gebhart/patrepeval huggingface dataset:
A Central Role for HER3 in HER2 -Amplified Breast Cancer: Implications for Targeted Therapy (2008)

Epidermal growth factor receptor (EGFR) and HER3 each form heterodimers with HER2 and have independently been implicated as key coreceptors that drive HER2-amplified breast cancer. Some studies suggest a dominant role for EGFR, a notion of renewed interest given the development of dual HER2/EGFR small-molecule inhibitors. Other studies point to HER3 as the primary coreceptor. To clarify the relative contributions of EGFR and HER3 to HER2 signaling, we studied receptor knockdown via small interfering RNA technology across a panel of six HER2-overexpressing cell lines. Interestingly, HER3 was as critical as HER2 for maintaining cell proliferation in most cell lines, whereas EGFR was dispensable. Induction of HER3 knockdown in the HER2-overexpressing BT474M1 cell line was found to inhibit growth in three-dimensional culture and induce rapid tumor regression of in vivo xenografts. Furthermore, preferential phosphorylation of HER3, but not EGFR, was observed in HER2-amplified breast cancer tissues. Given these data suggesting HER3 as an important therapeutic target, we examined the activity of pertuzumab, a HER2 antibody that inhibits HER3 signaling by blocking ligand-induced HER2/HER3 heterodimerization. Pertuzumab inhibited ligand-dependent morphogenesis in three-dimensional culture and induced tumor regression in the heregulin-dependent MDA-MB-175 xenograft model. Importantly, these activities of pertuzumab were distinct from those of trastuzumab, a monoclonal antibody currently used for treatment of HER2-amplified breast cancer patients. Our data suggest that inhibition of HER3 may be more clinically relevant than inhibition of EGFR in HER2-amplified breast cancer and also suggest that adding pertuzumab to trastuzumab may augment therapeutic benefit by blocking HER2/HER3 signaling.
Growth imbalance and altered expression of cyclins B1, A, E, and D3 in MOLT-4 cells synchronized in the cell cycle by inhibitors of DNA replication. (1995)

Expression of cyclins at the translational level is generally studied by immunoblotting lysates of cells synchronized in the cycle. Most methods used to synchronize transformed cells induce growth imbalance. The aim of the present study was to analyze levels of cyclins B1, A, E, and D3 in the respective phases of the cycle in synchronized human leukemic MOLT-4 cells, correlate them with total cellular protein content (reflecting growth imbalance), and compare the synchronized cells with cells from unperturbed, asynchronous cultures. Expression of cyclins detected immunocytochemically in individual permeabilized cells was analyzed by multiparameter flow cytometry, which made it possible to relate position of the cell in the cell cycle with cyclin expression. Cells synchronized at the G1-S boundary by thymidine, mimosine, or aphidicolin had about 40% increased total protein and 4-5 fold higher levels of cyclins E and B1 compared to their G1 counterparts from unperturbed cultures. Expression of cyclin A in synchronized cells was 2-fold higher, while expression of cyclin D3 was essentially unaltered. The synchronized cells traversing S phase after release from the block had elevated but decreasing levels of cyclins E, B1, and A. Although the cyclin expression of cells reentering G1 was similar to that of their counterparts from asynchronous cultures, the total protein content was still elevated by about 30%. The data indicate that due to different degrees of imbalance in total protein and individual cyclin content, levels of cyclins detected by immunoblotting of cell lysates from synchronized cultures may not be representative of their expression in unperturbed cells. The elevated level of cyclin B1 in the cells arrested at the G1-S boundary may reflect the increased half-life of this protein, stabilized as the result of the overexpression of cyclin E.
Human renal cell carcinoma antigen-specific CTLs: antigen-driven selection and long-term persistence in vivo. (1998)

Renal cell carcinomas (RCCs) are thought to be immunogenic, because cytokine-induced and even spontaneous tumor regression has been observed in a significant number of patients. However, little is known about the nature of immune responses that might lead to tumor regression. We studied naturally arising human T-cell responses against RCC by combining molecular analyses of T-cell receptor (TCR) usage in primary tumors in situ with functional analyses of tumor-infiltrating lymphocytes (TILs) in vitro. TILs of patient 26 that were cultured in vitro showed a human leukocyte antigen (HLA-A*0201)-restricted cytotoxic activity specific for autologous tumor cells. These tumor-derived lymphocytes were dominated by a family of T cells expressing V alpha20- and V beta22-positive TCRs. Their specificity-conferring third complementarity-determining regions were highly homologous with respect to the loop length and selection of particular amino acids in both TCR chains. These characteristics are similar to those reported for antigen-selected murine T cells recognizing immunodominant epitopes of non-self proteins. To evaluate the biological significance of these CTLs in vivo, we analyzed the corresponding TCR transcripts in the cryopreserved tumor material of patient 26 and in a second HLA-A*0201-positive RCC patient whose tumor cells were also lysed by TIL-26. The in situ TIL populations of both patients used related families of highly homologous TCRs, supporting the contention that immunodominant responses directed against a shared tumor-associated antigen occurred in both individuals in vivo. Furthermore, in the absence of overt metastatic disease, the tumor antigen-specific CTLs of patient 26 were shown to persist in the periphery 4 years after removal of the primary tumor. These results demonstrate that antigen-driven T-cell responses specific for spontaneously arising carcinomas developed in these patients and showed long-term persistence, even in the absence of immunotherapy.
Application of Kogelnik’s two-wave theory to deep, slanted, highly efficient, relief transmission gratings (1991)

Deep photoresist gratings, slanted as well as unslanted, were produced holographically in clear Shipley 1400 photoresist. The diffraction efficiencies of these gratings were measured as a function of incident angle for three wavelengths with polarization perpendicular to the plane of incidence. It is shown that the results agree fairly well with those predicted by Kogelnik's two-wave theory, indicating that these relief gratings behave like volume holograms. An explanation in terms of thin and thick gratings is given, and practical conclusions are drawn from these observations.
Sobolev Training for Neural Networks (2017)

At the heart of deep learning we aim to use neural networks as function approximators - training them to produce outputs from inputs in emulation of a ground truth function or data creation process. In many cases we only have access to input-output pairs from the ground truth, however it is becoming more common to have access to derivatives of the target output with respect to the input - for example when the ground truth function is itself a neural network such as in network compression or distillation. Generally these target derivatives are not computed, or are ignored. This paper introduces Sobolev Training for neural networks, which is a method for incorporating these target derivatives in addition the to target values while training. By optimising neural networks to not only approximate the function's outputs but also the function's derivatives we encode additional information about the target function within the parameters of the neural network. Thereby we can improve the quality of our predictors, as well as the data-efficiency and generalization capabilities of our learned function approximation. We provide theoretical justifications for such an approach as well as examples of empirical evidence on three distinct domains: regression on classical optimisation datasets, distilling policies of an agent playing Atari, and on large-scale applications of synthetic gradients. In all three domains the use of Sobolev Training, employing target derivatives in addition to target values, results in models with higher accuracy and stronger generalisation.
Contribution of femoral and proximal sciatic nerve branches to the sensory innervation of hindlimb digits in the rat (2000)

The present study was performed to investigate the possibility of "aberrant" innervation of the tips of the hindlimb digits in the rat, i.e., from other sources than the femoral and the main sciatic branches (tibial, peroneal, sural). Cutaneous injections of fluorescent tracers in the digits were combined with either selective nerve transections to restrict afferent routes followed by detection of labeled neurons in dorsal root ganglia (DRGs), or by a delayed application of a second tracer to afferent nerves under study to detect double labeled neurons in DRGs. The results show that the tips of the digits were represented in DRGs L3-6. The femoral nerve afferents from digits 1 and 2 projected primarily to DRG L3 and to a smaller extent to DRG L4. A small number of neurons from primarily medial digits 1 and 2, but also from lateral digits 3-5, were found to project to DRGs L4 and L5 via a proximal branch that leaves the sciatic nerve near the sciatic notch and runs distally in the posterior part of the thigh, here called the musculocutaneous nerve of the hindlimb. We also have some evidence indicating innervation of the tips of the digits from the posterior cutaneous nerve of the thigh. Aberrant innervation such as that described here might contribute to remaining and perhaps abnormal sensibility after nerve injury and is of interest for the interpretation of results in experimental studies of collateral and regenerative sprouting after such injury.
An implementation of the FP-growth algorithm (2005)

The FP-growth algorithm is currently one of the fastest approaches to frequent item set mining. In this paper I describe a C implementation of this algorithm, which contains two variants of the core operation of computing a projection of an FP-tree (the fundamental data structure of the FP-growth algorithm). In addition, projected FP-trees are (optionally) pruned by removing items that have become infrequent due to the projection (an approach that has been called FP-Bonsai). I report experimental results comparing this implementation of the FP-growth algorithm with three other frequent item set mining algorithms I implemented (Apriori, Eclat, and Relim).
Purification and Reconstitution of Chloride Channels from Kidney and Trachea (1989)

Chloride channels mediate absorption and secretion of fluid in epithelia, and the regulation of these channels is now known to be defective in cystic fibrosis. Indanyl-oxyacetic acid 94 (IAA-94) is a high-affinity ligand for the chloride channel, and an affinity resin based on that structure was developed. Solubilized proteins from kidney and trachea membranes were applied to the affinity matrix, and four proteins with apparent molecular masses of 97, 64, 40, and 27 kilodaltons were eluted from the column by excess IAA-94. A potential-dependent 36Cl- uptake was observed after reconstituting these proteins into liposomes. Three types of chloride channels with single-channel conductances of 26, 100, and 400 picosiemens were observed after fusion of these liposomes with planar lipid bilayers. Similar types of chloride channels have been observed in epithelia.
Multipoint connection routeing (1990)

Abstract Among other potential services envisioned for broadband ISDN networks, multipoint connnection services have drawn much attention from the standards arena as well as research communities. These services include conference calls, video lectures, etc. where more than two endpoint CPEs are involved in communication. In this paper we investigate representative multipoint connection routeing algorithms from a number of viewpoints: computational complexity, call set‐up complexity, dynamic reconfiguration, robustness to node failures and bandwidth efficiency. These algorithms are either known in the literature or a simple generalization of point‐to‐point routeing algorithms. An interesting conclusion of our study is that the use of multiple point‐to‐point connections for multipoint calls is a viable solution in many cases of interest. This solution would eliminate much of the additional call‐handling complexity that may be otherwise introduced by more sophisticated multipoint routeing algorithms.
Calcium-sensing receptor: a sensor and mediator of ischemic preconditioning in the heart (2010)

As a G protein-coupled receptor, the extracellular Ca(2+)-sensing receptor (CaSR) responds to changes not only in extracellular Ca(2+), but also to many other ligands. CaSR has been found to be expressed in the hearts and cardiovascular system. In this study, we confirmed that CaSR is expressed in mouse cardiomyocytes and showed that it is predominantly localized in caveolae. The goal of this study was to investigate whether CaSR plays a cardioprotective role in ischemic preconditioning (IPC). Hearts from C57BL/6J mice (male, 12-16 wk) were perfused in the Langendorff mode and subjected to the following treatments: 1) control perfusion; 2) perfusion with a specific CaSR antagonist, NPS2143; 3) IPC (four cycles of 5 min of global ischemia and 5 min of reperfusion); or 4) perfusion with NPS2143 before and during IPC. Following these treatments, hearts were subjected to 20 min of no-flow global ischemia and 120 min of reperfusion. Compared with control, IPC significantly improved postischemic left ventricular functional recovery and reduced infarct size. Although NPS2143 perfusion alone did not change the hemodynamic function and did not change the extent of postischemic injury, NPS2143 treatment abolished cardioprotection of IPC. Through immunoblot analysis, it was demonstrated that IPC significantly increased the levels of phosphorylated ERK1/2, AKT, and GSK-3β, which were also prevented by NPS2143 treatment. Taken together, the distribution of CaSR in caveolae along with NPS2143-blockade of IPC-induced cardioprotective signaling suggest that the activation of CaSR during IPC is cardioprotective by a process involving caveolae.
Determination of Ibuprofen in human plasma by high-performance liquid chromatography: validation and application in pharmacokinetic study (2000)

A specific method for the simultaneous determination of S-(+)Ibuprofen and R-(-)Ibuprofen enantiomers in human plasma is described. Adopting a high-performance liquid chromatographic (HPLC) system with spectrofluorometer detector, the compounds were extracted from plasma in alcohol medium and were separated on C18 column, using a solution of acetonitrile-water-acetic acid-triethylamine as mobile phase. The limit of quantitation was 0.1 microg/mL for both compounds. The method was validated by intra-day assays at three concentration levels and was used in a kinetic study in healthy volunteers. During the study we carried out inter-day assays to confirm the feasibility of the method.
Efficacy of eribulin in women with metastatic breast cancer: a pooled analysis of two phase 3 studies (2014)

Data from two phase 3 studies of eribulin were pooled in analyses initially requested by the European Medicines Agency to assess whether specific patient subgroups, previously treated with an anthracycline and a taxane, benefited from eribulin. Study 305/EMBRACE included women after two-to-five lines of chemotherapy for advanced breast cancer who were randomized to eribulin mesylate (1.4 mg/m(2) on days 1 and 8 every 21 days) or treatment of physician's choice. In Study 301, patients who had received up to two prior chemotherapy regimens for advanced disease were randomized to eribulin (as above) or capecitabine (1.25 g/m(2) b.i.d. on days 1-14 every 21 days). In the pooled population, overall survival (OS), progression-free survival and response rates were analysed in the intent-to-treat population and selected subgroups. Overall, 1,062 patients were randomized to eribulin and 802 patients to control. Median OS was 15.2 months with eribulin versus 12.8 months with control (hazard ratio [HR] 0.85; 95% CI 0.77, 0.95; P = 0.003). In all subgroups assessed, OS data favoured eribulin; significant improvements occurred in some subgroups, notably in women with human epidermal growth factor receptor 2 (HER2)-negative disease (HR 0.82; P = 0.002), although the effect in those with HER2-negative but hormone-receptor-positive disease did not reach statistical significance; benefits were also seen, among others, in those with estrogen-receptor-negative and triple-negative disease. Eribulin improves OS in various patient subgroups with advanced/metastatic breast cancer who had previously received an anthracycline and a taxane. Women with HER2-negative disease are among those who may obtain benefit from eribulin.
Structure−Activity Studies of Substituted Quinoxalinones as Multiple-Drug-Resistance Antagonists (2000)

A significant problem in the clinical treatment of cancer relates to the development of tumor resistance to many chemotherapeutic agents. Acquired drug resistance is often mediated through overexpression of membrane transport proteins that effectively efflux anticancer agents. Two of the best-studied transporters, P-glycoprotein (Pgp) and MRP1, have pharmacological properties that only partially overlap. In our search for improved drug-resistance antagonists, we have identified a family of substituted quinoxalines that selectively antagonizes Pgp over MRP1. Consequently, a focused library of congeners was designed and synthesized starting with a parent bromomethylquinoxalinone. This parent quinoxalinone was then condensed with a series of phenols to yield a family of substituted phenoxymethylquinoxalinones. These compounds were evaluated for their toxicity toward drug-sensitive MCF-7 breast carcinoma cells and for their abilities to antagonize Pgp and MRP1 in drug-resistant cell lines (NCI/ADR and MCF-7/VP, respectively). The results of this structure-activity study indicate that compounds with carbonyl substitutions of the phenoxy group (ester, amide, or ketone moieties) demonstrate excellent antagonism of Pgp while having relatively low toxicity toward drug-sensitive cells. Importantly, none of these compounds antagonized MRP1. Because of their transporter selectivity, we predict that substituted quinoxalinones may be more effective MDR modulators in vivo than are nonselective transporter antagonists.
Reconstitution of Mitogen-activated Protein Kinase Phosphorylation Cascades in Bacteria (1997)

Mitogen-activated protein (MAP) kinase pathways include a three-kinase cascade terminating in a MAP kinase family member. The middle kinase in the cascade is a MAP/extracellular signal-regulated kinase (ERK) kinase or MEK family member and is highly specific for its MAP kinase target. The first kinase in the cascade, a MEK kinase (MEKK), is characterized by its ability to activate one or more MEK family members. A two-plasmid bacterial expression system was employed to express active forms of the following MEK and MAP kinase family members: ERK1, ERK2, alpha-SAPK, and p38 and their upstream activators, MEK1, -2, -3, and -4. In each kinase module, the upstream activator, a constitutively active mutant of MEK1 or MEKK1, was expressed from a low copy plasmid, while one or two downstream effector kinases were expressed from a high copy plasmid with different antibiotic resistance genes and origins of replication. Consistent with their high activity, ERK1 and ERK2 were doubly phosphorylated on Tyr and Thr, were recognized by an antibody specific to the doubly phosphorylated forms, and were inactivated by either phosphoprotein phosphatase 2A or phosphotyrosine phosphatase type 1. Likewise, activated p38 and alpha-stress-activated protein kinase could also be inactivated by either phosphatase, and alpha-stress-activated protein kinase was recognized by an antibody specific to the doubly phosphorylated forms. These three purified, active MAP kinases have specific activities in the range of 0.6-2.3 micromol/min/mg. Coexpression of protein kinases with their substrates in bacteria is of great value in the preparation of numerous phosphoproteins, heretofore not possible in procaryotic expression systems.
Double-shot depth-resolved displacement field measurement using phase-contrast spectral optical coherence tomography (2006)

We describe a system for measuring sub-surface displacement fields within a scattering medium using a phase contrast version of spectral Optical Coherence Tomography. The system provides displacement maps within a 2-D slice extending into the sample with a sensitivity of order 10 nm. The data for a given deformation state is recorded in a single image, potentially allowing sub-surface displacement and strain mapping of moving targets. The system is based on low cost components and has no moving parts. The theoretical basis for the system is presented along with experimental results from a simple well-controlled geometry consisting of independently-tilting glass sheets. Results are validated using standard two-beam interferometry. A modified system was used to measure through-the-thickness phase changes within a porcine cornea due to displacements produced by an increase in the intraocular pressure.
A Combined Assay of Cell Viability and in Vitro Cytotoxicity with a Highly Water-Soluble Tetrazolium Salt, Neutral Red and Crystal Violet. (1996)

Cell viability and in vitro cytotoxicity assay methods were developed using a combination of dyes, 4-[3-(4-iodophenyl)-2-(4-nitrophenyl)-2H-5-tetrazolio]-1,3-benzene disulfonate (WST-1), neutral red (NR) and crystal violet (CV), with HeLa cells as a bioindicatior. As WST-1 produces a highly water soluble and non-cytotoxic formazan dye, ti allows each assay to be carried out in one culture dish. The combined cell viability assay using WST-1, NR and CV gave an absorbance that correlated linearly with the number of cells over the range 1000 to 50,000 cells/well. The combined assay was applied to the evaluation of IC50 values for sodium dodecyl sulfate as a model toxicant, which yielded similar values to those obtained with each assay independently.
Distinction of Tris(diimine)ruthenium(II) enantiomers chiral by virtue of helical chirality: temperature‐dependent deuterium NMR spectroscopy in partially oriented phases (2006)

2H NMR spectra of perdeuterated tris(diimine)ruthenium(II) complexes have been recorded in lyotropic liquid crystalline phase formed by the chiral polypeptide, poly-gamma-benzyl-L-glutamate (PBLG) and co-solvents. It is demonstrated that the left- and right-rotation isomers of these octahedral metal complexes with D3 symmetry can be distinguished. The effects of temperature and ligand size on spectral resolution were also studied. Although in the case of free bipyridine ligands excellent optical resolution could be obtained at room temperature in the complexes studied, the increase in ligand size has a detrimental effect on the resolution. This can be compensated to some extent by elevating the sample temperature and decreasing the deuterium relaxation rates, but the available temperature range and therefore the applicability of the technique are limited.