinity between isotypes. These differences, and varying abilities of the isotypes to fix complement and bind FcRs, could help coordinate the humoral defenses over the time course of a response. We therefore propose a Temporal Model of human IgE and IgG function in which early emergence of IgE sensitizes sentinel mast cells while switching to IgG3 recruits FcγR-mediated functions to the early response. IgG1 then emerges as the major effector of antigen clearance, and subsequently IgG2 competes with IgG1 to produce immune complexes that slow the inflammatory drive. Persisting antigen may finally stimulate high affinity IgG4 that outcompetes other isotypes and can terminate IgG1/FcγR-mediated activation via the inhibitory FcγRIIB. In this way, IgG antibodies of different subclasses, at different concentrations and with sometimes opposing functions deliver cohesive, protective immune function.
A Distributed Logical Filter for Connected Row Convex Constraints (2017)

Filtering denotes any method whereby an agent updates its belief state—its knowledge of the state of the world—from a sequence of actions and observations. Popular filtering techniques like Kalman and particle filters maintain compact representations of the belief state at all times. However, these techniques cannot be applied to situations where the world is described using constraints instead of stochastic models. In such cases, the belief state is a logical formula describing all possible world states. In this paper, we first review a logical filtering algorithm for connected row convex (CRC) constraints. CRC constraints are representationally very powerful; and the filtering algorithm for CRC constraints is a logical equivalent of the Kalman filter. We later study the CRC filtering algorithm in distributed settings where nodes of a network are interested in different subsets of variables from a larger system. We deduce its reducibility to the problem of distributed path consistency (PC) and prove the compactness of the belief state representations maintained at each node at all times.
Virtual Network Mapping with Traffic Matrices (2011)

Network virtualization allows multiple logical networks to coexist on the same physical infrastructure. A key problem that needs to be solved in this context is management of substrate network resources, in particular when mapping virtual network requests to the substrate. Several efficient algorithms have been proposed to provide effective solutions, but they assume that the virtual network request topology is given. In this paper, we show that the use of these topology-based requests may limit the efficiency of physical network usage. As an alternative, we propose a problem formulation and mapping algorithm that is based on traffic matrices to specify virtual network requests.
Near-infrared spectrophotometric monitoring of stroke-related changes in the protein and lipid composition of whole gerbil brains (1993)

Strokes are a critical problem in the U.S. that affect more than 500,000 people annually. Research into the causes of stroke and testing of drug therapies to reduce ischemic and postischemic damage to the brain is frustrated by an inability to continuously follow the physical and chemical events that occur during ischemia and reperfusion in vivo. Near-IR spectrometry is used in this paper to observe stroke-induced changes in the lipids and proteins of whole brain samples and in intact subjects. The examination of whole brains is made possible by a combination of hardware and software techniques designed to make the sample presentation to the spectrometer more reproducible. Near-IR spectrophotometry of brain tissue discriminates between adult (3-4 months of age) and aged (18-20 months of age) brains as well as between brains exposed to 5- and 10-min ischemia. The near-IR analytical method has many applications in aging and stroke research, including the noninvasive determination of age from brain spectra obtained transcranially, simultaneous multicomponent analysis of lipids and proteins, and quantification of edema.
Structured learning algorithm for detection of nonobstructive and obstructive coronary plaque lesions from computed tomography angiography (2015)

Visual identification of coronary arterial lesion from three-dimensional coronary computed tomography angiography (CTA) remains challenging. We aimed to develop a robust automated algorithm for computer detection of coronary artery lesions by machine learning techniques. A structured learning technique is proposed to detect all coronary arterial lesions with stenosis [Formula: see text]. Our algorithm consists of two stages: (1) two independent base decisions indicating the existence of lesions in each arterial segment and (b) the final decision made by combining the base decisions. One of the base decisions is the support vector machine (SVM) based learning algorithm, which divides each artery into small volume patches and integrates several quantitative geometric and shape features for arterial lesions in each small volume patch by SVM algorithm. The other base decision is the formula-based analytic method. The final decision in the first stage applies SVM-based decision fusion to combine the two base decisions in the second stage. The proposed algorithm was applied to 42 CTA patient datasets, acquired with dual-source CT, where 21 datasets had 45 lesions with stenosis [Formula: see text]. Visual identification of lesions with stenosis [Formula: see text] by three expert readers, using consensus reading, was considered as a reference standard. Our method performed with high sensitivity (93%), specificity (95%), and accuracy (94%), with receiver operator characteristic area under the curve of 0.94. The proposed algorithm shows promising results in the automated detection of obstructive and nonobstructive lesions from CTA.
High-Performance Blue InGaN Laser Diodes With Single-Quantum-Well Active Layers (2007)

The authors report on the high-performance blue laser diodes (LDs) with an emission wavelength of ~448 nm employing InGaN single-quantum-well (QW) active layers. At 100-mW continuous-wave (CW) output power, operation current and voltage are, respectively, 150 mA and 5.3 V, corresponding to the wall plug efficiency of >12%, a record value for the single-mode InGaN LDs with blue wavelengths. The single QW blue LD showed normal temperature dependence of light output-current curves with the characteristic temperature of 170 K. In addition, we demonstrate a high level of catastrophic optical damage of >300 mW and long device lifetime under CW operation condition at room temperature.
Error Tolerant Multimedia Stream Processing: There's Plenty of Room at the Top (of the System Stack) (2012)

There is a growing realization that the expected fault rates and energy dissipation stemming from increases in CMOS integration will lead to the abandonment of traditional system reliability in favor of approaches that offer reliability to hardware-induced errors across the application, runtime support, architecture, device and integrated-circuit (IC) layers. Commercial stakeholders of multimedia stream processing (MSP) applications, such as information retrieval, stream mining systems, and high-throughput image and video processing systems already feel the strain of inadequate system-level scaling and robustness under the always-increasing user demand. While such applications can tolerate certain imprecision in their results, today's MSP systems do not support a systematic way to exploit this aspect for cross-layer system resilience. However, research is currently emerging that attempts to utilize the error-tolerant nature of MSP applications for this purpose. This is achieved by modifications to all layers of the system stack, from algorithms and software to the architecture and device layer, and even the IC digital logic synthesis itself. Unlike conventional processing that aims for worst-case performance and accuracy guarantees, error-tolerant MSP attempts to provide guarantees for the expected performance and accuracy. In this paper we review recent advances in this field from an MSP and a system (layer-by-layer) perspective, and attempt to foresee some of the components of future cross-layer error-tolerant system design that may influence the multimedia and the general computing landscape within the next ten years.