gebhart/patrepeval huggingface dataset:
Soft-Failure Detection, Localization, Identification, and Severity Prediction by Estimating QoT Model Input Parameters (2021)

The performance of optical devices can degrade because of aging and external causes like, for example, temperature variations. Such degradation might start with a low impact on the Quality of Transmission (QoT) of the supported lightpaths (soft-failure). However, it can degenerate into a hard-failure if the device itself is not repaired or replaced, or if an external cause responsible for the degradation is not properly addressed. In this work, we propose comparing the QoT measured in the transponders with the one estimated using a QoT tool. Those deviations can be explained by changes in the value of input parameters of the QoT model representing the optical devices, like noise figure in optical amplifiers and reduced Optical Signal to Noise Ratio in the Wavelength Selective Switches. By applying reverse engineering, the value of those modeling parameters can be estimated as a function of the observed QoT of the lightpaths. Experiments reveal high accuracy estimation of modeling parameters, and results obtained by simulation show large anticipation of soft-failure detection and localization, as well as accurate identification of degradations before they have a major impact on the network.
Computational modeling of complex bioenergetic mechanisms that modulate CD4+ T cell effector and regulatory functions (2022)

We built a computational model of complex mechanisms at the intersection of immunity and metabolism that regulate CD4+ T cell effector and regulatory functions by using coupled ordinary differential equations. The model provides an improved understanding of how CD4+ T cells are shaping the immune response during Clostridioides difficile infection (CDI), and how they may be targeted pharmacologically to produce a more robust regulatory (Treg) response, which is associated with improved disease outcomes during CDI and other diseases. LANCL2 activation during CDI decreased the effector response, increased regulatory response, and elicited metabolic changes that favored Treg. Interestingly, LANCL2 activation provided greater immune and metabolic modulation compared to the addition of exogenous IL-2. Additionally, we identified gluconeogenesis via PEPCK-M as potentially responsible for increased immunosuppressive behavior in Treg cells. The model can perturb immune signaling and metabolism within a CD4+ T cell and obtain clinically relevant outcomes that help identify novel drug targets for infectious, autoimmune, metabolic, and neurodegenerative diseases.
Nondestructive thickness measurement of DCG films (1992)

Dichromated gelatin (DCG) films are coated on substrates to make holographic optical elements (HOEs) by using various techniques. It is necessary to measure the thickness of these films before and after exposure and processing. It is also necessary to estimate the variation of the thickness at different areas of the substrate. This thickness range is usually between 5 03μm and 50 μm. The principle of the method is based on the measurements on the Haidinger fringes generated by the film. For ease of observation and measurement, a commercial Fizeau type interferometer such as ZYGO has been used. The simple modification to observe the Haidinger fringes with the Fizeau type interferometer will be described. The thickness of the film is related to the diameters of the Haidinger fringes. It is possible to estimate the thickness quickly by counting the number of fringes. A more accurate estimate can be obtained by the measurement of the diameters of the fringes and by using this data in a formula that will be described. It is possible to estimate the thickness of the film to within +1 μm. The method is entirely nondestructive.
Speech presence probability estimation based on temporal cepstrum smoothing (2010)

We propose a novel, robust estimator for the probability of speech presence at each time-frequency point in the short-time discrete Fourier domain. While existing estimators perform quite reliably in stationary noise environments, they usually exhibit a large false-alarm rate in nonstationary noise that results in a great deal of noise leakage when applied to a speech enhancement task. The proposed estimator overcomes this problem by temporally smoothing the cepstrum of the a posteriori signal-to-noise ratio (SNR), and yields considerably less noise leakage and low speech distortions in both, stationary and nonstationary noise as compared to state-of-the-art estimators. Especially in babble noise, this results in large SNR improvements.
Oxide mediated epitaxy of CoSi2 on silicon (1996)

Uniform, single-crystal CoSi2 layers have been grown on Si by the technique of oxide mediated epitaxy (OME). Deposition of a thin layer of cobalt (1–3 nm) onto surfaces covered with a thin silicon oxide layer and annealing at 500–700 °C led to the growth of epitaxial, essentially uniform, CoSi2 layers on the (100), (110), and (111) surfaces of Si. The nucleation and growth of silicide apparently occurred subsurface, leaving the silicon oxide layer largely on the surface of the silicide after the growth. On all surfaces, thicker (10–30 nm), excellent quality, CoSi2 single-crystal thin films have been grown by repeated growth sequences. Experimental results are presented along with a discussion on the possible roles played by the thin oxide layer in promoting the epitaxial growth of silicide.
Clinical outcomes and functional recovery after temporomandibular joint replacement: a six-month follow-up study (2020)

International audience
Pixel‐wise assessment of cardiovascular magnetic resonance first‐pass perfusion using a cardiac phantom mimicking transmural myocardial perfusion gradients (2020)

The unique transmural perfusion pattern in the phantom allows effective pixel-wise assessment of first-pass perfusion acquisition protocols and quantification algorithms before their introduction into routine clinical use.
Polyphenol, Conditioning, and Conservation Effects on Protein Fractions and Degradability in Forage Legumes (2009)

Forage legume proteins were fractionated by the Cornell Net Carbohydrate and Protein System or ruminally incubated to assess how conditioning and conservation methods interact with polyphenols (condensed tannins or o ‐quinones) to alter protein degradability. The presence of polyphenols, conditioning by maceration rather than rolls, and conservation as hay rather than silage shifted protein fractions from buffer‐soluble to detergent‐extractable forms. Rumen undegradable protein (RUP) calculated from protein fractions for roll‐conditioned hays averaged 281 g kg −1 for alfalfa ( Medicago sativa L.), 309 g kg −1 for high‐tannin birdsfoot trefoil ( Lotus corniculatus L.), and 352 g kg −1 for o ‐quinone–containing red clover ( Trifolium pratense L.). Roll‐conditioned silages had lower RUP, averaging 132 g kg −1 for alfalfa, 161 g kg −1 for high‐tannin trefoil, and 241 g kg −1 for clover. Maceration increased calculated RUP by 67 to 124 g kg −1 ; responses were greatest in clover and high‐tannin trefoil. Rumen in situ residual protein (RP) was comparable to calculated RUP for silage, but ∼75 g kg −1 higher for hay. Hay RP also indicated a greater impact of tannins and a smaller impact of maceration on protein degradability. Discrepancies between calculated RUP, in situ RP, and previous protease RUP estimates indicate that routine methods for estimating RUP must be refined so that polyphenol‐containing forages can be properly characterized for feeding to ruminant livestock.
Epigenetic Activation of SOX11 in Lymphoid Neoplasms by Histone Modifications (2011)

Recent studies have shown aberrant expression of SOX11 in various types of aggressive B-cell neoplasms. To elucidate the molecular mechanisms leading to such deregulation, we performed a comprehensive SOX11 gene expression and epigenetic study in stem cells, normal hematopoietic cells and different lymphoid neoplasms. We observed that SOX11 expression is associated with unmethylated DNA and presence of activating histone marks (H3K9/14Ac and H3K4me3) in embryonic stem cells and some aggressive B-cell neoplasms. In contrast, adult stem cells, normal hematopoietic cells and other lymphoid neoplasms do not express SOX11. Such repression was associated with silencing histone marks H3K9me2 and H3K27me3. The SOX11 promoter of non-malignant cells was consistently unmethylated whereas lymphoid neoplasms with silenced SOX11 tended to acquire DNA hypermethylation. SOX11 silencing in cell lines was reversed by the histone deacetylase inhibitor SAHA but not by the DNA methyltransferase inhibitor AZA. These data indicate that, although DNA hypermethylation of SOX11 is frequent in lymphoid neoplasms, it seems to be functionally inert, as SOX11 is already silenced in the hematopoietic system. In contrast, the pathogenic role of SOX11 is associated with its de novo expression in some aggressive lymphoid malignancies, which is mediated by a shift from inactivating to activating histone modifications.
Airway Smooth Muscle in Bronchial Tone, Inflammation, and Remodeling (2007)

Airway smooth muscle (ASM) plays a pivotal role in modulating bronchomotor tone but also orchestrates and perpetuates airway inflammation and remodeling. Despite substantial research, there remain important unanswered questions. In 2006, the National Heart, Lung, and Blood Institute sponsored a workshop to define new directions in ASM biology. Important questions concerning the key functions of ASM include the following: Does developmental dysregulation of ASM function promote airway disease, what key signaling pathways in ASM evoke airway hyperresponsiveness in vivo, do alterations in ASM mass affect excitation-contraction coupling, and can ASM modulate airway inflammation and remodeling in a physiologically relevant manner? This workshop identified critical issues in ASM biology to delineate areas for scientific investigation in the identification of new therapeutic and diagnostic approaches in asthma, chronic obstructive pulmonary disease, and cystic fibrosis.
A stable optic-flow based method for tracking colonoscopy images (2008)

In this paper, we focus on the robustness and stability of our algorithm to plot the position of an endoscopic camera (during a colonoscopy procedure) on the corresponding pre-operative CT scan of the patient. The colon has few topological landmarks, in contrast to bronchoscopy images, where a number of registration algorithms have taken advantage of features such as anatomical marks or bifurcations. Our method estimates the camera motion from the optic-flow computed from the information contained in the video stream. Optic-flow computation is notoriously susceptible to errors in estimating the motion field. Our method relies on the following features to counter this, (1) we use a small but reliable set of feature points (sparse optic-flow field) to determine the spatio-temporal scale at which to perform optic-flow computation in each frame of the sequence, (2) the chosen scales are used to compute a more accurate dense optic flow field, which is used to compute qualitative parameters relating to the main motion direction, and (3) the sparse optic-flow field and the main motion parameters are then combined to estimate the camera parameters. A mathematical analysis of our algorithm is presented to illustrate the stability of our method, as well as comparison to existing motion estimation algorithms. We present preliminary results of using this algorithm on both a virtual colonoscopy image sequence, as well as a colon phantom image sequence.
Opposing effect of Lactobacillus on in vitro Klebsiella pneumoniae in biofilm and in an in vivo intestinal colonisation model (2017)

Beneficial bacteria represent potential sources of therapy, particularly in the battle against antibiotic-resistant pathogens. The Gram-negative bacillus Klebsiella pneumoniae is not only a paradigm of multi-resistant opportunistic pathogen, but it is also able to colonise the human intestine and displays a high capacity to form biofilm. In this study, the anti-biofilm activity of 140 neutralised Lactobacillus supernatants was assessed against K. pneumoniae. Among the 13 strains whose supernatant significantly impaired biofilm formation, Lactobacillus plantarum CIRM653 was selected because it was also able to impair K. pneumoniae preformed biofilm, independently of a bactericidal effect. Mixed K. pneumoniae/L. plantarum CIRM653 biofilms had reduced tridimensional structures associated with a significant decrease in K. pneumoniae biomass. Further investigation showed that L. plantarum CIRM653 supernatant induced transcriptional modifications of K. pneumoniae biofilm-related genes, including down-regulation of the quorum sensing-related lsr operons and over-expression of type 3 pili structure genes. Increased production of type 3 pili was validated by Western-blot, hemagglutination and adhesion assays. L. plantarum CIRM653 activity against K. pneumoniae was also assessed in a murine intestinal colonisation model: a constant faecal pathogen burden was observed, as against a gradual decrease in the control group. These results reveal that an in vitro a priori attracting anti-biofilm activity of Lactobacillus might be counterbalanced by an in vivo behaviour in a complex microbiota environment with potential deleterious dispersal of highly adherent K. pneumoniae cells, raising the question of the accuracy of in vitro assays in screening of beneficial microbes.
Pain and Overuse in High School Baseball Pitchers During a Season (2018)

Over half of adolescent baseball pitchers retrospectively recall throwing arm pain during a baseball season, leading to the institution of pitch count regulations across high school baseball; however, how pain varies throughout the season is unknown. PURPOSE: The purpose of this study was to determine the prevalence of pain and overuse symptoms occurring in high school baseball pitchers throughout a high school baseball season. METHODS: 97 pitchers were enrolled in the research study from eight central and southern Ohio high schools. Weekly surveys were sent via text message to assess overuse and pain using a validated questionnaire throughout the season (11 weeks). 44 of the 60 participants who met all inclusion criteria responded a minimum of 80% of the time and were included in the analysis. Descriptive statistics and prevalence of overuse and pain were calculated weekly throughout the season. RESULTS: The final participant pool maintained an average weekly completion rate of 91.8±0.2%. 34.8±7.9% of participants reported symptoms of overuse each week, with peak prevalence occurring in the 4th week of practice (45.5%), and trending downwards with 26.2% reporting overuse in the final week of the season. Prevalence of severe overuse, determined by a report of moderate or greater effect on training or performance, was low throughout the season (4.0±1.8%). Of those who did experience any symptom of overuse, the mean weekly overuse score was 22.0±3.1 out of 100 (mild overuse). Pain prevalence showed similar trends, with 28.5±7.6% of participants reporting pain during the season, with the peak occurring in week 4 of practice (40.9%), and trending down with 19.0% experiencing pain in the final week. The majority who experienced pain reported mild pain (81.3±7.1%), with few experiencing moderate pain (18.0±7.1%), and only one report of severe pain occurring in week 3. CONCLUSION: Prevalence of pain and overuse symptoms varies over the course of a high school baseball season, peaking within the first five weeks of the season, though most pain is mild. Further research is needed to determine whether increases in pain at this time are preceded by an initial period of chronic overuse or more acute changes in workload.
Human Plasmacytoid Dendritic Cells Efficiently Capture HIV-1 Envelope Glycoproteins via CD4 for Antigen Presentation (2013)

Advances in HIV-1 vaccine clinical trials and preclinical research indicate that the virus envelope glycoproteins (Env) are likely to be an essential component of a prophylactic vaccine. Efficient Ag uptake and presentation by dendritic cells (DCs) is important for strong CD4(+) Th cell responses and the development of effective humoral immune responses. In this study, we examined the capacity of distinct primary human DC subsets to internalize and present recombinant Env to CD4(+) T cells. Consistent with their specific receptor expression, skin DCs bound and internalized Env via C-type lectin receptors, whereas blood DC subsets, including CD1c(+) myeloid DCs, CD123(+) plasmacytoid DCs (PDCs), and CD141(+) DCs exhibited a restricted repertoire of C-type lectin receptors and relied on CD4 for uptake of Env. Despite a generally poor capacity for Ag uptake compared with myeloid DCs, the high expression of CD4 on PDCs allowed them to bind and internalize Env very efficiently. CD4-mediated uptake delivered Env to EEA1(+) endosomes that progressed to Lamp1(+) and MHC class II(+) lysosomes where internalized Env was degraded rapidly. Finally, all three blood DC subsets were able to internalize an Env-CMV pp65 fusion protein via CD4 and stimulate pp65-specific CD4(+) T cells. Thus, in the in vitro systems described in this paper, CD4-mediated uptake of Env is a functional pathway leading to Ag presentation, and this may therefore be a mechanism used by blood DCs, including PDCs, for generating immune responses to Env-based vaccines.
Rapid Cross-Linking of Elastin-like Polypeptides with (Hydroxymethyl)phosphines in Aqueous Solution (2007)

In situ gelation of injectable polypeptide-based materials is attractive for minimally invasive in vivo implantation of biomaterials and tissue engineering scaffolds. We demonstrate that chemically cross-linked elastin-like polypeptide (ELP) hydrogels can be rapidly formed in aqueous solution by reacting lysine-containing ELPs with an organophosphorous cross-linker, beta-[tris(hydroxymethyl)phosphino]propionic acid (THPP) under physiological conditions. The mechanical properties of the cross-linked ELP hydrogels were largely modulated by the molar concentration of lysine residues in the ELP and the pH at which the cross-linking reaction was carried out. Fibroblasts embedded in ELP hydrogels survived the cross-linking process and were viable after in vitro culture for 3 days. DNA quantification of ELP hydrogels with encapsulated fibroblasts indicated that there was no significant difference in DNA content between day 0 and day 3 when ELP hydrogels were formed with an equimolar ratio of THPP and lysine residues of the ELPs. These results suggest that THPP cross-linking may be a biocompatible strategy for the in situ formation of cross-linked hydrogels.
Intrinsic and Extrinsic Damping in Polycrystalline Fe Thin Films (2021)

We examine magnetic relaxation in polycrystalline Fe films with strong and weak crystallographic texture. Out-of-plane ferromagnetic resonance (FMR) measurements reveal Gilbert damping parameters of $\approx$ 0.0024 for Fe films with thicknesses of 4-25 nm, regardless of their microstructural properties. The remarkable invariance with film microstructure strongly suggests that intrinsic Gilbert damping in polycrystalline Fe is a local property of nanoscale crystal grains, with limited impact from grain boundaries and film roughness. By contrast, the in-plane FMR linewidths of the Fe films exhibit distinct nonlinear frequency dependences, indicating the presence of strong extrinsic damping. To fit our experimental data, we have used a grain-to-grain two-magnon scattering model with two types of correlation functions aimed at describing the spatial distribution of inhomogeneities in the film. However, neither of the two correlation functions is able to reproduce the experimental data quantitatively with physically reasonable parameters. Our finding points to the need to further examine the fundamental impact of film microstructure on extrinsic damping.
The Search for a Practical Iterative Detector for Magnetic Recording (2004)

The striking benefits of iterative detection have generated strong interest in the disk drive signal processing area, but thus far application of this technology has been rather limited. We review the benefits that the most interesting iterative detectors have over the industry-standard partial-response maximum-likelihood (PRML) detectors, and examine the hardware complexity issues that have so far stood in the way of practical implementations.
Why are metal foams stable? (2006)

Although metal foams are becoming accepted engineering materials, the reason for their stability in the liquid state is still under dispute. Liquid metal foams contain solid constituents which according to the existing models stabilize foam films by either modifying the curvature of the liquid/gas (L∕G) interfaces, or by forming particle bridges across metallic films and transmitting repulsive “disjoining” forces mechanically. Using high-resolution synchrotron tomography and a quantitative three-dimensional image analysis the authors show that there is little evidence for such curvature changes or particle bridges. The authors conclude that the main stabilizing action must be due to interactions between neighboring particles attached to L∕G interfaces.
Flickr's API Signature Forgery Vulnerability (2009)

Many methods require the user to be logged in. At present there is only one way to accomplish this. Users should be authenticated using the Flickr Authentication API. Any applications wishing to use the Flickr Authentication API must have already obtained a Flickr's API Key. An 8-byte long 'shared secret' for the API Key is then issued by Flickr and cannot be changed by the users. This secret is used in the signing process, which is required for all API calls using an authentication token. In addition, calls to the flickr.auth.* methods and login URLs pointing to the auth page on Flickr must also be signed. For more details, please read the Flickr Authentication API Spec [1].
The development of modified denture base materials (1983)

This work has been undertaken in an attempt to develop improved materials for the construction of dentures. In particular, a material was sought that would combine radiopacity with high impact resistance. Eight particulate radiopaque glasses were prepared and incorporated into poly(methyl methacrylate) denture base material, and the properties of the resultant composites were measured. Experiments were also carried out with glass fiber fillers, which were found to increase impact strength. It was shown that the incorporation of both a particulate radiopaque glass and glass fiber, 20% of each, yielded composites with improved properties.
UVA1 phototherapy for genital lichen sclerosus (2006)

UVA1 therapy may be of benefit in the management of vulval LS, a disease that is often poorly responsive to standard therapies. The therapy is well tolerated and could provide an acceptable therapeutic option for patients with severe disease.
Deep Reinforcement Learning for Dialogue Generation (2016)

Recent neural models of dialogue generation offer great promise for generating responses for conversational agents, but tend to be shortsighted, predicting utterances one at a time while ignoring their influence on future outcomes. Modeling the future direction of a dialogue is crucial to generating coherent, interesting dialogues, a need which led traditional NLP models of dialogue to draw on reinforcement learning. In this paper, we show how to integrate these goals, applying deep reinforcement learning to model future reward in chatbot dialogue. The model simulates dialogues between two virtual agents, using policy gradient methods to reward sequences that display three useful conversational properties: informativity (non-repetitive turns), coherence, and ease of answering (related to forward-looking function). We evaluate our model on diversity, length as well as with human judges, showing that the proposed algorithm generates more interactive responses and manages to foster a more sustained conversation in dialogue simulation. This work marks a first step towards learning a neural conversational model based on the long-term success of dialogues.