gebhart/patrepeval huggingface dataset:
Characterization of a Novel Golgi Apparatus-Localized Latency Determinant Encoded by Human Cytomegalovirus (2009)

Human cytomegalovirus (HCMV) exists indefinitely in infected individuals by a yet poorly characterized latent infection in hematopoietic cells. We previously demonstrated a requirement for the putative UL138 open reading frame (ORF) in promoting a latent infection in CD34(+) hematopoietic progenitor cells (HPCs) infected in vitro. In our present study, we have identified two coterminal transcripts of 2.7 and 3.6 kb and a 21-kilodalton (kDa) protein (pUL138) that are derived from the UL138 locus with early-late gene kinetics during productive infection. The UL138 transcripts and protein are detected in both fibroblasts and HPCs. A recombinant virus, FIX-UL138(STOP), that synthesizes the UL138 transcripts but not the protein exhibited a partial loss-of-latency phenotype in HPCs, similar to the phenotype observed for the UL138-null recombinant virus. This finding suggests that the UL138 protein is required for latency, but it does not exclude the possibility that the UL138 transcripts or other ORFs also contribute to latency. The mechanisms by which pUL138 contributes to latency remain unknown. While the 86- and 72-kDa immediate-early proteins were not detected in HPCs infected with HCMV in vitro, pUL138 did not function directly to suppress expression from the major immediate-early promoter in reporter assays. Interestingly, pUL138 localizes to the Golgi apparatus in infected cells but is not incorporated into virus particles. The localization of pUL138 to the Golgi apparatus suggests that pUL138 contributes to HCMV latency by a novel mechanism. pUL138 is the first HCMV protein demonstrated to promote an infection with the hallmarks of latency in CD34(+) HPCs.
The taming of the shrew: mitigating low-rate TCP-targeted attack (2010)

A Shrew attack, which uses a low-rate burst carefully designed to exploit TCP's retransmission timeout mechanism, can throttle the bandwidth of a TCP flow in a stealthy manner. While such an attack can significantly degrade the performance of all TCP-based protocols and services including Internet routing (e.g., BGP), no existing scheme clearly solves the problem in real network scenarios. In this paper, we propose a simple protection mechanism, called SAP (Shrew Attack Protection), for defending against a Shrew attack. Rather than attempting to track and isolate Shrew attackers, SAP identifies TCP victims by monitoring their drop rates and preferentially admits those packets from the victims with high drop rates to the output queue. This is to ensure that well-behaved TCP sessions can retain their bandwidth shares. Our simulation results indicate that under a Shrew attack, SAP can prevent TCP sessions from closing, and effectively enable TCP flows to maintain high throughput. SAP is a destination-port-based mechanism and requires only a small number of counters to find potential victims, which makes SAP readily implementable on top of existing router mechanisms.
EFFECTS OF CHRONIC EXCESS SALT INGESTION (1962)

Using the genetic technique of selective inbreeding, it has been possible to quickly develop two statistically separable populations from one unselected strain of Sprague-Dawley rats. One of these is very sensitive, the other very resistant, to the development of experimental hypertension from a high salt diet. It was suggested that similar genetic factors operate in man.
Small RNA Expression Profiling by High-Throughput Sequencing: Implications of Enzymatic Manipulation (2012)

Eukaryotic regulatory small RNAs (sRNAs) play significant roles in many fundamental cellular processes. As such, they have emerged as useful biomarkers for diseases and cell differentiation states. sRNA-based biomarkers outperform traditional messenger RNA-based biomarkers by testing fewer targets with greater accuracy and providing earlier detection for disease states. Therefore, expression profiling of sRNAs is fundamentally important to further advance the understanding of biological processes, as well as diagnosis and treatment of diseases. High-throughput sequencing (HTS) is a powerful approach for both sRNA discovery and expression profiling. Here, we discuss the general considerations for sRNA-based HTS profiling methods from RNA preparation to sequencing library construction, with a focus on the causes of systematic error. By examining the enzymatic manipulation steps of sRNA expression profiling, this paper aims to demystify current HTS-based sRNA profiling approaches and to aid researchers in the informed design and interpretation of profiling experiments.
Risk of Selecting De Novo Drug-Resistance Mutations during Structured Treatment Interruptions in Patients with Chronic HIV Infection (2005)

Genotypic mutations are selected during STI in a high proportion of patients (especially in patients receiving NNRTIs or lamivudine). Approximately one-half of selected mutations were archived mutations. Patients who had archived mutations did not have a higher risk of accumulating new mutations than did patients who were infected with wild-type virus before the STI.
α7 and α8 Nicotinic Receptor Subtypes Immunopurified from Chick Retina have Different Immunological, Pharmacological and Functional Properties (1997)

Nicotinic receptors are present in the chick retina, but their structure and functional characteristics are still unclear. Using anti-alpha7 and anti-alpha8 subunit-specific antibodies, we immunopurified the alpha7 and alpha8 subtypes of chick retina neuronal nicotinic receptors. When analysed by sodium dodecyl sulphate-polyacrylamide gel electrophoresis, the two purified subtypes consistently showed a similar peptide composition characterized by the presence of two major peptides of M(r) 58 +/- 1 and 54 +/- 1 kDa, and two minor peptides of 67 and 61 +/- 1 kDa. In the alpha7 subtype, the 58 kDa peptide was recognized by anti-alpha7 but not by anti-alpha8 antibodies; in the alpha8 subtype, the 58 kDa peptide was recognized only by anti-alpha8 antibodies. The alpha7 subtype had a single class of [125I]alpha-bungarotoxin binding sites with a K(D) value of 1.2 nM, whereas the purified alpha8 subtype had two classes of binding sites, one with a K(D) of 5.5 nM and the other with very high affinity (KD 52 pM), but present in only 8% of the receptors. Competition binding experiments also showed the presence on the alpha8 subtype of high- and low-affinity classes of binding sites; the affinity for cholinergic drugs of the former was greater than that of the single class present on the alpha7 subtype. When reconstituted in planar lipid bilayers, both subtypes formed ligand-gated cation channels with major conductance levels of 42 and 52 pS but with different lifetimes; the two channels were activated by agonists and blocked by d-tubocurarine and the glycinergic antagonist strychnine. In line with the binding data, the reconstituted alpha8 subtype had greater agonist sensitivity than the alpha7 subtype.
Correcting <scp>N</scp>euromuscular <scp>D</scp>eficits <scp>W</scp>ith <scp>G</scp>ene <scp>T</scp>herapy in <scp>P</scp>ompe <scp>D</scp>isease (2015)

Our data provide new mechanistic insight into the pathology of Pompe disease and suggest that early systemic correction to both neural and muscle tissues may be essential for successful correction of neuromuscular function in Pompe disease. Ann Neurol 2015;78:222-234.
Broadband spectral phase control with a tapered deformable mirror in a 4-f pulse shaper (2007)

We propose a simple technique for introducing a higher-order group velocity dispersion by bending a tapered deformable mirror in a 4-f pulse shaper. We design the taper shape and demonstrate a preliminary experiment of the spectral phase control in the wavelength range from 700 nm to 900 nm.
Mixed Alkylsilane Functionalized Surfaces for Simultaneous Wetting and Homeotropic Anchoring of Liquid Crystals (2011)

Surfaces functionalized with a self-assembled monolayer (SAM) formed from a mixture of two alkylsilanes with different chain lengths have been designed to simultaneously improve the liquid crystal (LC) wettability and promote homeotropic anchoring of the LC. Most chemically functionalized surfaces (e.g., long alkyl chain SAMs) that promote homeotropic alignment of LC possess low surface energy and result in poor LC wettability, inhibiting LC infiltration into microstructured surfaces and sometimes resulting in LC dewetting from the surface. However, a surface modified with a mixed SAM of octadecyltriethoxysilane (C18) and ethyltriethoxysilane (C2) exhibited very low LC contact angle while providing homeotropic anchoring. Ellipsometry was used to correlate the bulk concentration of C18 in the deposition solution to the surface coverage of C18 in the mixed monolayer; these bulk and surface concentrations were found to be equal within experimental uncertainty. The LC contact angle was found to depend nonmonotically with the surface coverage density, with a minimum (14.4 ± 0.1°) at a C18 surface coverage of 0.26 ± 0.08. Homeotropic LC anchoring was achieved at a C18 surface coverage of ≥0.11 ± 0.04, in the regime where a minimum in the LC contact angle was observed. The practical application of this approach to surface modification was demonstrated using a micropillar array sensor substrate. When the array was functionalized with a conventional C18 SAM, the LC did not infiltrate the array and exhibited a contact angle of 47.4 ± 0.5°. However, the LC material successfully infiltrated and wetted the same microstructured substrate when functionalized with a C18/C2 mixed SAM, while still exhibiting the desired homeotropic anchoring.
Generation of Leishmania mutants lacking antibiotic resistance genes using a versatile hit-and-run targeting strategy (2004)

The development of a method to create defined mutants of Leishmania parasites lacking foreign genes conferring resistance to antibiotics has both experimental and practical applications. Mutants deficient in specific virulence genes have potential as attenuated live vaccines, but these can only be of clinical relevance if the antibiotic resistance genes used for selection of the mutants are subsequently removed. In addition, the limited number of antibiotic resistance genes that can be used for genetic manipulation of Leishmania means that a system for recycling them for subsequent use would be highly beneficial when multiple genetic modifications are wanted. In the method we report here, a cassette carrying in tandem the hygromycin resistance gene as a positive marker and thymidine kinase gene as a negative marker is first integrated into the locus of interest and then replaced by a null targeting fragment containing no exogenous DNA. The application of this hit-and-run strategy for removal of one allele of the CPB cysteine peptidase gene array of Leishmania infantum is described.
<title>Use of discrete-state Markov process for Chinese-character recognition</title> (1990)

In this paper, an intelligent optical Chinese character recognition system using discrete-state Markov process has been developed to solve the input problem of Chinese characters. The doubly stochastic process encodes the distortion and similarity among patterns of a class through a stochastical and evaluating approach. A simple feature extraction is employed in our experiments, which is the histogram of the projected profiles. A character class is modeled by a 7-state Markov process, while the recognition rate for 5401 multi-font character classes reaches 97% on average for inside test and 92% on average for outside test.
25.6 A 70.5-to-85.5GHz 65nm phase-locked loop with passive scaling of loop filter (2015)

To support 16-QAM modulation in E-band applications, phase-locked loops (PLLs) are required to have wide a frequency tuning range from 71 to 86GHz and low phase noise of −90dBc/Hz @1MHz [1], which are still very challenging even with aggressive CMOS scaling [2]. Another issue associated with PLLs is the difficulty to integrate on-chip loop filters. Active loop filters are employed to scale down the loop filter capacitors and enable them to be fully integrated on-chip [3]. However, this method suffers from large active noise induced by the op-amp. Moreover, as the capacitance is reduced, the resistor value has to be increased to maintain the same zero frequency, leading to higher thermal noise and limiting achievable scaling factor. Another method is to integrate digital loop filters in all-digital PLLs (ADPLLs) [4]. Unfortunately, the quantization noise of digitally-controlled oscillators (DCOs) becomes a bottleneck to achieve good phase noise due to their limited frequency resolution. Furthermore, E-band DCO oscillation frequency is more sensitive to capacitor variation, making it even more difficult to achieve high frequency resolution. To address these issues, this paper proposes a 70.5-to-85.5GHz PLL with an injection-locked frequency tripler (ILFM3) and passive scaling to increase the effective capacitor for the loop filter by 100 times.
Ion implantation synthesized copper oxide-based resistive memory devices (2011)

Copper oxide resistive memory layers have been synthesized by ion implantation. Devices fabricated from off-stoichiometric Cu2O exhibited unipolar switching in forward/reverse bias without a forming voltage. The on-state conduction of these devices is likely dominated by a metallic filament, which ruptures via Joule heating to transition the device to the high resistance off-state. Technology scaling was achieved by oxygen implanting copper filled vias. The resulting via-based memory devices exhibited unipolar resistive switching down to 48 nm in diameter.
High-performance 8—14- µm Pb<sub>1-x</sub>Sn<sub>x</sub>Te photodiodes (1975)

Photovoltaic detectors of Pb <inf xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">1-x</inf> Sn <inf xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">x</inf> Te, sensitive in the 8- 14-µm spectral region, with near-theoretical performance characteristics, have been fabricated by a surface inversion technique. These detectors have exhibited quantum efficiencies of up to 45 percent limited by surface reflection), zero-bias resistance-area products of 21 Ωċcm <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sup> and background-limited detectivities of 1.5 × 10 <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">11</sup> cm ċ Hz <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">1/2</sup> /W. A theoretical model consistent with experimental results is presented. Such high-performance devices are useful in guidance, reconnaissance, surveillance, ranging, and communication systems.
Maximum SNR prefiltering for MIMO systems (2005)

In this paper, we derive a class of FIR prefilters for MIMO systems that maximize the signal-to-noise ratio (SNR) defined as the sum of SNRs for the output branches with uncorrelated noise. This definition is motivated by an analysis of the pairwise error probability. The maximum-SNR (MSNR) class of prefilters includes decision feedback equalization (DFE) and channel shortening equalization (CSE) prefilters. The feedback taps are completely suppressed by the CSE prefilter and not suppressed at all by the DFE prefilter. The MSNR class includes hybrid prefilters which are a combination of CSE and DFE prefilters. Hybrid prefilters allow middle ground for suppressing feedback taps which is desirable for equalization using decision feedback sequence estimation (DFSE). We show simulation results for joint DFSE demodulation of two 8-PSK modulated cochannel EDGE users using a single antenna receiver. We find that a hybrid prefilter performs best for this example.
Tunable dispersion compensating grating in a 10Gbit/s 100-220km step index fibre link (1995)

Chirped fibre gratings are of particular interest for compensating the dispersion (~17ps/nm.km @ 1.55µm) of installed step index (SI) fibre links since they are compact, low-loss, polarisation-insensitive and offer high negative-dispersion. In this paper we present a detailed investigation of the bandwidth-dispersion trade-off for a fixed (40mm) length tunable linearly-chirped fibre grating. In addition we demonstrate that such a grating can precisely compensate the dispersion in a 10Gbit/s transmission experiment for SI fibre lengths in the range 103-216km.
Transport of vacuum arc plasma through straight and curved magnetic ducts (1989)

We report on an experimental investigation of the transport of a metal vapor vacuum arc plasma through straight and curved magnetic solenoids for the case of an iron plasma and for magnetic field strength up to 650 G. We find that the fraction of plasma transported increases with magnetic field strength and saturates at a field at which the ion gyroradius equals the radius of the plasma channel. The magnetic field strength at the cathode location, where the plasma is injected into the solenoid, was found to be important, and for the present work the injection efficiency optimizes at a field of about 150 G.
Design of electronic seal system based on PKI (2011)

To ensure the integrity and non-repudiation of electronic documents received or sent by e-government affairs and protects their confidentially and effectiveness in transmission, this paper presents a solution for the electronic seal system based on PKI security system with a core of CA, and detailedly designs every module of the electronic seal system. It can resolve the safety problem of electronic document's stamp and signature, and assures the authenticity and reliability of electronic documents.
Ligation of 4-1BB (CDw137) Regulates Graft-Versus-Host Disease, Graft-Versus-Leukemia, and Graft Rejection in Allogeneic Bone Marrow Transplant Recipients (2001)

4-1BB is expressed on activated CD4(+) and CD8(+) T cells; its ligand, 4-1BB ligand is expressed on APCs. Despite expression on both T cell subpopulations, 4-1BB has been reported to predominantly affect CD8(+) T cell responses. By quantifying graft-vs-host disease alloresponses in vivo, we demonstrate that both CD4(+) and CD8(+) T cell-mediated alloresponses are regulated by 4-1BB/4-1BB ligand interactions to approximately the same extent. 4-1BB receptor-facilitated CD4(+) T cell-mediated alloresponses were partly CD28 independent. In two distinct marrow graft rejection systems, host CD8(+) and CD4(+) T cells each separately contributed to host anti-donor T cell-mediated allograft rejection. alpha 4-1BB mAb increased the graft-vs-leukemia effect of a suboptimal number of donor splenocytes given later post bone marrow transplantation by bolstering allogeneic responses resulting in leukemia elimination. In summary, 4-1BB ligation is a potent regulator of CD4(+) and CD8(+) T cell-mediated allogeneic responses in vivo. Modifying the ligation of 4-1BB represents a new approach to altering the graft-vs-host disease and graft-vs-leukemia effects of allogeneic T cells post bone marrow transplantation.
Iron-Sulfur Cluster-dependent Catalysis of Chlorophyllide a Oxidoreductase from Roseobacter denitrificans (2014)

Bacteriochlorophyll a biosynthesis requires the stereo- and regiospecific two electron reduction of the C7-C8 double bond of chlorophyllide a by the nitrogenase-like multisubunit metalloenzyme, chlorophyllide a oxidoreductase (COR). ATP-dependent COR catalysis requires interaction of the protein subcomplex (BchX)2 with the catalytic (BchY/BchZ)2 protein to facilitate substrate reduction via two redox active iron-sulfur centers. The ternary COR enzyme holocomplex comprising subunits BchX, BchY, and BchZ from the purple bacterium Roseobacter denitrificans was trapped in the presence of the ATP transition state analog ADP·AlF4(-). Electron paramagnetic resonance experiments revealed a [4Fe-4S] cluster of subcomplex (BchX)2. A second [4Fe-4S] cluster was identified on (BchY/BchZ)2. Mutagenesis experiments indicated that the latter is ligated by four cysteines, which is in contrast to the three cysteine/one aspartate ligation pattern of the closely related dark-operative protochlorophyllide a oxidoreductase (DPOR). In subsequent mutagenesis experiments a DPOR-like aspartate ligation pattern was implemented for the catalytic [4Fe-4S] cluster of COR. Artificial cluster formation for this inactive COR variant was demonstrated spectroscopically. A series of chemically modified substrate molecules with altered substituents on the individual pyrrole rings and the isocyclic ring were tested as COR substrates. The COR enzyme was still able to reduce the B ring of substrates carrying modified substituents on ring systems A, C, and E. However, substrates with a modification of the distantly located propionate side chain were not accepted. A tentative substrate binding mode was concluded in analogy to the related DPOR system.
<i>p</i>-type conduction in Mg-doped GaN and Al0.08Ga0.92N grown by metalorganic vapor phase epitaxy (1994)

Temperature dependences of the hole concentration and Hall mobility in Mg-doped GaN and Al0.08Ga0.92N grown by metalorganic vapor phase epitaxy were measured by the van der Pauw method over a wide temperature range from 100 to 500 K. Assuming that the effective mass of holes in Al0.08Ga0.92N is equal to that of GaN, the activation energy of the Mg shallow acceptor in Al0.08Ga0.92N is estimated to be about 35 meV deeper than that in GaN.
MATIN: A Random Network Coding Based Framework for High Quality Peer-to-Peer Live Video Streaming (2013)

In recent years, Random Network Coding (RNC) has emerged as a promising solution for efficient Peer-to-Peer (P2P) video multicasting over the Internet. This probably refers to this fact that RNC noticeably increases the error resiliency and throughput of the network. However, high transmission overhead arising from sending large coefficients vector as header has been the most important challenge of the RNC. Moreover, due to employing the Gauss-Jordan elimination method, considerable computational complexity can be imposed on peers in decoding the encoded blocks and checking linear dependency among the coefficients vectors. In order to address these challenges, this study introduces MATIN which is a random network coding based framework for efficient P2P video streaming. The MATIN includes a novel coefficients matrix generation method so that there is no linear dependency in the generated coefficients matrix. Using the proposed framework, each peer encapsulates one instead of n coefficients entries into the generated encoded packet which results in very low transmission overhead. It is also possible to obtain the inverted coefficients matrix using a bit number of simple arithmetic operations. In this regard, peers sustain very low computational complexities. As a result, the MATIN permits random network coding to be more efficient in P2P video streaming systems. The results obtained from simulation using OMNET++ show that it substantially outperforms the RNC which uses the Gauss-Jordan elimination method by providing better video quality on peers in terms of the four important performance metrics including video distortion, dependency distortion, End-to-End delay and Initial Startup delay.
A generalised design technique for traceback survivor memory management in Viterbi decoders (2002)

There are number of algorithms available for the design of traceback survivor memory units in Viterbi (1967) decoders. Perhaps the best description of the traceback algorithms was given by Feygin et al. (1993), where four separate algorithms were presented. These four algorithms, however, can all be encapsulated in the description of two broader algorithms. In addition a new implementation technique is presented for one family of algorithms. As a result a host of new, low complexity implementations of survivor memory units become possible.