gebhart/patrepeval huggingface dataset:
The NVAX CPU Chip: Design Challenges, Methods, and CAD Tools. (1992)

The NVAX CPU chip is a 1.3 million transistor, VAX microprocessor designed in Digital&amp;apos;s 0.75micrometer CMOS-4 technology. It has a typical cycle time of 12 ns under worst-case operating conditions. The goal of the chip design team was to design a high-performance, robust, and reliable chip, within the constraints of a short schedule. Design strategies were developed to achieve this goal, including organization of a chip design flow and new implementation and verification methods. New proprietary CAD tools also played important roles in the chip development. Introduction The NVAX CPU chip is a 1.3 million transistor, VAX microprocessor designed in Digital&amp;apos;s 0.75micrometer fourth-generation complementary metaloxide semiconductor (CMOS-4) technology. The implementation of the NVAX CPU chip posed many design and complexity management challenges. The combination of the chip performance goal, the high level of integration, and the small feature sizes of the CMOS-4 technology increased the...
Near 1 kW of Continuous-Wave Power From a Single High-Efficiency Diode-Laser Bar (2007)

Near 1 kW of continuous-wave output power has been obtained from a single 1-cm-wide diode-laser bar. Mounted on a water-cooled microchannel heat sink, the operating wavelength was near 940 nm (at ~400 W) and the measured thermal resistance was as low as 0.08degC/W. Maximum power conversion efficiencies (PCEs) of 70% and 67% were obtained from high-fill-factor bars with cavity lengths of 4 and 5 mm, respectively. A maximum PCE of 72.2% was achieved with 3-mm broad-area single emitters. On-going lifetime data may signal the stable operation at unprecedented powers.
NFATc1 Targets Cyclin A in the Regulation of Vascular Smooth Muscle Cell Multiplication during Restenosis (2008)

Platelet-derived growth factor BB (PDGF-BB) induced cyclin A expression and CDK2 activity in vascular smooth muscle cells (VSMC). Inhibition of nuclear factors of activated T cell (NFAT) activation by cyclosporin A (CsA) and VIVIT suppressed PDGF-BB-induced cyclin A expression and CDK2 activity, resulting in blockade of VSMC in the G(1) phase. In addition, CsA- and VIVIT-mediated inhibition of NFATs and small interfering RNA-targeted down-regulation of cyclin A levels suppressed PDGF-BB-induced VSMC DNA synthesis. PDGF-BB also induced cyclin A mRNA levels in VSMC in an NFAT-dependent manner. Cloning and bioinformatic analysis of rat cyclin A promoter revealed the presence of NFAT-binding elements, and PDGF-BB induced the binding of NFATs to these regulatory sequences in a CsA- and VIVIT-sensitive manner. Chromatin immunoprecipitation analysis showed that NFATc1 binds to the cyclin A promoter in response to PDGF-BB in a VIVIT-sensitive manner. Furthermore, PDGF-BB induced cyclin A promoter-luciferase reporter gene activity in VSMC, and it was inhibited by both CsA and VIVIT. Balloon injury induced cyclin A expression and CDK2 activity in rat carotid arteries, and these responses were also blocked by VIVIT. In addition, VIVIT attenuated balloon injury-induced SMC proliferation, resulting in reduced restenosis. Down-regulation of NFATc1 by its small interfering RNA inhibited PDGF-BB-induced cyclin A expression and DNA synthesis both in rat and human VSMC. Together, these findings demonstrate that the cyclin A-CDK2 complex may be a potential effector of NFATs, specifically NFATc1, in mediating SMC multiplication leading to neointima formation. Therefore, NFATs may be used as target molecules for the development of therapeutic agents against vascular diseases such as restenosis.
Protocol design contests (2014)

In fields like data mining and natural language processing, design contests have been successfully used to advance the state of the art. Such contests offer an opportunity to bring the excitement and challenges of protocol design---one of the core intellectual elements of research and practice in networked systems---to a broader group of potential contributors, whose ideas may prove important. Moreover, it may lead to an increase in the number of students, especially undergraduates or those learning via online courses, interested in pursuing a career in the field. We describe the creation of the infrastructure and our experience with a protocol design contest conducted in MIT's graduate Computer Networks class. This contest involved the design and evaluation of a congestion-control protocol for paths traversing cellular wireless networks. One key to the success of a design contest is an unambiguous, measurable objective to compare protocols. In practice, protocol design is the art of trading off conflicting goals with each other, but in this contest, we specified that the goal was to maximize $\log(\mbox{throughput}/\mbox{delay})$. This goal is a good match for applications such as video streaming or videoconferencing that care about high throughput and low interactive delays. Some students produced protocols whose performance was better than published protocols tackling similar goals. Furthermore, the convex hull of the set of all student protocols traced out a tradeoff curve in the throughput-delay space, providing useful insights into the entire space of possible protocols. We found that student protocols diverged in performance between the training and testing traces, indicating that some students had overtrained ("overfitted") their protocols to the training trace. Our conclusion is that, if designed properly, such contests could benefit networking research by making new proposals more easily reproducible and amenable to such "gamification," improve networked systems, and provide an avenue for outreach.
Abnormal Pulmonary Artery Endothelial-Smooth Muscle Cell Interactions in Experimental Congenital Diaphragmatic Hernia (CDH) (2014)

Acker, Shannon N. MD; Seedorf, Gregory; Abman, Steve H. MD; Nozik-Grayck, Eva MD; Partrick, David A. MD, FACS; Gien, Jason MD Author Information
Distinct representations of configural and part information across multiple face-selective regions of the human brain (2015)

Several regions of the human brain respond more strongly to faces than to other visual stimuli, such as regions in the amygdala (AMG), superior temporal sulcus (STS), and the fusiform face area (FFA). It is unclear if these brain regions are similar in representing the configuration or natural appearance of face parts. We used functional magnetic resonance imaging of healthy adults who viewed natural or schematic faces with internal parts that were either normally configured or randomly rearranged. Response amplitudes were reduced in the AMG and STS when subjects viewed stimuli whose configuration of parts were digitally rearranged, suggesting that these regions represent the 1st order configuration of face parts. In contrast, response amplitudes in the FFA showed little modulation whether face parts were rearranged or if the natural face parts were replaced with lines. Instead, FFA responses were reduced only when both configural and part information were reduced, revealing an interaction between these factors, suggesting distinct representation of 1st order face configuration and parts in the AMG and STS vs. the FFA.
Intrahepatic Cholangiocarcinoma: An International Multi-Institutional Analysis of Prognostic Factors and Lymph Node Assessment (2011)

Although tumor size provides no prognostic information, tumor number, vascular invasion, and LN metastasis were associated with survival. N1 status adversely affected overall survival and also influenced the relative effect of tumor number and vascular invasion on prognosis. Lymphadenectomy should be strongly considered for ICC, because up to 30% of patients will have LN metastasis.
Enhanced Multi-Hop Vehicular Broadcast (MHVB) for Active Safety Applications (2007)

This paper, focuses on the "enhancement" of multi- hop vehicular broadcast (MHVB). The protocol is fundamentally a flooding algorithm with special characteristics in order to efficiently disseminate information such as the positions and the velocities of the vehicles for the sake of active safety applications. The main purpose of this paper is to show the performance improvements obtained by adding more special characteristics to the existing version of MHVB. The enhancement procedure is carried out in two steps: by changing the shape of the backfire region in the algorithm and by introducing a new Dynamic Scheduling algorithm which prioritizes the packet transmission based upon "processing" of the received packets from the other vehicles. The key point in the proposal made to enhance the broadcast protocol is the balance between the application requirement and the performance of the protocol.
A Micromechanical Bending Stage for Studying Mechanical Properties of Materials Using Nanoindenter (2015)

An analytical and computational model of a novel bending stage is presented. The stage applies bending moments on micro/nanoscale beam specimens using a nanoindenter. In uniaxial tests, any flaw within the entire volume of the specimen may lead to fracture before material yields. The new stage minimizes the volume of material under a uniaxial state of stress in the specimen, but maximizes bending stress over a small volume such that high stresses can be reached within a small volume on the specimen without a premature failure by fracture. The analytical model of the stage accounts for the geometric nonlinearity of the sample, but assumes simplified boundary conditions. It predicts the deflection and stresses in the specimen beam upon loading. The numerical model of the stage and the specimen employing a finite element (FE) package tests the validity of the analytical model. Good agreement between analytical and numerical results shows that the assumptions in the analytical model are reasonable. Therefore, the analytical model can be used to optimize the design of the stage and the specimen. A design of the stage is presented that results in axial/bending stress &lt; 2% in the sample. In order to test the feasibility of the proposed design, a 3D printed stage and a sample are fabricated using the Polyamide PA2200. Bending test is then carried out employing an indenter. Elastic modulus of PA2200 is extracted from the load-deflection data. The value matches closely with that reported in the literature.
A role for microwave processing in the dry preservation of mammalian cells (2008)

Dry preservation involves removing water from samples so that degradative biochemical processes are slowed and extended storage is possible. Recently this approach has been explored as a method for preserving living mammalian cells. The current work explores the use of microwave processing to enhance evaporation rates and to improve drying uniformity, thereby overcoming some of the challenges in this field. Mouse macrophage cells (J774) were pre-incubated in full complement media containing 50 mM trehalose, for 18-h, to allow for endocytosis of trehalose. Droplets of experimental and control (no intracellular trehalose) cell suspensions were placed on coverslips in a microwave cavity. Water was evaporated using intermittent microwave heating (600 W, 30 s intervals). Samples were dried to various moisture levels, rehydrated, and then survival was assessed after a 45-min recovery period using Calcein-AM/PI fluorescence and Trypan Blue exclusion assays. The metabolic activity of dried cells (4.3 gH(2)O/gdw) was assessed after rehydration using a resazurin reduction assay. Apoptosis levels were also measured. Post- rehydration survival correlated with the final moisture content achieved, consistent with other drying methods. Intracellular trehalose provided protection against injury associated with moisture loss. Metabolic assays revealed normal growth in surviving cells, and these survival levels were consistent with results from apoptosis assays (P > 0.05). Brightfield and fluorescence images of microwave-dried samples revealed a uniform distribution of cells within the dried matrix and profilometry analysis demonstrated that solids were uniformly distributed throughout the sample. Microwave-processing successfully facilitated rapid and uniform dehydration of cell-based samples.
Third-Harmonic Generation at 1594 nm in a KTP Ridge Optical Waveguide (2021)

International audience
Mitomycin C-treated dendritic cells inactivate autoreactive T cells: Toward the development of a tolerogenic vaccine in autoimmune diseases (2008)

Treatment of autoimmune diseases remains a challenge for immunological research. An ideal therapy should inhibit the immune reaction against the diseased organ and leave the rest of the immune response intact. Our previous studies showed that donor-derived dendritic cells (DCs) treated in vitro with mitomycin C (MMC) suppress rat heart allograft rejection if injected into recipients before transplantation. Here we analyze their efficacy in controlling autoimmunity. MMC-DCs loaded with myelin-basic-protein (MBP) inhibited specific T cells derived from multiple sclerosis patients in vitro. If coincubated with MMC-DCs, T cells were arrested in the G(0)/G(1) cell cycle phase. Microarray gene scan showed that MMC influences the expression of 116 genes in DCs, one main cluster comprising apoptotic and the second cluster immunosuppressive genes. Apparently, the combination of apoptosis with expression of tolerogenic molecules renders MMC-DCs suppressive. MBP-loaded MMC-DCs also inhibited mouse T cells in vitro and, in contrast to MBP-loaded naïve DCs, did not induce experimental autoimmune encephalitis. Most importantly, mice vaccinated with inhibitory DCs became resistant to the disease. Whereas this is not the first report on generation of suppressive DCs, it delineates a method using a clinically approved drug at nontoxic concentrations, which yields irreversibly changed DCs, effective across species in vitro and in vivo.
Bioluminescence Measurement of Time-Dependent Dynamic Changes of CYP-Mediated Cytotoxicity in CYP-Expressing Luminescent HepG2 Cells (2021)

We sought to develop a cell-based cytotoxicity assay using human hepatocytes, which reflect the effects of drug-metabolizing enzymes on cytotoxicity. In this study, we generated luminescent human hepatoblastoma HepG2 cells using the mouse artificial chromosome vector, in which click beetle luciferase alone or luciferase and major drug-metabolizing enzymes (CYP2C9, CYP2C19, CYP2D6, and CYP3A4) are expressed, and monitored the time-dependent changes of CYP-mediated cytotoxicity expression by bioluminescence measurement. Real-time bioluminescence measurement revealed that compared with CYP-non-expressing cells, the luminescence intensity of CYP-expressing cells rapidly decreased when the cells were treated with low concentrations of aflatoxin B1 or primaquine, which exhibits cytotoxicity in the presence of CYP3A4 or CYP2D6, respectively. Using kinetics data obtained by the real-time bioluminescence measurement, we estimated the time-dependent changes of 50% inhibitory concentration (IC<sub>50</sub>) values in the aflatoxin B1- and primaquine-treated cell lines. The first IC<sub>50</sub> value was detected much earlier and at a lower concentration in primaquine-treated CYP-expressing HepG2 cells than in primaquine-treated CYP-non-expressing cells, and the decrease of IC<sub>50</sub> values was much faster in the former than the latter. Thus, we successfully monitored time- and concentration-dependent dynamic changes of CYP-mediated cytotoxicity expression in CYP-expressing luminescent HepG2 cells by means of real-time bioluminescence measurement.
Comparison of modal analysis and equivalent circuit representation of E -plane arm of the jerusalem cross (1982)

Transmission coefficients predicted by modal analysis agree well with measurements, but an LC equivalent circuit gives satisfactory results for normal incidence only. The two methods predict similar phases for the induced currents. The modal method&apos;s account of the current distribution is illustrated for two resonant frequencies in the E-plane.
BETWEEN ANGELS AND LOVERS (The Architect's Proper Embrace) (1998)

For architect-authors from antiquity and the Renaissance, the architectural treatise served as an expressive vehicle for performing a curious act: the subsuming of forbidden space as the proper “property” of architecture. While devoting much textual space to delimiting the categories of high and low, inside and outside, authors of the early treatises—among them Vitruvius, Alberti, Palladio, Colonna and Filarete—have effectively defined the forbidden, low and outside space as a proper place within the urban, architectural order; this, to appeal to a generalized, cultural fixation on “propriety.” Reflecting on the moral imperatives of these old stories of architecture may perhaps motivate contemporary architects to embrace architecture more as “angels and lovers” than as the owners of afield.
Eflapegrastim, a novel and potent long-acting GCSF for reducing chemotherapy-induced neutropenia: Integrated results from two phase III trials in breast cancer patients. (2019)

539 Background: Eflapegrastim (E) is a novel long-acting GCSF comprised of recombinant human GCSF covalently linked to human IgG4 Fc fragment via a PEG linker (MW, 72 kDa). E showed increased potency vs pegfilgrastim (P) in preclinical and Phase I and II trials. Two identically designed Phase III pivotal trials (NCT02643420, NCT02953340) were conducted globally with a fixed dose of 13.2 mg E containing 3.6 mg GCSF to evaluate E vs P (6 mg) in pts receiving chemotherapy for early-stage breast cancer. Methods: Each open-label trial randomized pts 1:1 to a single subcutaneous dose of E 13.2 mg/0.6 mL or P 6 mg/0.6 mL on Day 2 of each of four 21-day cycles following Day 1 adj/neoadj docetaxel 75 mg/m 2 + cyclophosphamide 600mg/m 2 (TC). The primary endpoint was to demonstrate E non-inferiority (NI) to P as measured by mean duration of severe neutropenia (DSN) in Cycle 1. Results: A total 643 intent-to-treat pts (314 E/329 P) with median age 60 yrs (24–88) were enrolled. Cycle 1 mean (SD) DSN was 0.24 (0.581) vs 0.36 (0.789) days for E and P, confirming NI (p &lt; .0001) and suggesting statistical superiority (p &lt; .029). DSN NI was also shown across cycles 2–4. Among subgroups, including elderly (≥65 yrs) and overweight ( &gt; 75kg) pts, DSN was reduced for E vs P. In Cycle 1, E showed an absolute risk reduction for severe neutropenia of 6.5% vs P (27.1% relative risk reduction, p &lt; .043). Neutropenic complications (hospitalization and/or anti-infective use) were 2.9% and 4.0% for E and P (p = ns). Incidence of FN was low for both E and P, 1.6% vs 1.8% in Cycle 1 and 3.2% vs 3.0% overall. ANC profiles showed sustained increased levels for E vs P in the recovery phase across all cycles. Safety profiles were similar for E and P, including primarily for expected hematologic AEs and for bone pain and other musculoskeletal pain. Conclusions: These integrated pivotal trial results confirm a similar safety profile and non-inferiority in reducing neutropenic risk for E at a lower GCSF dose vs P. The data also suggests the potential for increased potency of E to deliver improved clinical benefit, a possibility that warrants further clinical trials. Clinical trial information: NCT02643420, NCT02953340.
Enhancing the representation of functional connectivity networks by fusing multi‐view information for autism spectrum disorder diagnosis (2018)

Functional connectivity network provides novel insights on how distributed brain regions are functionally integrated, and its deviations from healthy brain have recently been employed to identify biomarkers for neuropsychiatric disorders. However, most of brain network analysis methods utilized features extracted only from one functional connectivity network for brain disease detection and cannot provide a comprehensive representation on the subtle disruptions of brain functional organization induced by neuropsychiatric disorders. Inspired by the principles of multi-view learning which utilizes information from multiple views to enhance object representation, we propose a novel multiple network based framework to enhance the representation of functional connectivity networks by fusing the common and complementary information conveyed in multiple networks. Specifically, four functional connectivity networks corresponding to the four adjacent values of regularization parameter are generated via a sparse regression model with group constraint ( l<sub>2,1</sub> -norm), to enhance the common intrinsic topological structure and limit the error rate caused by different views. To obtain a set of more meaningful and discriminative features, we propose using a modified version of weighted clustering coefficients to quantify the subtle differences of each group-sparse network at local level. We then linearly fuse the selected features from each individual network via a multi-kernel support vector machine for autism spectrum disorder (ASD) diagnosis. The proposed framework achieves an accuracy of 79.35%, outperforming all the compared single network methods for at least 7% improvement. Moreover, compared with other multiple network methods, our method also achieves the best performance, that is, with at least 11% improvement in accuracy.
Taxonomic identifiation, anti-trypanosomal activity, metabolomics analyses and GenBank accession data of Mediterranean marine sponge associated actinomycetes (2015)

Marine sponge-associated actinomycetes are considered as promising sources for the discovery of novel biologically active compounds. In the present study, a total of 64 actinomycetes were isolated from 12 different marine sponge species that had been collected offshore the islands of Milos and Crete, Greece, eastern Mediterranean. The isolates were affiliated to 23 genera representing 8 different suborders based on nearly full length 16S rRNA gene sequencing. Four putatively novel species belonging to genera Geodermatophilus, Microlunatus, Rhodococcus and Actinomycetospora were identified based on a 16S rRNA gene sequence similarity of &lt; 98.5% to currently described strains. Eight actinomycete isolates showed bioactivities against Trypanosma brucei brucei TC221 with half maximal inhibitory concentration (IC50) values &lt;20 µg/mL. Thirty four isolates from the Milos collection and 12 isolates from the Crete collection were subjected to metabolomic analysis using high resolution LC-MS and NMR for dereplication purposes. Two isolates belonging to the genera Streptomyces (SBT348) and Micromonospora (SBT687) were prioritized based on their distinct chemistry profiles as well as their anti-trypanosomal activities. These findings demonstrated the feasibility and efficacy of utilizing metabolomics tools to prioritize chemically unique strains from microorganism collections and further highlight sponges as rich source for novel and bioactive actinomycetes.