gebhart/patrepeval huggingface dataset:
LDPC decoder strategies for achieving low error floors (2008)

One of the most significant impediments to the use of LDPC codes in many communication and storage systems is the error-rate floor phenomenon associated with their iterative decoders. The error floor has been attributed to certain subgraphs of an LDPC codepsilas Tanner graph induced by so-called trapping sets. We show in this paper that once we identify the trapping sets of an LDPC code of interest, a sum-product algorithm (SPA) decoder can be custom-designed to yield floors that are orders of magnitude lower than the conventional SPA decoder. We present three classes of such decoders: (1) a bi-mode decoder, (2) a bit-pinning decoder which utilizes one or more outer algebraic codes, and (3) three generalized-LDPC decoders. We demonstrate the effectiveness of these decoders for two codes, the rate-1/2 (2640,1320) Margulis code which is notorious for its floors and a rate-0.3 (640,192) quasi-cyclic code which has been devised for this study. Although the paper focuses on these two codes, the decoder design techniques presented are fully generalizable to any LDPC code.
Self-Purification in Semiconductor Nanocrystals (2006)

Doping of nanocrystals is an important and very difficult task. "Self-purification" mechanisms are often claimed to make this task even more difficult, as the distance a defect or impurity must move to reach the surface of a nanocrystal is very small. We show that self-purification can be explained through energetic arguments and is an intrinsic property of defects in semiconductor nanocrystals. We find the formation energies of defects increases as the size of the nanocrystal decreases. We analyze the case of Mn-doped CdSe nanocrystals and compare our results to experimental findings.
ThruChip Interface for Heterogeneous Chip Stacking (2013)

This paper presents a wireless inter-chip link using inductive coupling, namely ThruChip Interface (TCI). TCI is a digital CMOS circuit solution in a standard CMOS technology. It is much less expensive than TSV (Through Silicon Via) but bears comparison in performance. Delay time and energy dissipation will scale down by scaling device size and chip thickness. As the inductive coupling enables interface among chips under different supply voltages, TCI is suitable for heterogeneous integration. A 90nm 8-core processor under 1.0V power supply and two 65nm SRAM's under 1.2V power supply are stacked and AC-coupled by TCI at 19.2Gb/s. Power dissipation and area efficiency of the link is 1pJ/b and 0.15mm2/Gbps respectively, which is 1/30 and 1/3 in comparison with the conventional DDR2 interface.
High-Speed Wavelength-Swept Semiconductor Laser Using a Diffraction Grating and a Polygon Scanner in Littrow Configuration (2007)

High-speed tuning of an extended-cavity semiconductor laser is demonstrated using a scanning polygon filter. We achieved a tuning rate of 7714-nm/ms with 65 mW of power over a wavelength range of 135-nm and with an instantaneous line-width ~ 0.13 nm.
Evaluation of a sensor for low interface pressure applications (2000)

An ultra-thin, small sensor has recently been developed, "FlexiForce" (Tekscan, Boston, MA, USA), which may be effective for the measurement of low interface pressure between the skin, support surfaces and pressure garments. To evaluate the suitability of the sensor for these applications, drift, repeatability, linearity, hysteresis and curvature effects were tested under laboratory conditions. The drift was 1.7-2.5%/logarithmic time, the repeatability was 2.3-6.6% and the linearity was 1.9-9.9% in the range of forces of 10-50 g applied. The hysteresis was 5.4% on average. The output offset of the sensor increased with decreasing radius of curvature for radii less than 32 mm compared with a flat surface when no pressure was applied. The sensitivity to pressure decreased with curvature for radii less than 32 mm. It was found that the sensor had acceptable drift, repeatability, linearity and hysteresis. However, a significant curvature effect was observed indicating that the sensor is suitable for direct measurement on surfaces with the radii greater than 32 mm under static conditions.
Inhibition of Pectinase and Cellulase by Certain Plants (1962)

1. The water-soluble leaf extracts from 61 plant species in 32 families were screened for their ability to inhibit two hydrolytic fungal enzymes, cellulase and pectinase. 2. Leaf extracts from 29 species inhibited pectinase and extracts from 14 inhibited cellulase. 3. The leaves from muscadine grape, persimmon, dogwood, blueberry, sericea, blackberry, raspberry, and rose were considered good sources for the pectinase inhibitor as measured against cucumber-flower pectinase and a commercial pectinase. 4. In general, cellulase inhibition by the different plant species was less pronounced than that observed for pectinase. The first five species listed in the previous paragraph gave strong inhibition of cucumber-flower cellulase. Muscadine grape and persimmon were the only two species which inhibited the commercial cellulase enzyme 19AP, and then only moderate to weak inhibition was obtained.
Surfactant Gel Foam/Emulsion: History and Field Application in Western Canadian Sedimentary Basin (2005)

Abstract Surfactant gels were introduced into the Western Canadian Sedimentary Basin (WCSB) as fracturing fluids in 1998. These fluids proved to be successful for propped fracture stimulations in shallow gas wells. About the same time, it was found that surfactant gels could be foamed with nitrogen or emulsified with a high quality (volume fraction) of liquid CO2. Since their inception in the Canadian market, surfactant gel foams/emulsions have been used in coal-bed methane (CBM) and also in the stimulation of deeper, higher temperature applications. This paper will discuss the use of these fluids in the WCSB as well as the chemistry of the fluids, laboratory conductivity measurements which show proppant pack retained conductivities of greater than 96%, and their application in more than 3,100 oil and gas producing zones. The fluids have been used in a variety of formations and in wells with permeability's from 0.1 millidarcies to 10 Darcies, depths in excess of 3000 m (10000 feet) and bottom-hole temperatures up to 100 °C (212 °F). For water-sensitive formations, foamed surfactant gel fracturing costs are significantly less in comparison to hydrocarbon, CO2, or methanol-based fluids.
The Influence of DNA Sequence on the Immunostimulatory Properties of Plasmid DNA Vectors (1998)

To determine the influence of DNA sequence on immunostimulatory properties of vaccine vectors, we tested the induction of in vitro and in vivo immune responses by plasmids modified to contain extended runs of dG sequences. Studies with oligonucleotides indicate that dG sequences can directly stimulate B cells as well as enhance the activity of immunostimulatory CpG motifs because of interaction with the macrophage scavenger receptor (MSR); this receptor can bind a variety of polyanions including dG sequences. To modify vectors, we introduced stretches of 20-60 dG residues into the pCMV-beta and pSG5rab.gp vectors and measured the ability of these plasmids to induce IL-12 and IFN-gamma production by murine splenocytes. The induction of in vivo antibody responses to rabies glycoprotein was also assessed with the pSG5rab.gp vectors. In in vitro cultures, cytokine production induced by plasmids with and without dG sequences was similar. Furthermore, the addition of dG sequences to pSG5rab.gp vectors failed to enhance the anti-rabies glycoprotein response to immunization. To assess further mechanisms by which plasmids stimulate macrophages, we measured the effects of MSR ligands on in vitro cytokine induction. In in vitro cultures, poly(G), dG30, and fucoidan inhibited IL-12 induction by plasmids. IL-12 induction was also inhibited by mammalian DNA but was unaffected by polyanions that are not MSR ligands. Together, these results suggest that the addition of 20 to 60-base dG sequences to plasmids does not significantly affect their properties as immunostimulators or vaccines. Furthermore, these results suggest that MSR ligands can block cytokine induction by plasmid DNA whether or not the plasmid contains extended runs of dG.
Vascular repair processes mediated by transforming growth factor-beta. (2001)

These results identify TGF-beta isoforms as the major mediators of adventitial fibrosis and negative remodeling after arterial injury, which is a major cause for restenosis following angioplasty.
Antiproteases as Therapeutics to Target Inflammation in Cystic Fibrosis (2010)

Cystic Fibrosis (CF) is the most common fatal inherited disease of Caucasians, affecting about 1 in 3000 births. Patients with CF have a recessive mutation in the gene encoding the CF transmembrane conductance regulator (CFTR). CFTR is expressed in the epithelium of many organs throughout the exocrine system, however, inflammation and damage of the airways as a result of persistent progressive endobronchial infection is a central feature of CF. The inflammatory response to infection brings about a sustained recruitment of neutrophils to the site of infection. These neutrophils release various pro-inflammatory compounds including proteases, which when expressed at aberrant levels can overcome the endogenous antiprotease defence mechanisms of the lung. Unregulated, these proteases can exacerbate inflammation and result in the degradation of structural proteins and tissue damage leading to bronchiectasis and loss of respiratory function. Other host-derived and bacterial proteases may also contribute to the inflammation and lung destruction observed in the CF lung. Antiprotease strategies to dampen the excessive inflammatory response and concomitant damage to the airways remains an attractive therapeutic option for CF patients.
Blockage of NF-κB Signaling by Selective Ablation of an mRNA target by 2-5A Antisense Chimeras (1994)

Activation of 2-5A-dependent ribonuclease by 5'-phosphorylated, 2',5'-linked oligoadenylates, known as 2-5A, is one pathway of interferon action. Unaided uptake into HeLa cells of 2-5A linked to an antisense oligonucleotide resulted in the selective ablation of messenger RNA for the double-stranded RNA (dsRNA)-dependent protein kinase PKR. Similarly, purified, recombinant human 2-5A-dependent ribonuclease was induced to selectively cleave PKR messenger RNA. Cells depleted of PKR activity were unresponsive to activation of nuclear factor-kappa B (NF-kappa B) by the dsRNA poly(I):poly(C), which provides direct evidence that PKR is a transducer for the dsRNA signaling of NF-kappa B.
FM and AM mode locking of the homogeneous laser - Part I: Theory (1970)

A new general analysis for mode-locked operation of a homogeneously broadened laser with either internal phase (FM) or amplitude (AM) modulation is presented in this paper. In this analysis, a complex Gaussian pulse is followed through one pass around the laser cavity. Approximations are made to the line shape and modulation characteristics to keep the pulse Gaussian. After one round trip, a self-consistent solution is required. This yields simple analytic expressions for the pulse length, frequency chirp, and bandwidth of the mode-locked pulses. The analysis is further extended to include effects of detuning of the modulator, in which case analytical expressions are obtained for the phase shift of the pulse within the modulation cycle, the shift of the pulse spectrum off line center, the change in pulse length, and the change in power output. Numerical results for a typical Nd:YAG laser are given. In the case of the FM mode-locked laser it is found that there is a frequency chirp on the pulse and that this causes pulse compression and stretching when the modulator is detuned. Etalon effects and dispersion effects are also considered.
Quantification of Circulating DNA: In the Preparation Lies the Rub (2001)

Although cell-free nucleic acids were first described in the 1940s (1), it was not until tumor-specific DNA sequences were detected in the plasma of cancer patients (2) that they started to attract the interest of the wider scientific community. Because the placenta shares numerous features with malignant tissues, such as a high rate of cell turnover and the expression of certain protooncogenes, these seminal reports prompted Lo and colleagues to examine whether fetal DNA could be detected in an analogous manner in the plasma of pregnant women. This hypothesis indeed proved to be true, and in 1997 Lo et al. (3) described the presence of fetal DNA circulating in maternal plasma and serum. This observation has been one of the most important for those attempting to develop safe and efficacious methods for prenatal diagnosis of fetal genetic traits. The reason for this interest is that current methods of obtaining fetal material for prenatal diagnosis rely on invasive procedures such as amniocentesis or chorionic villus sampling, both of which are associated with a procedure-related fetal loss rate of almost 1% (4). Although concerted efforts had been made to develop noninvasive, and hence risk-free, alternative prenatal diagnostic methods using fetal cells enriched from the blood of pregnant women, …
Modification of the Campylobacter jejuni N-Linked Glycan by EptC Protein-mediated Addition of Phosphoethanolamine (2012)

Campylobacter jejuni is the major worldwide cause of bacterial gastroenteritis. C. jejuni possesses an extensive repertoire of carbohydrate structures that decorate both protein and non-protein surface-exposed structures. An N-linked glycosylation system encoded by the pgl gene cluster mediates the synthesis of a rigidly conserved heptasaccharide that is attached to protein substrates or released as free oligosaccharide in the periplasm. Removal of N-glycosylation results in reduced virulence and impeded host cell attachment. Since the N-glycan is conserved, the N-glycosylation system is also an attractive option for glycoengineering recombinant vaccines in Escherichia coli. To determine whether non-canonical N-glycans are present in C. jejuni, we utilized high throughput glycoproteomics to characterize C. jejuni JHH1 and identified 93 glycosylation sites, including 34 not previously reported. Interrogation of these data allowed the identification of a phosphoethanolamine (pEtN)-modified variant of the N-glycan that was attached to multiple proteins. The pEtN moiety was attached to the terminal GalNAc of the canonical N-glycan. Deletion of the pEtN transferase eptC removed all evidence of the pEtN-glycan but did not globally influence protein reactivity to patient sera, whereas deletion of the pglB oligosaccharyltransferase significantly reduced reactivity. Transfer of eptC and the pgl gene cluster to E. coli confirmed the addition of the pEtN-glycan to a target C. jejuni protein. Significantly reduced, yet above background levels of pEtN-glycan were also observed in E. coli not expressing eptC, suggesting that endogenous E. coli pEtN transferases can mediate the addition of pEtN to N-glycans. The addition of pEtN must be considered in the context of glycoengineering and may alter C. jejuni glycan-mediated structure-function interactions.
Inhibitory effect of the polyinosinic‐polycytidylic acid/cationic liposome on the progression of murine B16F10 melanoma (2006)

Cellular proteins, retinoic acid inducible gene-I and Toll-like receptor 3, sense dsRNA including polyinosinic-polycytidylic acid (PIC) to stimulate innate immune response. The local administration of PIC has been demonstrated to be effective in anti-tumor immunotherapy. However, the effects of PIC delivered cross the cell membrane have not yet been examined. To address this issue, we used a complex of PIC and cationic liposome (PIC liposome) and examined its anti-tumor effects in vitro and in vivo. PIC liposome could directly suppress the growth of B16F10 melanoma in vitro and repeated peritumoral injections of PIC liposome inhibited melanoma growth in a dose-dependent manner. This treatment induced tyrosinase-related protein-2 (TRP-2)-tetramer(+) CD8(+) cells in the lymph nodes. As the mechanism for its anti-tumor immune response, we showed that the intradermal injection of PIC liposome induced the maturation of dendritic cells (DC). Moreover, the intratumoral injection of immature DC after treatment with PIC liposome significantly increased the number of TRP-2-specific IFN-gamma-producing cells in the lymph nodes as well as spleen, which resulted in an augmentation of the anti-tumor immune response. These studies demonstrate the potential of peritumoral injection of PIC liposome as immunotherapy for malignant melanoma.
A clinical rating scale for progressive supranuclear palsy (2007)

We devised a Progressive Supranuclear Palsy (PSP) Rating Scale comprising 28 items in six categories: daily activities (by history), behaviour, bulbar, ocular motor, limb motor and gait/midline. Scores range from 0 to 100, each item graded 0-2 (six items) or 0-4 (22 items). Inter-rater reliability is good, with intra-class correlation coefficient for the overall scale of 0.86 (95% CI 0.65-0.98). A single examiner applied the PSPRS at every visit for 162 patients. Mean rate of progression was 11.3 (+/-11.0) points per year. Neither onset age nor gender correlated well with rate of progression. Median actuarially corrected survival was 7.3 years. The PSPRS score was a good independent predictor of subsequent survival (P < 0.0001). For example, for patients with scores from 40 to 49, 3-year survival was 41.9% (95% CI 31.0-56.6) but 4-year survival was only 17.9% (95% CI 10.2-31.5). For those patients, likelihood or retaining some gait function was 51.7% (40.0-66.9) at 1 year but only 6.5% (1.8-23.5) at 3 years. We conclude that the PSPRS is a practical measure that is sensitive to disease progression and could be useful as a dependent variable in observational or interventional trials and as an indicator of prognosis in clinical practice.
Elucidating the Sole Contribution from Electromagnetic Near‐Fields in Plasmon‐Enhanced Cu2O Photocathodes (2015)

Despite many promising reports of plasmon‐enhanced photocatalysis, the inability to identify the individual contributions from multiple enhancement mechanisms has delayed the development of general design rules for engineering efficient plasmonic photocatalysts. Herein, a plasmonic photocathode comprised of Au@SiO 2 (core@shell) nanoparticles embedded within a Cu 2 O nanowire network is constructed to exclusively examine the contribution from one such mechanism: electromagnetic near‐field enhancement. The influence of the local electromagnetic field intensity is correlated with the overall light‐harvesting efficiency of the device through variation of the SiO 2 shell thickness (5–22 nm) to systematically tailor the distance between the plasmonic Au nanoparticles and the Cu 2 O nanowires. A threefold increase in device photocurrent is achieved upon integrating the Au@SiO 2 nanoparticles into the Cu 2 O nanowire network, further enabling a 40% reduction in semiconductor film thickness while maintaining photocathode performance. Photoelectrochemical results are further correlated with photoluminescence studies and optical simulations to confirm that the near‐field enhancement is the sole mechanism responsible for increased light absorption in the plasmonic photocathode.
Relationship between evolutionary rate and cellular location among the Inv/Spa invasion proteins of Salmonella enterica. (1995)

For 21 strains of Salmonella enterica, nucleotide sequences were obtained for three invasion genes, spaO, spaP, and spaQ, of the chromosomal inv/spa complex, the products of which form a protein export system required for entry of the bacteria into nonphagocytic host cells. These genes are present in all eight subspecies of the salmonellae, and homologues occur in a variety of other bacteria, including the enteric pathogens Shigella and Yersinia, in which they are plasmid borne. Evolutionary diversification of the invasion genes among the subspecies of S. enterica has been generally similar in pattern and average rate to that of housekeeping genes. However, the range of variation in evolutionary rate among the invasion genes is unusually large, and there is a relationship between the evolutionary rate and cellular location of the invasion proteins, possibly reflecting diversifying selection on exported proteins in adaptation to variable host factors in extracellular environments. The SpaO protein, which is hypervariable in S. enterica and exhibits only 24% sequence identity with its homologues in Shigella and Yersinia, is secreted. In contrast, the membrane-associated proteins SpaP, SpaQ, and InvA are weakly polymorphic and have > 60% sequence identity with the corresponding proteins of other enteric bacteria. Acquisition of the inv/spa genes may have been a key event in the evolution of the salmonellae as pathogens, following which the invention of flagellar phase shifting facilitated niche expansion to include warm-blooded vertebrates.
Genetic alterations responsible for reduced susceptibility to vancomycin in community-associated MRSA strains of ST72 (2017)

Based on the genomic data, molecular experiments and PAP and cell wall analyses, we propose that a single mutation of vraR is associated with the reduced susceptibility to vancomycin in MRSA and further treatment failure.
Synthesis, Structure−Activity Relationships, and Drug Resistance of β-d-3‘-Fluoro-2‘,3‘-Unsaturated Nucleosides as Anti-HIV Agents (2004)

Our recent studies demonstrated that d- and l-2'-fluoro-2',3'-unsaturated nucleosides (d- and l-2'-F-d4Ns) display moderate to potent antiviral activities against HIV-1 and HBV. As an extension of these findings, beta-d-3'-fluoro-2',3'-unsaturated nucleosides were synthesized as potential antiviral agents. The key intermediate (2S)-5-(1,3-dioxolan)-1-benzoyloxy-3,3-difluoropentan-2-ol 6 was prepared from 2,3-O-isopropylidene-d-glyceraldehyde 1, which was converted to 5-O-benzoxy-d-2-deoxy-3,3-difluoropentofuranosyl acetate 7 by the ring-closure reaction under acidic conditions. The acetate 7 was condensed with silylated purine and pyrimidine bases, which produced the alpha and beta isomers. The 3',3'-difluoro nucleosides were then treated with t-BuOK to give the desired 3'-fluoro-unsaturated nucleosides. We studied the structure-activity relationships of d-3'-fluoro-2',3'-unsaturated nucleosides against HIV-1 in human peripheral blood mononuclear cells, from which we found that the cytosine derivative 26 was the most potent among the synthesized compounds. To understand the mode of action and drug resistance profile, with particular regard to the role of fluorine, we performed the molecular modeling studies of the cytidine analogue d-3'F-d4C and found a good correlation between calculated relative binding energies and activity/resistance data. Our model also shows interactions of the 3'-fluorine and the 2',3' double bond, which can be correlated to the observed biological data. Differences between fluorine substitution at the 3' and 2' positions may account for the higher cross-resistance with lamivudine observed in the 2'-fluorinated series.
Parkinsonism With 'On-Off' Phenomena (1979)

Continuous intravenous infusion of levodopa was used for eight days to manage a parkinsonian patient with "on-off" fluctuations who underwent abdominoperineal resection for carcinoma of the rectum. Reasonable control of parkinsonism was obtained initially with small doses of levodopa, but more than 4 g daily were eventually required. No adverse effects on cardiac rhythm, blood pressure, or gastrointestinal function occurred. Frequent adjustment of levodopa dosage was necessary in view of continuing "on-off" fluctuations. Severe akinesia, which can cause dysphagia, respiratory complications, and venous stasis in the legs, can benefit from this method of management after major abdominal surgery in a patient with advanced parkinsonism.