gebhart/patrepeval huggingface dataset:
Through-thickness temperature gradients in double-layered magneto-optical media for direct overwrite (1990)

The effect of through-thickness temperature gradients in thin films irradiated by short laser pulses is described, together with its application to direct overwrite. We found by simulation that through-thickness temperature gradients become substantial when a medium is irradiated by short laser pulses of the order of 1 ns which is the characteristic time of heat diffusivity. This effect qualitatively explains why in writing experiments on a double-layered medium short pulses expand the laser power range for a writing process.
Safety and immunogenicity of the novel H4:IC31 tuberculosis vaccine candidate in BCG-vaccinated adults: Two phase I dose escalation trials (2017)

ClinicalTrials.gov, NCT02066428 and NCT02074956.
Model management and the automation of computer system operations (2002)

A report is presented on efforts to develop and manage a model of a real-time computer system. The computer systems of interest are large-scale, IBM mainframe computers that run the MVS operating system. The model interacts with both the computer system itself, and with heterogeneous software modules designed to control and manage the computer system. The work indicates that even in rule-based environments, an object-oriented status-model manager provides valuable functionality.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Rapid degradation of CdSe∕ZnS colloidal quantum dots exposed to gamma irradiation (2008)

Effects of Cs137 gamma irradiation on photoluminescent properties of CdSe∕ZnS colloidal quantum dots are reported. Optical degradation is evaluated by tracking the dependence of photoluminescence intensity on irradiation dose. CdSe∕ZnS quantum dots show poor radiation hardness, and severely degrade after less than 20kR exposure to 662keV gamma photons.
Structures of [M2(dimen)4](Y)2 (M = Rh, Ir; dimen = 1,8-Diisocyanomenthane; Y = PF6, Tetrakis[3,5-bis(trifluoromethyl)phenyl]borate, B(C6H5)4) Crystals Featuring an Exceptionally Wide Range of Metal−Metal Distances and Dihedral Twist Angles (1996)

The binuclear complexes [M2(dimen)4](Y)2 (M = Rh, Ir; dimen = 1,8-diisocyanomenthane; Y = PF6, tetrakis[3,5-bis(trifluoromethyl)phenyl]borate), and B(C6H5)4) have face-to-face structures with M−M distances between 3.60 and 4.48 Å, and square-planar unit twist angles between 0 and 17.2°. Ligand flexing and out-of-plane bending of the metal centers accommodate M−M distances longer than 3.9 Å; addition of a torsional deformation produces a twisted conformation for shorter M−M distances (<3.9 Å). Spectroscopic data indicate that there are two or more deformational isomers of Ir2(dimen)42+ in solution.
Thirty-Day Mortality After Total Knee Arthroplasty (2001)

Factors that were associated with a significantly increased mortality after total knee arthroplasty included an age of more than seventy years, primary (as compared with revision) knee surgery, use of a cemented prosthesis, preexisting cardiopulmonary disease, and simultaneous bilateral arthroplasty.
A unified model for The Multi-level Virtual Conductor (2014)

The Multi-level Virtual Conductor (MLVC) is a bidirectional DC-DC converter that has been controlled in a designated strategy so as to allow it to behave like a conductor has a voltage difference between its terminals. It is considered, in the MLVC, that both input and output of a bi-directional DC-DC converter are independent current sources. These current sources can be considered as a load or as power supply based on its polarity. Therefore, two control loops are required to stabilize the terminals voltages at a certain voltage difference in between. Accordingly, the controller design becomes a very complicated process. To facilitate this dilemma; one solution is to design the controller according to two stages. First stage: design the controller according to one loop control to stabilize one terminal voltage. While the second stage: design the controller according to one loop control to stabilize the other terminal voltage. Then design the controller of the MLVC based on the design considerations of the two cases. However this solution is an effective one and it begets good results. But, it is a heavy burden to perform the design procedure twice. Thus, this paper presents a unified model for the MLVC in order to ease the design procedures. This unified model helps to simplify the controller design process. The proposed unified model is investigated analytically and experimentally. Moreover, both of the frequency response and the transient response are analytically and experimentally studied, as well.
Deletion of a previously uncharacterized flagellar-hook-length control gene fliK modulates the σ 54-dependent regulon in Campylobacter jejuni (2007)

A previously unannotated, putative fliK gene was identified in the Campylobacter jejuni genome based on sequence analysis; deletion mutants in this gene had a 'polyhook' phenotype characteristic of fliK mutants in other genera. The mutants greatly overexpressed the sigma(54)-dependent flagellar hook protein FlgE, to form unusual filamentous structures resembling straight flagella in addition to polyhooks. The genome sequence reveals only one gene predicted to encode an orthologue of the NtrC-family activator required for sigma(54)-dependent transcription. Hence, all sigma(54)-dependent genes in the genome would be overexpressed in the fliK mutant together with flgE. Microarray analysis of genome-wide transcription in the mutant showed increased transcription of a subset of genes, often downstream of sigma(54)-dependent promoters identified by a quality-predictive algorithm applied to the whole genome. Assessment of genome-wide transcription in deletion mutants in rpoN, encoding sigma(54), and in the sigma(54)-activator gene flgR, showed reciprocally reduced transcription of genes that were overexpressed in the fliK mutant. The fliA (sigma(28))-dependent regulon was also analysed. Together the data clearly define the roles of the alternative sigma factors RpoN and FliA in flagellar biogenesis in C. jejuni, and identify additional putative members of their respective regulons.
Chemical Composition and Antimicrobial Activity of the Essential Oils ofPistacia lentiscusvar.chia (1999)

The chemical composition of the three essential oils obtained by steam distillation of the mastic gum, leaves and twigs of Pistacia lentiscus var. chia, was studied by GC/MS. Sixty nine constituents were identified from the oils. alpha-Pinene, myrcene, trans-caryophyllene and germacrene D were found to be the major components. The in vitro antimicrobial activity of the three essential oils and of the resin (total, acid and neutral fraction) against six bacteria and three fungi is reported.
Challenges of analog and I/O scaling in 10nm SoC technology and beyond (2014)

Continuous process-level and system-level innovation has driven Moore's Law scaling for the last fifty years, and will continue to do so in the next decades. In the last two decades, there has been an acceleration of new materials and devices into semiconductor manufacturing, such as low-k, strained Si, high-k, and FinFET, in order to continue process and cost scaling. At the same time, ever increasing component integration on SoCs has further driven cost scaling, allowing the current mobile era to take shape. In the next decade, the focus of SoC innovation will be on patterning and low-resistance materials on the process side, and multi-die package integration on the system side.
An Experimental Investigation of Digging Via Localized Fluidization, Tested With RoboClam: A Robot Inspired by Atlantic Razor Clams (2016)

The Atlantic razor clam, Ensis directus, burrows underwater by expanding and contracting its valves to fluidize the surrounding soil. Its digging method uses an order of magnitude less energy than would be needed to push the clam directly into soil, which could be useful in applications such as anchoring and sensor placement. This paper presents the theoretical basis for the timescales necessary to achieve such efficient digging and gives design parameters for a device to move at these timescales. It then uses RoboClam, a robot designed to imitate the razor clam's movements, to test the design rules. It was found that the minimum contraction time is the most critical timescale for efficient digging and that efficient expansion times vary more widely. The results of this paper can be used as design rules for other robot architectures for efficient digging, optimized for the size scale and soil type of the application.
Ed Carstensen, advisor and mentor to the shockwave lithotripsy program project group (2017)

In the 1980s shockwave lithotripsy emerged as a revolutionary advancement for the treatment of kidney stones. Initial studies with patients showed SWL to be highly effective. The technology was elegant, outcomes exceptionally positive and early tests suggested treatment was safe. As experience with SWL grew, limitations surfaced. A key finding was that SWs have the potential to induce significant trauma to the kidney. Our group convinced the NIH it was time to conduct a rigorous assessment to characterize the adverse effects of SWL and determine the mechanisms of SW action in stone breakage and tissue injury. The NIH Program Project Grant mechanism mandated we establish a panel of external advisors to help guide our work. We needed expertise in physical acoustics, cavitation and animal models of ultrasound exposure. We wanted a leading expert. We were extremely fortunate to land Ed Carstensen. Ed worked with us for nearly 15 years, well into our third renewal cycle. He was a brilliant scientist, a man dedicated to the highest standards of conduct in research. Ed taught us a great deal, he inspired by example and had an exceptional influence on our work and on the greater field of lithotripsy research. [Work supported by NIH-DK43881.]
PSP based DCG-FGT transistor Model: Full characterization procedure (2012)

Full characterization of a new DCG-FGT (Dual-Control-Gate Floating-Gate Transistor) transistor model for static and transient simulations is presented. The model is running under electrical simulator (ELDO) and is characterized thanks to ICCAP software. It has been validated on an advanced STMicroelectronics technology. The final objective of this work is to provide an accurate and scalable model available in design framework.
Transient Vibration Response of Transformer Coil sunder External Short Circuit. (Nonlinear Vibration Analsis of a Fluid-Structure Interacted Problem). (1994)

A new simulation method to treat the fluid-structure interacted nonlinear problem is presented. In this method, the transformer coils are modeled as a multiple-degree-of-freedom system, which consists of lumped masses and nonlinear springs. The insulation oil in the gap between the lumped masses is regarded as a one-dimensional uncompressible fluid flow including viscous resistance. A good correlation is achieved between the experimental and analytical results using an actual scale model transformer in the verification.
True blue: S‐opsin is widely expressed in different animal species (2012)

Colour vision in animals is an interesting, fascinating subject. In this study, we examined a wide variety of species for expression of S-opsin (blue sensitive) and M-/L-opsin (green-red sensitive) in retinal cones using two novel monoclonal antibodies specific for peptides from human opsins. Mouse, rat and hare did not express one of the investigated epitopes, but we could clearly prove existence of cones through peanut agglutinin labelling. Retinas of guinea pig, dog, wolf, marten, cat, roe deer, pig and horse were positive for S-opsin, but not for M-/L-opsin. Nevertheless all these species are clearly at least dichromats, because we could detect further S-opsin negative cones by labelling with cone arrestin specific antibody. In contrast, pheasant and char had M-/L-opsin positive cones, but no S-opsin expressing cones. Sheep, cattle, monkey, men, pigeon, duck and chicken were positive for both opsins. Visual acuity analyzed through density of retinal ganglion cells revealed least visual discrimination by horses and highest resolution in pheasant and pigeon. Most mammals studied are dichromats with visual perception similar to red-green blind people.
A Linear Time Algorithm for Finding Minimum Cutsets in Reducible Graphs (1979)

The analysis of many processes modeled by directed graphs requires the selection of a subset of vertices which cut all the cycles in the graph. Reducing the size of such a cutset usually leads to a simpler and more efficient analysis, but the problem of finding minimum cutsets in general directed graphs is known to be $NP$-complete. In this paper we show that in reducible graphs (and thus in almost all the “practical” flowcharts of programs), minimum cutsets can be found in linear time. We further show that the linear algorithm can check its own applicability to a given graph, thus eliminating the need of prechecking (in nonlinear time) whether it is reducible or not. An immediate application of this result is in program verification systems based on Floyd’s inductive assertions method.
Bacterial Biofilms and Their Implications in Pathogenesis and Food Safety (2021)

Biofilm formation is an integral part of the microbial life cycle in nature. In food processing environments, bacterial transmissions occur primarily through raw or undercooked foods and by cross-contamination during unsanitary food preparation practices. Foodborne pathogens form biofilms as a survival strategy in various unfavorable environments, which also become a frequent source of recurrent contamination and outbreaks of foodborne illness. Instead of focusing on bacterial biofilm formation and their pathogenicity individually, this review discusses on a molecular level how these two physiological processes are connected in several common foodborne pathogens such as <i>Listeria monocytogenes</i>, <i>Staphylococcus aureus</i>, <i>Salmonella enterica</i> and <i>Escherichia coli</i>. In addition, biofilm formation by <i>Pseudomonas aeruginosa</i> is discussed because it aids the persistence of many foodborne pathogens forming polymicrobial biofilms on food contact surfaces, thus significantly elevating food safety and public health concerns. Furthermore, in-depth analyses of several bacterial molecules with dual functions in biofilm formation and pathogenicity are highlighted.
Social Synchrony: Predicting Mimicry of User Actions in Online Social Media (2009)

We propose a computational framework to predict synchrony of action in online social media. Synchrony is a temporal social network phenomenon in which a large number of users are observed to mimic a certain action over a period of time with sustained participation from early users. Understanding social synchrony can be helpful in identifying suitable time periods of viral marketing. Our method consists of two parts - the learning framework and the evolution framework. In the learning framework, we develop a DBN based representation that includes an understanding of user context to predict the probability of user actions over a set of time slices into the future. In the evolution framework, we evolve the social network and the user models over a set of future time slices to predict social synchrony. Extensive experiments on a large dataset crawled from the popular social media site Digg (comprising ~7 M diggs) show that our model yields low error (15.2 plusmn 4.3%) in predicting user actions during periods with and without synchrony. Comparison with baseline methods indicates that our method shows significant improvement in predicting user actions.
Abstract 5141: Macrophage transcriptomic signature validation in scRNA seq and overall survival differences in urothelial carcinoma (2023)

Abstract Introduction: While the prognostic value of immune system biomarkers has been well explored, role of cancer associated macrophages in bladder cancer(BC) is unclear due to lack of consistent results, coupled with tissue nonspecific transcriptomic signature. Methodology: Data acquisition from 3,936 patients of The Cancer Genome Atlas (TCGA) in addition to Gene Expression Omninus (GEO) data sets GSE13507, GSE16945, GSE48277, GSE32894, GSE149582, as well as European Genotype Phenotype EGAS000001004507 was obtained. Tumor associated macrophages M1 and M2 were defined utilizing 188 and 159 gene expression profiles via xCell computational algorithm. To obtain bladder tissue residence macrophage signatures, scRNA seq was performed on tissue collected from surgical resection of 5 HG bladder cancer patients and 2 healthy controls. CellRanger software package with default parameters was utilized giving a total of 8,068 cells. FindAllMarkers was utilized for integration of DEG genes (cancer vs control) among the cluster and identification of BC macrophage specific markers. Endpoint of OS were measured in months from the time of cystectomy to follow up. Results: Surprisingly, presence of M1 infiltration was found to be associated with improved OS in two out of eight cohorts only (GSE32894, GSE70691, p&amp;lt;0.001), while the remainder detected no significant difference. Similarly, no association with OS was detected among all 8 cohorts with M2 infiltration. To improve our understanding of tissue specific markers of macrophage population in bladder, we then analyzed macrophage clusters detected within scRNAseq of BC patients compared to healthy. Gene ontology enrichment analysis of functions within tumor specific macrophages demonstrated an exaggerated expression of mTORC1 signaling, PI3K/AKT/mTOR signaling, TGF beta and EGF receptor pathways compared to non-cancer controls. Reanalysis of 22 tissue specific markers for M1/M2 infiltration showed no difference in any of the 8 cohorts with M1 high vs low infiltration. Similarly, addition of M2 infiltration as predictive marker yielded no further associations with OS in all but one cohort (GSE32894, p=0.00041), where high M2 tumor presence was associated with improved OS. Conclusion: Our study represents the largest TAMs evaluation of BC across 8 cohorts with additional scRNA seq exploration of tissue specific signatures, demonstrating no association with OS in bladder cancer. Citation Format: Laura Bukavina, Spencer Bell, Daniel Geynisman, Ilaha Isali, Daniel Ranti, John Sfakianos, Henkel Valentine, Adam Calaway, Alexander Kutikov, Andres Correa, Robert Uzzo, Lee Ponsky, Philip Abbosh. Macrophage transcriptomic signature validation in scRNA seq and overall survival differences in urothelial carcinoma. [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 5141.
Impact of HIV-1 Resistance-Associated Mutations on Susceptibility to Doravirine: Analysis of Real-World Clinical Isolates (2021)

Clinical management of human immunodeficiency virus type-1 (HIV-1) infection may be negatively impacted by either acquired or transmitted drug resistance. Here, we aim to extend our understanding of the impact of resistance-associated mutations (RAMs) on the susceptibility of clinical isolates to the nonnucleoside reverse transcriptase inhibitor (NNRTI) doravirine. Clinical isolates from people living with HIV-1 undergoing routine testing for susceptibility to doravirine and other approved NNRTIs (etravirine, rilpivirine, efavirenz, and nevirapine) were collected from August 2018 to August 2019. Susceptibility in the presence/absence of NNRTI and nucleos(t)ide reverse transcriptase inhibitor (NRTI) mutations was determined using cutoffs for relative fold change in inhibition (ratio of the 50% inhibitory concentration [IC<sub>50</sub>] of patient virus compared with the IC<sub>50</sub> of a wild-type reference strain). Biological cutoffs of 3- to 15-fold change were investigated for doravirine, with preestablished cutoffs used for the other NNRTIs. Of 4,070 clinical isolates, 42.9% had ≥1 NNRTI RAM. More isolates were susceptible to doravirine (92.5-96.7%) than to etravirine (91.5%), rilpivirine (89.5%), efavirenz (81.5%), or nevirapine (77.5%). Based on a 3-fold cutoff, doravirine susceptibility was retained in 44.7-65.8% of isolates resistant to another NNRTI and 28.5% of isolates resistant to all other tested NNRTIs. The presence of NRTI RAMs, including thymidine analog mutations, was associated with doravirine hypersusceptibility in some isolates, particularly in the absence of NNRTI RAMs. These results support the favorable resistance profile of doravirine and are of particular importance given the challenge posed by both acquired and transmitted resistance.
MOP and NOP receptor interaction: Studies with a dual expression system and bivalent peptide ligands (2022)

Opioids targeting mu;μ (MOP) receptors produce analgesia in the peri-operative period and palliative care. They also produce side effects including respiratory depression, tolerance/dependence and addiction. The N/OFQ opioid receptor (NOP) also produces analgesia but is devoid of the major MOP side effects. Evidence exists for MOP-NOP interaction and mixed MOP-NOP ligands produce analgesia with reduced side effects. We have generated a HEKMOP/NOP human expression system and used bivalent MOP-NOP and fluorescent ligands to (i) probe for receptor interaction and (ii) consequences of that interaction. We used HEKMOP/NOP cells and two bivalent ligands; Dermorphin-N/OFQ (MOP agonist-NOP agonist; DeNO) and Dermorphin-UFP101 (MOP agonist-NOP antagonist; De101). We have determined receptor binding profiles, GTPγ[35S] binding, cAMP formation and ERK1/2 activation. We have also probed MOP and NOP receptor interactions in HEK cells and hippocampal neurones using the novel MOP fluorescent ligand, DermorphinATTO488 and the NOP fluorescent ligand N/OFQATTO594. In HEKMOP/NOP MOP ligands displaced NOP binding and NOP ligands displaced MOP binding. Using fluorescent probes in HEKMOP/NOP cells we demonstrated MOP-NOP probe overlap and a FRET signal indicating co-localisation. MOP-NOP were also co-localised in hippocampal tissue. In GTPγ[35S] and cAMP assays NOP stimulation shifted the response to MOP rightwards. At ERK1/2 the response to bivalent ligands generally peaked later. We provide evidence for MOP-NOP interaction in recombinant and native tissue. NOP activation reduces responsiveness of MOP activation; this was shown with conventional and bivalent ligands.
Effect of Sintering Temperature for Die-shear Strength of Non-pressure Sintering Copper Paste on Metal Plating (2022)

Die-bonding technology using Cu sinter pastes is an attractive and important joint method for power devices operating at higher temperatures. This paper describes the effect of sintering temperatures on die-shear strengths of non-pressure sintered copper (sCu) onto six different metal platings (Cu, Ni, Electroless Ni, Pd, Ag, and Au). The die-shear strengths of sCu on the metal plating under sintering temperatures (225-350 °C) in H <inf xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</inf> gas were measured. As the sintering temperatures increased, the shear strengths on the Cu, Ni, and ENi plating increased, whereas those on the Pd, Ag, and Au plating decreased. By analyzing the element distribution on the bonding interfaces using SEM/EDX, it was found that the self- and non-diffusion couples (sCu:Cu, sCu:Ni, sCu:ENi) can keep the high shear strengths and the diffused couples (sCu:Pd, sCu:Ag, sCu:Au) can deteriorate the shear strengths.
Polyacrylonitrile Single‐Walled Carbon Nanotube Composite Fibers (Adv. Mater. 2004, 1, 58) (2004)

Abstract To view the original paper use http://dx.doi.org/10.1002/adma.200305456 .