gebhart/patrepeval huggingface dataset:
Functional Mapping of YadA- and Ail-Mediated Binding of Human Factor H to<i>Yersinia enterocolitica</i>Serotype O:3 (2008)

Yersinia enterocolitica is an enteric pathogen that exploits diverse means to survive in the human host. Upon Y. enterocolitica entry into the human host, bacteria sense and respond to variety of signals, one of which is the temperature. Temperature in particular has a profound impact on Y. enterocolitica gene expression, as most of its virulence factors are expressed exclusively at 37 degrees C. These include two outer membrane proteins, YadA and Ail, that function as adhesins and complement resistance (CR) factors. Both YadA and Ail bind the functionally active complement alternative pathway regulator factor H (FH). In this study, we characterized regions on both proteins involved in CR and the interaction with FH. Twenty-eight mutants having short (7 to 41 amino acids) internal deletions within the neck and stalk of YadA and two complement-sensitive site-directed Ail mutants were constructed to map the CR and FH binding regions of YadA and Ail. Functional analysis of the YadA mutants revealed that the stalk of YadA is required for both CR and FH binding and that FH appears to target several conformational and discontinuous sites of the YadA stalk. On the other hand, the complement-sensitive Ail mutants were not affected in FH binding. Our results also suggested that Ail- and YadA-mediated CR does not depend solely on FH binding.
An Overview of Energy-Efficient Hardware Accelerators for On-Device Deep-Neural-Network Training (2021)

Deep Neural Networks (DNNs) have been widely used in various artificial intelligence (AI) applications due to their overwhelming performance. Furthermore, recently, several algorithms have been reported that require on-device training to deliver higher performance in real-world environments and protect users’ personal data. However, edge/mobile devices contain only limited computation capability with battery power, so an energy-efficient DNN training processor is necessary to realize on-device training. Although there are a lot of surveys on energy-efficient DNN inference hardware, the training is quite different from the inference. Therefore, analysis and optimization techniques targeting DNN training are required. This article aims to provide an overview of energy-efficient DNN processing that enables on-device training. Specifically, it will provide hardware optimization techniques to overcomes the design challenges in terms of distinct dataflow, external memory access, and computation. In addition, this paper summarizes key schemes of recent energy-efficient DNN training ASICs. Moreover, we will also show a design example of DNN training ASIC with energy-efficient optimization techniques.
Smoothing Data with Fourier Transformations<sup>1</sup> (1974)

Abstract The natural variability of agronomic data often masks underlying true curves. A relatively new Fourier transform data smoothing technique, when tested on several sets of noisy agronomic data, gave very satisfactory reductions of this variability. The data were smoothed by computing the Fourier transform, setting high frequency noise components of the resulting variance spectrum to zero, and then computing the inverse Fourier transform. The key to the technique's success lies in the fact that the data were dominated by relatively low frequencies of variation which could be separated from the higher frequency noise. This simple, lucid interpretation of the filtering action makes Fourier transform smoothing even more attractive than other methods whose filtering action is not so intuitively obvious. The technique was superior to two other methods in extracting a true curve from noisy artificial data.
Microcytic anemia, erythropoietic protoporphyria, and neurodegeneration in mice with targeted deletion of iron-regulatory protein 2 (2005)

Iron-regulatory proteins (IRPs) 1 and 2 posttranscriptionally regulate expression of transferrin receptor (TfR), ferritin, and other iron metabolism proteins. Mice with targeted deletion of IRP2 overexpress ferritin and express abnormally low TfR levels in multiple tissues. Despite this misregulation, there are no apparent pathologic consequences in tissues such as the liver and kidney. However, in the central nervous system, evidence of abnormal iron metabolism in IRP2-/- mice precedes the development of adult-onset progressive neurodegeneration, characterized by widespread axonal degeneration and neuronal loss. Here, we report that ablation of IRP2 results in iron-limited erythropoiesis. TfR expression in erythroid precursors of IRP2-/- mice is reduced, and bone marrow iron stores are absent, even though transferrin saturation levels are normal. Marked overexpression of 5-aminolevulinic acid synthase 2 (Alas2) results from loss of IRP-dependent translational repression, and markedly increased levels of free protoporphyrin IX and zinc protoporphyrin are generated in IRP2-/- erythroid cells. IRP2-/- mice represent a new paradigm of genetic microcytic anemia. We postulate that IRP2 mutations or deletions may be a cause of refractory microcytic anemia and bone marrow iron depletion in patients with normal transferrin saturations, elevated serum ferritins, elevated red cell protoporphyrin IX levels, and adult-onset neurodegeneration.
Synthesis of Organic Pillared MFI Zeolite as Bifunctional Acid–Base Catalyst (2015)

Organic pillared MFI zeolite has been synthesized by detemplation of diquaternary ammonium surfactant ([C22H45–N+(CH3)2–C6H12–N+(CH3)2–C6H13]Br2, C22-6-6) and intercalation of arylic silsesquioxane (1,4-bis(triethoxysilyl)benzene, BTEB) molecules between multilamellar MFI layers. The acid extraction and UV light radiation were sequentially employed for removal of C22-6-6 surfactant located not only between MFI layers but also in the zeolite micropores. The removal of the C22-6-6 template using a nonthermal calcination method prevents the condensation of external silanol groups of zeolitic layers stacked next to each other, which allows intercalation of BTEB molecules between the zeolitic layers and their successive reaction with the silanol groups to form the organic pillared zeolite structure. A post-treatment amination of the resultant zeolite sample introduced amino groups in the organic BTEB pillars. The acid sites from the zeolite framework aluminum and basic sites from the amino groups in BTEB pillars endow organic pillared MFI bifunctionality for cascade catalytic reactions. The synthesis of organic pillared MFI is a new addition to the structural modifications of lamellar zeolite with more open structures for processing bulky molecules. The resultant inorganic–organic hybrid zeolite structure creates new opportunities for potential applications of lamellar zeolites with tailored physicochemical properties.
<scp>gerud</scp> 2.0: a computer program for the reconstruction of parental genotypes from half‐sib progeny arrays with known or unknown parents (2005)

Abstract Large groups of related progeny, as can be collected from discrete egg masses or fruits, present excellent opportunities for parentage analysis by allowing the reconstruction of parental genotypes. Current techniques of parental genotypic reconstruction require the knowledge of at least one parental genotype. Here, I present a new computer program that reconstructs parental genotypes when no parents are known, provided that the progeny array contains only full and half siblings. The prospects for successfully reconstructing parental genotypes for such progeny arrays with unknown parents are nearly as good as those for the case when one parent is known with certainty.
The Alpha Catalytic Subunit of Protein Kinase CK2 Is Required for Mouse Embryonic Development (2007)

Protein kinase CK2 (formerly casein kinase II) is a highly conserved and ubiquitous serine/threonine kinase that is composed of two catalytic subunits (CK2alpha and/or CK2alpha') and two CK2beta regulatory subunits. CK2 has many substrates in cells, and key roles in yeast cell physiology have been uncovered by introducing subunit mutations. Gene-targeting experiments have demonstrated that in mice, the CK2beta gene is required for early embryonic development, while the CK2alpha' subunit appears to be essential only for normal spermatogenesis. We have used homologous recombination to disrupt the CK2alpha gene in the mouse germ line. Embryos lacking CK2alpha have a marked reduction in CK2 activity in spite of the presence of the CK2alpha' subunit. CK2alpha(-/-) embryos die in mid-gestation, with abnormalities including open neural tubes and reductions in the branchial arches. Defects in the formation of the heart lead to hydrops fetalis and are likely the cause of embryonic lethality. Thus, CK2alpha appears to play an essential and uncompensated role in mammalian development.
Marginal zone macrophages and their role in the immune response against T‐independent type 2 antigens: modulation of the cells with specific antibody (1989)

Marginal zone macrophages are strategically positioned in the marginal zone of the spleen and are thought to play an important role in the initiation of the immune response to T-independent type 2 responses. The cells are characterized by high phagocytic activity and by the selective uptake of neutral polysaccharides. In the mouse marginal zone macrophages react specifically with the monoclonal antibody ER-TR9. Injection of the antibody resulted in a complete abrogation of the uptake of neutral polysaccharides by the cells in vivo, although the cells were still capable of taking up latex and carbon particles. The complete blockade of the polysaccharide uptake did not result in an altered humoral immune response against this antigen. When the antibody ER-TR9 was coupled to the toxin gelonin a complete elimination of the marginal zone macrophages could be established in vivo. However, complete elimination did not result in changes of the immune responses against 2,4,6-trinitrophenylated Ficoll, suggesting that the marginal zone macrophages are either not involved in this type of response, or that their function can be taken over by other cells. The possible role of these cells and the importance of the spleen in the immune response against bacterial antigens is discussed.
Unanswerable queries in a spontaneous speech task (2002)

This paper outlines the general strategies followed in developing the CMU (Carnegie Mellon University) speech understanding system. Our system is oriented toward the extraction of information relevant to a task. It uses a flexible frame-based parser. Our system handles phenomena that are natural in spontaneous speech, for example, restarts, repeats and grammatically ill-formed utterances. It maintains a history of the key features of the dialogue. It can resolve elliptical, anaphoric and other indirect references. In general, the system may not be able to generate a database response to a query for a number of reasons, for example, the user may inquire about information not in the database. These unanswerable (Class X) queries constituted about 30% of the data in the November 92 ARPA Spoken Language Systems benchmark evaluation. We will present some results which indicate that the perplexity of the unanswerable queries is significantly higher than the perplexity of the remaining data. In this paper, we focus on our attempts to improve the performance of CMU's Spoken Language System on the unanswerable queries. The system has been used to model an air travel information service (ATIS) task. In the December 93 DARPA Spoken Language Systems benchmark evaluation, the CMU ATIS system correctly answered 90.7% transcript inputs and 86.8% speech inputs. These were the best numbers reported for the evaluation.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Digitising VHF FM sound broadcasting with DRM+ (DRM mode E) (2009)

This paper summarizes and discusses findings on compatibility of the forthcoming DRM mode E into classical VHF FM sound broadcasting. The results are based on theoretical considerations, lab measurements, field trials and radio network planning exercises. In addition, the status of the ongoing work towards a comprehensive DRM mode E coverage study including first results hereof are given.
Automated Assessment in Learning and Teaching Programming Languages using Virtual Learning Environment (2019)

The paper investigates the impact of different types of e-learning course activities on the first-year university students' results in the introductory programming course. The primary goal of three years of research is to uncover the role of a few types of activities, especially the purpose of an automated assessment. Despite the education systems function supported the automated assessment of source code is one of the most useful tools of programming learning, there are only a few researches inspected its effectiveness and impact. The paper compares involved groups of students, their motivation and expectations collected via a set of questionnaires. It investigates the significance of automated assessment of source code in the educational process. The results show significant differences between groups with and without the use of automated assessment were not proven. Finally, the authors researched the relationship between the number of solved tasks and the student's outcomes of the evaluation and identified a positive correlation.
Control and visualization system for managed self-organization network (2011)

We propose the managed self-organizing network concept considering the unexpected network changes caused by the future applications, and implement the control and visualization system for it. In the managed self-organizing network, multiple virtual networks are accommodated on a single optical infrastructure. Each virtual network is controlled based on self-organizing mechanism by attractor selection algorithm that models behavior where living organisms adapt to unknown changes in their surrounding environments. On the other hand, the physical resource management server dynamically manages the resource allocation for each virtual network to optimize the utilization of total network resources. Our implemented system efficiently visualizes the behavior of managed self-organizing network with time variability, and network filtering and clustering functions are implemented for visualization of large and multiple virtual networks.
Non-Destructive Testing of Concrete: A Review of Methods (2015)

This paper reviews the most common non-destructive testing (NDT) methods of concrete structures as utilized by the structural engineering industry. The fundamentals of NDT methods are explored in regards to their potential, limitations, inspection techniques and interpretations. The factors that influence the success of NDT methods are discussed and ways to mediate their influence are recommended. Reference is made to standard guidelines for the application and interpretation of the discussed NDT methods. NDT of concrete was found to be gaining increasing acceptance as a means of evaluating the strength, uniformity, durability and other properties of existing concrete structures. Perceptions of NDT inadequacy were attributable to lack of understanding construction materials and NDT methods themselves. The intent of this paper is to address these concerns by identifying and describing the most common successful methods of NDT as applied to concrete structures.
A characterization of sharing in parallel programs and its application to coherency protocol evaluation (1988)

In this paper we use trace-driven simulation to analyze the memory reference patterns of write shared data in several parallel applications. We first develop a characterization of write sharing (based on the notion of a write run), and then examine the traces, using metrics derived from the characterization. The results indicate that the amount of write sharing in all programs is small; and that it is characterized by short to medium sequences of per processor references, with little contention for either data or locks. We determine to what extent this analysis can be used to predict the coherency overhead of write-invalidate and write-broadcast protocols. We develop a simple model of write sharing from the write run characterization. By applying the results of the sharing analysis to the model, weighted by machine-specific cycle costs for carrying out coherency-related bus operations, we can estimate relative protocol performance. We compare these results to those from detailed architectural simulations. The simulation results indicate that (1) neither protocol dominates in performance; and that (2) the write run model is a good predictor of protocol performance when the unit of the coherency operations matches that in the sharing analysis. This is the case for the write-broadcast protocols, in which one word is broadcast for each write to shared data. However, in Berkeley Ownership, a write-invalidate protocol, the unit of coherency is an entire cache block. When the block size is large, performance for this protocol is quite sensitive to the memory reference patterns within the block.
Multiple Roles for the T7 Promoter Nontemplate Strand during Transcription Initiation and Polymerase Release (2004)

Transcription initiation begins with recruitment of an RNA polymerase to a promoter. Polymerase-promoter interactions are retained until the nascent RNA is extended to 8-12 nucleotides. It has been proposed that accumulation of "strain" in the transcription complex and RNA displacement of promoter-polymerase interactions contribute to releasing the polymerase from the promoter, and it has been further speculated that too strong a promoter interaction can inhibit the release step, whereas a weak interaction may facilitate release. We examined the effects of partial deletion of the nontemplate strand on release of T7 RNA polymerase from the T7 promoter. T7 polymerase will initiate from such partially single-stranded promoters but binds them with higher affinity than duplex promoters. We found that release on partially single-stranded promoters is strongly inhibited. The inhibition of release is not due to an indirect effect on transcription complex structure or loss of specific polymerase-nontemplate strand interactions, because release on partially single-stranded templates is recovered if the interaction with the promoter is weakened by a promoter base substitution. This same substitution also appears to allow the polymerase to escape more readily from a duplex promoter. Our results further suggest that template-nontemplate strand reannealing drives dissociation of abortive transcripts during initial transcription and that loss of interactions with either the nontemplate strand or duplex DNA downstream of the RNA lead to increased transcription complex slippage during initiation.
PLACEMENT OF ACTIVE ADJUSTABLE STIFFNESS SYSTEM TO MULTISTORY BUILDINGS (INTERSTORY-LINKAGE METHOD) : Active seismic response controlled structures (1993)

The placement of the active controllers (AC) is one of the important issues, in the research of the active seismic response control. As the placement method of the Active Adjustable Stiffness system (A 2 S 2), an interstory linkage method is adopted, and an interstory displacement (IS) control and a typical point displacement (TP) control are defined as the selfbalancing adaptive control. These control algorithms as well as the placement mode and the extent of the adjustable, stiffness values are the design parameters for the A 2 S 2, and we obtained the seismic response, process by the numerical analysis with these design parameters to show the required performance property of the A 2 S 2. Furthermore we evaluate the seismic response process by means of the nonstationary power spectra. Also we proposed the multi-point control for the TP control to reduce the higher vibration mode.
Tactile Stimulation by Repetitive Lateral Movement of Midair Ultrasound Focus (2019)

We report a new vibrotactile modulation method of midair ultrasound focus, namely, lateral modulation (LM), in which the focus quickly moves along a small cyclic trajectory and provides stronger and clearer vibrotactile stimuli than those by the conventional amplitude modulation (AM) method. Midair ultrasound haptics has an essential technical advantage of offering remote, non-contact, and pinpoint tactile stimuli on device-free bare skin. On the other hand, lack of clarity in the presented vibrotactile sensation has often been pointed out, and until now, an AM focus has been valid only on glabrous skin. Our main scientific contribution of the article is to verify the LM method, with the following experimental findings newly obtained. We confirmed that with the same maximum output amplitude of the ultrasound phased arrays, LM stimuli with circular focal trajectories were sensed stronger than AM stimuli by glabrous skin and hairy skin in a modulation frequency of 10-200 Hz. We also found that the detection threshold in glabrous skin mainly depended on the focal speed, whereas the tendency in hairy skin was different from that. With these results, we discuss a basis of perceptional mechanism that responds to LM stimuli, along with practical aspects of potential applications.
High Shear Homogenization of Lignin to Nanolignin and Thermal Stability of Nanolignin‐Polyvinyl Alcohol Blends (2014)

A new method to prepare nanolignin using a simple high shear homogenizer is presented. The kraft lignin particles with a broad distribution ranging from large micron- to nano-sized particles were completely homogenized to nanolignin particles with sizes less than 100 nm after 4 h of mechanical shearing. The (13) C nuclear magnetic resonance (NMR) and (31) P NMR analysis showed that there were no major changes in the chemical composition between the starting kraft lignin particles and the nanolignin obtained after 4 h of mechanical treatment. The nanolignin particles did not show any change in molecular weight distribution and polydispersity compared to the original lignin particles. The nanolignin particles when used with polyvinyl alcohol (PVA) increased the thermal stability of nanolignin/PVA blends more effectively compared to the original lignin/PVA blends.
Thermodynamic and Electrochemical Studies of the Electron Transfer Reactions of Hemoglobin (1992)

Heme containing proteins function as oxygen carriers, electron carriers or enzymes in biological systems. Of particular interest to this investigation is the ability of heme proteins to serve as electron carriers. The heme group, an iron atom bound to the four nitrogens of a porphyrin ring system, is the characteristic structural feature in common to all heme proteins. The iron atom serves as the site of oxidation or reduction during electron transfer. However, heme proteins exhibit significantly different thermodynamic and kinetic properties for electron transfer reactions. These differences between heme proteins must be due to the protein structure and the location of the heme group within the molecule. Although hemoglobin functions physiologically as an oxygen carrier rather than an electron carrier it is an ideal molecule to use as a model for the study of the electron transfer reactions of heme proteins. This is because it is readily available, has a moderate cost and has a known and documented structure.
Moderate Pulmonary Arterial Hypertension in Male Mice Lacking the Vasoactive Intestinal Peptide Gene (2007)

Deletion of the VIP gene leads to spontaneous expression of moderately severe PAH in mice during air breathing. Although not an exact model of idiopathic PAH, the VIP-/- mouse should be useful for studying molecular mechanisms of PAH and evaluating potential therapeutic agents. VIP replacement therapy holds promise for the treatment of PAH, and mutations of the VIP gene may be a factor in the pathogenesis of idiopathic PAH.