gebhart/patrepeval huggingface dataset:
Heat-transfer enhancing features for handler tray-type device carriers (1998)

Many test handlers process semiconductor devices in trays which must be rapidly heated or cooled by a forced air flow to a desired test temperature and then back to ambient temperature. This paper describes a new design feature for test-handler tray that significantly increases the rate of convective heat transfer to the tray and the devices in the tray. The improved tray incorporates lateral ribs which breakup thermal boundary layers and enhance mixing. This enhanced heat transfer is especially important in new test-in-tray handlers whose operating speeds can be limited by thermal response times.
Silibinin Sensitizes Human Glioma Cells to TRAIL-Mediated Apoptosis via DR5 Up-regulation and Down-regulation of c-FLIP and Survivin (2007)

Silibinin, a flavonoid isolated from Silybum marianum, has been reported to have cancer chemopreventive and therapeutic effects. Here, we show that treatment with subtoxic doses of silibinin in combination with tumor necrosis factor-related apoptosis-inducing ligand (TRAIL) induces rapid apoptosis in TRAIL-resistant glioma cells, but not in human astrocytes, suggesting that this combined treatment may offer an attractive strategy for safely treating gliomas. Although the proteolytic processing of procaspase-3 by TRAIL was partially blocked in glioma cells, cotreatment with silibinin efficiently recovered TRAIL-induced caspase activation in these cells. Silibinin treatment up-regulated DR5, a death receptor of TRAIL, in a transcription factor CHOP-dependent manner. Furthermore, treatment with silibinin down-regulated the protein levels of the antiapoptotic proteins FLIP(L), FLIP(S), and survivin through proteasome-mediated degradation. Taken together, our results show that the activity of silibinin to modulate multiple components in the death receptor-mediated apoptotic pathway is responsible for its ability to recover TRAIL sensitivity in TRAIL-resistant glioma cells.
DNA topoisomerase II can drive changes in higher order chromosome architecture without enzymatically modifying DNA (1998)

Topoisomerase II has been suggested to play a major role in chromosome organization based on its DNA decatenating activity and its ability to mediate direct binding interactions between DNA and nuclear matrix. However, this latter point remains controversial. Here we address the question of whether the chromatin binding activity of Topoisomerase II is sufficient to modify chromosome form using whole mammalian chromosomes in vitro. Intact chromosomes were microsurgically removed from living cells and disassembled by treatment with protease or heparin. When these disassembled chromosomes were incubated with recombinant human Topoisomerase II, the enzyme became incorporated into chromatin and reassembly resulted, leading to almost complete restoration of pre-existing chromosome shape and position within minutes. Chromosome reconstitution by Topoisomerase II was dose-dependent, saturable, and appeared to be controlled stoichiometrically, rather than enzymatically. Similar reassembly was observed in the absence of ATP and when a catalytically inactive thermosensitive Topoisomerase II mutant was used at the restrictive temperature. Chromosome recondensation also could be induced after the strand-passing activity of Topoisomerase II was blocked by treatment with an inhibitor of its catalytic activity, amsacrine. When a non-hydrolyzable beta,gamma-imido analog of ATP (AMP-PNP) was used to physiologically fix bound Topoisomerase II enzyme in a closed form around DNA, subsequent chromosome disassembly was prevented in the presence of high salt. These data suggest that Topoisomerase II may control higher order chromatin architecture through direct binding interactions, independently of its well-known catalytic activity.
Spp1 (osteopontin) promotes TGFβ processing in fibroblasts of dystrophin-deficient muscles through matrix metalloproteinases (2019)

Duchenne muscular dystrophy (DMD) is caused by mutations in the gene encoding dystrophin. Prior work has shown that DMD progression can vary, depending on the genetic makeup of the patient. Several modifier alleles have been identified including LTBP4 and SPP1. We previously showed that Spp1 exacerbates the DMD phenotype in the mdx mouse model by promoting fibrosis and by skewing macrophage polarization. Here, we studied the mechanisms involved in Spp1's promotion of fibrosis by using both isolated fibroblasts and genetically modified mice. We found that Spp1 upregulates collagen expression in mdx fibroblasts by enhancing TGFβ signaling. Spp1's effects on TGFβ signaling are through induction of MMP9 expression. MMP9 is a protease that can release active TGFβ ligand from its latent complex. In support for activation of this pathway in our model, we showed that treatment of mdx fibroblasts with MMP9 inhibitor led to accumulation of the TGFβ latent complex, decreased levels of active TGFβ and reduced collagen expression. Correspondingly, we found reduced active TGFβ in Spp1-/-mdxB10 and Mmp9-/-mdxB10 muscles in vivo. Taken together with previous observations of reduced fibrosis in both models, these data suggest that Spp1 acts upstream of TGFβ to promote fibrosis in mdx muscles. We found that in the context of constitutively upregulated TGFβ signaling (such as in the mdxD2 model), ablation of Spp1 has very little effect on fibrosis. Finally, we performed proof-of-concept studies showing that postnatal pharmacological inhibition of Spp1 reduces fibrosis and improves muscle function in mdx mice.
The Squamous Cell Carcinoma Antigen 2 Inhibits the Cysteine Proteinase Activity of a Major Mite Allergen, Der p 1 (2004)

The squamous cell carcinoma antigens 1 (SCCA1) and SCCA2 belong to the ovalbumin-serpin family. Although SCCA1 and SCCA2 are closely homologous, these two molecules have distinct properties; SCCA1 inhibits cysteine proteinases such as cathepsin K, L, and S, whereas SCCA2 inhibits serine proteinases such as cathepsin G and human mast cell chymase. Although several intrinsic target proteinases for SCCA1 and SCCA2 have been found, the biological roles of SCCA1 and SCCA2 remain unknown. A mite allergen, Der p 1, is one of the most immunodominant allergens and also acts as a cysteine proteinase probably involved in the pathogenesis of allergic diseases. We have recently shown that both SCCA1 and SCCA2 are induced by two related Th2-type cytokines, IL-4 and IL-13, in bronchial epithelial cells and that SCCA expression is augmented in bronchial asthma patients. In this study, we explored the possibility that SCCA proteins target Der p 1, and it turned out that SCCA2, but not SCCA1, inhibited the catalytic activities of Der p 1. We furthermore analyzed the inhibitory mechanism of SCCA2 on Der p 1. SCCA2 contributed the suicide substrate-like mechanism without formation of a covalent complex, causing irreversible impairment of the catalytic activity of Der p 1, as SCCA1 does on papain. In addition, resistance to cleavage by Der p 1 also contributed to the inhibitory mechanism of SCCA2. These results suggest that SCCA2 acts as a cross-class serpin targeting an extrinsic cysteine proteinase derived from house dust mites and that it may have a protective role against biological reactions caused by mites.
A Three-Monoclonal Antibody Combination Potently Neutralizes BoNT/G Toxin in Mice (2023)

Equine-derived antitoxin (BAT<sup>®</sup>) is the only treatment for botulism from botulinum neurotoxin serotype G (BoNT/G). BAT<sup>®</sup> is a foreign protein with potentially severe adverse effects and is not renewable. To develop a safe, more potent, and renewable antitoxin, humanized monoclonal antibodies (mAbs) were generated. Yeast displayed single chain Fv (scFv) libraries were prepared from mice immunized with BoNT/G and BoNT/G domains and screened with BoNT/G using fluorescence-activated cell sorting (FACS). Fourteen scFv-binding BoNT/G were isolated with K<sub>D</sub> values ranging from 3.86 nM to 103 nM (median K<sub>D</sub> 20.9 nM). Five mAb-binding non-overlapping epitopes were humanized and affinity matured to create antibodies hu6G6.2, hu6G7.2, hu6G9.1, hu6G10, and hu6G11.2, with IgG K<sub>D</sub> values ranging from 51 pM to 8 pM. Three IgG combinations completely protected mice challenged with 10,000 LD<sub>50</sub>s of BoNT/G at a total mAb dose of 6.25 μg per mouse. The mAb combinations have the potential for use in the diagnosis and treatment of botulism due to serotype G and, along with antibody combinations to BoNT/A, B, C, D, E, and F, provide the basis for a fully recombinant heptavalent botulinum antitoxin to replace the legacy equine product.
Measurement of residual phase noise and longitudinal-mode linewidth in a hybridly mode-locked external linear cavity semiconductor laser (2002)

We report measurements of the residual phase-noise knee position and longitudinal-mode linewidth of a hybridly mode-locked external linear cavity semiconductor laser as a function of laser cavity length. Excellent agreement between these measurements suggests a direct relationship between rms pulse-to-pulse timing jitter and average longitudinal-mode linewidth. This relationship leads to a fundamental limit in the timing jitter of mode-locked lasers.
B-type natriuretic peptide and serum unbound free fatty acid levels after contemporary percutaneous coronary intervention. (2008)

PCI using short inflation times and coronary stenting are associated with a trend toward increased BNP levels at 18-24 hours post-PCI and a transient significant rise in FFAu levels.
Aarhus Regenerative Orthopaedics Symposium (AROS) (2016)

The combination of modern interventional and preventive medicine has led to an epidemic of ageing. While this phenomenon is a positive consequence of an improved lifestyle and achievements in a society, the longer life expectancy is often accompanied by decline in quality of life due to musculoskeletal pain and disability. The Aarhus Regenerative Orthopaedics Symposium (AROS) 2015 was motivated by the need to address regenerative challenges in an ageing population by engaging clinicians, basic scientists, and engineers. In this position paper, we review our contemporary understanding of societal, patient-related, and basic science-related challenges in order to provide a reasoned roadmap for the future to deal with this compelling and urgent healthcare problem.
Left Atrial Strain as Sensitive Marker of Left Ventricular Diastolic Dysfunction in Heart Failure (2020)

The findings of this analysis suggest that LA strain could be a useful parameter in the evaluation of DD in patients with heart failure and sinus rhythm, irrespective of LVEF.
Supplementary Data from Targeting BET Proteins BRD2 and BRD3 in Combination with PI3K-AKT Inhibition as a Therapeutic Strategy for Ovarian Clear Cell Carcinoma (2023)

&lt;p&gt;Supplementary Table 5. The results of RNA-Seq.&lt;/p&gt;
Multiple Genetic Pathways Involving Amino Acid Position 143 of HIV-1 Integrase Are Preferentially Associated with Specific Secondary Amino Acid Substitutions and Confer Resistance to Raltegravir and Cross-Resistance to Elvitegravir (2013)

Y143C,R substitutions in HIV-1 integrase define one of three primary raltegravir (RAL) resistance pathways. Here we describe clinical isolates with alternative substitutions at position 143 (Y143A, Y143G, Y143H, and Y143S [Y143A,G,H,S]) that emerge less frequently, and we compare the genotypic and phenotypic profiles of these viruses to Y143C,R viruses to reconcile the preferential selection of Y143C,R variants during RAL treatment. Integrase amino acid sequences and RAL susceptibility were characterized in 117 patient isolates submitted for drug resistance testing and contained Y143 amino acid changes. The influence of specific Y143 substitutions on RAL susceptibility and their preferential association with particular secondary substitutions were further defined by evaluating the composition of patient virus populations along with a large panel of site-directed mutants. Our observations demonstrate that the RAL resistance profiles of Y143A,G,H,S viruses and their association with specific secondary substitutions are similar to the well-established Y143C profile but distinct from the Y143R profile. Y143R viruses differ from Y143A,C,G,H,S viruses in that Y143R confers a greater reduction in RAL susceptibility as a single substitution, consistent with a lower resistance barrier. Among Y143A,C,G,H,S viruses, the higher prevalence of Y143C viruses is the result of a lower genetic barrier than that of the Y143A,G,S viruses and a lower resistance barrier than that of the Y143H viruses. In addition, Y143A,C,G,H,S viruses require multiple secondary substitutions to develop large reductions in RAL susceptibility. Patient-derived viruses containing Y143 substitutions exhibit cross-resistance to elvitegravir.
A Robotic Interface for Retrieval of Distributed Multimedia Content (2005)

In a social setting, it is often beneficial to have a partner that is alert of the environment and the circumstances and is able to communicate information that otherwise does not come to our awareness. Typically, these are human companions, however a robotic partner may be an alternate solution. For a robotic partner to be successful, it must naturally interact with its user, and be able to retrieve data and analyze its content. In this paper we present Iolaus, a robotic partner for social settings. Iolaus can be implemented as a robotic parrot perched on the user s shoulder, or as an attentive companion similar to a seeing eye dog. When the user enters a new social setting the robot can be asked and should attempt to answer questions regarding people and surroundings, very similar to a human partner. In this phase of the project, we are using the Sony Aibo robot dog to implement Iolaus s information retrieval component demonstrating how a human-robot interface can help the user access a vast amount of distributed information and multimedia content in a socially acceptable manner.
Polymerization of (E)‐1,3‐Pentadiene and (E)‐2‐methyl‐1,3‐pentadiene with neodymium catalysts: Examination of the factors that affect the stereoselectivity (2013)

ABSTRACT (E)‐1,3‐Pentadiene (EP) and (E)‐2‐methyl‐1,3‐pentadiene (2MP) were polymerized to cis ‐1,4 polymers with homogeneous and heterogeneous neodymium catalysts to examine the influence of the physical state of the catalyst on the polymerization stereoselectivity. Data on the polymerization of (E)‐1,3‐hexadiene (EH) are also reported. EP and EH gave cis ‐1,4 isotactic polymers both with the homogeneous and with the heterogeneous system, whereas 2MP gave an isotactic cis ‐1,4 polymer with the heterogeneous catalyst and a syndiotactic cis ‐1,4 polymer, never reported earlier, with the homogeneous one. For comparison, the results obtained with the soluble CpTiCl 3 ‐based catalyst (Cp = cyclopentadienyl), which gives cis ‐1,4 isotactic poly(2MP), are examined. A tentative interpretation is given for the mechanism of the formation of the stereoregular polymers obtained and a complete NMR characterization of the cis ‐1,4‐syndiotactic poly(2MP) is reported. © 2013 Wiley Periodicals, Inc. J. Polym. Sci., Part A: Polym. Chem. 2013, 51, 3227–3232
Rare HIV-1 transmitted/founder lineages identified by deep viral sequencing contribute to rapid shifts in dominant quasispecies during acute and early infection (2017)

In order to inform the rational design of HIV-1 preventive and cure interventions it is critical to understand the events occurring during acute HIV-1 infection (AHI). Using viral deep sequencing on six participants from the early capture acute infection RV217 cohort, we have studied HIV-1 evolution in plasma collected twice weekly during the first weeks following the advent of viremia. The analysis of infections established by multiple transmitted/founder (T/F) viruses revealed novel viral profiles that included: a) the low-level persistence of minor T/F variants, b) the rapid replacement of the major T/F by a minor T/F, and c) an initial expansion of the minor T/F followed by a quick collapse of the same minor T/F to low frequency. In most participants, cytotoxic T-lymphocyte (CTL) escape was first detected at the end of peak viremia downslope, proceeded at higher rates than previously measured in HIV-1 infection, and usually occurred through the exploration of multiple mutational pathways within an epitope. The rapid emergence of CTL escape variants suggests a strong and early CTL response. Minor T/F viral strains can contribute to rapid and varied profiles of HIV-1 quasispecies evolution during AHI. Overall, our results demonstrate that early, deep, and frequent sampling is needed to investigate viral/host interaction during AHI, which could help identify prerequisites for prevention and cure of HIV-1 infection.
Inhibition of thymocyte positive selection by natural MHC: peptide ligands (1999)

The 3A9 transgenic mouse line carries the rearranged TCR genes from a T cell hybridoma that recognizes hen egg lysozyme peptide 46 – 61 in the context of MHC class II Ak molecules. As expected, positive selection of immature 3A9 thymocytes to become mature CD4+ 8− T cells was efficient on the “selecting” CBA (H-2k ) genetic background but not on the “non-selecting” C57BL/6 (H-2b ) background. Surprisingly, positive selection was also inefficient on the CBA × C57BL/6 F1 background (H-2kb ). We present evidence that expression of Abβ molecules on thymus epithelium (in conjunction with Abα or Akα molecules) inhibits the positive selection of 3A9 thymocytes mediated by Akα : Akβ complexes, in a process evocative of peptide antagonism of mature T cells.
41.2: Judder‐Induced Edge Flicker in Moving Objects (2001)

Abstract The threshold motion rates that produce edge flicker were determined as a function of contrast, luminance and sampling frequency. A passive filtering scheme, called the Movieola filter, appears to mitigate this artifact. The Movieola filter produces interpolated frames based on a passive two‐tap discrete dissolve. It is simple to implement and therefore relatively inexpensive to manufacture.
Interplay between genetic regulation of phosphate homeostasis and bacterial virulence (2014)

Bacterial pathogens, including those of humans, animals, and plants, encounter phosphate (Pi)-limiting or Pi-rich environments in the host, depending on the site of infection. The environmental Pi-concentration results in modulation of expression of the Pho regulon that allows bacteria to regulate phosphate assimilation pathways accordingly. In many cases, modulation of Pho regulon expression also results in concomitant changes in virulence phenotypes. Under Pi-limiting conditions, bacteria use the transcriptional-response regulator PhoB to translate the Pi starvation signal sensed by the bacterium into gene activation or repression. This regulator is employed not only for the maintenance of bacterial Pi homeostasis but also to differentially regulate virulence. The Pho regulon is therefore not only a regulatory circuit of phosphate homeostasis but also plays an important adaptive role in stress response and bacterial virulence. Here we focus on recent findings regarding the mechanisms of gene regulation that underlie the virulence responses to Pi stress in Vibrio cholerae, Pseudomonas spp., and pathogenic E. coli.
Activation of the p53 Transcriptional Program Sensitizes Cancer Cells to Cdk7 Inhibitors (2017)

Cdk7, the CDK-activating kinase and transcription factor IIH component, is a target of inhibitors that kill cancer cells by exploiting tumor-specific transcriptional dependencies. However, whereas selective inhibition of analog-sensitive (AS) Cdk7 in colon cancer-derived cells arrests division and disrupts transcription, it does not by itself trigger apoptosis efficiently. Here, we show that p53 activation by 5-fluorouracil or nutlin-3 synergizes with a reversible Cdk7<sup>as</sup> inhibitor to induce cell death. Synthetic lethality was recapitulated with covalent inhibitors of wild-type Cdk7, THZ1, or the more selective YKL-1-116. The effects were allele specific; a CDK7<sup>as</sup> mutation conferred both sensitivity to bulky adenine analogs and resistance to covalent inhibitors. Non-transformed colon epithelial cells were resistant to these combinations, as were cancer-derived cells with p53-inactivating mutations. Apoptosis was dependent on death receptor DR5, a p53 transcriptional target whose expression was refractory to Cdk7 inhibition. Therefore, p53 activation induces transcriptional dependency to sensitize cancer cells to Cdk7 inhibition.
Uploading and Temperature-Controlled Release of Polymeric Colloids via Hydrophilic Emulsion-Templated Porous Polymers (2010)

Porous cross-linked poly(N-isopropylacrylamide) (PNIPAM) was prepared using high internal phase emulsions as templates. The materials could absorb a large volume of water and swell largely at room temperature. When the aqueous phase was heated above the lower critical solution temperature (LCST) of PNIPAM, the swollen structure could contract and squeeze some of the absorbed liquids out. This capability was utilized in the uploading at room temperature and then release of polystyrene colloids by increasing the temperature above the LCST. The thermoresponsive porous PNIPAM acted like a pump to load and then release the polymer colloids. The multicycles of loading and release were demonstrated to show its efficiency. Importantly, it showed that most of the PS colloids from the second upload onward could be released during the heating cycle.
Water-Assisted Transformation of Aluminum Alloys to Ceramic Nanowires and Aerogels (2023)

Ceramic nanowires (NWs) and their-based aerogels hold great promise for manufacturing and applications of polymer nanocomposites with otherwise unattainable mechanical and thermal properties. Unfortunately, conventional routes for the synthesis of ceramic NWs commonly suffer from the use of costly or toxic chemicals, low production rate, and complex and expensive procedures. Here, we report on a water-assisted route for the cost-effective, scalable transformation of bulk aluminum–lithium alloys into ceramic alumina NWs and aerogels. In this study, we employ water as the intermediary solvent for dealloying to form monolithic porous Li-doped aluminum metal, which can then be converted to ultralong metal–organic NWs, then to hydroxide NWs after hydrolysis and finally to NW aerogels after freeze-drying. As a high-performance thermal interface material for electronic devices, the oxidized alumina NW aerogels infiltrated with epoxy show significantly improved thermal properties. Our study shows great potential for the scalable production of ceramic NWs using a low-cost and environmental-friendly route for various applications.
Photonic Arbitrary Waveform Generation Technology (2006)

Abstract : Modelocked semiconductor lasers emit short ( 1 GHz) and can be utilized for a wide variety of applications, but are typically geared towards time domain applications, e.g., optical time division multiplexed optical links, optical sampling, etc. Additionally, the periodic nature of optical pulse generation from modelocked semi conductor diode lasers also makes these devices ideal candidates for the generation of high quality optical frequency combs, or multiple wavelengths, in addition to the ultra short temporally stable, high peak intensity optical pulses that one is accustomed to. Modelocked semiconductor lasers are used to generate a set of phase locked optical frequencies on a periodic grid. The periodic and phase coherent nature of the optical frequency combs make it possible for the realization of high performance optical and RF arbitrary waveform synthesis. The resulting optical frequency components can be used for communication applications relying on direct detection, dense WDM, coherent detection WDM, OTDM, and OCDMA. This report highlights recent results in the use of optical frequency combs generated from semiconductors for optical and RF arbitrary waveform generation.