gebhart/patrepeval huggingface dataset:
Time-Frequency Transforms for Radar Imaging and Signal Analysis (2002)

Introduction: radar electronic backscattering radar signals radar ambiguity function and matched filter synthetic aperture radar imaging. Time-frequency transforms: linear transforms bilinear transforms. Detection and extraction of signal noise: time-varying frequency filtering SNR improvement in time-frequency domain CFAR detection in joint time-frequency domain signal extraction in joint time-frequency domain. Time-frequency analysis of radar range profiles: electromagnetic phenomenology embedded in backscattered data time-frequency representation of range profiles application of high-resolution time-frequency techniques to scattering data extraction of dispersive scattering features from radar imagery using time-frequency processing. Time-frequency based image formation: radar imaging of moving targets motion compensation time-frequency based image formation radar imaging of manoeuvring targets radar imaging of multiple targets. Motion compensation in inverse synthetic aperture radar imaging using time-frequency techniques: motion compensation algorithms time-frequency based motion compensation motion compensation examples of simulated and measured data presence of three-dimensional target motion. Synthetic aperture radar imaging of moving target: radar signatures of moving targets effect of target motion on SAR imaging detection and imaging of moving targets SAR imaging of moving targets using time-frequency transforms. Time-frequency transform for analysis of micro-doppler phenomena: vibration induced micro-doppler rotation induced micro-doppler examples. Trends in time-frequency transforms for radar applications.
From Alzheimer's disease to skin tumors: The catenin connection (2001)

Proceedings of the National Academy of Sciences (PNAS), a peer reviewed journal of the National Academy of Sciences (NAS) - an authoritative source of high-impact, original research that broadly spans the biological, physical, and social sciences.
The Basic Principles of Chimeric Antigen Receptor Design (2013)

CARs are a new class of drugs with great potential for cancer immunotherapy. Upon their expression in T lymphocytes, CARs direct potent, targeted immune responses that have recently shown encouraging clinical outcomes in a subset of patients with B-cell malignancies. This review focuses on the design of CARs, including the requirements for optimal antigen recognition and different modalities to provide costimulatory support to targeted T cells, which include the use of second- and third generation CARs, costimulatory ligands, chimeric costimulatory receptors, and cytokines.
Inability of truncated recombinant Osp A proteins to elicit protective immunity to Borrelia burgdorferi in mice. (1993)

The murine immune response to Borrelia burgdorferi (Bb), the etiologic agent of Lyme disease, is characterized by the development of antibodies reactive with the outer surface protein (Osp) A. It has been demonstrated that passive immunization of mice with at least some Osp A antibodies, including an Osp A mAb (CIII.78) that binds to a conformational epitope in the carboxyl-terminus of Osp A, provides protection against Bb challenge. Active immunization of mice with Osp A also confers protection, making Osp A a candidate for a vaccine Ag. To determine the regions of the Osp A protein that can elicit protective immunity, we immunized boosted mice with overlapping recombinant truncated fragments of Osp A, then challenged them with Bb. All groups of mice developed IgG Osp A antibodies detectable by immunoblotting with sera diluted at least 5000-fold. As expected, vaccination with full-length recombinant Osp A protected mice from challenge infection. In contrast, none of the mice vaccinated with the truncated Osp A proteins demonstrated immunity, even those immunized with an Osp A fragment binding the neutralizing mAb CIII.78. Osp A antibodies contained in the truncated Osp A antisera also failed to immunoprecipitate in vitro translated full-length Osp A and did not bind, as demonstrated by indirect immunofluorescence, to live or acetone-fixed Bb. Taken together, these results suggest that neutralizing Osp A antibodies are induced by vaccination with the full-length recombinant Osp A protein but not by vaccination with recombinant fragments.
Activity-dependent Neuroprotective Protein Constitutes a Novel Element in the SWI/SNF Chromatin Remodeling Complex (2007)

Complete deficiency in activity-dependent neuroprotective protein (ADNP), a heterochromatin 1-binding protein, results in dramatic changes in gene expression, neural tube closure defects, and death at gestation day 9 in mice. To further understand the cellular roles played by ADNP, the HEK293 human embryonic kidney cell line that allows efficient transfection with recombinant DNA was used as a model for the identification of ADNP-interacting proteins. Recombinant green fluorescent protein (GFP)-ADNP was localized to cell nuclei. When nuclear extracts were subjected to immunoprecipitation with specific GFP antibodies followed by polyacrylamide gel electrophoresis, several minor protein bands were observed in addition to GFP-ADNP. In-gel protein digests followed by mass spectrometry identified BRG1, BAF250a, and BAF170, all components of the SWI/SNF (mating type switching/sucrose nonfermenting) chromatin remodeling complex, as proteins that co-immunoprecipitate with ADNP. These results were verified utilizing BRG1 antibodies. ADNP short hairpin RNA down-regulation resulted in microtubule reorganization and changes in cell morphology including reduction in cell process formation and cell number. These morphological changes are closely associated with the SWI/SNF complex multifunctionality. Taken together, the current study uncovers a molecular basis for the essential function of the ADNP gene and protein.
A Review of Biomedical Centrifugal Microfluidic Platforms (2016)

Centrifugal microfluidic or lab-on-a-disc platforms have many advantages over other microfluidic systems. These advantages include a minimal amount of instrumentation, the efficient removal of any disturbing bubbles or residual volumes, and inherently available density-based sample transportation and separation. Centrifugal microfluidic devices applied to biomedical analysis and point-of-care diagnostics have been extensively promoted recently. This paper presents an up-to-date overview of these devices. The development of biomedical centrifugal microfluidic platforms essentially covers two categories: (i) unit operations that perform specific functionalities, and (ii) systems that aim to address certain biomedical applications. With the aim to provide a comprehensive representation of current development in this field, this review summarizes progress in both categories. The advanced unit operations implemented for biological processing include mixing, valving, switching, metering and sequential loading. Depending on the type of sample to be used in the system, biomedical applications are classified into four groups: nucleic acid analysis, blood analysis, immunoassays, and other biomedical applications. Our overview of advanced unit operations also includes the basic concepts and mechanisms involved in centrifugal microfluidics, while on the other hand an outline on reported applications clarifies how an assembly of unit operations enables efficient implementation of various types of complex assays. Lastly, challenges and potential for future development of biomedical centrifugal microfluidic devices are discussed.
Altering the biochemical state of individual cultured cells and organelles with ultramicroelectrodes (1998)

We describe an efficient technique for the selective chemical and biological manipulation of the contents of individual cells. This technique is based on the electric-field-induced permeabilization (electroporation) in biological membranes using a low-voltage pulse generator and microelectrodes. A spatially highly focused electric field allows introduction of polar cell-impermeant solutes such as fluorescent dyes, fluorogenic reagents, and DNA into single cells. The high spatial resolution of the technique allows for design of, for example, cellular network constructions in which cells in close contact with each other can be made to possess different biochemical, biophysical, and morphological properties. Fluorescein, and fluo-3 (a calcium-sensitive fluorophore), are electroporated into the soma of cultured single progenitor cells derived from adult rat hippocampus. Fluo-3 also is introduced into individual submicrometer diameter processes of thapsigargin-treated progenitor cells, and a plasmid vector cDNA construct (pRAY 1), expressing the green fluorescent protein, is electroporated into cultured single COS 7 cells. At high electric field strengths, observations of dye-transfer into organelles are proposed.
BAFF and APRIL: A Tutorial on B Cell Survival (2003)

BAFF, a member of the TNF family, is a fundamental survival factor for transitional and mature B cells. BAFF overexpression leads to an expanded B cell compartment and autoimmunity in mice, and elevated amounts of BAFF can be found in the serum of autoimmune patients. APRIL is a related factor that shares receptors with BAFF yet appears to play a different biological role. The BAFF system provides not only potential insight into the development of autoreactive B cells but a relatively simple paradigm to begin considering the balancing act between survival, growth, and death that affects all cells.
Disease Severity and Immune Activity Relate to Distinct Interkingdom Gut Microbiome States in Ethnically Distinct Ulcerative Colitis Patients (2016)

Despite years of research, the etiology of UC remains enigmatic. Diagnosis is difficult and the patient population heterogeneous, which represents a significant barrier to the development of more effective, tailored therapy. In this study, we demonstrate the clinical utility of the gut microbiome in stratifying UC patients by identifying the existence of four distinct interkingdom pathogenic microbiotas within the UC patient population that are compositionally and metabolically distinct, covary with clinical markers of disease severity, and drive discrete CD4(+) T-cell expansions ex vivo These findings offer new insight into the potential value of the gut microbiome as a tool for subdividing UC patients, opening avenues to the development of more personalized treatment plans and targeted therapies.
Synthesis of stereoregular ROMP polymers using molybdenum and tungsten imido alkylidene initiators (2011)

Three of the four possible structures for polymers formed from an achiral monomer through a single ROMP polymerization step have been prepared for a small collection of monomers. Trans,syndiotactic structures have been prepared through chain end control, cis,isotactic polymers have been prepared through enantiomorphic site control, and cis,syndiotactic polymers have been prepared through stereogenic metal control. Stereogenic metal control at the metal center as a means of forming syndiotactic polymers is virtually unknown. Synthesis of ROMP polymers with a regular structure that contain alternating enantiomers from a racemic mixture of monomers is a natural consequence of stereogenic metal control. Ruthenium catalysts do not display ROMP specificities analogous to those described here, perhaps since alkylidene isomers have not been observed for Ru catalysts and the barrier to rotation of the carbene in a generic NHC dichloride Ru catalyst has been calculated to be relatively low.
Identification of a single nucleotide change in the hypoxanthine-guanine phosphoribosyltransferase gene (HPRTYale) responsible for Lesch-Nyhan syndrome. (1989)

Complete deficiency of hypoxanthine-guanine phosphoribosyltransferase (HPRT) causes the Lesch-Nyhan syndrome. Previous characterization of a mutant form of HPRT, HPRTYale, from a subject with the Lesch-Nyhan syndrome revealed normal mRNA and protein concentrations, no residual catalytic activity, and cathodal migration upon PAGE. We have cloned and sequenced HPRTYale cDNA. The nucleotide sequence of full-length HPRTYale cDNA revealed a single nucleotide substitution compared with normal HPRT cDNA: G----C at nucleotide position 211. This transversion predicts substitution of arginine for glycine at amino acid position 71, explaining the cathodal migration of HPRTYale. Chou-Fasman secondary structure analysis predicts a change in the probability of beta-turn formation in the region containing the mutation. Inclusion of the bulky arginine side chain in place of glycine probably disrupts protein folding as well. Cloning mutant forms of cDNA allows identification of specific mutations, provides insight into mutational mechanisms, and facilitates structure-function analysis of mutant proteins.
FAK overexpression is correlated with tumour invasiveness and lymph node metastasis in oesophageal squamous cell carcinoma (2003)

Focal adhesion kinase (p125(FAK); 'FAK') is a tyrosine kinase that is localised to cellular focal adhesions and is associated with a number of other proteins, such as integrin adhesion receptors. We performed an immunohistochemical analysis of FAK protein expression to determine the relationship between FAK overexpression and clinicopathological factors in oesophageal squamous cell carcinoma (ESCC). We examined tissue specimens that had been removed from 91 patients with thoracic oesophageal cancer who had undergone surgery between 1983 and 2001. Immunohistochemical staining was performed by the standard streptavidin-biotin method. Seven human ESCC cell lines-TE-1, TE-2, TE-8, TE-13, TE-15, TT, and TTn-and one immortalized human keratinocyte cell line-HaCaT-were used in Western blot analysis. Immunostaining of FAK was seen in the cytoplasm of cancer cells, particularly in cells located in the invasive fronts of cancer nests. FAK overexpression was detected in 54 of the 91 patients (59.3%). Significant correlations were observed between FAK overexpression and cell differentiation (P=0.0057), depth of tumour invasion (P=0.0023), presence of regional lymph node metastasis (P=0.0097), number of lymph node metastases (P=0.0026), and disease stage (P=0.012). The survival rates of patients with FAK-overexpressing cancer were significantly lower than those of patients without FAK-overexpression cancer (P=0.006). The 5-year survival rate of patients without FAK overexpression was 69%, whereas that of patients with FAK overexpression was 38%. On Western blot analysis, FAK was expressed at a high level in TE-1, TE-8, TE-15, and TT cells, at a moderate level in TE-2 and TTn cells, and at a low level in TE13 and HaCaT cells. FAK phosphorylation at tyrosine 397 was demonstrated in proportion to the intensity of FAK in all cell lines except TE15 and HaCaT. In conclusion, FAK overexpression of ESCC was related to cell differentiation, tumour invasiveness, and lymph node metastasis. Consequently, patients with ESCC who had FAK overexpression had a poor prognosis.
[Expression of androgen receptor in breast carcinoma and its relationship with estrogen receptor, progesterone receptor and HER2 status]. (2010)

AR has a high positive rate in breast carcinoma, and may be an ideal therapeutic target for breast carcinoma, especially for the triple negative subtype.
DNA double strand break repair via non-homologous end-joining. (2013)

DNA double-stranded breaks (DSB) are among the most dangerous forms of DNA damage. Unrepaired DSBs results in cells undergoing apoptosis or senescence whereas mis-processing of DSBs can lead to genomic instability and carcinogenesis. One important pathway in eukaryotic cells responsible for the repair of DSBs is non-homologous end-joining (NHEJ). In this review we will discuss the interesting new insights into the mechanism of the NHEJ pathway and the proteins which mediate this repair process. Furthermore, the general role of NHEJ in promoting genomic stability will be discussed.
STAT3 Plays a Critical Role in KRAS -Induced Pancreatic Tumorigenesis (2011)

The STAT3 transcription factor is an important regulator of stem cell self-renewal, cancer cell survival, and inflammation. In the pancreas, STAT3 is dispensable for normal development, whereas the majority of pancreatic ductal adenocarcinomas (PDAC) show constitutive activation of STAT3, suggesting its potential as a therapeutic target in this cancer. Here, we sought to define the mechanisms of STAT3 activation and its functional importance in PDAC pathogenesis. Large-scale screening of cancer cell lines with a JAK2 inhibitor that blocks STAT3 function revealed a more than 30-fold range in sensitivity in PDAC, and showed a close correlation of sensitivity with levels of tyrosine-phosphorylated STAT3 and of the gp130 receptor, an upstream signaling component. Correspondingly, upregulation of the IL6/LIF-gp130 pathway accounted for the strong STAT3 activation in PDAC subsets. To define functions of STAT3 in vivo, we developed mouse models that test the impact of conditional inactivation of STAT3 in KRAS-driven PDAC. We showed that STAT3 is required for the development of the earliest premalignant pancreatic lesions, acinar-to-ductal metaplasia (ADM) and pancreatic intraepithelial neoplasia (PanIN). Moreover, acute STAT3 inactivation blocked PDAC initiation in a second in vivo model. Our results show that STAT3 has critical roles throughout the course of PDAC pathogenesis, supporting the development of therapeutic approaches targeting this pathway. Moreover, our work suggests that gp130 and phospho-STAT3 expression may be effective biomarkers for predicting response to JAK2 inhibitors.
Ultrahigh Frequency Carbon Nanotube Transistor Based on a Single Nanotube (2007)

Single-walled carbon nanotube field-effect transistors (CNT FETs) are predicted to have intrinsic cutoff frequencies approaching the THz range. Here ldquointrinsicrdquo means that the parasitic capacitance due to fringing fields is negligible compared to the gate-source capacitance required to modulate the conductance. In practice, although there are strategies proposed to mitigate this based on parallel arrays of CNT FETs, this parasitic capacitance dominates most geometries (even aligned arrays to date). In this work we show nanotube transistor performance with maximum stable gain above 1 GHz (even including the parasitics) by combining ldquoon-chiprdquo the electrical properties of 100 CNT FETs fabricated on one long nanotube. This also solves the problem of impedance matching by boosting the on current to a large (mA) value, and at the same time allows one to extract properties of each individual CNT FET, since they are identical in electrical characteristics as they are made out of the same CNT. This strategy opens the door to applications of carbon nanotube devices in the RF and microwave frequency range, a technologically relevant portion of the spectrum for both wired and wireless electronics, that has been (until now) incompatible with nanotube device technology.
Sequential SPECT and Optical Imaging of Experimental Models of Prostate Cancer with a Dual Modality Inhibitor of the Prostate‐Specific Membrane Antigen (2011)

One reagent for two techniques: Compound [111In]1 provides a platform for sequential radionuclide and optical imaging of prostate cancer through targeting of the prostate-specific membrane antigen. Because the same subject can be dual-imaged after one injection of the agent, these findings support rapid clinical translation. Detailed facts of importance to specialist readers are published as ”Supporting Information”. Such documents are peer-reviewed, but not copy-edited or typeset. They are made available as submitted by the authors. Please note: The publisher is not responsible for the content or functionality of any supporting information supplied by the authors. Any queries (other than missing content) should be directed to the corresponding author for the article.
Low-cost WDM passive optical network with directly-modulated self-seeding reflective SOA (2006)

A novel scheme facilitating self-seeding reflective semiconductor optical amplifiers as colourless upstream transmitters in a low-cost WDM-PON solution, eliminating centralised broadband sources and active temperature control, is experimentally demonstrated. A single passive broadband filter is used to reflect broadband ASE light from all transmitters for self-seeding. Direct modulation of the incoherent upstream channels shows no significant penalty after 21 km of transmission.
Analysis of production, purification, and cytolytic potential of bi‐specific antibodies reactive with ovarian‐carcinoma‐associated antigens and the T‐cell antigen CD3 (1993)

OV-TL3 and MOv 18 MAbs, due to their restricted specificity, have been successfully used to visualize ovarian cancer in patients and might therefore be used to develop therapies for ovarian cancer. The bi-specific MAbs alpha T3/OC2 and alpha OC/TR (both being combinations of MOv18 and alpha CD3) have been shown to lyse ovarian tumor cells in vitro. To evaluate the relative merits of MOv18/CD3 and OV-TL 3/CD3, the present study was undertaken in which the bi-specific MAbs alpha T3/OC2 and alpha OC/TR, and a newly developed bi-specific MAb, OV-TL 3/CD3, were highly purified and compared for specificity, stability, purification and cytolytic potential. The dual specificity of the hybrid-hybridoma supernatants was analyzed by immunohistochemistry, and by testing bi-specific MAb-mediated cytotoxicity against relevant target cells in the presence of effector cells. Stability testing of bi-specific MAb-producing hybridomas showed that, after sub-cloning, clones stably produced up to 40% bi-specific MAb even after prolonged in vitro culture. The purification of the bi-specific fractions was performed with protein A and by ion-exchange high-pressure liquid chromatography, depending on the sub-class combination of the bi-specific MAb. The purified bi-specific MAbs were tested for their ability to mediate target-cell lysis with the use of cytotoxic T-cell clones and activated peripheral-blood lymphocytes. The purified alpha T3/OC2, alpha OC/TR, and OV-TL3/CD3 were all able to mediate highly specific lysis of various ovarian-carcinoma cell lines. No correlation was found between the level of antigen expression and bi-specific MAb-mediated cytolysis.
Store depletion and calcium influx (1997)

Calcium influx in nonexcitable cells regulates such diverse processes as exocytosis, contraction, enzyme control, gene regulation, cell proliferation, and apoptosis. The dominant Ca2+ entry pathway in these cells is the store-operated one, in which Ca2+ entry is governed by the Ca2+ content of the agonist-sensitive intracellular Ca2+ stores. Only recently has a Ca2+ current been described that is activated by store depletion. The properties of this new current, called Ca2+ release-activated Ca2+ current (ICRAC), have been investigated in detail using the patch-clamp technique. Despite intense research, the nature of the signal that couples Ca2+ store content to the Ca2+ channels in the plasma membrane has remained elusive. Although ICRAC appears to be the most effective and widespread influx pathway, other store-operated currents have also been observed. Although the Ca2+ release-activated Ca2+ channel has not yet been cloned, evidence continues to accumulate that the Drosophila trp gene might encode a store-operated Ca2+ channel. In this review, we describe the historical development of the field of Ca2+ signaling and the discovery of store-operated Ca2+ currents. We focus on the electrophysiological properties of the prototype store-operated current ICRAC, discuss the regulatory mechanisms that control it, and finally consider recent advances toward the identification of molecular mechanisms involved in this ubiquitous and important Ca2+ entry pathway.