gebhart/patrepeval huggingface dataset:
Bond Graph Modeling Procedures for Fault Detection and Isolation of Complex Flow Processes (2001)

Many models for fault detection and isolation (FDI) will contain multi-port energy storage and flow-dependencies due to convection. Converting these models into qualitative ones leads to ambiguities that can be eliminated by analysis of boundary conditions. In this study the example of an automotive cooling system is used to demonstrate how these issues can be handled. Furthermore, time constants in the models need to correspond to the bandwidth of the data acquisition system. In order to achieve this, parameters leading to irrelevant time constants can be eliminated by assigning relatively small and large parameters to be zero or infinite respectively. However, this may result in (i) discontinuities and (ii) zero order causal paths (&amp;quot;algebraic loops&amp;quot;). Compensation of qualitative e#ects instead of reversal is shown to be an adequate solution for these problems.
Dynamics of Adatom Motion under the Influence of Mutual Interactions:O/Ru(0001) (1999)

The diffusive motion of O atoms adsorbed on Ru(0001) was observed on the atomic scale by scanning tunneling microscopy with temporal resolution of $\ensuremath{\approx}10\mathrm{ms}$ at room temperature. From statistical analysis of the changes of the atom configurations in sequences of more than 1000 images, mean residence times of oxygen atoms in the neighborhood of other oxygen atoms were extracted. The residence times vary by more than 1 order of magnitude over distances of three lattice constants, indicating the necessity of including the lateral interaction in modeling collective phenomena such as surface diffusion or reactions.
Breakdown of dimethyl sulphide by mixed cultures and byThiobacillus thioparus (1986)

Dimethyl sulphide (DMS) was degraded by acclimatized activated sludge and by a mixed culture of Thiobacillus thioparus TK-1 and Pseudomonas sp. AK-2. While both these organisms persisted in stable co-culture on DMS, it was found that T. thioparus TK-1 and the derived strain TK-m grew in pure culture on DMS, and oxidized DMS with an apparent Km of 4.5 × 10−5 M. During growth, all the DMS-sulphur was oxidized stoichiometrically to sulphate but no methanol was detected in pure cultures of TK-m. DMS-carbon was probably converted to CO2, since the fixation of 14CO2 was progressively diluted during growth of a culture on 14CO2 and DMS. Growth yields were consistent with autotrophic growth, dependent on the oxidation of the methyl residues to CO2 (probably with formaldehyde as a first intermediate) and the sulphide to sulphate. The organism thus appears to exhibit a mixture, from the one substrate, of chemolithotrophic and methylotrophic energy generation supporting autotrophic growth with CO2 fixation.
Are ultrafine submicron sized gliadin fibrous materials suitable as bio-absorbents? Processing and post-treatment derived structures and functional properties (2022)

Gliadins were electrospun into ultrafine fibrous membrane-like materials to evaluate their processability and suitability as bio-absorbents. From a wide range of tested protein concentrations and processing conditions, 15 and 20% protein solutions were optimal to produce uniform fibers with sizes <1 μm. The results showed that the 20% gliadin solution produced uniform round fibers, while 15% gliadin solution resulted in formation of diverse morphologies such as round and flat-ribbon shaped fibers. Importantly, post-heat treatment of fibrous materials at 130 °C for 2 h increased crosslinking of gliadin protein and improved functionality of fibers. Heat-treatment induced formation of higher amounts of α-helices and random coils, though no change in β-sheets were observed. With post heat-treatment, the fibrous gliadin materials indicated crosslinking of proteins by inter and intramolecular disulphide, hydrogen bonding and other weaker protein interactions. The newly fabricated gliadin fibrous material demonstrated certain stability and ability to absorb and “lock” defibrinated sheep blood, suggesting a support from submicron sized structural morphology of the material. For further development steps of gliadin-based fibrous materials, new efforts are needed in modification of gliadins to maintain the ultrafine structures and improve their strength in order to explore them as bio-absorbents or even scaffolds.
Cooperative Spectrum Sharing Protocol with Selective Relaying System (2011)

In this paper, we propose a two-phase protocol based on cooperative relaying for a secondary system to achieve spectrum access along with a selective relaying primary system. The primary system comprises of a transmitter-receiver pair PT-PR and M relays R <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">i</sub> , i G {1,2,⋯ , M}. The secondary system is a multi-user system with N transmitters R <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">i</sub> , i ϵ {M +1, M + 2, ⋯ , M + N } which intend to communicate with a common receiver SR. In the proposed protocol, terminals R <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">i</sub> , i ϵ M <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">1</sub> = {1, 2, ⋯ , M + Q} are designated as possible candidates for assisting the primary system while the remaining secondary transmitters R <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">i'</sub> , i' ϵ M <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sub> = {M + Q + 1, M + Q + 2, ⋯ ,M + N} are chosen as possible candidates for secondary spectrum access, where 0 ≤ Q ≤ N. The relaying terminal R <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">p</sub> , p ϵ M <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">1</sub> which achieves the request target rate for the primary system and has the best channel to PR, is first selected from M <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">1</sub> to serve as a decode-and-forward (DF) relay for the primary system. With the cooperation of R <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">p</sub> , the primary system is able to tolerate some interference lower than a certain threshold in the relaying phase, without degrading its outage performance. The secondary transmitter R <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">s</sub> , s ϵ M <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sub> which satisfies this interference constraint and optimizes the outage performance for the secondary system, is then selected from M <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sub> to access the spectrum band simultaneously when R <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">p</sub> is relaying the primary signal. Analytical and simulation results confirm the efficiency of the proposed spectrum sharing protocol. We show that there exists an optimal value for Q and both primary and secondary systems are able to achieve better outage performance with increasing N.
Substantially Modified Ratios of Effector to Regulatory T Cells During Chemotherapy in Ovarian Cancer Patients Return to Pre-Treatment Levels at Completion: Implications for Immunotherapy (2012)

Ovarian cancer is the leading cause of death from gynaecological malignancy. Despite improved detection and treatment options, relapse rates remain high. Combining immunotherapy with the current standard treatments may provide an improved prognosis, however, little is known about how standard chemotherapy affects immune potential (particularly T cells) over time, and hence, when to optimally combine it with immunotherapy (e.g., vaccines). Herein, we assess the frequency and ratio of CD8+ central memory and effector T cells as well as CD4+ effector and regulatory T cells (Tregs) during the first 18 weeks of standard chemotherapy for ovarian cancer patients. In this pilot study, we observed increased levels of recently activated Tregs with tumor migrating ability (CD4+CD25hiFoxp3+CD127-CCR4+CD38+ cells) in patients when compared to controls. Although frequency changes of Tregs as well as the ratio of effector T cells to Tregs were observed during treatment, the Tregs consistently returned to pre-chemotherapy levels at the end of treatment. These results indicate T cell subset distributions associated with recurrence may be largely resistant to being "re-set" to healthy control homeostatic levels following standard treatments. However, it may be possible to enhance T effector to Treg ratios transiently during chemotherapy. These results suggest personalized immune monitoring maybe beneficial when combining novel immuno-therapeutics with standard treatment for ovarian cancer patients.
Engineered adenovirus serotypes for overcoming anti-vector immunity (2009)

Adenovirus (Ad)-based gene transfer has been successfully utilised in gene therapy and vaccine applications. To date, an increasing number of human clinical trials utilise recombinant Ad-based vectors as a gene transfer platform. In particular, progress has been made recently in utilising Ad-based vectors as a vaccine platform in HIV, cancer immunotherapy approaches and in vaccination for other infections. Despite these successes, the scientific and bio-industrial communities have recently recognised that innate and pre-existing immunity against Ad vectors can constitute a serious obstacle to the development and application of this technology. It is essential to overcome vector-mediated immune responses, such as production of inflammatory cytokines and pre-existing immunity to Ad, because the induction of these responses not only shortens the period of gene expression but also leads to serious side effects. This review focuses on the biology of Ad infection and the approaches that are being adopted to overcome immunity against the Ad-based vectors.
Coq6 Is Responsible for the C4-deamination Reaction in Coenzyme Q Biosynthesis in Saccharomyces cerevisiae (2015)

The yeast Saccharomyces cerevisiae is able to use para-aminobenzoic acid (pABA) in addition to 4-hydroxybenzoic acid as a precursor of coenzyme Q, a redox lipid essential to the function of the mitochondrial respiratory chain. The biosynthesis of coenzyme Q from pABA requires a deamination reaction at position C4 of the benzene ring to substitute the amino group with an hydroxyl group. We show here that the FAD-dependent monooxygenase Coq6, which is known to hydroxylate position C5, also deaminates position C4 in a reaction implicating molecular oxygen, as demonstrated with labeling experiments. We identify mutations in Coq6 that abrogate the C4-deamination activity, whereas preserving the C5-hydroxylation activity. Several results support that the deletion of Coq9 impacts Coq6, thus explaining the C4-deamination defect observed in Δcoq9 cells. The vast majority of flavin monooxygenases catalyze hydroxylation reactions on a single position of their substrate. Coq6 is thus a rare example of a flavin monooxygenase that is able to act on two different carbon atoms of its C4-aminated substrate, allowing its deamination and ultimately its conversion into coenzyme Q by the other proteins constituting the coenzyme Q biosynthetic pathway.
Dynamic resource adaptation in beyond LTE-A TDD heterogeneous networks (2013)

Dynamic downlink and uplink resource adaptation in TDD (Time Domain Duplex) systems by flexibly changing the ratio of time slots for downlink and uplink transmissions is studied under Heterogonous Network (HetNet) scenarios. The time-scale of the resource adaptation and the interference management between downlink and uplink transmissions from different cells are important factors in determining the achievable level of resource efficiency, user experience and energy saving in TDD systems. In this paper, we apply the dynamic downlink and uplink resource adaptation in multi-cell macro-pico scenarios with co-channel interference. The performance is evaluated in system level for LTE-Advanced TDD configurations. Reconfiguration rates of 10 msec and 640 msec are considered as the time-scale of the dynamic resource adaptation. In addition, the time domain inter-cell interference coordination between the macro cells and the pico cells is applied for handling the high level of interference from macro cells to pico cells in the downlink multi-cell dynamic simulations.
CYCLIC TESTING OF 1:40 SCALE CANTILEVER RC ELEMENTS WITH DIGITALLY MANUFACTURED REINFORCEMENT (2021)

CYCLIC TESTING OF 1:40 SCALE CANTILEVER RC ELEMENTS WITH DIGITALLY MANUFACTURED REINFORCEMENT - 8th International Conference on Computational Methods in Structural Dynamics and Earthquake Engineering - 28-30 June 2021, Streamed from Athens, Greece
Tunable opto-electronic oscillator with an intracavity Fabry-Perot etalon (2010)

An optically tunable optoelectronic oscillator(OEO) scheme with 1000 finesse intracavity Fabry-Perot etalon is demonstrated at 10GHz. Optical single side band modulation is implemented and resulted in 10-20dB higher SNR than standard dual side band modulation.
Theoretical and experimental study of monopole phased array antennas (1985)

A theoretical and experimental investigation of the mutual coupling in large two-dimensional periodic planar phased arrays of thin cylindrical monopoles is addressed. A plane wave representation of the active input impedance is used to analyze an infinite array of monopoles. A finite array analysis is used to compute the center element gain pattern and input impedance as a function of the array size and element position. The center element gain pattern is shown to have omnidirectional vertical polarization with a null on-axis and peak gain in the vicinity of <tex xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">50\deg</tex> from broadside. Measurements of the element gain pattern and mutual coupling for a 121-element passively terminated monopole square lattice array are shown to be in good agreement with the theory. The results of the infinite array analysis are compared to theoretical and experimental data in the literature for hexagonal lattice arrays.
Effects of Combined Tristetraprolin/Tumor Necrosis Factor Receptor Deficiency on the Splenic Transcriptome (2016)

Tristetraprolin (TTP) acts by binding to AU-rich elements in certain mRNAs, such as tumor necrosis factor (TNF) mRNA, and increasing their decay rates. TTP knockout mice exhibit a profound inflammatory syndrome that is largely due to increased TNF levels. Although TTP's effects on gene expression have been well studied in cultured cells, little is known about its functions in intact tissues. We performed deep RNA sequencing on spleens from TTP knockout mice that were also deficient in both TNF receptors ("triple knockout" mice) to remove the secondary effects of excess TNF activity. To help identify posttranscriptionally regulated transcripts, we also compared changes in mature mRNA levels to levels of transiently expressed pre-mRNA. In the triple knockout spleens, levels of 3,014 transcripts were significantly affected by 1.5-fold or more, but only a small fraction exhibited differential mRNA/pre-mRNA changes suggestive of increased mRNA stability. Transferrin receptor mRNA, which contains two highly conserved potential TTP binding sites, was significantly upregulated relative to its pre-mRNA. This was reflected in increased transferrin receptor expression and increased splenic iron/hemosiderin deposition. Our results suggest that TTP deficiency has profound effects on the splenic transcriptome, even in the absence of secondary increases in TNF activity.
A MHC class I B locus allele-restricted simian immunodeficiency virus envelope CTL epitope in rhesus monkeys. (1995)

In light of the importance of virus-specific CTL in the control of the spread of the AIDS virus, it will be important to assess the generation of these effector cell responses in trials of novel vaccine strategies for the prevention of AIDS virus infections. To facilitate such studies in the simian immunodeficiency virus (SIV)/macaque model for AIDS, we have defined a rhesus monkey SIVmac CTL epitope carboxy terminus to both the CD4-binding and V4 regions of the envelope glycoprotein. We also used one-dimensional isoelectric focusing to characterize the MHC class I molecule of the rhesus monkey that binds this 9-amino-acid SIVmac envelope fragment. Cloning and sequencing of the cDNA encoding this rhesus monkey MHC class I molecule demonstrated that it is a newly described HLA-B homologue, Mamu-B*01. The definition of this viral CTL epitope and its restricting MHC class I molecule will facilitate the use of the SIVmac/rhesus monkey model for studies of envelope-based vaccine strategies for the prevention of AIDS.
Use of Reverse Phase Protein Microarrays and Reference Standard Development for Molecular Network Analysis of Metastatic Ovarian Carcinoma (2005)

Cancer can be defined as a deregulation or hyperactivity in the ongoing network of intracellular and extracellular signaling events. Reverse phase protein microarray technology may offer a new opportunity to measure and profile these signaling pathways, providing data on post-translational phosphorylation events not obtainable by gene microarray analysis. Treatment of ovarian epithelial carcinoma almost always takes place in a metastatic setting since unfortunately the disease is often not detected until later stages. Thus, in addition to elucidation of the molecular network within a tumor specimen, critical questions are to what extent do signaling changes occur upon metastasis and are there common pathway elements that arise in the metastatic microenvironment. For individualized combinatorial therapy, ideal therapeutic selection based on proteomic mapping of phosphorylation end points may require evaluation of the patient's metastatic tissue. Extending these findings to the bedside will require the development of optimized protocols and reference standards. We have developed a reference standard based on a mixture of phosphorylated peptides to begin to address this challenge.
Screening strategies for obtaining novel, biologically active, fungal secondary metabolites from marine habitats (2008)

Abstract To determine the best sources of novel, biologically active metabolites, both endophytic fungi (plant isolates) and fungi associated with algae were isolated from plants and algae from marine habitats of the North, Baltic and Mediterranean Seas, Atlantic Ocean, and Gulf of Mexico. Following preselection of the isolates according to taxon and metabolic profiles, almost all were active in at least one of the tests for antibacterial, antifungal, and/or herbicidal activities. Metabolites isolated from the culture extracts belonged to diverse structural groups; 42% were previously unknown structures. Compared to fungi associated with algae, endophytic fungi were a better source of novel metabolites and antifungal culture extracts; they produced a higher number of metabolites per fungus. Microsphaeropsis spp. and Coniothyrium spp. synthesized the highest numbers of novel metabolites per isolate, and Geniculosporium , Nodulisporium and Phomopsis the greatest numbers of metabolites per isolate. Based on the proportion of novel to known metabolites, endophytic fungi from marine environments equalled endophytes from terrestrial habitats. Metabolic profiles (HPLC-DAD) of the saprophytic, marine fungi belonging to Dendryphiella spp. from diverse temperate and subtropical locations revealed that geographical source of the isolates had little qualitative effect on secondary metabolite production in this genus.
Temporal secretory patterns of growth hormone in male meat‐type chickens of lines selected for body weight gain or food conversion (1991)

1. The pronounced episodic release of chicken growth hormone (cGH) in male broiler chicks, as well as its peak interval of about 90 min was confirmed in this study. 2. Lines selected for 6-week body weight (GL line) or for food conversion between 3 and 6 weeks of age (FC line) not only differ in the selection criteria but also in percentage abdominal fat. 3. The overall mean plasma GH concentration was higher in the FC line in both experiments, and this was only caused by peak amplitudes which were almost twice as high as in the FC line. Peak intervals were identical in both selected lines. 4. These observations suggest that decreased abdominal fat and increased protein efficiency may be genetically linked to increased plasma GH peak amplitude. This, and earlier observations on the effectiveness of pulsatile administration of cGH on the growth of broilers suggest that the biological function of GH may depend on its secretory pattern rather than its mean concentration in plasma.
Supplementary Methods from Proteasome Inhibition Causes Regression of Leukemia and Abrogates BCR-ABL–Induced Evasion of Apoptosis in Part through Regulation of Forkhead Tumor Suppressors (2023)

Supplementary Methods from Proteasome Inhibition Causes Regression of Leukemia and Abrogates BCR-ABL–Induced Evasion of Apoptosis in Part through Regulation of Forkhead Tumor Suppressors
Reducing Computational Complexity of Neural Networks in Optical Channel Equalization: From Concepts to Implementation (2023)

In this paper, a new methodology is proposed that allows for the low-complexity development of neural network (NN) based equalizers for the mitigation of impairments in high-speed coherent optical transmission systems. In this work, we provide a comprehensive description and comparison of various deep model compression approaches that have been applied to feed-forward and recurrent NN designs. Additionally, we evaluate the influence these strategies have on the performance of each NN equalizer. Quantization, weight clustering, pruning, and other cutting-edge strategies for model compression are taken into consideration. In this work, we propose and evaluate a Bayesian optimization-assisted compression, in which the hyperparameters of the compression are chosen to simultaneously reduce complexity and improve performance. Next, this paper presents four distinct metrics (RMpS, BoP, NABS, and NLGs) that are discussed here that can be used to evaluate the amount of computing complexity required by various compression algorithms. These measurements can serve as a benchmark for evaluating the relative effectiveness of various NN equalizers when compression approaches are used. In conclusion, the trade-off between the complexity of each compression approach and its performance is evaluated by utilizing both simulated and experimental data in order to complete the analysis. By utilizing optimal compression approaches, we show that it is possible to design an NN-based equalizer that is simpler to implement and has better performance than the conventional digital back-propagation (DBP) equalizer with only one step per span. This is accomplished by reducing the number of multipliers used in the NN equalizer after applying the weighted clustering and pruning algorithms. Furthermore, we demonstrate that an equalizer based on NN can also achieve superior performance while still maintaining the same degree of complexity as the full electronic chromatic dispersion compensation block. We conclude our analysis by highlighting open questions and existing challenges, as well as possible future research directions.
Diffusion Tensor Imaging of the Optic Tracts in Multiple Sclerosis: Association with Retinal Thinning and Visual Disability (2010)

Optic-tract diffusion abnormalities are associated with retinal damage, suggesting that both may be related to optic-nerve injury, but do not appear to contribute strongly to visual disability in multiple sclerosis.