gebhart/patrepeval huggingface dataset:
Applications of coding in network communications (2012)

This thesis uses the tool of network coding to investigate fast peer-to-peer file distribution, anonymous communication, robust network construction under uncertainty, and prioritized transmission. 
In a peer-to-peer file distribution system, we use a linear optimization approach to show that the network coding framework significantly simplifies analysis even in scenarios where the optimal solution does not require coding. We also study the effect of requiring reciprocity and the impact of dynamically changing network scenarios. 
Second, we investigate anonymous routing in peer-to-peer networks. The goal is to design and analyze a peer-to-peer system that hides the identities of source and sink pairs against adversarial nodes. We first propose a protocol for subgraph construction signaling. The protocol uses path diversity rather than cryptographic keys. We prove information theoretic security of the proposed protocol. We investigate a variety of deterministic and randomized subgraph designs. We also give a reverse path construction mechanism, with which a sink can reply to the source without knowing the source identity. We next investigate anonymous data transmission using network coding. Again, path diversity (with network coding) is used to hide the identities of source and sink pairs. We investigate the effect of subgraph shape on anonymity and congestion arising from traffic shaping constraints, demonstrating the tradeoff between the two through simulations. 
Third, we study the problem of network construction under uncertainty about link-loss rates. We prove that both maximizing throughput and minimizing cost are coNP-hard problems. We find polynomial time-solvable solutions that outperform other deterministic approaches. 
Lastly, we investigate strategies for communication under a system that prioritizes data based on the worth of data and the probability of successful transmission. Only the highest priority data is transmitted when communication is very limited.
A role for iron in oxidant-mediated ischemic injury to intestinal microvasculature (1987)

Recent reports in the literature suggest that iron plays an important role in free radical-mediated injury in biological systems. To assess the role of iron-catalyzed oxidant production in ischemia-reperfusion injury, we examined the influence of deferoxamine (an iron chelator) and apotransferrin (iron transporting protein) on the increased intestinal vascular permeability produced by 1 h of ischemia and reperfusion. Both agents were administered intravascularly as a constant infusion, beginning 5 min before reperfusion. Capillary osmotic reflection coefficients were derived from the relationship between lymph-to-plasma protein concentration ratio and lymph flow in the feline small bowel. Vascular permeability in control intestinal preparations was 0.08 +/- 0.005, however it increased significantly to 0.40 +/- 0.03 in preparations subjected to 1 h of ischemia and 30 min of reperfusion. Vascular permeability in the deferoxamine-(0.15 +/- 0.009) and apotransferrin- (0.17 +/- 0.002) treated animals were significantly lower (P less than 0.01) than in the untreated group. Treatment with iron-loaded deferoxamine or transferrin did not offer any protection against ischemic injury. These findings support the hypothesis that iron plays an important role in the formation of hydroxyl radicals after reperfusion of the ischemic bowel.
Volumetric multislice gagCEST imaging of articular cartilage: Optimization and comparison with T1rho (2016)

We demonstrated the feasibility and optimization of multislice GagCEST mapping of articular cartilage. Volumetric analysis and decreased scan times will help to advance the clinical utility of GagCEST imaging of articular cartilage. Magn Reson Med 77:1134-1141, 2017. © 2016 International Society for Magnetic Resonance in Medicine.
PI3K/AKT Signaling Regulates H3K4 Methylation in Breast Cancer (2016)

Post-translational histone H3 modifications regulate transcriptional competence. The mechanisms by which the epigenome is regulated in response to oncogenic signaling remain unclear. Here we show that H3K4me3 is increased in breast tumors driven by an activated PIK3CA allele and that inhibition of PI3K/AKT signaling reduces promoter-associated H3K4me3 in human breast cancer cells. We show that the H3K4 demethylase KDM5A is an AKT target and that phosphorylation of KDM5A regulates its nuclear localization and promoter occupancy. Supporting a role for KDM5A in mediating PI3K/AKT transcriptional effects, the decreased expression in response to AKT inhibition of a subset of cell-cycle genes associated with poor clinical outcome is blunted by KDM5A silencing. Our data identify a mechanism by which PI3K/AKT signaling modulates the cancer epigenome through controlling H3K4 methylation and suggest that KDM5A subcellular localization and genome occupancy may be pharmacodynamic markers of the activity of PI3K/AKT inhibitors currently in clinical development.
Auditory-modeling inspired methods of feature extraction for robust automatic speech recognition (2002)

This paper proposes a technique of extracting robust feature vectors for ASR. The technique is inspired by work related to auditory modeling. It involves first filtering the speech signal through a bank of band-pass filters, which are based on a model of the human cochlea. Autocorrelation functions (ACF) are computed on the filters' outputs. Then the individual ACFs are scaled by their corresponding voice indices (VIs), which use information related to the pitch. A summed ACF is then obtained by summing the individual ACFs across the bands. Feature vectors are then computed using standard cepstral analysis, by treating the summed ACF as a regular ACF. Finally, frame indices (FIs) weigh the feature vectors in the time domain. The effectiveness of the proposed techniques, compared to LPCC and MFCC, are demonstrated by comparing the results obtained from simple recognition experiments.
Der f 34, a Novel Major House Dust Mite Allergen Belonging to a Highly Conserved Rid/YjgF/YER057c/UK114 Family of Imine Deaminases (2016)

The high prevalence of house dust mite (HDM) allergy is a growing health problem worldwide, and the characterization of clinically important HDM allergens is a prerequisite for the development of diagnostic and therapeutic strategies. Here, we report a novel HDM allergen that belongs structurally to the highly conserved Rid/YjgF/YER057c/UK114 family (Rid family) with imine deaminase activity. Isolated HDM cDNA, named der f 34, encodes 128 amino acids homologous to Rid-like proteins. This new protein belongs to the Rid family and has seven conserved residues involved in enamine/imine deaminase activity. Indeed, we demonstrated that purified Der f 34 had imine deaminase activity that preferentially acted on leucine and methionine. Native Der f 34 showed a high IgE binding frequency as revealed by two-dimensional immunoblotting (62.5%) or ELISA (68%), which was comparable with those of a major HDM allergen Der f 2 (77.5 and 79%, respectively). We also found that Der f 34 showed cross-reactivity with another prominent indoor allergen source, Aspergillus fumigatus. This is the first report showing that the Rid family imine deaminase represents an additional important pan-allergen that is conserved across organisms. The high prevalence of house dust mite (HDM) allergy is a growing health problem worldwide, and the characterization of clinically important HDM allergens is a prerequisite for the development of diagnostic and therapeutic strategies. Here, we report a novel HDM allergen that belongs structurally to the highly conserved Rid/YjgF/YER057c/UK114 family (Rid family) with imine deaminase activity. Isolated HDM cDNA, named der f 34, encodes 128 amino acids homologous to Rid-like proteins. This new protein belongs to the Rid family and has seven conserved residues involved in enamine/imine deaminase activity. Indeed, we demonstrated that purified Der f 34 had imine deaminase activity that preferentially acted on leucine and methionine. Native Der f 34 showed a high IgE binding frequency as revealed by two-dimensional immunoblotting (62.5%) or ELISA (68%), which was comparable with those of a major HDM allergen Der f 2 (77.5 and 79%, respectively). We also found that Der f 34 showed cross-reactivity with another prominent indoor allergen source, Aspergillus fumigatus. This is the first report showing that the Rid family imine deaminase represents an additional important pan-allergen that is conserved across organisms.
ChemInform Abstract: A CONVENIENT SYNTHESIS OF O‐ALKYL THIOESTERS FROM ESTERS (1984)

Abstract Aus den Estern (I) werden die Thiono‐ester (II) durch Behandlung mit LDA, Trimethylchlorsilan und Schwefelwasserstoff hergestellt.
Tiny Video Networks (2021)

Abstract Automatic video understanding is becoming more important for applications where real‐time performance is crucial and compute is limited: for example, automated video tagging, robot perception, activity recognition for mobile devices. Yet, accurate solutions so far have been computationally intensive. We propose efficient models for videos—Tiny Video Networks—which are video architectures, automatically designed to comply with fast runtimes and, at the same time are effective at video recognition tasks. The TVNs run at faster‐than‐real‐time speeds and demonstrate strong performance across several video benchmarks. These models not only provide new tools for real‐time video applications, but also enable fast research and development in video understanding. Code and models are available.
Utilizing the Spatial Information Provided by Channel Norm Feedback in SDMA Systems (2008)

<para xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink"> To achieve high performance, in terms of reliability and throughput, in future multiple-antenna communication systems, it is essential to fully exploit the spatial dimensions of the wireless propagation channel. In multiuser communication systems, the throughput can be significantly increased by simultaneously transmitting to several users in the same time-frequency slot by means of <emphasis emphasistype="boldital">spatial-division multi-access</emphasis> (SDMA). A major limiting factor for downlink SDMA transmission is the amount of <emphasis emphasistype="boldital">channel-state information</emphasis> (CSI) that is available at the transmitter. In most cases, CSI can be measured/estimated only at the user terminals and must be fed back to the base station. This procedure typically constrains the amount of CSI that can be conveyed to the base station. Herein, we develop several low-complexity, as well as optimized, SDMA downlink resource-allocation schemes that are particularly suitable for systems utilizing statistical channel information and partial CSI feedback. </para>
EPIPOLYTHIOPIPERAZINEDIONE ANTIBIOTICS FROM PENICILLIUM TURBATUM (1974)

A group of epipolythiopiperazinedione antibiotics was obtained from the fermentation broth of Penicillium turbatum. The fermentation, isolation, biological properties and structure elucidation of three metabolites of this group are discussed.
Protective Effect of New Formulation of Carnosine+Hyaluronic Acid on the Inflammation and Cartilage Degradation in the Experimental Model of Osteoarthritis (2020)

Osteoarthritis (OA) is a disease that currently has no cure. There are numerous studies showing that carnosine and hyaluronic acid (HA) have a positive pharmacological action during joint inflammation. For this reason, the goal of this research was to discover the protective effect of a new HA+Carnosine formulation (FidHycarn) on the inflammatory response and on the cartilage degradation in in vivo experimental model of OA. This model was induced by a single intra-articular (i.ar.) injection of 25&amp;micro;l normal saline having 1mg of monosodium iodoacetate solution (MIA) in the knee joint. MIA injection caused histological alterations and degradation of cartilage as well as behavioral changes. Oral treatment with FidHycarn ameliorated the macroscopic signs, improved thermal hyperalgesia and weight distribution of hind paw as well as decreased histological and radiographic alterations. The oxidative damage was analyzed by evaluating the levels of nitrotyrosine and inducible nitric oxide synthase (iNOS) that were significantly reduced in FidHycarn rats. Moreover, the levels of pro-inflammatory cytokines and chemokines were also significantly reduced by FidHycarn. However, interestingly, in more cases, the effects of FidHycarn were not statistically different to Naproxen used as positive control. Thus, the new formulation containing Carnosine and HA could represent an interesting therapeutic strategy to combat osteoarthritis.
Retroviral Expression of MUC-1 Human Tumor Antigen with Intact Repeat Structure and Capacity to Elicit Immunity In Vivo (1998)

MUC-1 mucin is an epithelial cell antigen whose aberrant expression plays a role in autoimmunity and tumor immunity and is thus an attractive candidate for immunotherapy of gene therapy. Because the MUC-1 cDNA is composed almost entirely of 60-bp tandem repeats and is susceptible to homologous recombination, it presents a special challenge to cloning and expression in viral vectors. Nevertheless, we have been successful in constructing a retroviral vector (MFG-MUC-1) with a 22-tandem repeat MUC-1 cDNA. Both stable and transient packaging cell lines are capable of producing high-titer retroviruses that can transfer the expression of MUC-1 to murine 3T3 cells. Transduced cells express uniformly high levels of MUC-1 on their surface, and western blot analysis reveals that the molecule expressed is of full length and extensively glycosylated. We have used the MFG-MUC-1 vector to stably transduce an immortalized murine dendritic cell line and show that immunization of mice with transduced cells elicits specific immune responses to mucin. The ability of this vector to transfer expression of the MUC-1 tumor antigen to potent antigen-presenting cells is expected to be of use in the immunotherapy of epithelial cancers.
Precision broadband wavemeter for millimeter and submillimeter range (1996)

A precise, broadband, Fabry-Perot wavemeter has been designed and built to measure wavelengths in the millimeter and submillimeter range. The design of the wavemeter is novel in that it enhances the fundamental mode over a wide band and permits determination of the exact longitudinal index of the mode. With the use of an exact mode number in wavelength calculations, high measurement accuracies, to the extent permissible by the quality factor of the resonator, can be obtained. The wavemeter was tested by measuring well-known spectral lines of the OCS molecule in the frequency range of 72-607 GHz. Measurement of 24 OCS lines demonstrated an accuracy of better than 2/spl times/10/sup -5/ in relative units and 0.87/spl times/10/sup -5/ in rms units for frequency/wavelength. A discussion of further development and automation of the wavemeter is included.
A Review of Laying Hens' Behavior (2015)

Domestic fowl still tend to exhibit very similar behavior such as perching, nesting and dust-bathing to their ancestor, Red Jungle Fowl (Gallus gallus), even though they have been domesticated for 8,000 years. If given the opportunity, they choose high place for staying at night, a dark place for laying eggs and do dust bath in litter area. Therefore, these behaviors are considered for very important role in improving the welfare of laying hens. In EU and some countries, farmers must provide perches, nests and litter for the housing of laying hens. An understanding of behavior can lead to enhance physical health, emotional condition and welfare of laying hens. Unfortunately, there is little information on behavior of laying hens in Korea. Therefore, we researched the literature on certain behavior of laying hens.
Energetic and Socioeconomic Justification for Solar-Powered Desalination Technology for Rural Indian Villages (2014)

This paper provides justification for solar-powered electrodialysis desalination systems for rural Indian villages. It is estimated that 11% of India’s 800 million people living in rural areas do not have access to an improved water source. If the source’s quality in regards to biological, chemical, or physical contaminants is also considered, this percentage is even higher. User interviews conducted by the authors and in literature reveal that users judge the quality of their water source based on its aesthetic quality (taste, odor, and temperature). Seventy-three percent of Indian villages rely on groundwater as their primary drinking supply. However, saline groundwater underlies approximately 60% of the land area in India. Desalination is necessary in order to improve the aesthetics of this water (by reducing salinity below the taste threshold) and remove contaminants that cause health risks. Both technical and socioeconomic factors were considered to identify the critical design requirements for inland water desalination in India. An off-grid power system is among those requirements due to the lack of grid access or intermittent supply, problems faced by half of Indian villages. The same regions in India that have high groundwater salinity also have the advantage of high solar potential, making solar a primary candidate. Within the salinity range of groundwater found in inland India, electrodialysis would substantially reduce the energy consumption to desalinate compared to reverse osmosis, which is the standard technology used for village-level systems. This energy savings leads to a smaller solar array required for electrodialysis systems, translating to reduced capital costs.
Source Isolation: A Seismic Shift For Seabed Seismic Productivity (2018)

Seabed seismic data have proven critical for addressing long-standing challenges in seismic imaging both for exploration and especially optimizing reservoir development and management, including broadband data acquisition, full azimuth acquisition, gas clouds or removal of multiples to name a few. Historically, OBS acquisition has been expensive and an increased focus on receiver efficiency and source efficiency is essential to bring the cost down. The Marine Autonomous Seismic System (MASS) is a miniaturized long-battery life 4-component node designed for efficient OBS acquisition (Steen-Hansen, 2017). The compact size allows for handling large numbers of receivers during operations in an automated manner. With such significant advances on the receiver side, a step change is needed for source side technology where little has happened since the advent of flip/flop acquisition in the early 1980’s.
The Effect of Substance P on an Intervertebral Disc Rat Organ Culture Model (2016)

N/A.
Phospholipid-bound Tissue Factor Modulates both Thrombin Generation and APC-mediated Factor Va Inactivation (1999)

Hemostasis is initiated by tissue factor (TF) exposed on cellular phospholipid (PL) membranes, leading to thrombin generation. The binding of thrombin to thrombomodulin (TM), activates the protein C pathway, resulting in the inactivation of factors Va and VIIIa by activated protein C (APC) and a negative feedback effect on thrombin generation. A new assay system was developed for simultaneous measurement of thrombin and APC generation in defibrinated plasma induced by large unilamellar PL vesicles complexed with full-length recombinant TF (TF:PL). TF:PL preparations with a low TF concentration induced an initial rate of thrombin generation below 100 nM/min, and resulted in less thrombin formation in the presence of TM than in its absence. In contrast, TF:PL preparations with a high concentration of TF induced a higher rate of thrombin generation, and APC-mediated feedback inhibition did not occur, despite maximal APC generation. We used the same TF:PL surfaces to study factor Va inactivation by APC in a non-plasma reaction system, and found an inverse correlation between TF surface density and the rate of factor Va inactivation. This observation suggests a previously unrecognized hemostatic effect of TF, namely a non-enzymatic surface density-based inhibition of the anticoagulant effect of APC. In this model, high concentrations and surface density of TF exert complementary effects by promoting the regular procoagulant cascade and by inhibiting the protein C pathway, thereby maximizing hemostasis after vascular injury.
Alternative Splicing of In-Frame Exon Associated with Premature Termination Codons: Implications for Readthrough Therapies (2012)

The correction of premature termination codons (PTCs) by agents that promote readthrough represents a promising emerging tool for the treatment of many genetic diseases. The efficiency of the treatment, however, varies depending on the stop codon itself and the amount of correctible transcripts related to the efficiency of nonsense-mediated decay. In the current study, a screen by in vitro minigene assay of all six PTCs described in exon 15 of the CFTR gene demonstrated alternative splicing to differing degrees for five of them. Of the five, PTC mutations c.2537G>A (p.Trp846*(UAG) ) and c.2551C>T (p.Arg851*) cause the greatest proportion of transcripts lacking exon 15; both mutations altering exonic splicing regulatory elements. In order to increase the amount of full-length transcripts, different pharmacological treatments were performed showing both negative and positive effects on exon inclusion for the same mutation. Therefore, the total amount of transcripts together with the splicing profile should be assessed to anticipate and improve efficacy of readthrough therapy.
1,3-Dipolar Cycloadditions of Diazo Compounds in the Presence of Azides (2016)

The diazo group has untapped utility in chemical biology. The tolerance of stabilized diazo groups to cellular metabolism is comparable to that of azido groups. However, chemoselectivity has been elusive, as both groups undergo 1,3-dipolar cycloadditions with strained alkynes. Removing strain and tuning dipolarophile electronics yields diazo group selective 1,3-dipolar cycloadditions that can be performed in the presence of an azido group. For example, diazoacetamide but not its azido congener react with dehydroalanine residues, as in the natural product nisin.
Physiologic Testosterone Levels in Normal Men Suppress High-Density Lipoprotein Cholesterol Levels (1992)

Experimental hypogonadism induced by administration of a GnRH antagonist results in a statistically significant increase in HDL cholesterol, including HDL2 and HDL3. These effects are most likely due to decreased androgen levels because they are reversed by administration of antagonist together with testosterone. Our results imply that androgen levels in the normal adult male range have a suppressive effect on HDL cholesterol concentration and may contribute to the increased risk for coronary artery disease in men.
Apparatus for investigating low energy ion-molecule reactors and its application to the reactive scattering of N<sup>+</sup> by H<sub>2</sub> (1974)

An apparatus was designed and constructed for measuring the scattering of ions from neutral molecules in a laboratory energy range of 6 to 50 eV. A beam of monoenergetic ions of a specified mass is generated by ionizing the parent neutral in an electron impact source and chen passing the resulting ions through a magnetic momentum analyzer and electrostatic focusing system. The ion beam then passes through a collision cell which contains the neutral target molecules. The scattering ions are detected by a detection system which consists of a crossed electric and magnetic field velocity filter, a quadrupole mass filter and a magnetic electron multiplier. The primary ion source and collision cell are mounted on a rotable cable in a large vacuum chamber and the detection system is mounted on the side of the vacuum chamber. This arrangement allows intensity distributions as a function of angle, mass and velocity to be determined.