gebhart/patrepeval huggingface dataset:
The zinc‐binding region (ZBR) fragment of Emi2 can inhibit APC/C by targeting its association with the coactivator Cdc20 and UBE2C‐mediated ubiquitylation (2014)

Anaphase-promoting complex or cyclosome (APC/C) is a multisubunit ubiquitin ligase E3 that targets cell-cycle regulators. Cdc20 is required for full activation of APC/C in M phase, and mediates substrate recognition. In vertebrates, Emi2/Erp1/FBXO43 inhibits APC/C-Cdc20, and functions as a cytostatic factor that causes long-term M phase arrest of mature oocytes. In this study, we found that a fragment corresponding to the zinc-binding region (ZBR) domain of Emi2 inhibits cell-cycle progression, and impairs the association of Cdc20 with the APC/C core complex in HEK293T cells. Furthermore, we revealed that the ZBR fragment of Emi2 inhibits in vitro ubiquitin chain elongation catalyzed by the APC/C cullin-RING ligase module, the ANAPC2-ANAPC11 subcomplex, in combination with the ubiquitin chain-initiating E2, E2C/UBE2C/UbcH10. Structural analyses revealed that the Emi2 ZBR domain uses different faces for the two mechanisms. Thus, the double-faced ZBR domain of Emi2 antagonizes the APC/C function by inhibiting both the binding with the coactivator Cdc20 and ubiquitylation mediated by the cullin-RING ligase module and E2C. In addition, the tail region between the ZBR domain and the C-terminal RL residues [the post-ZBR (PZ) region] interacts with the cullin subunit, ANAPC2. In the case of the ZBR fragment of the somatic paralogue of Emi2, Emi1/FBXO5, these inhibitory activities against cell division and ubiquitylation were not observed. Finally, we identified two sets of key residues in the Emi2 ZBR domain that selectively exert each of the dual Emi2-specific modes of APC/C inhibition, by their mutation in the Emi2 ZBR domain and their transplantation into the Emi1 ZBR domain.
Design and evaluation of two block coded modulation schemes (2002)

Presents a study on the design and evaluation of two block coded modulation systems. One of the systems uses a binary construction and quadrature amplitude modulation. The other utilizes a ternary construction and phase modulation. The performance of the two coded schemes are compared theoretically with those of uncoded schemes of the same bandwidth, average power and transmission rate. The ternary scheme is also evaluated practically by computer simulations. Furthermore, the sub-optimum detection algorithm which is used in the ternary scheme is surveyed from the computational complexity and the memory requirement viewpoints.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Bounds on expansion in LZ'77-like coding (2004)

This paper investigates the maximum increase in number of phrases that results from changing one symbol in a string that has been parsed using an LZ'77-like algorithm. We provide upper and lower bounds to the maximum expansion as a function of the position of the changed symbol and of the string length.
Field‐evolved resistance to Bt maize in sugarcane borer (Diatraea saccharalis) in Argentina (2017)

Abstract BACKGROUND Maize technologies expressing Bacillus thuringiensis (Bt) insecticidal proteins are widely used in Argentina to control sugarcane borer ( Diatraea saccharalis Fabricius). Unexpected D. saccharalis damage was observed to Bt maize events TC1507 (expressing Cry1F) and MON 89034 × MON 88017 (expressing Cry1A.105 and Cry2Ab2) in an isolated area of San Luis Province. Diatraea saccharalis larvae were sampled from MON 89034 × MON 88017 fields in the area to generate a resistant strain (RR), which was subsequently characterized in plant and diet bioassays. RESULTS Survivorship of the RR strain was high on TC1507 leaf tissue, intermediate on MON 89034 × MON 88017, and low on MON 810 (expressing Cry1Ab). The RR strain had high resistance to Cry1A.105 (186.74‐fold) and no resistance to Cry2Ab2 in diet bioassays. These results indicate resistance to Cry1F and Cry1A.105 (and likely cross‐resistance between them) but not to Cry1Ab or Cry2Ab2. Resistance to MON 89034 × MON 88017 was functionally recessive. Reviews of grower records suggest that resistance initially evolved to Cry1F, conferring cross‐resistance to Cry1A.105, with low refuge compliance as the primary cause. A mitigation plan was implemented in San Luis that included technology rotation, field monitoring, and grower education on best management practices (BMPs) including refuges. CONCLUSION In the affected area, the resistance to Cry1F and Cry1A.105 is being managed effectively through use of MON 89034 × MON 88017 and MON 810 in combination with BMPs, and no spread of resistance to other regions has been observed. © 2017 The Authors. Pest Management Science published by John Wiley &amp; Sons Ltd on behalf of Society of Chemical Industry.
Payoff-based Inhomogeneous Partially Irrational Play for potential game theoretic cooperative control: Convergence analysis (2012)

This paper investigates learning algorithm design in potential game theoretic cooperative control, where it is in general required for agents' collective action to converge to the most efficient equilibria while standard game theory aims at just computing a Nash equilibrium. In particular, the equilibria maximizing the potential function should be selected in case the utility functions are already aligned to a global objective function. In order to meet the requirement, this paper develops a learning algorithm called Payoff-based Inhomogeneous Partially Irrational Play (PIPIP). The main feature of PIPIP is to allow agents to make irrational decisions with a specified probability, i.e. agents can choose an action with a low utility from the past actions stored in the memory. We then prove convergence in probability of the collective action to the potential function maximizers. Finally, the effectiveness of the present algorithm is demonstrated through simulation on a sensor coverage problem.
Comparison of buffering strategies for asymmetric packet switch modules (1991)

The performance of a class of asymmetric packet switch modules with channel grouping is analyzed. The switch module considered has n inputs and m outputs. A packet destined for a particular output address (out of g) needs to access only one of the r available physical output ports: m=gr. These switch modules are the key building blocks in many large multistage switch architectures. The focus is on the performance of input-buffered and output-buffered switch modules under geometrically bursty traffic. A combination of exact derivation, numerical analysis, and simulation yields the saturation throughput of input-buffered switch modules and the mean delay of the input-buffered and output-buffered switch modules. Tables and formulas useful for traffic engineering are presented. The results show that increasing the number of output ports per output address (r) can significantly improve switch performance, especially when traffic is bursty. Although output-buffered switch modules have significantly better performance than input-buffered switch modules when there are equal numbers of input and output ports, this performance difference becomes significantly smaller when the switch dimensions are asymmetric.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
The SVD beamformer with diverging waves: a proof-of-concept for fast aberration correction (2021)

The rise of ultrafast ultrasound imaging-with plane or diverging waves - paved the way to new applications of ultrasound in biomedical applications. However, propagation through complex layers (typically fat, muscle, and bone) hinder considerably the image quality, especially because of sound speed heterogeneities. In difficult-to-image patients, in the case of the hepatic steatosis for instance, a good image and a reliable sound speed quantification are crucial to provide a powerful non-invasive diagnosis tool. In this work, we proposed to adapt the singular value decomposition (SVD) beamformer method for diverging waves and thus present a novel aberration correction approach for widely used curved arrays. We probed its efficiency experimentally both<i>in vitro</i>and<i>in vivo</i>. Besides the proposed matrix formalism, we explored the physical meaning of the SVD of ultrafast data. Finally, we demonstrated the ability of the technique to improve the image quality and offer new perspectives particularly in quantitative liver imaging.
As-doped Si's complex permittivity and its effects on heating curve at 2.45 GHz frequency (2015)

An analysis to determine the complex permittivity of arsenic-doped silicon wafer at 2.45 GHz is presented based on closed-form analytical expressions for cylindrical symmetry. Experimental results in support with the numerical analysis and simulation results are also presented. This analysis will further help analyze the capacitive heating of doped and undoped silicon wafer at microwave frequency; hence, this paper is a precursor to elucidation of capacitive heating of silicon substrates placed between susceptors. This study indicates that when the dopant is added to the silicon the loss tangent decreases with increase in concentration but upon annealing the loss tangent becomes constant with respect to concentration of the dopant.
A multi-laboratory comparison of photon migration instruments and their performances: the BitMap exercise (2021)

Performance assessment and standardization are indispensable for instruments of clinical relevance in general and clinical instrumentation based on photon migration/diffuse optics in particular. In this direction, a multi-laboratory exercise was initiated with the aim of assessing and comparing their performances. 29 diffuse optical instruments belonging to 11 partner institutions of a European level Marie Curie Consortium BitMap1 were considered for this exercise. The enrolled instruments covered different approaches (continuous wave, CW; frequency domain, FD; time domain, TD and spatial frequency domain imaging, SFDI) and applications (e.g. mammography, oximetry, functional imaging, tissue spectroscopy). 10 different tests from 3 well-accepted protocols, namely, the MEDPHOT2 , the BIP3 , and the nEUROPt4 protocols were chosen for the exercise and the necessary phantoms kits were circulated across labs and institutions enrolled in the study. A brief outline of the methodology of the exercise is presented here. Mainly, the design of some of the synthetic descriptors, (single numeric values used to summarize the result of a test and facilitate comparison between instruments) for some of the tests will be discussed.. Future actions of the exercise aim at deploying these measurements onto an open data repository and investigating common analysis tools for the whole dataset.
Synthesis and Antiviral Evaluation of β‐D‐ and β‐L‐Pentofuranonucleoside Derivatives Bearing 5‐Trifluoromethylcytosine as the Base (2004)

Abstract For Abstract see ChemInform Abstract in Full Text.
Sensitivity analysis of optical scatterometry technique for high-aspect ratio trench measurement (2023)

For CMOS image sensors fabrication, deep trenches are commonly incorporated in the device to isolate the individual pixel one another within the pixel matrix. These etched structures typically exhibit a high aspect ratio of 1:20 and controlling such narrow and deep object is a challenge for inline metrology. In a manufacturing environment, the preferred method for trench height measurements remains the optical scatterometry (OCD) technique as being very sensitive and reliable. Still, it requires time and resources for model construction and validation. It appears then that an analysis of its predicted sensitivity could be a valuable pre-step before starting any activity on large periodical objects where OCD sensitivity can reach its limits. In this study, we tested this approach for deep trench structures with CD dimension in the range of 100nm to 1400nm and the depth from 100 nm to 5 μm. The periodicity (pitch) was fixed at CD*2. At first, 3D Mueller scatterometry signatures were modelled selecting spectroscopic ellipsometry acquisition configurations according to industrial most common ones. Thanks to an optimized RCWA (Rigorous Coupled Wave Analysis) code developed inhouse, calculation durations were reduced enough to allow massive data generation. By implementing a sensitivity analysis approach that uses Sobol coefficients, the sensitivity of the OCD metrology technique is here evaluated for each CD and depth values. More particulary, it will be illustrated by a CD range of &plusmn;10% of 350nm and with the depth of the trench varying from 100nm up to 5μm. As a results, a sensitivity frontier can be estimated at around 3μm, a critical depth value above which OCD in the given configuration is no more sensitive to the metrics determination. Such observation will be further discussed by analysis of convergence evaluation.
Progress in III-Nitride Tunnel Junctions for Optoelectronic Devices (2022)

The recent progress in III-nitride tunnel junction (TJ) contacts for optoelectronic devices is summarized in this review paper. Due to the rapid developments of various III-nitride based optoelectronic devices for different emerging applications, TJs are of interest for these devices to achieve more efficient device performance. This review paper first briefly describes the working principles of TJs and the advantages of employing TJs in optoelectronic devices. The significant advancements in III-nitride TJs realized by metalorganic chemical vapor deposition (MOCVD) and molecular beam epitaxy (MBE) are addressed, as well as their TJ device performances. Lastly, the critical challenges for employing III-nitride TJs in wide bandgap ultraviolet (UV) light emitters are discussed for future investigations.
Sufficient condition for the existence of interface states in some two-dimensional photonic crystals (2014)

There is no assurance that interface states can be found at the boundary separating two materials. While a strong perturbation typically favors wave localization, we show on the contrary that in some two-dimensional photonic crystals (PCs) possessing a Dirac-like cone at k = 0 derived from monopole and dipoles excitation, a small perturbation is sufficient to create interface states. The conical dispersion together with the flat band at the zone center generates the existence of gaps in the projected band structure and the existence of single mode interface states inside the projected band gaps stems from the geometric phases of the bulk bands. The underlying physics for the existence of an interface state is related to the sign change of the surface impedance in the gaps above and below the flat band. The established results are applicable for long wavelength regimes where there is only one propagating diffraction order for an interlayer scattering.
Shared Sensing and Communications in Sensor Networks : The Multihop Case (2006)

A joint sensing/communication problem is considered for sensor networks. Herein, the channel(s) between a source and destination are the parameters to be sensed and communicated over the network. Lower bounds on the end-to-end distortion are developed for a multihop, linear network. Internode communication is assumed to be done via an encode-and-forward approach. For a many-to-one topology with two hops, data aggregation and time-division communication approaches are compared. Asymptotic in the SNR, it is shown that a time-division approach is superior
Step-GRAND: A Low Latency Universal Soft-input Decoder (2023)

GRAND features both soft-input and hard-input variants that are well suited to efficient hardware implementations that can be characterized with achievable average and worst-case decoding latency. This paper introduces step-GRAND, a soft-input variant of GRAND that, in addition to achieving appealing average decoding latency, also reduces the worst-case decoding latency of the corresponding hardware implementation. The hardware implementation results demonstrate that the proposed step-GRAND can decode CA-polar code $(128,105+11)$ with an average information throughput of $47.7$ Gbps at the target FER of $\leq10^{-7}$. Furthermore, the proposed step-GRAND hardware is $10\times$ more area efficient than the previous soft-input ORBGRAND hardware implementation, and its worst-case latency is $\frac{1}{6.8}\times$ that of the previous ORBGRAND hardware.
Role of Neisseria meningitidis PorA and PorB Expression in Antimicrobial Susceptibility (2013)

FIG 1 Analysis of porin expression during MIC analysis.(A) Membrane proteins were isolated by Sarkosyl extraction, and 10 g was separated on 8 to 12% bis-Tris acrylamide gels prior to Coomassie staining.Lane 1, 9; lane 2, 9PorA; lane 3, 9PorB.(B) Samples from the last well showing turbidity were plated on BHI agar and immunoblotted with the PorA-specific MAb MN14C11.6.
Fin field effect transistor directionality impacts printing of implantation shapes (2018)

In modern integrated circuit (IC) fabrication processes, the photoresist receives considerable illumination energy that is reflected by underlying topography during optical lithography of implantation layers. Bottom antireflective coating (BARC) is helpful to mitigate the reflection. Often, however, BARC is not used, because its removal is technically challenging, in addition to its relatively high economic cost. Furthermore, the advanced technology nodes, such as 14/10-nm nodes, have introduced fin field effect transistor (FinFET), which makes reflection from nonuniform silicon substrates exceptionally complicated. Therefore, modeling reflection from topography becomes obligatory to accurately predict printing of implantation shapes. Typically, FinFET is always fixed in one direction in realistic designs. However, the same implantation rectangle may be oriented in either horizontal or vertical direction. Then, there are two types of relations between the critical dimension (CD) and FinFET, namely a parallel-to and a perpendicular-to relation. We examine the fin directionality impact on CD. We found that this impact may be considerable in some cases. We use our in-house rigorous optical topography simulator to reveal underlining physical reasons. One of the major causes of the CD differences is that in the parallel orientation, the solid sidewalls of the fins conduct considerable light reflections unlike for the perpendicular orientation. This finding can aid the compact modeling in optical proximity correction of implantation masks.
Increased Conception Rates in Beef Cattle Inseminated with Nanopurified Bull Semen1 (2014)

Aberrant sperm phenotypes coincide with the expression of unique sperm surface determinants that can be probed by objective, biomarker-based semen analysis and targeted as ligands for semen purification. This study evaluated a nanoparticle-based magnetic purification method that removes defective spermatozoa (∼30% of sample) from bull semen and improves sperm sample viability and fertilizing ability in vitro and in vivo. Two types of nanoparticles were developed: a particle coated with antibody against ubiquitin, which is present on the surface of defective spermatozoa, and a particle coated with the lectin peanut agglutinin, which binds to glycans exposed by acrosomal damage. In a 2 yr artificial insemination field trial with 798 cows, a conception rate of 64.5% ± 3.7% was achieved with a 10 × 10(6) sperm dose of peanut agglutinin-nanopurified spermatozoa, comparable to a control nonpurified full dose of 20 × 10(6) spermatozoa per dose (63.3% ± 3.2%) and significantly higher than a 10 × 10(6) sperm dose of nonpurified control semen (53.7% ± 3.2%; P < 0.05). A total of 466 healthy calves were delivered, and no negative side effects were observed in the inseminated animals or offspring. Because the method is inexpensive and can be fully integrated in current protocols for semen cryopreservation, it is feasible for use in the artificial insemination industry to improve fertility with reduced sperm dosage inseminations. Spermatology will benefit from nanopurification methodology by gaining new tools for the identification of candidate biomarkers of sperm quality such as binder of sperm protein 5 (BSP5), described in the present study.
Popularitätsbasierte Anpassung des Replikationsfaktors in verteilten Dateisystemen (2011)

Verteilte Dateisysteme erlauben es zusatzliche Replikate von Dateien anzulegen, um Client-Zugriffe auf mehrere Server zu verteilen. Bei einer einheitlichen Festlegung des Replikationsfaktors fur alle Dateien wird der beschrankte verfugbare Speicherplatz jedoch nicht effizient genutzt, da es nur einen geringen Anteil von Dateien gibt, die haufig angefragt werden, wahrend die restlichen Dateien unnotig Speicherplatz belegen.

Der erste Teil dieser Arbeit beschreibt daher ein Verfahren den Replikationsfaktor einer Datei in Abhangigkeit ihrer Popularitat festzulegen. Im Kontext des verteilten Dateisystems XtreemFS wurde dazu ein zentraler Dienst fur die dynamische Replikation implementiert und mit einem Trace simuliert. Die Auswertung zeigt, dass die popularitatsbasierte Anpassung ein geeignetes Verfahren ist den Replikationsfaktor dynamisch festzulegen, da bei einer wochentlichen Ermittlung der Popularitat weniger als durchschnittlich 3,1% zusatzliche Replikate angelegt wurden.

Da der Dienst selbst nicht mit einer beliebigen Anzahl von Dateien skaliert, muss er in mehrere Partitionen unterteilt und dezentral ausgefuhrt werden. Darum entwickelt der zweite Teil der Arbeit eine dezentrale Variante des Dienstes und zeigt, dass der Replikationsfaktor identisch zum zentralen Fall festgelegt werden kann. Nur im Fall eines Netzwerkausfalls oder nicht synchronisierter lokaler Uhren tritt eine Abweichung der Replikationsfaktoren auf, deren Ausmas in der Simulation untersucht wurde.
Microfabrication services at INO (2003)

MEMS (Micro Electro Mechanical Systems) technology has expanded widely over the last decade in terms of its use in devices and instrumentation for diverse applications. However, access to versatile foundry services for MEMS fabrication is still limited. At INO, the presence of a multidisciplinary team and a complete tool set allow us to offer unique MEMS foundry-type services. These services include: design, prototyping, fabrication, packaging and testing of various MEMS and MOEMS devices. The design of a device starts with the evaluation of different structures adapted to a given application. Computer simulation tools, like IntelliSuite, ANSYS or custom software are used to evaluate the mechanical, optical, thermal and electromechanical performances. Standard IC manufacturing techniques such as metal, dielectric and semiconductor film deposition and etching as well as photolithographic pattern transfer are available. In addition, some unique techniques such as on-wafer lithography by laser writing, gray-scale mask lithography, thick photoresist lithography, selective electroplating, injection moulding and UV-assisted moulding are available to customers. The hermetic packaging and a novel patented wafer-level micropackaging are also applied. This multifaceted expertise has been utilized to manufacturing of several types of MEMS devices as well as complex instruments including micromirror-type devices, microfilters, IR microbolometric detector arrays, complete cameras and multipurpose sensors.