gebhart/patrepeval huggingface dataset:
Quantum limit of optical magnetometry in the presence of ac Stark shifts (2000)

We analyze systematic (classical) and fundamental (quantum) limitations of the sensitivity of optical magnetometers resulting from ac Stark shifts. We show that in contrast to absorption-based techniques, the signal reduction associated with classical broadening can be compensated in magnetometers based on phase measurements using electromagnetically induced transparency (EIT). However due to ac Stark--associated quantum noise the signal-to-noise ratio of EIT-based magnetometers attains a maximum value at a certain laser intensity. This value is independent on the quantum statistics of the light and defines a standard quantum limit of sensitivity. We demonstrate that an EIT-based optical magnetometer in Faraday configuration is the best candidate to achieve the highest sensitivity of magnetic-field detection and give a detailed analysis of such a device.
Selective inhibition of the cytopathic effect of type A influenza viruses by oligodeoxynucleotides covalently linked to an intercalating agent (1987)

Oligodeoxynucleotides covalently linked to an acridine derivative were targeted to part of the 3'-terminal sequence which is common to the eight RNAs of type A influenza viruses. The cytopathic effect of the virus on MDCK cells in culture was strongly decreased by a heptanucleotide covalently attached to the acridine ring. Control experiments using other oligonucleotide sequences showed that the effect was specific for the complementary sequence of the 3'-terminal region of the viral RNAs. The RNA transcriptase reaction of a type A virus was also selectively inhibited in vitro by the heptanucleotide-acridine conjugate. A type B influenza virus was used as a control. The common sequence at the 3' end of its eight viral RNAs is different from that of type A viruses. Three mismatches were expected with the heptanucleotide which was fully complementary to type A viral RNAs. This heptanucleotide had no effect on the cytopathic effect of a type B influenza virus. These results demonstrate that viral RNAs are specific targets for the oligonucleotide-acridine conjugate that inhibits the cytopathic effect of type A influenza viruses.
Photonic crystal structures with submicrometer spatial resolution achieved by high-power femtosecond laser-induced photopolymerization (2000)

We demonstrate in this paper a fabrication of three- dimensional microstructures using photopolymerization of resin by two-photon absorption. When a tightly focused laser beam was scanned in a light-curling liquid, solidified rods were formed following the trace of the scanning. If the solidification was arranged to occur along the frame of a microstructure, a designed spatial pattern would be transformed into material object. Due to a quadratic dependence of photopolymerization rate on the laser pulse energy, the size of solidified voxels was controlled down to submicrometer order. Infrared transmission measurement exhibited pronounced band gap effects from thus-fabricated photonic crystal structures.
Ferromagnetic Resonance Characterization of Magnetic Nanowires for Biolabel Applications (2018)

Ferromagnetic resonance (FMR) characterization is widely applied to extract dynamic magnetic properties from nanowires and thin films. This paper discusses the possibility of establishing a biomarker labeling system with ferromagnetic nanowires and coplanar waveguide (CPW) based FMR detection techniques. The results have validated the possibility and show the potential of ferromagnetic nanowire based biolabels.
Expression of bcl-2 in fetal tissues suggests a role in morphogenesis. (1993)

We have studied the distribution of the bcl-2 protein in fetal tissues, in an effort to uncover patterns of expression that may elucidate the potential role of bcl-2 during development. We find that bcl-2 is expressed in many hematolymphoid and non-hematolymphoid tissues, most abundantly in placental trophoblast. In tissues of endocrine and neural derivation and in stem-cell populations of colonic and some stratified epithelia, bcl-2 seems to be involved in tissue homeostasis. However, in developing proximal nephrons of the kidney and other sites characterized by inductive interactions between epithelium and mesenchyme, bcl-2 is apparently involved in morphogenesis, possibly by mediating the formation of condensations of cells that are "committed" to the formation of more differentiated structures. The distribution of bcl-2-protein expression in fetal tissues is consistent with its previously described role in promoting cell survival, presumably by preventing apoptosis in lymphoid and other tissues where cell death represents an active regulatory process. Expression of bcl-2 protein is more widespread in fetal than adult tissues. Our observations therefore represent supportive evidence for the importance of inducible cell survival as a regulatory process in normal homeostasis and morphogenesis in many fetal tissues and structures.
DNA RECOGNITION BY PROTEINS WITH THE HELIX-TURN-HELIX MOTIF (1990)

The Hippo pathway was initially discovered in Drosophila melanogaster as a key regulator of tissue growth. It is an evolutionarily conserved signaling cascade regulating numerous biological processes, including cell growth and fate decision, organ size ...Read More
The Navigation Potential of Signals of Opportunity-Based Time Difference of Arrival Measurements (2005)

This research introduces the concept of navigation potential, NP, to quantify the intrinsic ability to navigate using a given signal. NP theory is a new, information theory-like concept that provides a theoretical performance limit on estimating navigation parameters from a received signal that is modeled through a stochastic mapping of the transmitted signal and measurement noise. NP theory is applied to SOP-based TDOA systems in general as well as for the Gaussian case. Furthermore, the NP is found for a received signal consisting of the transmitted signal, multiple delayed and attenuated replicas of the transmitted signal, and measurement noise. Multipath-based NP captures the dominant error source foreseen in SOP-based navigation systems and may be more indicative of actual system performance than non-multipath-based metrics. NP theory applies to signals other than SOP. As an example, NP is used to bound GPS correlation error performance for the multipath and no-multipath case.
Purification and characterization of an extracellular peptide factor that affects two different developmental pathways in Bacillus subtilis. (1996)

We have purified and characterized an extracellular peptide factor that serves as a cell density signal for both competence development and sporulation in Bacillus subtilis. This competence and sporulation stimulating factor (CSF) was purified from conditioned medium (culture supernatant) based on its ability to stimulate expression of srfA (comS) in cells at low cell density. CSF is a 5-amino-acid peptide, glu-arg-gly-met-thr (ERGMT), that is, the carboxy-terminal 5 amino acids of the 40-amino-acid peptide encoded by phrC. No detectable CSF was produced in a phrC null mutant. The activity of chemically synthesized CSF (ERGMT) was virtually indistinguishable from that of CSF that was purified from culture supernatants. At relatively low concentrations (1-10 nM), CSF stimulated expression of srfA, whereas high concentrations of CSF stimulated the ability of cells at low cell density to sporulate. Stimulation of srfA expression by CSF requires the oligopeptide permease encoded by spo0K, a member of the ATP-binding-cassette family of transporters, and the putative phosphatase encoded by rapC, the gene immediately upstream of phrC. RapC was found to be a negative regulator of srfA expression, suggesting that the target of RapC is the transcription factor encoded by comA. We propose that CSF is transported into the cell by the Spo0K oligopeptide permease and stimulates competence gene expression by inhibiting (either directly or indirectly) the RapC phosphatase.
Carrier-induced suppression of the antibody response to a 'self' hapten. (1991)

Immunization of male rats and monkeys with gonadotropin-releasing hormone (GnRH) conjugated to a carrier results in a dramatic atrophy of the prostate. GnRH, linked to either diphtheria toxoid or tetanus toxoid as carrier, is now being evaluated for its use in the immunotherapy of hormone-dependent prostate enlargement in men. This report deals with the phenomenon of carrier-induced, epitope-specific regulation in the GnRH-carrier system. In experiments designed to assess the influence of the carrier on antibody responses to the 'self' hapten GnRH, we show that preimmunization with carriers diphtheria toxoid and tetanus toxoid results in a strain-dependent inhibition of anti-GnRH responses in mice. Results of adoptive transfer experiments indicate that T cells from carrier-presensitized mice are responsible for suppression of anti-haptenic antibodies and that T cells from conjugate-immunized mice, on the other hand, can actually help overcome hyporesponsiveness.
Artificial Chemokines: Combining Chemistry and Molecular Biology for the Elucidation of Interleukin-8 Functionality (2008)

How can we understand the contribution of individual parts or segments to complex structures? A typical strategy to answer this question is simulation of a segmental replacement followed by realization and investigation of the resulting effect in structure-activity studies. For proteins, this problem is commonly addressed by site-directed mutagenesis. A more general approach represents the exchange of whole secondary structure elements by rationally designed segments. For a demonstration of this possibility we identified the alpha-helix at the C-terminus of human interleukin-8 (hIL-8). Since this chemokine possesses four conserved cysteine residues, it can easily be altered by ligation strategies. A set of different segments, which are able to form amphiphilic helices, was synthesized to mimic the C-terminal alpha-helix. Beside sequences of alpha-amino acids, oligomers of non-natural beta(3)-amino acids with the side chains of canonical amino acids were introduced. Such beta-peptides form helices, which differ from the alpha-helix in handedness and dipole orientation. Variants of the semisynthetic hIL-8 proteins demonstrated clearly that the exact side chain orientation is of more importance than helix handedness and dipole orientation. The activity of a chimeric protein with a beta-peptide helix that mimics the side chain orientation of the native alpha-helix most perfectly is comparable to that of the native hIL-8. Concepts like this could be a first step toward the synthesis of proteins consisting of large artificial secondary structure elements.
Recent Results on the Biology of Hodgkin and Reed-Sternberg cells: II. Continuous Cell Lines (1993)

The relative scarcity of Hodgkin (H) and Reed-Sternberg (RS) cells within biopsies from cases with Hodgkin's disease (HD) is an impediment to the analysis of the nature and function of these cells. Continuous cell lines as uniform and permanently available sources of cells provide a valid alternative. Development of HD cell lines has proven to be rather difficult when compared with the results on leukemia and Non-Hodgkin lymphoma cells. Only a few cell lines containing cells that resemble in-vivo H-RS cells have been established. Because the in-vitro culture conditions favor the self-propagation of residual normal cells, e.g. Epstein-Barr virus transformed B-lymphoblastoid cells or monocyte/macrophage monolayers, early attempts at culturing HD tissue resulted mainly in the generation of such cell lines. Even for the bona fide HD cell lines it is difficult to prove that the immortalized cells originated from an H-RS cell. These 13 HD cell lines have been extensively characterized in a large variety of aspects. These data have resulted in widely varying conclusions about the nature of the cell lines. It is apparent that all HD cell lines are unique among hematopoietic cell lines and are also different from one another. No conclusive evidence towards the origin of the cells has been obtained for some cell lines, while others could be operationally, albeit not always unequivocally, assigned to the T- or B-cell or monocyte-macrophage lineages. The overall phenotypes are often not concordant with those of normal hematopoietic cells; some cell lines show clearly mixed lineage attributes. The artifactual expansion of non-HRS cells in culture and the acquisition or loss of certain properties during the adaptation to culture systems cannot be excluded. There was also a bias for the establishment of cell lines from cases with advanced clinical stages, nodular sclerosing subtype and pleural effusions. The extensive analysis of a few cell lines has provided a wealth of information useful for the understanding of the biology of H-RS cells. The striking heterogeneity could be reflective of a biologically heterogeneous disease.
The preclinical development of regorafenib for the treatment of colorectal cancer (2014)

In order to better predict the efficacy of kinase inhibitors and to utilize them more efficiently, our understanding of drug discovery, the approaches for kinase profiling, and technologies needed for their development are paramount. Indeed, the authors believe that the field should better explore the use of predictive biomarkers that might be able to better assess these therapeutics. Pharmaceutical scientists must also consider the cost effectiveness of the targeted agents developed as a number of the drugs developed are very expensive.
Speech-gesture driven multimodal interfaces for crisis management (2003)

Emergency response requires strategic assessment of risks, decisions, and communications that are time critical while requiring teams of individuals to have fast access to large volumes of complex information and technologies that enable tightly coordinated work. The access to this information by crisis management teams in emergency operations centers can be facilitated through various human-computer interfaces. Unfortunately, these interfaces are hard to use, require extensive training, and often impede rather than support teamwork. Dialogue-enabled devices, based on natural, multimodal interfaces, have the potential of making a variety of information technology tools accessible during crisis management. This paper establishes the importance of multimodal interfaces in various aspects of crisis management and explores many issues in realizing successful speech-gesture driven, dialogue-enabled interfaces for crisis management. This paper is organized in five parts. The first part discusses the needs of crisis management that can be potentially met by the development of appropriate interfaces. The second part discusses the issues related to the design and development of multimodal interfaces in the context of crisis management. The third part discusses the state of the art in both the theories and practices involving these human-computer interfaces. In particular, it describes the evolution and implementation details of two representative systems, Crisis Management (XISM) and Dialog Assisted Visual Environment for Geoinformation (DAVE/spl I.bar/G). The fourth part speculates on the short-term and long-term research directions that will help addressing the outstanding challenges in interfaces that support dialogue and collaboration. Finally, the fifth part concludes the paper.
Mobilization of bone marrow-derived stem cells after myocardial infarction and left ventricular function: simply effects of optimized drug treatment? (2005)

Mobilization of bone marrow-derived stem cells after myocardial infarction and left ventricular function: simply effects of optimized drug treatment?We read with interest the recent article by Leone et al. 1 regarding the mobilization of CD34 þ cells from bone marrow after myocardial infarction (MI) and the effects on left ventricular function.ACE-inhibitors and statins are administered on a routine basis to patients with acute MI and are likely to contribute to enhance levels of CD34 þ cells. 2,3Indeed, the present paper identifies the use of statins after MI as the best independent predictor of increased mobilization of stem cells.In animal models, however, Nygren et al. 4 were unable to detect any increase in peripheral blood progenitor or stem cell activity following MI when animals were without drug treatment.These findings could not be attributed to the trapping of potentially mobilized cells, as no progenitor cells were detected in the infarcted myocardium or in the spleen.Likewise, the findings of Leone et al. 1 that 1 year after MI the levels of CD34 þ cells were still three-fold higher when compared with the time before MI are difficult to explain by MI or acute release of inflammatory mediators which mobilize stem cells such as VEGF.We postulate that these findings are the result of an optimized drug therapy of patients following MI, including the use of statins, ACE-inhibitors, and other potentially stem cell-mobilizing agents.The finding of Leone et al. 1 that the amount of mobilized stem cells is highly variable and does not correlate to the size and severity of MI also points to a multimodal regulation of stem cell mobilization after MI.Interestingly, the finding that CD34 þ cell concentration was an independent predictor for global and regional improvement of the left ventricular function 1 year after MI, but not early after MI, may suggest that CD34 þ cells could be used as a diagnostic tool to identify patients with a high risk of developing heart failure after MI and who should therefore receive specifically intensive drug therapy.
Noninvasive mapping of human trigeminal brainstem pathways (2008)

The human trigeminal system mediates facial pain and somatosensory processing. The anatomic location of neuronal substrates and axonal pathways of the trigeminal system have previously been characterized with conventional in vitro methods. The present investigation implemented diffusion tensor imaging (DTI) and probabilistic tractography to first segment the peripheral trigeminal circuitry, trigeminal nerve branches (ophthalmic, maxillary, and mandibular nerves), ganglion, and nerve root. Subsequent segmentations involved the spinal trigeminal and trigeminal thalamic tracts, which respectively convey information to the spinal trigeminal nuclei and ventral thalamic regions. This latter procedure also identified 1) spinal thalamic (anterolateral [AL]) system pathways (propagating pain and temperature information from the body), 2) trigeminal lemniscus (TL; touch and face position), and 3) medial lemniscus (ML; touch and limb position). The anatomic location of the identified pain and somatosensory pathways compared well with previous functional findings in the human trigeminal system, as well as the tract position in human histological cross sections. Probabilistic tractography may be a useful method to further comprehend the functional and structural properties of trigeminal and other related systems. Application of DTI to map pain and somatosensory pathways in conjunction with a characterization of function properties of pain and somatosensory processing would further define the systematic changes that occur in trigeminal pathology.
Ribonucleoside Analogue That Blocks Replication of Bovine Viral Diarrhea and Hepatitis C Viruses in Culture (2002)

A base-modified nucleoside analogue, beta-D-N(4)-hydroxycytidine (NHC), was found to have antipestivirus and antihepacivirus activities. This compound inhibited the production of cytopathic bovine viral diarrhea virus (BVDV) RNA in a dose-dependant manner with a 90% effective concentration (EC(90)) of 5.4 microM, an observation that was confirmed by virus yield assays (EC(90) = 2 microM). When tested for hepatitis C virus (HCV) replicon RNA reduction in Huh7 cells, NHC had an EC(90) of 5 microM on day 4. The HCV RNA reduction was incubation time and nucleoside concentration dependent. The in vitro antiviral effect of NHC was additive with recombinant alpha interferon-2a and could be prevented by the addition of exogenous cytidine and uridine but not of other natural ribo- or 2'-deoxynucleosides. When HCV RNA replicon cells were cultured in the presence of increasing concentrations of NHC (up to 40 micro M) for up to 45 cell passages, no resistant replicon was selected. Similarly, resistant BVDV could not be selected after 20 passages. NHC was phosphorylated to the triphosphate form in Huh7 cells, but in cell-free HCV NS5B assays, synthetic NHC-triphosphate (NHC-TP) did not inhibit the polymerization reaction. Instead, NHC-TP appeared to serve as a weak alternative substrate for the viral polymerase, thereby changing the mobility of the product in polyacrylamide electrophoresis gels. We speculate that incorporated nucleoside analogues with the capacity of changing the thermodynamics of regulatory secondary structures (with or without introducing mutations) may represent an important class of new antiviral agents for the treatment of RNA virus infections, especially HCV.
The Emerging Role of EpCAM in Cancer and Stem Cell Signaling (2009)

Initially discovered as a dominant antigen on colon carcinomas, the epithelial cell adhesion molecule (EpCAM) was considered a mere cell adhesion molecule and reliable surface-binding site for therapeutic antibodies. Recent findings can better explain the relevance of EpCAM's high-level expression on human cancers and cancer propagating cells, and its negative prognostic potential for survival of patients with certain cancers. EpCAM has oncogenic potential and is activated by release of its intracellular domain, which can signal into the cell nucleus by engagement of elements of the wnt pathway.
Thoracic spinal cord stimulation improves functional status and relieves symptoms in patients with refractory angina pectoris: the first placebo-controlled randomised study (2007)

In this first placebo-controlled trial to apply SCS in patients with refractory angina, improvement in functional status and symptoms was revealed in phases with conventional or subthreshold stimulation, in comparison to a low-output (placebo) phase.
Demographic Estimation from Face Images: Human vs. Machine Performance (2014)

Demographic estimation entails automatic estimation of age, gender and race of a person from his face image, which has many potential applications ranging from forensics to social media. Automatic demographic estimation, particularly age estimation, remains a challenging problem because persons belonging to the same demographic group can be vastly different in their facial appearances due to intrinsic and extrinsic factors. In this paper, we present a generic framework for automatic demographic (age, gender and race) estimation. Given a face image, we first extract demographic informative features via a boosting algorithm, and then employ a hierarchical approach consisting of between-group classification, and within-group regression. Quality assessment is also developed to identify low-quality face images that are difficult to obtain reliable demographic estimates. Experimental results on a diverse set of face image databases, FG-NET (1K images), FERET (3K images), MORPH II (75K images), PCSO (100K images), and a subset of LFW (4K images), show that the proposed approach has superior performance compared to the state of the art. Finally, we use crowdsourcing to study the human perception ability of estimating demographics from face images. A side-by-side comparison of the demographic estimates from crowdsourced data and the proposed algorithm provides a number of insights into this challenging problem.