gebhart/patrepeval huggingface dataset:
Data from Heterogeneity of Circulating Tumor Cell–Associated Genomic Gains in Breast Cancer and Its Association with the Host Immune Response (2023)

&lt;div&gt;Abstract&lt;p&gt;Tumor cells that preferentially enter circulation include the precursors of metastatic cancer. Previously, we characterized circulating tumor cells (CTC) from patients with breast cancer and identified a signature of genomic regions with recurrent copy-number gains. Through FISH, we now show that these CTC-associated regions are detected within the matched untreated primary tumors of these patients (21% to 69%, median 55.5%, &lt;i&gt;n&lt;/i&gt; = 19). Furthermore, they are more prevalent in the metastases of patients who died from breast cancer after multiple rounds of treatment (70% to 100%, median 93%, samples &lt;i&gt;n&lt;/i&gt; = 41). Diversity indices revealed that higher spatial heterogeneity for these regions within primary tumors is associated with increased dissemination and metastasis. An identified subclone with multiple regions gained (MRG clone) was enriched in a posttreatment primary breast carcinoma as well as multiple metastatic tumors and local breast recurrences obtained at autopsy, indicative of a distinct early subclone with the capability to resist multiple lines of treatment and eventually cause death. In addition, multiplex immunofluorescence revealed that tumor heterogeneity is significantly associated with the degree of infiltration of B lymphocytes in triple-negative breast cancer, a subtype with a large immune component. Collectively, these data reveal the functional potential of genetic subclones that comprise heterogeneous primary breast carcinomas and are selected for in CTCs and posttreatment breast cancer metastases. In addition, they uncover a relationship between tumor heterogeneity and host immune response in the tumor microenvironment.&lt;/p&gt;Significance:&lt;p&gt;As breast cancers progress, they become more heterogeneous for multiple regions amplified in circulating tumor cells, and intratumoral spatial heterogeneity is associated with the immune landscape.&lt;/p&gt;&lt;/div&gt;
Optimistic active messages (1994)

Recent networks and network interfaces promise remarkable communication performance with very little overhead, but current software structures impose substantial overhead that prevents applications from achieving the benefits of these new architectures. We propose a new software structure that eliminates much of the overhead while preserving the ease of programming of current systems. Our architecture relies on the compiler to bridge the gap between high-level application programs and low-level communication primitives. The compiler incorporates application code into message handlers using a new runtime mechanism called optimistic active messages.
Active and Passive Greenhouse Gas Profiling in the Atmosphere Using Near Infrared Tunable Diode Lasers (2019)

The development of two laser-based sensors for horizontal and vertical profiling of greenhouse gas levels in the atmosphere including an auto-aligning, open-path instrument and a new variant on laser heterodyne radiometry are presented. (tel: + 1202.994.7474, e-mail: houston@gwu.edu). © 2019 Miller, Bailey, Flores, and Bomse
Expression of an enzymatically active polymerase of human hepatitis B virus in a coupled transcription-translation system (1999)

Genome replication of hepadnavirus proceeds by reverse transcription from a viral pregenomic RNA template by a virally encoded polymerase that possesses protein-priming, reverse transcriptase, DNA polymerase, and RNase H activities. Characterization of this enzyme has been hampered by failure to purify an active enzyme from virions and difficulties in expressing an active polymerase in heterologous systems. In this study, we constructed human hepatitis B virus polymerase cDNA under the control of a phage T7 promoter and expressed it in a rabbit reticulocyte lysate-coupled transcription-translation system. In vitro site-directed mutagenesis confirmed that the recombinant polymerase cDNA produced three products: a full-length protein (approximately 94 kDa), an internally initiated protein (approximately 81 kDa), and an N-terminal protein (approximately 40 kDa). The in vitro expressed polymerase possessed protein priming activity, as demonstrated by 32P-dGTP-labeling of the full size polymerase and the N-terminal portion of the molecule in an in vitro priming assay. The polymerase also exhibited polymerization activity, as detected in an in vitro polymerase assay by incorporation of radionucleotides into acid-precipitable polynucleotides and by synthesis of human hepatitis B virus (HBV) specific DNA with product lengths between 100 and 500 nucleotides. In addition, the polymerase was found to use an RNA sequence bearing HBV DR1/epsilon stem-loop motif as a template for DNA synthesis. Both the protein-priming and the reverse transcription activities of this recombinant polymerase are dependent on the RNA fragment containing the HBV DR1/epsilon stem-loop sequence known to be required for the polymerase activities. The in vitro systems used in this study will be applicable to further functional and biochemical studies of this enzyme.
A Pitch-Matched Low-Noise Analog Front-End With Accurate Continuous Time-Gain Compensation for High-Density Ultrasound Transducer Arrays (2022)

This article presents a compact analog front-end (AFE) circuit for ultrasound receivers with linear-in-dB continuous gain control for time-gain compensation (TGC). The AFE consists of two variable-gain stages, both of which employ a novel complementary current-steering network (CCSN) as the interpolator to realize continuously variable gain. The first stage is a trans-impedance amplifier (TIA) with a hardware-sharing inverter-based input stage to save power and area. The TIA’s output couples capacitively to the second stage, which is a class-AB current amplifier (CA). The AFE is integrated into an application-specific integrated circuit (ASIC) in a 180-nm high-voltage BCD technology and assembled with a <inline-formula xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink"> <tex-math notation="LaTeX">$100~\mu \text{m}$ </tex-math></inline-formula> -pitch PZT transducer array of <inline-formula xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink"> <tex-math notation="LaTeX">$8\times $ </tex-math></inline-formula> 8 elements. Both electrical and acoustic measurements show that the AFE achieves a linear-in-dB gain error below ±0.4 dB within a 36-dB gain range, which is <inline-formula xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink"> <tex-math notation="LaTeX">$&gt; 2\times $ </tex-math></inline-formula> better than the prior art. Per channel, the AFE occupies 0.025 mm 2 area, consumes 0.8 mW power, and achieves an input-referred noise density of 1.31 pA / <inline-formula xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink"> <tex-math notation="LaTeX">$\surd $ </tex-math></inline-formula> Hz.
Errata: Transcranial low-level laser therapy (810 nm) temporarily inhibits peripheral nociception: photoneuromodulation of glutamate receptors, prostatic acid phophatase, and adenosine triphosphate (2016)

[This corrects the article DOI: 10.1117/1.NPh.3.1.015003.].
Identification of Streptococcus intermedius Central Nervous System Infection by Use of PCR and Electrospray Ionization Mass Spectrometry (2012)

We describe the utility of PCR and electrospray ionization with mass spectrometry (PCR/ESI-MS) of culture-negative cerebrospinal fluid (CSF) in order to identify Gram-positive cocci noted on a Gram stain of CSF from a previously healthy 26-year-old man with community-acquired pneumonia (CAP) and multiple brain abscesses. CSF samples were obtained 2 weeks apart, first by lumbar puncture and 2 weeks later from an external ventricular drain that was inserted into the right ventricle. Both CSF cultures were negative. A Gram stain of bronchoalveolar lavage (BAL) fluid was notable for many Gram-positive cocci (GPC), but cultures of BAL fluid and subcarinal lymph node biopsy tissue were negative. PCR/ESI-MS detected Streptococcus intermedius, a common cause of brain abscesses, in both CSF samples as well as in the fixed tissue from the biopsy. This unique case confirms S. intermedius pulmonary infection as the source of metastatic CNS infection and reveals the potential of PCR/ESI-MS to detect a streptococcal pathogen not captured by conventional cultures.
Depressed-clad large mode area amplifier fiber with selective doping yielding near diffraction-limited beam quality (2013)

Large mode area (LMA) optical fibers are finding widespread use nowadays in high power fiber lasers and amplifiers. The lower numerical apertures allow for larger core diameters and therefore reduced intensity of guided lightwaves whilst preserving the near single-mode guidance. As the core diameter is made larger though, conventional LMA fibers support a growing number of modes and beam propagation factor - M <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sup> - gets worse unless provision is made to avoid the latter (even if bending-induced losses as a result of coiling the fiber to a prescribed diameter is assumed). Diverse strategies have been reported in the literature in the last decade or so to address the aforementioned issue. Selective doping [1-2] and multi-layer claddings with depressed index inner layer [3] are two such schemes. The former favors the amplification of the fundamental mode through confinement of rare-earth dopants to the central portion of the core whereas the latter results in increased differential bending losses as a result of the lower effective numerical aperture seen by higher-order modes (HOMs). Both of these methods are shown herein to be quite effective at suppressing HOMs for fibers with large core diameters when implemented all together.
Inside Cover: Synchronized Synthesis of Peptide‐Based Macrocycles by Digital Microfluidics (Angew. Chem. Int. Ed. 46/2010) (2010)

A microfluidic technique for synchronized chemical synthesis has been developed and applied to the formation of peptide-based macrocycles and analogues with side chains appended during ring-opening. A. R. Wheeler and co-workers describe this digital microfluidic technique, in which discrete droplets of samples and reagents are controlled by electric potentials applied to an array of electrodes coated with a hydrophobic insulator, in their Communication on page 8625 ff. Artwork: M. Jebrail/S. Youhanna.
A Single Factor Underlies the Metabolic Syndrome: A confirmatory factor analysis (2006)

These analyses support the current clinical definition of the metabolic syndrome, as well as the existence of a single factor that links all of the core components.
<title>Special sensor ultraviolet spectrographic imager: an instrument description</title> (1992)

We describe the Special Sensor Ultraviolet Spectrographic Imager (SSUSI). This instrument consists of a scanning imaging spectrograph (SIS) whose field-of-view is scanned from horizon to horizon and a nadir-looking photometer system (NPS). The SIS produces simultaneous multispectral images over the spectral range 1 150 to 1800A. The NPS consists of three photometers with filters designed to monitor the airglow at 4278A and 6300A and the terrestrial albedo near 6300A. SSUSI will fly on the DMSP Block 5D3 satellites S-16 thru S-19. The instruments will be calibrated at the Applied Physics Laboratory's Optical Calibration Facility.
Electro‐Optic Response in a Racemic Smectic C Liquid Crystal (2005)

The structure and properties of chiral and racemic smectic liquid crystals are presented. Remarkably, an electrical-field response of a racemic modification in its tilted smectic C phase is discovered. The switching behavior is similar to that observed for conventional, chiral, ferroelectric liquid crystals. The Figure shows unidirectional switched states in a racemic material.
Quantum plasmons with optical-range frequencies in doped few-layer graphene (2017)

Although plasmon modes exist in doped graphene, the limited range of doping achieved by gating restricts the plasmon frequencies to a range that does not include visible and infrared. Here we show, through the use of first-principles calculations, that the high levels of doping achieved by lithium intercalation in bilayer and trilayer graphene shift the plasmon frequencies into the visible range. To obtain physically meaningful results, we introduce a correction of the effect of plasmon interaction across the vacuum separating periodic images of the doped graphene layers, consisting of transparent boundary conditions in the direction perpendicular to the layers; this represents a significant improvement over the Exact Coulomb cutoff technique employed in earlier works. The resulting plasmon modes are due to local field efffects and the non-local response of the material to external electromagnetic fields, requiring a fully quantum mechanical treatment. We describe the features of these quantum plasmons, including the dispersion relation, losses and field localization. Our findings point to a strategy for fine-tuning the plasmon frequencies in graphene and other two dimensional materials.
Wavefield separation using a volume distribution of three component recordings (1999)

By making multiple three component (3C) measurements around a volume so that the rate of change of the wavefield in all directions can be estimated, it is possible to calculate the divergence and the curl of the wavefield which in turns corresponds to P‐ and S‐waves. The volume may be of arbitrary shape, but the equations for wavefield separation are simplified if the volume has a known shape such as that of a tetrahedron. The dimensions of the volume should be smaller than approximately one fifth of the minimum wavelength of the recorded wavefield. A field test was carried out in Oman in April 1998. With a lack of distinct P‐ and S‐waves in the data, the technique was instead evaluated on the airwave‐induced ground motion. The airwave arrival was found to consist mainly of vertical motion that decays with depth. The wavefield separation technique was successfully tested on this arrival.
SPECTRAL SIGNATURES OF ACETONE VAPOR FROM ULTRAVIOLET TO MILLIMETER WAVELENGTHS (2008)

This paper presents comparative analysis of different wavelength ranges for the spectroscopic detection of acetone vapor. We collected and analyzed original absorption line spectra arising from electronic transitions in the ultraviolet, near-infrared vibrational overtones, mid-infrared fundamentals, THz torsional modes, and mm-wave rotational transitions. Peak absorption cross sections of prominent spectral features are determined. The relative merit of each spectral range for sensing is considered, taking into account the absorption strength, available technology, and possible interferences.
Supplemental Methods, Supplemental Tables 1-2, Supplemental Figures 1-4 from AACR Project GENIE: Powering Precision Medicine through an International Consortium (2023)

&lt;p&gt;Supplemental Methods. Supplemental Table 1: Ã¢â,¬â€¹Genomic Data Characterization by Center. Supplemental Table 2: Ã¢â,¬â€¹Gene Panels Submitted by Each Center. Figure S1: Number of putative germline SNPs per sample, before and after uniform germline filtering. Figure S2Ã¢â,¬â€¹. Distribution of total somatic mutation burden per sample stratified by sequencing panel. Figure S3: Ã¢â,¬â€¹Log-scale comparison of mutation frequencies at hotspot sites between GENIE (data aggregated from all sequencing panels) and cancerhotspots.org (CHS) using a binomial test. Figure S4:Ã¢â,¬â€¹ Comparison of mutation frequencies at hotspot sites in each GENIE sequencing panel with cancerhotspots.org (CHS) using a binomial test.&lt;/p&gt;
22-nm FD-SOI Embedded MRAM Technology for Low-Power Automotive-Grade-l MCU Applications (2018)

We demonstrate 22-nm FD-SOI 40Mb embedded MRAM (eMRAM) macros for automotive-grade-l (Auto-G1) MCU applications, highlighting sub-ppm to bit error rate and zero failure after 1M endurance cycles across Auto-G1 operating temperature range (-40∼150 °C). Read disturbance characterization with external field also reveals that 40Mb eMRAM macro is capable of active-mode magnetic immunity > 500 Oe at 150 °C. In addition, based on 22-nm eMRAM macro data, we review the effects of magnetic tunnel junction (MTJ) size on reliability and examine scalability of eMRAM technology beyond 22 nm.
Bifurcation analysis of bubble dynamics in fluidized beds (2007)

We use a low-dimensional, agent-based bubble model to study the changes in the global dynamics of fluidized beds in response to changes in the frequency of the rising bubbles. The computationally based bifurcation analysis shows that at low frequencies, the global dynamics is attracted towards a fixed point since the bubbles interact very little with one another. As the frequency of injection increases, however, the global dynamics undergoes a series of bifurcations to new behaviors that include highly periodic orbits, chaotic attractors, and intermittent behavior between periodic orbits and chaotic sets. Using methods from time-series analysis, we are able to approximate nonlinear models that allow for long-term predictions and the possibility of developing control algorithms.
Poly(ADP-ribose) polymerase inhibition in cancer therapy: are we close to maturity? (2009)

More patient-compliant orally available PARP-1 inhibitor clinical candidates, along with their possible use as single agents in specific, molecularly defined cancer indications, increase the expectations for this therapeutic approach. The growing understanding of the biological role of other PARPs, such as Tankyrase 1, may be of interest as new potential targets. Besides the classical NAD-mimicking pharmacophore, additional compounds, which either do not resemble nicotinamide or exploit different binding sites, are emerging.
Myeloid-derived suppressor cells (2013)

While conventional anticancer therapies, including surgical resection, radiotherapy, and/or chemotherapy, are relatively efficient at eliminating primary tumors, these treatment modalities are largely ineffective against metastases. At least in part, this reflects the rather inefficient delivery of conventional anticancer agents to metastatic lesions. We have recently demonstrated that myeloid-derived suppressor cells (MDSCs) can be used as cellular missiles to selectively deliver a radioisotope-coupled attenuated variant of <i>Listeria monocytogenes</i> to both primary and metastatic neoplastic lesions in mice with pancreatic cancer. This novel immunotherapeutic intervention robustly inhibited tumor growth while promoting a dramatic decrease in the number of metastases.
Inhibitory effect of opiates on LPS mediated release of TNF and IL-8 (2012)

Most patients with advanced cancer experience severe pain and are often treated with opiates. Cancer patients are especially susceptible to opportunistic infections due to treatment with immunosuppressive and cytostatic drugs. Since opiates have been demonstrated to have immunomodulatory effects, it is of clinical importance to evaluate potential differences between commonly used opiates with regard to their effect on the immune system. The aim of this study was to evaluate the effect of morphine, tramadol, fentanyl and ketobemidone on the functioning of the immune system with special reference to TNF and IL-8 release. Method. U-937 cells were preincubated with different concentrations of opioids followed by stimulation with LPS 100 μg/ml for three hours. The effect of opioids on the levels of cytokine mRNA was studied using RT-PCR. Erk and Akt phosphorylation was also measured by Western blot. Results. All opioids with the exception of fentanyl were capable of inhibiting TNF release from U-937 cells. Morphine had no effect on IL-8 release but the effect of other opiates was almost the same as the effect on TNF. All opioids with the exception of fentanyl were capable of inhibiting production of mRNA for TNF and IL-8. The observed effects of opiates were not always reversible by naloxone, suggesting that the effects might be mediated by other receptors or through a non-receptor mediated direct effect. Although preliminary evidence suggests the involvement of Erk and Akt pathways, further studies are needed to unravel the intracellular pathways involved in mediating the effects of opiates. Our data suggests that the order of potency with regard to inhibition of cytokine release is as follows: tramadol > ketobemidone > morphine > fentanyl. Conclusion. Further studies are needed to understand the clinical implications of the observed immunosuppressive effects of tramadol and ketobemidone and to improve opioid treatment strategies in patients with cancer.
Power Consumption of Rotary Blood Pumps: Pulsatile Versus Constant‐Speed Mode (2014)

We investigated the power consumption of a HeartMate III rotary blood pump based on in vitro experiments performed in a cardiovascular simulator. To create artificial-pulse mode, we modulated the pump speed by decreasing the mean speed by 2000 rpm for 200 ms and then increasing speed by 4000 rpm (mean speeds plus 2000 rpm) for another 200 ms, creating a square waveform shape. The HeartMate III was connected to a cardiovascular simulator consisting of a hydraulic pump system to simulate left ventricle pumping action, arterial and venous compliance chambers, and an adjustable valve for peripheral resistance to facilitate the desired aortic pressure. The simulator operated based on Suga's elastance model to mimic the Starling response of the heart, thereby reproducing physiological blood flow and pressure conditions. We measured the instantaneous total electrical current and voltage of the pump to evaluate its power consumption. The aim was to answer these fundamental questions: (i) How does pump speed modulation affect pump power consumption? (ii) How does the power consumption vary in relation to external pulsatile flow? The results indicate that speed modulation and external pulsatile flow both moderately increase the power consumption. Increasing the pump speed reduces the impact of external pulsatile flow.
Effects of Hypothermia on Cerebral Metabolism, Blood Flow, and Autoregulation (2004)

Deep hypothermia, achieved by lowering body temperature to the range of 20-25jC, has been used for decades to improve theoutcome from high-risk surgical procedures. At the laboratory level, hypothermia is one of the most robust neuroprotectants studied to date. Experimentally, decreases in body and brain temperature have consistently produced marked reductions in brain injury and improvement in a variety of behavioral parameters. Unfortunately, the benefits of hypothermia can be offset by undesirable side effects such as cardiac arrhythmias, shivering, coagulopathies, and reduced resistance to infection (see Chapter 6)—all of which become more serious as the depth of cooling increases.