gebhart/patrepeval huggingface dataset:
HER2 As Therapeutic Target for Overcoming ATP-Binding Cassette Transporter–Mediated Chemoresistance in Small Cell Lung Cancer (2012)

Small cell lung cancer (SCLC) easily acquires multidrug resistance after successful initial therapy. Overexpression of ATP-binding cassette (ABC) transporters is important for the multidrug resistance. Among them, ABCB1 and ABCG2 are known to be upregulated in chemoresistant SCLC cells. We found that human epidermal growth factor receptor 2 (HER2) expressions are also upregulated in chemoresistant SBC-3/ETP, SBC-3/SN-38, and SBC-3/CDDP cells, compared with chemosensitive SBC-3 cells. Lapatinib, a tyrosine kinase inhibitor of HER2, could not suppress proliferation of these HER2-positive SCLC cells alone but successfully restored chemosensitivity to etoposide and SN-38 with a clinically applicable concentration. The reversal effect of lapatinib was thought to be caused by inhibition of drug efflux pump functions of ABC transporters, although lapatinib itself has been reported to be a substrate for them. Moreover, knocking down of HER2 by an short interfering RNA weakened the effect of lapatinib on ABCB1, indicating the involvement of HER2 in the inhibitory mechanisms. Notably, we showed that caveolin-1 and Src play key roles in modulating ABCB1 function via HER2 inactivation. In SBC-3/ETP cells, dephosphorylation of HER2 by lapatinib activates Src and successively leads to increased caveolin-1 phosphorylation. Through this process, caveolin-1 dissociates from HER2 and strengthens association with ABCB1, and finally impairs the pump functions. Furthermore, we showed that treatment by lapatinib in combination with etoposide or irinotecan significantly suppresses the growth of subcutaneous SBC-3/ETP and SBC-3/SN-38 tumors in mice, respectively. Collectively, these results indicate that combination therapy with lapatinib and cytotoxic agents could conquer ABC transporter-mediated chemoresistance especially in HER2-positive SCLC.
Synthetic Zero Air Reference Material for High Accuracy Greenhouse Gas Measurements (2018)

The purity analysis of zero air is a significant contributor to the uncertainty in preparing reference materials of high impact greenhouse gases, limiting progress toward coherent and comparable measurements required to assess climate trends. We have produced a commutable synthetic zero air reference material with an oxygen, nitrogen, and argon matrix closely matching atmospheric composition. This is the critical step in preventing systematic biases from pressure broadening effects when using these reference materials to calibrate instruments based on optical spectroscopy. The amount fractions of carbon dioxide, methane, and carbon monoxide, which are present as minor impurities in the zero air reference material, have been accurately quantified using a novel dilution device that can generate gas mixtures of these components at trace amount fractions. These developments will have a significant impact on advancing the state of the art in high accuracy reference materials and for baseline calibration of spectroscopic instrumentation.
A METHOD FOR THE ESTIMATION OF SUGAR IN SMALL QUANTITIES OF BLOOD (1915)

The red color obtained by heating a dextrose solution with picric acid and sodium carbonate is employed as the basis of the present method for the determination of blood sugar, the reaction being so delicate that it is possible to determine the dextrose in as little as 0.5 c.c. of blood. Following is the method in detail as ordinarily used by us.Two c.c. of blood are drawn from a vein through a hypodermic needle into an Ostwald pipette, a little potassium oxalate in the tip of the pipette preventing clotting. The blood is discharged immediately into a 25 c.c. volumetric flask containing 10 c.c. of N/100 acetic acid previously heated in a boiling water bath. The pipette is rinsed once with distilled water. The flask is replaced in the boiling water bath and shaken occasionally for five minutes. After cooling, 1 c.c. of 5 per cent. dialyzed iron (Merck) is added to precipitate any protein still in solution. Distilled water is added to the mark, the contents of the flask are filtered, and an aliquot of the c...
Compact All-InP Laser-Vector-Modulator for Generation and Transmission of 100-Gb/s PDM-QPSK and 200-Gb/s PDM-16-QAM (2013)

A compact indium phosphide (InP)-based integrated transmitter assembly consisting of a tunable laser and a double-nested Mach-Zehnder modulator (vector modulator) was successfully used for the generation of Nyquist-prefiltered quadrature phase shift keying (QPSK) and 16-ary quadrature amplitude modulation (16-QAM) signals at 32 Gbaud. With external polarization division multiplexing (PDM) emulation and digital coherent detection, we realized data rates of 128 Gb/s with PDM-QPSK and 256 Gb/s with PDM-16-QAM from a commercially available small-form factor device originally designed for 40-Gb/s direct-detection differential QPSK applications. We transmitted these two signals over 8000 and 960 km of standard single mode fiber, respectively. We also compared the performance of the integrated transmitter with a LiNbO3 based vector modulator, using a high-performance 100-kHz external-cavity laser and a low-cost 200-kHz to 400-kHz integrated laser assembly as optical local oscillators. The all-InP integrated laser-vector-modulator transmitter was found to be a viable solution for long-haul 100 and 200-Gb/s coherent optical transmission systems.
Rate controlling in off line 3D video coding using evolution strategy (2009)

In this paper, we propose a rate control technique for 3D video using subjective quality for off line video coding. We propose to use Video Quality Metric (VQM) with an evolution strategy (ES) algorithm, which is capable of identifying the best possible quantization parameters for each 16times16 macroblock, of both colour and depth map videos, to encode the 3D sequence such that it would maximize the subjective quality of the entire video sequence subjected to the target bit rate. Simulation results suggest that the proposed technique can improve the RD performance of the H.264/AVC codec significantly. With the proposed technique, up to 35% bit rate reduction can be achieved at the same video quality. Furthermore, results show that the proposed technique can improve the subjective quality of the encoded video significantly for video sequences especially with high motion.
High power heating in the ion cyclotron range of frequencies in the Wisconsin Tokapole II (1981)

Fast wave heating at the second, third and fourth harmonics of the ion cyclotron resonance, and slow wave heating at the fundamental in a single ion species hydrogen plasma, are found to be in good agreement with warm plasma theory at RF power levels <or=130 kW. Ion heating is negligible off an eigenmode. Ion body temperatures are more than doubled to 75 eV from the 35 eV ohmically heated case with tails comprising 8% of the plasma at 320 eV. No deleterious effects except a non-disruptive 10% shortening of the discharge length caused by impurity influx are noted. A passive mode tracking technique allows approximately=40% increase in power deposition in a passing eigenmode over that of a fixed frequency RF source. Ion temperatures are limited by charge exchange due to the <50 eV central temperature and the small 13 cm radius current channel.
Research of Anomaly Detection Based on Time Series (2009)

With the continuous deterioration of the network environment, a variety of viruses, Trojans continue to affect the security of the network. Through the network traffic anomaly detection and analysis can efficiently find problems existing in the network. This paper discusses the network traffic flow data predict and network anomaly detection, network traffic prediction using ARMA model, network anomaly detection using the exponential smoothing model. ARMA model supplies the expectation value to abnormal detection, at the same time exponential smoothing model can restoration historical flow data, making the following traffic forecast more accurate. A network traffic predict and network anomaly detection system has been developed, with which can find network anomaly and send alarms, thus improve network stability and robustness.
pH-activatable near-infrared fluorescent probes for detection of lysosomal pH inside living cells (2014)

Four near-infrared fluorescent probes (A, B, C and D) have been synthesized, characterized, and evaluated for detection of lysosomal pH inside living cells. The fluorescent probes display highly sensitive and selective fluorescent response to acidic pH as the acidic pH results in drastic structural changes from spirocyclic (non-fluorescent) forms to ring-opening (fluorescent) forms of the fluorescent probes. The fluorescence intensities of the fluorescent probes (B, C and D) increase significantly by more than 200-fold from pH 7.4 to 4.2. The fluorescent probe D bearing the N-(2-hydroxyethyl) ethylene amide residue possesses the advantages of high sensitivity, excellent photostability, good cell membrane permeability, strong pH dependence, and low auto-fluorescence background. It has been successfully applied to selectively stain lysosomes and detect lysosomal pH changes inside normal endothelial and breast cancer cells.
Side-chain Packing Using SE(3)-Transformer (2021)

Predicting protein side-chains is important for both protein structure prediction and protein design. Modeling approaches to predict side-chains such as SCWRL4 have become one of the most widely used tools of its type due to fast and highly accurate predictions. Motivated by the recent success of AlphaFold2 in CASP14, our group adapted a 3D equivariant neural network architecture to predict protein side-chain conformations, specifically within a protein-protein interface, a problem that has not been fully addressed by AlphaFold2.
Accelerated photobleaching of nonlinear optical polymer for the formation of optical waveguide (1994)

The photobleaching process in nonlinear optical polymer thin film is shown to be accelerated by the addition of a photosensitizer. Photobleaching time has been effectively reduced by a factor of 3–5. Refractive indices of both unbleached and fully bleached film with benzyldimethylketal (BDK) is higher than those of the film without BDK. Nonlinear optical properties of the optical copolymer with photosensitizer were little affected by the addition of the photosensitizer. Optical loss of the waveguide formed by the technique is comparable to that of waveguide without photosensitizer.
Seasonal changes in selectivity for individual song in the songbird auditory forebrain (2011)

Seasonal differences in song behaviour and anatomy of the song control system are well documented in songbirds. Although seasonal effects on songbird vocal production have been studied extensively, relatively less work has been done on seasonal effects on songbird auditory processing. The European starling (Sturnus vulgaris) has proven to be a remarkably interesting model to study the relationship between social/breeding behaviour plasticity and auditory processing. Starlings are highly social songbirds with songs that show different levels of variations that reflect not only species-specific but also individual-specific identity. Taking advantage of the whole-brain approach allowed by functional Magnetic Resonance Imaging (fMRI), we measured the neural responses to these songs in medetomidine-anesthetized adult male starlings (N=9) in both the breeding and the non-breeding seasons. Subjects were exposed to species-specific songs (universally-shared male songs), individual male conspecific songs (used in individual recognition) and synthetic pure tones. The direct comparison of the neural activation elicited by songs used in individual recognition, as compared to species-specific songs, revealed that perception of individual male songs induced a greater activity in the regions analogous to the auditory cortex of mammals (Field L and caudomedial nidopallium (NCM)). There were however differences between Field L and NCM according to the season. Whereas Field L showed the same selectivity for individual male songs in both seasons, NCM (more specifically the most caudal part of NCM) showed this selectivity only during the breeding season. In the non-breeding season, selectivity for individual male songs was not present anymore in caudal NCM. Responses to synthetic pure tone stimuli remained unchanged between the seasons, indicating that this seasonal change in selectivity for individual stimuli in caudal NCM was not due to a change in auditory perception as a whole. Finally, the data seems to suggest lateralization of selectivity for individual songs towards the right hemisphere, which is somewhat similar to the right-hemisphere specialization for the recognition of faces observed in humans. These results suggest that seasons impact auditory processing as well as vocal production. A differential representation of sounds with distinct biological significance is thus observed between seasons, which opens questions about a potential neural substrate for the extraction of biologically relevant information used in vocal communication.
From Budapest to Bar Harbor (2005)

inflammatory responses generated during bone injury may lead to PGE 2 -stimulated angiogenesis, 3 chondrogenesis, 4 osteogenesis, 4 and now osteoclastogenesis via differentiation of resident monocytic precursors. Since osteoclasts are essential factors in the transition of cartilage to bone, this may be the key to understanding how this process is coordinately regulated. Thus, the study by Han et al provides significant insights to our understanding of bone tissue engineering.
Transmembrane orientation of the fibronectin receptor complex (integrin) demonstrated directly by a combination of immunocytochemical approaches. (1988)

The avian 140-KD cell adhesion receptor or "integrin," a complex of three glycoproteins with molecular masses averaging 140 KD, interacts with extracellular fibronectin and forms a linkage complex that co-localizes with intracellular actin. To probe the molecular interactions involved in this linkage complex, we used monoclonal antibodies and a combination of immunolocalization approaches to determine whether any component was transmembrane. Immunoadsorption and immunoblotting experiments demonstrated that anti-120-KD Mabs recognized the band 3 component of integrin isolated from chicken embryo fibroblasts (CEF) by JG22E immunoaffinity chromatography, and they co-localize with anti-fibronectin and polyclonal anti-integrin at cell contact sites in double-labeling experiments. Immunofluorescence experiments involved comparisons of double-labeled intact cells or substrate-attached, ventral plasma membrane "rip-off" fragments, using anti-fibronectin and each of the anti-120-KD Mabs. The extracellular faces of living intact cells were strongly labeled by a majority (approximately 70%) of the anti-120-KD Mabs at fibronectin-membrane attachment sites. The remainder (approximately 30%) labeled intact cells weakly or not at all. However, although the anti-120-KD Mab ES186 did not stain living cells, it did demonstrate positive staining above substratum contact sites over entire isolated rip-off membranes. In contrast, Mabs directed against putative extracellular epitopes and anti-fibronectin antibodies did not label these sites at the center of rip-offs unless the membranes were detergent permeabilized. Proteolysis experiments suggested that the ES186 epitope was located at one end of the molecule, since removal of short fragments from integrin band 3 concomitantly removed or destroyed the ES186 epitope, whereas the extracellular epitopes still remained. These experiments directly demonstrate that integrin band 3 is a transmembrane polypeptide with at least one epitope recognized by anti-120-KD Mabs on the cytoplasmic side of the plasma membrane and at least one epitope on the extracellular cell surface.
Small, fat-filled lipid droplets remain spherical as they indent a nucleus, dilute the lamina, and cause rupture (2022)

Abstract The nucleus in many cell types is a stiff organelle, and yet fat-filled lipid droplets (FD’s) in the cytoplasm can be seen to indent and displace the nucleus. FD’s are phase-separated liquids with a poorly understood interfacial tension γ that determines how FD’s interact with other organelles. Here, micron-sized FD’s remain spherical as they indent both the nucleus and peri-nuclear actomyosin, dilute Lamin-B1 locally independent of Lamin-A,C, and trigger rupture with locally persistent accumulation in the nucleus of cGAS, a cytosolic DNA sensor. FD-nucleus interactions initiate rapid mis-localization of the essential DNA repair factor KU80, and nuclear rupture associates with DNA damage and perturbed cell cycle. Similar results are evident in FD-laden cells after constricted 3D-migration, which is impeded by FD’s. Spherical shapes of small FD’s are consistent with a high γ that we measure for FD’s mechanically isolated from fresh adipose tissue as ∼40_mN/m – which is far higher than other liquid condensates, but typical of oils in water and sufficiently rigid to disrupt cell structures.
Percutaneous implantation of the first repositionable aortic valve prosthesis in a patient with severe aortic stenosis (2008)

Successful percutaneous aortic valve replacement can be performed using the new self-expanding and repositionable Lotus valve for treatment of high-risk patients with aortic valve stenosis. Further studies are mandatory to assess device safety and efficacy in larger patient populations.
A Time-Optimal Self-Stabilizing Synchronizer Using A Phase Clock (2007)

A synchronizer with a phase counter (sometimes called asynchronous phase clock) is an asynchronous distributed algorithm, where each node maintains a local "pulse counter" that simulates the global clock in a synchronous network. In this paper, we present a time-optimal self-stabilizing scheme for such a synchronizer, assuming unbounded counters. We give a simple rule by which each node can compute its pulse number as a function of its neighbors' pulse numbers. We also show that some of the popular correction functions for phase clock synchronization are not self-stabilizing in asynchronous networks. Using our rule, the counters stabilize in time bounded by the diameter of the network, without invoking global operations. We argue that the use of unbounded counters can be justified by the availability of memory for counters that are large enough to be practically unbounded and by the existence of reset protocols that can be used to restart the counters in some rare cases where faults will make this necessary.
Environmental risk factors for inflammatory bowel disease. (2010)

Inflammatory bowel disease (IBD) is characterized by chronic inflammation of the gastrointestinal tract and is associated with significant morbidity. The etiology of IBD has been extensively studied during the last several decades; however, causative factors in disease pathology are not yet fully understood. IBD is thought to result from the interaction between genetic and environmental factors that influence the normal intestinal commensal flora to trigger an inappropriate mucosal immune response. Although many IBD susceptibility genes have been discovered, similar advances in defining environmental risk factors have lagged. A number of environmental risk factors have been explored, including smoking, appendectomy, oral contraceptives, diet, breastfeeding, infections/ vaccinations, antibiotics, and childhood hygiene. However, most of these factors have demonstrated inconsistent findings, thus making additional studies necessary to better understand the etiology of IBD.
Loss of LAMP5 interneurons drives neuronal network dysfunction in Alzheimer’s disease (2022)

In Alzheimer's disease (AD), where amyloid-β (Aβ) and tau deposits in the brain, hyperexcitation of neuronal networks is an underlying disease mechanism, but its cause remains unclear. Here, we used the Collaborative Cross (CC) forward genetics mouse platform to identify modifier genes of neuronal hyperexcitation. We found LAMP5 as a novel regulator of hyperexcitation in mice, critical for the survival of distinct interneuron populations. Interestingly, synaptic LAMP5 was lost in AD brains and LAMP5 interneurons degenerated in different AD mouse models. Genetic reduction of LAMP5 augmented functional deficits and neuronal network hypersynchronicity in both Aβ- and tau-driven AD mouse models. To this end, our work defines the first specific function of LAMP5 interneurons in neuronal network hyperexcitation in AD and dementia with tau pathology.
Seeded FEL Microbunching Experiments at the UCLA Neptune Laboratory (2010)

Seeded high‐gain FELs, which can generate very powerful radiation pulses in a relatively compact undulator and simultaneously modulate the electron beam longitudinally at the seed wavelength, are important tools for advanced accelerator development. A single‐pass 0.5–9 THz FEL amplifier‐buncher driven by a regular photoinjector is being built at the UCLA Neptune Laboratory. FEL interactions at 340 μm (1 THz) are considered for the first experiment, since time‐resolved measurements of longitudinal current distribution of the bunched beam using the RF deflecting cavity are possible. A design of a 0.2–2.0 μm FEL using the same undulators is presented. In this case the FEL is driven by a high‐peak current beam from the laser‐plasma accelerator tunable in the 100–300 MeV range.
Intersubband transitions in the communications wavelength range (/spl lambda//spl sim/1.55 /spl mu/m) In GaN/AlGaN multiple quantum wells (2001)

Summary form only given. Fueled by the recent success of mid-infrared quantum cascade lasers, optical devices based on intersubband (IS) transitions face a rising interest also in other wavelength ranges. In particular, the intrinsically ultrafast electron dynamics associated with IS-transitions warrants research into the latter for the communications wavelength range (/spl lambda//spl sim/1.55 /spl mu/m). Few material systems, however, provide a sufficiently large band-discontinuity for the quantum wells (QWs) to accommodate the large subband spacing needed for such short wavelengths, Sb-based materials or group-III-nitrides presently being the best candidates. The rapid success of GaN-based interband light emitting diodes and lasers makes this material system particularly attractive. We present the first IS-transitions in the communications wavelength range, with peak absorption wavelengths as short as 1.4 /spl mu/m.
Development of a MIP-Based QCM Sensor for Selective Detection of Penicillins in Aqueous Media (2021)

Pharmaceuticals wastes have been recognized as emerging pollutants to the environment. Among those, antibiotics in the aquatic environment are one of the major sources of concern, as chronic, low-dose exposure can lead to antibiotic resistance. Herein, we report on molecularly imprinted polymers (MIP) to recognize penicillin V potassium salt (PenV-K), penicillin G potassium salt (PenG-K), and amoxicillin sodium salt (Amo-Na), which belong to the most widespread group of antibiotics worldwide. Characterization and optimization led to two MIPs comprising methacrylic acid as the monomer and roughly 55% ethylene glycol dimethacrylate as the crosslinker. The obtained layers led to sensitive, selective, repeatable, and reusable sensor responses on quartz crystal microbalances (QCM). The LoD for PenV-K, PenG-K, and Amo-Na sensors are 0.25 mM, 0.30 mM, and 0.28 mM, respectively; imprinting factors reach at least around three. Furthermore, the sensors displayed relative selectivity factors of up to 50% among the three penicillins, which is appreciable given their structural similarity.