gebhart/patrepeval huggingface dataset:
Current aspects of optical performance monitoring and failure root cause analysis in optical WDM networks (2005)

Currently existing dense wavelength division multiplexing (DWDM) networks start to migrate from numerous point-to-point links towards meshed, transparent, optical networks with dynamically routed light paths. This increases the need for appropriate network monitoring and supervision methods. Optical performance monitoring (OPM) has to be cost-effective. Thus additional spendings for OPM have to be significantly smaller than the savings in OPEX due to increased reliability and ease of operation, administration, and maintenance (OAM). We elaborate on different advanced monitoring concepts. First, we discuss general failure scenarios in meshed networks. Then we describe software based failure root cause analysis and its implementation. We conclude that by implementing appropriate software algorithms in the network hardware effort can be significantly reduced. Finally, we assess different advanced OPM methods which may show up as useful to enable OPM in future optical networks.
Identification and Characterization of the RLIP/RALBP1 Interacting Protein Xreps1 in Xenopus laevis Early Development (2012)

We demonstrate here that RLIP/RalBP1, an effector of Ral involved in receptor-mediated endocytosis and in the regulation of actin dynamics during embryonic development, also interacts with Reps1. Although these two proteins are present early during embryonic development, they are active only at the end of gastrulation. Our results suggest that the interaction between RLIP and Reps1 is negatively controlled during the cleavage stage of development, which is characterized by rapid mitosis. Later in development, Reps1 is required for the normal function of the ectodermic cell, and its targeting into the plasma membrane affects the stability of the ectoderm.
10-OR: Combination Therapy with Anti-CD3 Antibody and Harmine plus Exendin-4 Enhances Remission from Recent-Onset Type 1 Diabetes. (2022)

Type 1 diabetes (T1D) results from loss of both immune tolerance and functional β-cells. Administration of harmine (H) plus exendin-4 (E) markedly induces human β-cell expansion. Anti-CD3 antibody treatment reduces C-peptide loss in T1D patients. Here, we tested whether combination therapy with anti-CD3 antibody and H+E enhances T1D remission in non-obese diabetic (NOD) mice. First, we tested whether H+E protects human β-cells against inflammation and ER stress. We found that H+E, but not the drugs alone, significantly reduced both thapsigargin- and cytokine-induced human β-cell apoptosis. Single-cell RNAseq of human islets treated with cytokines and H+E showed reduced IL1β and IFNγ signaling in β-cells. Apoptosis genes such as CYLD and RIPK1 were downregulated and prosurvival genes such as HIF1A and VEGFA were upregulated in β-cells of H+E-treated islets. Next, treatment of early-onset diabetic NOD mice with H+E (daily ip) for 8 weeks improved glucose homeostasis but failed to induce long-lasting immune tolerance and T1D remission. Therefore, we next treated early-onset diabetic NOD mice with low-dose anti-CD3 antibody daily for 3 days (40µg/day) followed by 8 weeks treatment with H+E or vehicle (V) (Alzet pumps) . Treatment with anti-CD3 and H+E eliminated hyperglycemia in 100% of the mice vs. only 20% remission in anti-CD3 and V-treated mice. CD3+ T cell numbers were significantly and similarly reduced (∼50%) in mice treated with H+E or V. Preliminary results indicate that activated T cells in pancreatic lymph nodes (PLNs) and islet insulitis were significantly reduced, and T regulatory cells in spleen and PLNs were increased in H+E-treated mice. TUNEL+ β-cells were decreased and Ki67+ β-cells were increased in the pancreas of H+E-treated mice. Collectively, these results indicate that combination therapy with low-dose anti-CD3 antibody and H+E enhances T1D remission in diabetic NOD mice by increasing β-cell viability and favoring immune tolerance. Disclosure G.Lu: None. R.Kang: None. Y.Li: None. P.Wang: None. C.Rosselot: None. R.J.Devita: None. A.F.Stewart: None. A.Garcia-ocana: Consultant; Sun Pharmaceutical Industries Ltd. Funding NIH DK105015
GDNF released from microspheres enhances nerve regeneration after delayed repair (2012)

Based on the positive outcome of the delivery system, we plan to study the delivery system over longer time courses of release and nerve regeneration.
The decomposition of YBa2Cu3O7−δ doped into Ba2YRuO6 (2008)

One of the persistent criticisms of claims for observation of superconductivity in Ba2YRu1−uCuuO6 (O6) is that the diamagnetism is actually due to the decomposition of the material into YBa2Cu3O7−δ and other phases. We report a series of experiments in which YBa2Cu3O7−δ is doped into Ba2YRuO6 and carried through a series of sintering steps which were followed by magnetization, neutron diffraction, and scanning electron microscopy/microprobe measurements. It was found that the dopant YBa2Cu3O7−δ decomposed and failed to reform with cooling. It is concluded that the O6 phase is the stable high-temperature phase. The Cu released from the Y123 decomposition doped the host Ba2YRuO6, in partial substitution for Ru. This doping resulted in a small diamagnetic response with an onset temperature of ∼84 K.
SAT-281 Chronic, Excess Growth Hormone Action Alters the Development and Aging of the Microbial Community in the Mouse Gut (2020)

Abstract Emerging evidence proposes that the gut microbiome has an vital role in host growth, metabolism and endocrinology. That is, gut microbes impact growth by potentially altering the growth hormone (GH)/insulin-like growth factor-1 axis. Our previous research has also shown that GH - in states of absence and excess - is associated with altered gut microbial composition, maturity and predictive metabolic function in mice. Moreover, both GH and the gut microbiome are implicated in development and aging. Yet, it is unknown how GH impacts the longitudinal microbiome. This study thus aimed to characterize the longitudinal changes in the gut microbial profile of bovine GH transgenic mice (a model of chronic, excess GH action and accelerated aging). Microbial composition was quantified from fecal pellets of the same bGH and control mice at 3, 6 and 12 months of age through 16S rRNA gene sequencing and QIIME 2. Additional bioinformatic analyses assessed the unique signature and predictive metabolic function of the microbiome. The bGH mice had a distinct microbial profile compared to controls longitudinally. At 3 months, bGH mice had increased Firmicutes and Actinobacteria, decreased Bacteroidetes, Proteobacteria and Campylobacterota, and a significant reduction in microbial richness and evenness. By 6 months, all of the aforesaid phyla were increased with the exception of Firmicutes. By 12 months, bGH mice exhibited dysbiosis with increased Firmicutes and Proteobacteria and reduced Bacteroidetes, microbial richness and evenness. Moreover, abundance in Firmicutes, Bacteroidetes and Campylobacterota were significantly explained by the combined effect of genotype and age (p = 0.006, 0.005 and 0.02, respectively). Across all timepoints, bGH mice had a significantly different microbiome compared to controls (p = 0.002), and the development of microbial richness and evenness were also significantly different in bGH mice (p = 0.034 and 0.023). Bacterial genera Lactobacillus, Ruminococcaceae and Lachnospiraceae were identified as a unique candidates in bGH mice across all timepoints. Likewise, metabolic pathways involved in biosynthesis of heme b, menaquinol, acetate and butyrate differentiated the longitudinal bGH microbiome. Collectively, these results show that chronic, excess GH impacts the development and aging of the gut microbiome. Notably, several of the stated bacterial genera and metabolic pathways were associated with GH in our previous study, suggesting that GH may influence the longitudinal presence of certain gut microbes and metabolic functions. Additional studies will be performed to further explore the GH-associated gut microbiome and its impact on host health. Research was partially funded by the John J. Kopchick MCB/TBS Fellowship, a fellowship from the Osteopathic Heritage Foundation and the MMPC at UC, Davis (NIH grant U240DK092993).
Exploiting the Anti-HIV-1 Activity of Acyclovir: Suppression of Primary and Drug-Resistant HIV Isolates and Potentiation of the Activity by Ribavirin (2012)

Multiple clinical trials have demonstrated that herpes simplex virus 2 (HSV-2) suppressive therapy using acyclovir (ACV) or valacyclovir in HIV-1/HSV-2-infected persons increased the patient's survival and decreased the HIV-1 load. It has been shown that the incorporation of ACV-monophosphate into the nascent DNA chain instead of dGMP results in the termination of viral DNA elongation and directly inhibits laboratory strains of HIV-1. We evaluated here the anti-HIV activity of ACV against primary HIV-1 isolates of different clades and coreceptor specificity and against viral isolates resistant to currently used drugs, including zidovudine, lamivudine, nevirapine, a combination of nucleoside reverse transcriptase inhibitors (NRTIs), a fusion inhibitor, and two protease inhibitors. We found that, at clinically relevant concentrations, ACV inhibits the replication of these isolates in human tissues infected ex vivo. Moreover, addition of ribavirin, an antiviral capable of depleting the pool of intracellular dGTP, potentiated the ACV-mediated HIV-1 suppression. These data warrant further clinical investigations of the benefits of using inexpensive and safe ACV alone or in combination with other drugs against HIV-1, especially to complement or delay highly active antiretroviral therapy (HAART) initiation in low-resource settings.
Data from Analysis of Mitosis and Antimitotic Drug Responses in Tumors by <i>In Vivo</i> Microscopy and Single-Cell Pharmacodynamics (2023)

&lt;div&gt;Abstract&lt;p&gt;Cancer relies upon frequent or abnormal cell division, but how the tumor microenvironment affects mitotic processes &lt;i&gt;in vivo&lt;/i&gt; remains unclear, largely due to the technical challenges of optical access, spatial resolution, and motion. We developed high-resolution &lt;i&gt;in vivo&lt;/i&gt; microscopy methods to visualize mitosis in a murine xenograft model of human cancer. Using these methods, we determined whether the single-cell response to the antimitotic drug paclitaxel (Ptx) was the same in tumors as in cell culture, observed the impact of Ptx on the tumor response as a whole, and evaluated the single-cell pharmacodynamics (PD) of Ptx (by &lt;i&gt;in vivo&lt;/i&gt; PD microscopy). Mitotic initiation was generally less frequent in tumors than in cell culture, but subsequently it proceeded normally. Ptx treatment caused spindle assembly defects and mitotic arrest, followed by slippage from mitotic arrest, multinucleation, and apoptosis. Compared with cell culture, the peak mitotic index in tumors exposed to Ptx was lower and the tumor cells survived longer after mitotic arrest, becoming multinucleated rather than dying directly from mitotic arrest. Thus, the tumor microenvironment was much less proapoptotic than cell culture. The morphologies associated with mitotic arrest were dose and time dependent, thereby providing a semiquantitative, single-cell measure of PD. Although many tumor cells did not progress through Ptx-induced mitotic arrest, tumor significantly regressed in the model. Our findings show that &lt;i&gt;in vivo&lt;/i&gt; microscopy offers a useful tool to visualize mitosis during tumor progression, drug responses, and cell fate at the single-cell level. &lt;i&gt;Cancer Res; 71(13); 4608–16. ©2011 AACR&lt;/i&gt;.&lt;/p&gt;&lt;/div&gt;
ChemInform Abstract: NOVEL FLUORINATED ANTIFOLATES. ENZYME INHIBITION AND CYTOTOXICITY STUDIES ON 2′‐ AND 3′‐FLUOROAMINOPTERIN (1983)

Abstract Analoga (V) des Aminopterins werden gemäß Formelschema synthetisiert.
Systemic CD14 Inhibition Attenuates Organ Inflammation in Porcine Escherichia coli Sepsis (2013)

Sepsis is an infection-induced systemic inflammatory response syndrome. Upstream recognition molecules, like CD14, play key roles in the pathogenesis. The aim of the present study was to investigate the effect of systemic CD14 inhibition on local inflammatory responses in organs from septic pigs. Pigs (n = 34) receiving Escherichia coli-bacteria or E. coli-lipopolysaccharide (LPS) were treated with an anti-CD14 monoclonal antibody or an isotype-matched control. Lungs, liver, spleen, and kidneys were examined for bacteria and inflammatory biomarkers. E. coli and LPS were found in large amounts in the lungs compared to the liver, spleen, and kidneys. Notably, the bacterial load did not predict the respective organ inflammatory response. There was a marked variation in biomarker induction in the organs and in the effect of anti-CD14. Generally, the spleen produced the most cytokines per weight unit, whereas the liver contributed the most to the total load. All cytokines were significantly inhibited in the spleen. Interleukin-6 (IL-6) was significantly inhibited in all organs, IL-1β and IP-10 were significantly inhibited in liver, spleen, and kidneys, and tumor necrosis factor, IL-8, and PAI-1 were inhibited only in the spleen. ICAM-1 and VCAM-1 was significantly inhibited in the kidneys. Systemic CD14-inhibition efficiently, though organ dependent, attenuated local inflammatory responses. Detailed knowledge on how the different organs respond to systemic inflammation in vivo, beyond the information gained by blood examination, is important for our understanding of the nature of systemic inflammation and is required for future mediator-directed therapy in sepsis. Inhibition of CD14 seems to be a good candidate for such treatment.
On Generating and Labeling Network Traffic with Realistic, Self-Propagating Malware (2021)

Research and development of techniques which detect or remediate malicious network activity require access to diverse, realistic, contemporary data sets containing labeled malicious connections. In the absence of such data, said techniques cannot be meaningfully trained, tested, and evaluated. Synthetically produced data containing fabricated or merged network traffic is of limited value as it is easily distinguishable from real traffic by even simple machine learning (ML) algorithms. Real network data is preferable, but while ubiquitous is broadly both sensitive and lacking in ground truth labels, limiting its utility for ML research. This paper presents a multi-faceted approach to generating a data set of labeled malicious connections embedded within anonymized network traffic collected from large production networks. Real-world malware is defanged and introduced to simulated, secured nodes within those networks to generate realistic traffic while maintaining sufficient isolation to protect real data and infrastructure. Network sensor data, including this embedded malware traffic, is collected at a network edge and anonymized for research use. Network traffic was collected and produced in accordance with the aforementioned methods at two major educational institutions. The result is a highly realistic, long term, multi-institution data set with embedded data labels spanning over 1.5 trillion connections and over a petabyte of sensor log data. The usability of this data set is demonstrated by its utility to our artificial intelligence and machine learning (AI/ML) research program.
Key improvements of the MEMS switch lifetime thanks to a dielectric-free design and contact reliability investigations in hot/cold switching operations (2013)

Dielectric charging and contact degradations are the two major challenges to improve the lifetime of series ohmic electrostatic MEMS switches. This paper details our approach and our main results to overcome the failures due to dielectric charging. We introduce a time predictive model for charge accumulation that we use as a design tool for reliability. The key parameters are listed and a new switch design is proposed to reduce the charging: the dielectric materials between the actuation electrodes are removed as much as possible. This dielectric-free design gives remarkable results in terms of dielectric charging sensitivity: the pull-in voltage decreases a little bit at initial times, and remains steady for longer time. The second major challenge, that remains to be considered, deals with the contact reliability. For that purpose, gold and ruthenium contacts have been investigated under several operating conditions. Gold contacts give good results in cold switching conditions whereas ruthenium suffers from surface contamination which increases quickly the contact resistance. In hot switching conditions, both materials are sensitive to material transfer mechanism, the failure rate being proportional to the open circuit voltage. Nevertheless, ruthenium seems more resistant to a material transfer than gold, and offers performances acceptable for some specific applications. A hermetic packaging at wafer level should allow to improve the contact reliability thanks to an efficient management of the surface contamination issue.
Polimerização RAFT em Miniemulsão (2013)

"Dentre as diversas técnicas para obter polímeros de maneira controlada, a técnica de Transferência Reversível de Cadeia por Adição-Fragmentação (RAFT) é tida como uma das mais versáteis, uma vez que é compatível com uma grande quantidade de monômeros, solventes, condições reacionais e sistemas de polimerização. Utilizando essa metodologia, é possível sintetizar polímeros com diversas arquiteturas e com excelente controle do tamanho das cadeias. Neste trabalho, é apresentada uma revisão da técnica de polimerização RAFT em sistemas de miniemulsão. As principais características da técnica de polimerização RAFT e uma ampla revisão dos estudos em miniemulsão são apresentadas, abrangendo mais de 152 referências. Também é abordado nesta revisão o uso da polimerização RAFT em miniemulsão para obtenção de polímeros para aplicações biotecnológicas."
Vessel Sampling and Blood Flow Velocity Distribution With Vessel Diameter for Characterizing the Human Bulbar Conjunctival Microvasculature (2015)

This was the first study to determine the sampling size of the vessels and the distribution histogram of the blood flow velocity and vessel diameter, which may lead to a better understanding of the human microvascular system of the bulbar conjunctiva.
High-Performance Computing and ABMS for High-Resolution COVID-19 Spreading Simulation (2022)

This paper presents an approach for the modeling and the simulation of the spreading of COVID-19 based on agent-based modeling and simulation (ABMS). Our goal is not only to support large-scale simulations but also to increase the simulation resolution. Moreover, we do not assume an underlying network of contacts, and the person-to-person contacts responsible for the spreading are modeled as a function of the geographical distance among the individuals. In particular, we defined a commuting mechanism combining radiation-based and gravity-based models and we exploited the commuting properties at different resolution levels (municipalities and provinces). Finally, we exploited the high-performance computing (HPC) facilities to simulate millions of concurrent agents, each mapping the individual’s behavior. To do such simulations, we developed a spreading simulator and validated it through the simulation of the spreading in two of the most populated Italian regions: Lombardy and Emilia-Romagna. Our main achievement consists of the effective modeling of 10 million of concurrent agents, each one mapping an individual behavior with a high-resolution in terms of social contacts, mobility and contribution to the virus spreading. Moreover, we analyzed the forecasting ability of our framework to predict the number of infections being initialized with only a few days of real data. We validated our model with the statistical data coming from the serological analysis conducted in Lombardy, and our model makes a smaller error than other state of the art models with a final root mean squared error equal to 56,009 simulating the entire first pandemic wave in spring 2020. On the other hand, for the Emilia-Romagna region, we simulated the second pandemic wave during autumn 2020, and we reached a final RMSE equal to 10,730.11.
Linearly-polarized lasing at 1180 nm using polarization-maintaining Yb-doped solid photonic bandgap fiber (2009)

Linearly-polarized lasing at 1180 nm is demonstrated by utilizing polarization maintaining Yb-doped solid photonic bandgap fiber. The extinction ratio of the output light between two lineary-polarized lights is more than 20 dB.
Combinations of β-Lactam or Aminoglycoside Antibiotics with Plectasin Are Synergistic against Methicillin-Sensitive and Methicillin-Resistant Staphylococcus aureus (2015)

Bacterial infections remain the leading killer worldwide which is worsened by the continuous emergence of antibiotic resistance. In particular, methicillin-sensitive (MSSA) and methicillin-resistant Staphylococcus aureus (MRSA) are prevalent and the latter can be difficult to treat. The traditional strategy of novel therapeutic drug development inevitably leads to emergence of resistant strains, rendering the new drugs ineffective. Therefore, rejuvenating the therapeutic potentials of existing antibiotics offers an attractive novel strategy. Plectasin, a defensin antimicrobial peptide, potentiates the activities of other antibiotics such as β-lactams, aminoglycosides and glycopeptides against MSSA and MRSA. We performed in vitro and in vivo investigations to test against genetically diverse clinical isolates of MSSA (n = 101) and MRSA (n = 115). Minimum inhibitory concentrations (MIC) were determined by the broth microdilution method. The effects of combining plectasin with β-lactams, aminoglycosides and glycopeptides were examined using the chequerboard method and time kill curves. A murine neutropenic thigh model and a murine peritoneal infection model were used to test the effect of combination in vivo. Determined by factional inhibitory concentration index (FICI), plectasin in combination with aminoglycosides (gentamicin, neomycin or amikacin) displayed synergistic effects in 76-78% of MSSA and MRSA. A similar synergistic response was observed when plectasin was combined with β-lactams (penicillin, amoxicillin or flucloxacillin) in 87-89% of MSSA and MRSA. Interestingly, no such interaction was observed when plectasin was paired with vancomycin. Time kill analysis also demonstrated significant synergistic activities when plectasin was combined with amoxicillin, gentamicin or neomycin. In the murine models, plectasin at doses as low as 8 mg/kg augmented the activities of amoxicillin and gentamicin in successful treatment of MSSA and MRSA infections. We demonstrated that plectasin strongly rejuvenates the therapeutic potencies of existing antibiotics in vitro and in vivo. This is a novel strategy that can have major clinical implications in our fight against bacterial infections.
New coater/developer technologies for CD control and defectivity reduction towards 5 nm and smaller nodes (2019)

Extreme ultraviolet (EUV) lithography is now being introduced for the mass production of 7 nm process. In order to meet process requirements for 7 nm node, continuous work on coater/developer has been done to improve CD uniformity and defectivity. However, further improvements are still required especially for 5 nm or smaller nodes because of the increasing impact of stochastic failures. 2 The probability of such failures quickly increases with CD size, resulting in a very narrow defect process window. Therefore, strict control of CD is getting crucial to ensure stable yield in the future nodes. In this paper, optimization of processes has been explored to improve not only local CD variations, but also wafer uniformity and stability across batch processing. We will also present our latest technologies for the reduction of in-film particles in coated films and the optimization of development/rinse process for the reduction of residues and collapses.