gebhart/patrepeval huggingface dataset:
Hybrid integration of silicon nanophotonics with 40nm-CMOS VLSI drivers and receivers (2011)

Oracle's scalable hybrid integration technology platform enables continuing improvements in performance and energy efficiency of photonic bridge chips by leveraging advanced CMOS technologies with maximum flexibility, which is critical for developing ultralow power high-performance photonic interconnects for future computing systems. Herein, we report on our second generation of photonic bridge chips comprising electronic drivers and receivers built in 40 nm bulk CMOS technology attached to nanophotonic devices, fabricated using SOI-photonic and 130 nm SOI-CMOS photonic technologies. Hybrid integration by flip-chip bonding is enabled by microsolder bump interconnects scaled down from our previous generation effort and fabricated on singulated dies by a novel batch processing technique based on component embedding. Generation-on-generation, the hybrid integrated Tx and Rx bridge chips achieved 2.3× and 1.7× improvement in energy efficiency, respectively, while operating at 2× the datarate (10 Gbps).
Differential reduction in cardiac and liver monolysocardiolipin acyltransferase-1 and reduction in cardiac and liver tetralinoleoyl-cardiolipin in the α-subunit of trifunctional protein heterozygous knockout mice (2015)

The contribution of α-subunit of trifunctional protein (αTFP) to cardiolipin (CL) (diphosphatidylglycerol) remodelling and mitochondrial supercomplex formation was examined in heart and liver mitochondria from wild-type (WT) and αTFP heterozygous knockout [Mtpa(+/−)] mice. Mtpa(+/−) mouse heart and liver exhibited an approximate 55% and 50% reduction in αTFP protein expression compared with WT respectively. Monolysocardiolipin (MLCL) acyltransferase (MLCL AT)-1 protein derived from αTFP was reduced by 30% in Mtpa(+/−) mouse heart but not in liver compared with WT. In vitro acylation of MLCL was significantly reduced in heart but not in liver mitochondria of Mtpa(+/−) mice compared with WT. CL mass was reduced and significant reductions in linoleate-containing CL species, in particular tetralinoleoyl-CL (L4-CL) and trilinoleoyl-CL (L3-MLCL) species, were observed in heart and liver mitochondria of Mtpa(+/−) mice compared with WT. Cardiac and liver mitochondrial supercomplex assembly and NADH dehydrogenase (complex I) activity within these supercomplexes were unaltered in both Mtpa(+/−) mouse heart and Mtpa(+/−) mouse liver compared with WT. The results indicate that αTFP may modulate CL molecular species composition in murine heart and liver. In addition, L4-CL might not be an essential requirement for mitochondrial supercomplex assembly.
DNA polymerase theta protects leukemia cells from metabolic-induced DNA damage (2022)

Leukemia cells accumulate DNA damage, but altered DNA repair mechanisms protect them from apoptosis. We showed here that formaldehyde generated by serine/1-carbon cycle metabolism contributed to the accumulation of toxic DNA-protein crosslinks (DPCs) in leukemia cells, especially in driver clones harboring oncogenic tyrosine kinases (OTKs: FLT3(internal tandem duplication [ITD]), JAK2(V617F), BCR-ABL1). To counteract this effect, OTKs enhanced the expression of DNA polymerase theta (POLθ) via ERK1/2 serine/threonine kinase-dependent inhibition of c-CBL E3 ligase-mediated ubiquitination of POLθ and its proteasomal degradation. Overexpression of POLθ in OTK-positive cells resulted in the efficient repair of DPC-containing DNA double-strand breaks by POLθ-mediated end-joining. The transforming activities of OTKs and other leukemia-inducing oncogenes, especially of those causing the inhibition of BRCA1/2-mediated homologous recombination with and without concomitant inhibition of DNA-PK-dependent nonhomologous end-joining, was abrogated in Polq-/- murine bone marrow cells. Genetic and pharmacological targeting of POLθ polymerase and helicase activities revealed that both activities are promising targets in leukemia cells. Moreover, OTK inhibitors or DPC-inducing drug etoposide enhanced the antileukemia effect of POLθ inhibitor in vitro and in vivo. In conclusion, we demonstrated that POLθ plays an essential role in protecting leukemia cells from metabolically induced toxic DNA lesions triggered by formaldehyde, and it can be targeted to achieve a therapeutic effect.
Monoclonal antibodies directed against lipopolysaccharide of legionella pneumophila serogroup 1 (1998)

The monoclonal antibodies (MAbs) against lipopolysaccharide of virulent strain of Legionella pneumophila serogroup 1 were produced. Three most productive hybrid clones (5F4, 5F10 and 2C9) were selected from fusions of mouse myeloma cells with spleen cells from BALB/c mice, immunized with bacterial outer membrane antigens. All generated clones were IgG-secreting. The MAbs had narrow strain specificity and showed no cross-reactions with other unrelated bacterial species. These antibodies were tested in sandwich ELISA. The results suggest that the MAbs could be used for diagnostic purposes.
Submicron Structures Technology and Research (1987)

Contains table of contents for Part I, table of contents for Section 1, description of Submicron Structures Laboratory research, reports on twelve research project and a list of publications.
Novel BAP degradation pathway during adventitious caulogenesis in Pinus pineaL. cotyledons (2011)

Cytokinins (CKs) are a group of phytohormones which probably regulate the growth, development, and metabolism of all plants. The aromatic CK benzyladenine (BA) has been widely applied in in vitro culture for inducing shoot organogenesis. Our study of endogenous cytokinin profiles during the caulogenic process based on mature cotyledons of stone pine (Pinus pinea L.) showed a novel metabolic pathway of aromatic cytokinins based on modification of purine skeleton. Methods Three-year-old mature seeds from two half-sibling selected families and open-pollinated trees of P. pinea were used [1] and the samples were collected following the Alonso et al.[2] procedure. Extraction and purification of cytokinins was based on the method described by Novak et al. [3], including modifications published later [4]. The samples were purified using a combination of a cation (SCX-cartridge) and anion [DEAE-Sephadex/ C18-cartridge] exchangers. Combination of high performance liquid chromatography (HPLC) with quadrupoletime of flight mass spectrometry (QqTOF) was used for accurate and sensitive identification and quantification of cytokinins.
Flux Melting of Metal-Organic Frameworks (2018)

Recent demonstrations of melting in the metal-organic framework (MOF) family have createdinterest in the interfacial domain between inorganic glasses and amorphous organic polymers. Thechemical and physical behaviour of porous hybrid liquids and glasses is of particular interest,though opportunities are limited by the inaccessible melting temperatures of many MOFs. Here,we show that the synthetic processing technique of flux melting, ‘borrowed’ from the inorganicdomain, may be applied to MOFs in order to melt materials which do not possess an accessibleliquid state in their pure form. We employ the high-temperature liquid state of one MOF as a solventfor a secondary, non-melting MOF component. Differential scanning calorimetry, small- and wideangleX-ray scattering, electron microscopy and X-ray total scattering techniques are used to showthe flux melting of the crystalline component within the liquid. Gas adsorption and positronannihilation lifetime spectroscopy measurements show that this results in enhanced, accessibleporosity to a range of guest molecules, in the resultant flux melted MOF glass.
Development of a Small Tactile Sensor for Robot Finger (2006)

This paper presents a new tactile sensor that can detect the vertical force and the shear force. This proposed tactile sensor detects an applied force as a change in electrical resistance in strain gauges attached to the surface. For outputs of this proposed sensor, the interaction occurs structurally, and the hysteresis also occurs since the force applying on the sensor is detected by the strain gauge attached to the surface. However, since the effects of the hysteresis are small and difficult to correct, we disregard the hysteresis, and only correct the interaction. Measurement of the vertical and shear forces applying on this proposed tactile sensor becomes possible after correcting the interaction. The experimental results show that three dimensional forces can measure using this proposed tactile sensor. This proposed tactile sensor has simple structure. Therefore, because of this structure, this tactile sensor can be made easily and realized as small size.
Representative Midwestern US Cycles: Synthesis and Applications (2013)

This paper proposed a set of representative real-world driving cycles in Midwestern US, which are capable of capturing the dependence of driving patterns on driving distance. Recent analyses of the real-world driving in USA show that most of certification cycles lead to underestimation of energy consumption per mile compared to the naturalistic driving patterns. Real-world driving is a mix of local driving and highway driving. Furthermore, the driving patterns show high dependency on the driving distance. To cover the wide range of real-world driving distances, five synthetic cycles are generated ranging from 4.78 miles to 40.71 miles following the real-world driving distance distribution. Each individual cycle is constructed by a stochastic process using the extracted driving information from the naturalistic trip data in the Midwestern US. While constructing the cycle set, the statistical criteria for validating the cycle representativeness are processed to capture the clear distance dependency and remove random variations. The synthesized cycles are subsequently used for Plug-in Hybrid Electric Vehicle (PHEVs) or Hybrid Electric Vehicle (HEVs) design and control studies for the assessment of the impact of electrified vehicles on the grid.
Nanoindentation hardness of particles used in magnetorheological finishing (MRF) (2000)

Knowledge of the hardness of abrasive particles that are used in polishing is a key to the fundamental understanding of the mechanisms of material removal. The magnetorheological-finishing process uses both magnetic and nonmagnetic abrasive particles during polishing. The nanohardnesses of the micrometer-sized magnetic carbonyl iron and nonmagnetic abrasive particles have been measured successfully by use of novel, to our knowledge, sample-preparation and nanoindentation techniques. Some of the results reported compare favorably with existing microhardness data found in the literature, whereas other results are new.
Edge-Coupled Active and Passive Wafer-Scale Measurements on 300mm Silicon Photonics Wafers (2021)

We perform wafer-scale measurements of silicon photonics components using broadband (100nm+) edge couplers and reflecting optical fiber probes for the first time. We demonstrate &lt;1dB/cm waveguide loss and 25GHz+ micro-ring modulators on 300mm wafers.
A 180 Myr-old female-specific genome region in sturgeon reveals the oldest known vertebrate sex determining system with undifferentiated sex chromosomes (2021)

Several hypotheses explain the prevalence of undifferentiated sex chromosomes in poikilothermic vertebrates. Turnovers change the master sex determination gene, the sex chromosome or the sex determination system (e.g. XY to WZ). Jumping master genes stay main triggers but translocate to other chromosomes. Occasional recombination (e.g. in sex-reversed females) prevents sex chromosome degeneration. Recent research has uncovered conserved heteromorphic or even homomorphic sex chromosomes in several clades of non-avian and non-mammalian vertebrates. Sex determination in sturgeons (Acipenseridae) has been a long-standing basic biological question, linked to economical demands by the caviar-producing aquaculture. Here, we report the discovery of a sex-specific sequence from sterlet (<i>Acipenser ruthenus</i>). Using chromosome-scale assemblies and pool-sequencing, we first identified an approximately 16 kb female-specific region. We developed a PCR-genotyping test, yielding female-specific products in six species, spanning the entire phylogeny with the most divergent extant lineages (<i>A. sturio, A. oxyrinchus</i> versus <i>A. ruthenus, Huso huso</i>), stemming from an ancient tetraploidization. Similar results were obtained in two octoploid species (<i>A. gueldenstaedtii, A. baerii</i>). Conservation of a female-specific sequence for a long period, representing 180 Myr of sturgeon evolution, and across at least one polyploidization event, raises many interesting biological questions. We discuss a conserved undifferentiated sex chromosome system with a ZZ/ZW-mode of sex determination and potential alternatives. This article is part of the theme issue 'Challenging the paradigm in sex chromosome evolution: empirical and theoretical insights with a focus on vertebrates (Part I)'.
Regulated underexpression and overexpression of the FliN protein of Escherichia coli and evidence for an interaction between FliN and FliM in the flagellar motor (1995)

The FliN protein of Escherichia coli is essential for the assembly and function of flagella. Here, we report the effects of regulated underexpression and overexpression of FliN in a fliN null strain. Cells that lack the FliN protein do not make flagella. When FliN is underexpressed, cells produce relatively few flagella and those made are defective, rotating at subnormal, rapidly varying speeds. These results are similar to what was seen previously when the flagellar protein FliM was underexpressed and unlike what was seen when the motility proteins MotA and MotB were underexpressed. Overexpression of FliN impairs motility and flagellation, as has been reported previously for FliM, but when FliN and FliM are co-overexpressed, motility is much less impaired. This and additional evidence presented indicate that FliM and FliN are associated in the flagellar motor, in a structure distinct from the MotA/MotB torque generators. A recent study showed that FliN might be involved in the export of flagellar components during assembly (A. P. Vogler, M. Homma, V. M. Irikura, and R. M. Macnab, J. Bacteriol. 173:3564-3572, 1991). We show here that approximately 50 amino acid residues from the amino terminus of FliN are dispensable for function and that the remaining, essential part of FliN has sequence similarity to a part of Spa33, a protein that functions in transmembrane export in Shigella flexneri. Thus, FliN might function primarily in flagellar export, rather than in torque generation, as has sometimes been supposed.
Conservation of the kinaselike regulatory domain is essential for activation of the natriuretic peptide receptor guanylyl cyclases. (1992)

The natriuretic peptide receptors, NPR-A and NPR-B, are two members of the newly described class of receptor guanylyl cyclases. The kinaselike domain of these proteins is an important regulator of the guanylyl cyclase activity. To begin to understand the molecular nature of this type of regulation, we made complete and partial deletions of the kinase domain in NPR-A and NPR-B. We also made chimeric proteins in which the kinase domains of NPR-A and NPR-B were exchanged or replaced with kinase domains from structurally similar proteins. Complete deletion of the kinase homology domain in NPR-A and NPR-B resulted in constitutive activation of the guanylyl cyclase. Various partial deletions of this region produced proteins that had no ability to activate the enzyme with or without hormone stimulation. The kinase homology domain can be exchanged between the two subtypes with no effect on regulation. However, structurally similar kinaselike domains, such as from the epidermal growth factor receptor or from the heat-stable enterotoxin receptor, another member of the receptor guanylyl cyclase family, were not able to regulate the guanylyl cyclase activity correctly. These findings suggest that the kinaselike domain of NPR-A and NPR-B requires strict sequence conservation to maintain proper regulation of their guanylyl cyclase activity.
A room temperature pulsed visible OPO with 1 watt output based on periodically-poled MgO doped stoichiometric LiTaO<inf>3</inf> (2006)

An efficient 532nm-pumped pulsed OPO that could be operated at room temperature using a PPMgSLT crystal is reported. ≫1.0 W total output for a 1.6W input (power conversion of 62.5%) was achieved.
Diverse Organic Field‐Effect Transistor Sensor Responses from Two Functionalized Naphthalenetetracarboxylic Diimides and Copper Phthalocyanine Semiconductors Distinguishable Over a Wide Analyte Range (2013)

Abstract Naphthalenetetracarboxylic diimide derivatives (octyl “8” NTCDI, dimethylaminopropyl “DMP” NTCDI) and copper phthalocyanine (CuPc) are used to form a diverse organic field‐effect transistor (OFET) sensor array. CuPc and 8‐NTCDI are p‐channel and n‐channel semiconductors, respectively, showing expected and opposing responses to analytes. DMP‐NTCDI, on the other hand, because of its ionizable side chain, shows response directions and magnitudes that are not correlated to those of the other two. The result is a distinct response pattern and unambiguous recognition ability for individual analytes. The differences are even more dramatic if the time evolution of the responses is considered. The three‐response patterns obtained from representative polar, nonpolar, acidic, and basic vapors are all different, showing the potential for this approach in rapid, low‐cost electronic detection of volatile compounds.
The Electrical Characteristics of Metal-Oxide-Semiconductor Field Effect Transistors Fabricated on Cubic Silicon Carbide (2003)

The n-channel metal-oxide-semiconductor field effect transistors (MOSFETs) were fabricated on cubic silicon carbide (3C-SiC) epitaxial layers grown on 3C-SiC substrates. The gate oxide of the MOSFETs was formed using pyrogenic oxidation at 1100 °C. The 3C-SiC MOSFETs showed enhancement type behaviors after annealing at 200 °C for 30 min in argon atmosphere. The maximum value of the effective channel mobility of the 3C-SiC MOSFETs was 260 cm2/V·s. The leakage current of gate oxide was of a few tens of nA/cm2 at an electric field range below 8.5 MV/cm, and breakdown began around 8.5 MV/cm.
Systemic Delivery and Pre-clinical Evaluation of Nanoparticles Containing Antisense Oligonucleotides and siRNAs (2008)

By virtue of their potential to selectively silence oncogenic molecules in cancer cells, antisense oligonucleotides (ASO) and small interfering RNAs (siRNAs) are powerful tools for development of tailored anti-cancer drugs. The clinical benefit of ASO/siRNA therapeutic is, however, hampered due to poor pharmacokinetics and biodistribution, and suboptimal suppression of the target in tumor tissues. Raf-1 protein serine/threonine kinase is a druggable signaling molecule in cancer therapy. Our laboratory has developed cationic liposomes for systemic delivery of raf ASO (LErafAON) and raf siRNA (LErafsiRNA) to human tumor xenografts grown in athymic mice. LErafAON is also the first ASO containing liposomal drug tested in humans. In this article, we primarily focus on a modified formulation of systemically delivered cationic liposomes containing raf antisense oligonucleotide (md-LErafAON). The cationic liposomes were prepared using dimyristoyl 1,2-diacyl-3-trimethylammonium-propane (DMTAP), phosphatidylcholine (PC), and cholesterol (CHOL). The toxicology, pharmacokinetics, biodistribution, target selectivity, and anti-tumor efficacy studies of md-LErafAON were conducted in mice. We demonstrate that md-LErafAON is the next generation of systemically delivered and well-tolerated antisense therapeutic suitable for clinical evaluation.
A cm-scale self-powered intelligent and secure IoT edge mote featuring an ultra-low-power SoC in 14nm tri-gate CMOS (2018)

Energy efficiency, performance and security of compact, self-powered, smart, secure and connected motes at the edge of IoT are critical for realizing intelligent, robust and sustainable end-to-end cyberphysical systems that deliver compelling new capabilities based on big data analytics. Integrated ultra-low-power compute [1] and wireless connectivity [2], neural-network-based inference accelerators [3], energy-efficient and compact multi-sensing front end and crypto engines, high density and low leakage embedded memory, and fine-grain power management are essential ingredients of the mote SoC.
Impact of cetyl trimethyl ammonium chloride on melting behaviour of long chain alcohols (2015)

National audience
A theoretical study of oxygen transfer including cell necrosis for the design of a bioartificial pancreas (2006)

In an extravascular bioartificial pancreas (BAP), islet functions are probably limited by diffusive mass transfer and local consumption, leading to low oxygenation. A mathematical model based on finite elements and focusing on local oxygen transport in both the alginate core and the islets of Langerhans has been proposed to help design an efficient pancreas supply. It was possible to randomly localize islets in a hollow fiber at different densities, and the effects of hypoxia and necrosis were included in the mass transfer simulations. Thorough study of the numerical results first led to the analysis of several relevant parameters, such as necrosis factor and efficacy in terms of insulin secretion, as a way to optimize fiber geometry. The approach was then to calculate the number of islets that needed to be implanted in order to obtain a correct response in terms of insulin secretion. In most configurations, it was found to be much higher than that of ultimately functional islets, because of hypoxia and necrosis. Fiber length should thus be adjusted accordingly. Finally, we demonstrated that the compromise to be found between the reduction of the number of implanted islets and fiber length and diameter did not correspond to realistic hollow fiber systems. The alternative of using flat geometry was also envisaged with more optimistic feasibility assessments.
Low-Bandwidth Channel Quality Indication for OFDMA Frequency Domain Packet Scheduling (2006)

In this paper we consider bandwidth-efficient means for the user equipment (UE) to conduct channel quality indication (CQI) for OFDMA frequency domain packet scheduling (FDPS). Using a UTRAN long-term evolution (LTE) system model, we find that a threshold-based CQI scheme can enable about 60% CQI bandwidth saving with less than 5-10% loss on system performance compared to near-ideal signaling. To sustain sufficient CQI reporting accuracy and high FDPS gain, we show that time- domain CQI averaging over multiple sub-frames is desirable although it lowers the mobility performance. Conducting the averaging on the UE side is most attractive from a signalling perspective. Combining averaging with lowered CQI reporting rate, FDPS can provide around 30-50% gain for LTE with a CQI reporting bandwidth as low as 10 kbit/s in a 20 MHz system (up to 3-5 km/h).
Structural proteins of Enterococcus faecalis bacteriophage φEf11 (2016)

ϕEf11, a temperate <i>Siphoviridae</i> bacteriophage, was isolated by induction from a root canal isolate of <i>Enterococcus faecalis</i>. Sequence analysis suggested that the ϕEf11 genome included a contiguous 8 gene module whose function was related to head structure assembly and another module of 10 contiguous genes whose products were responsible for tail structure assembly. SDS-PAGE analysis of virions of a ϕEf11 derivative revealed 11 well-resolved protein bands. To unify the deduced functional gene assignments emanating from the DNA sequence data, with the structural protein analysis of the purified virus, 6 of the SDS-PAGE bands were subjected to mass spectrometry analysis. 5 of the 6 protein bands analyzed by mass spectrometry displayed identical amino acid sequences to those predicted to be specified by 4 of the ORFs identified in the ϕEf11 genome. These included: ORF8 (predicted scaffold protein), ORF10 (predicted major head protein), ORF15 (predicted major tail protein), and ORF23 (presumptive antireceptor).