gebhart/patrepeval huggingface dataset:
Conformational Changes in Salivary Proline-Rich Protein 1 upon Adsorption to Calcium Phosphate Crystals (2007)

Conformational analyses of PRP1, a proline-rich acidic salivary protein and major component of the acquired enamel pellicle, have been carried out in solution and upon binding to two enamel prototypes, hydroxyapatite (HA) and carbonated hydroxyapatite (CHA), using Fourier transform infrared spectroscopy (FTIR) in attenuated total reflection (ATR) mode. We have shown for the first time that, in solution, large portions of PRP1 adopt the hydrated polyproline type II (PPII) helical structure in addition to the random coil structure, with the maximum absorbance of the amide I band around 1620 cm-1. Upon binding to HA or CHA, the protein undergoes significant conformational changes, loosing a considerable portion of hydrated PPII and random coil domains with a shift in the maximum absorbance to 1666 cm-1, indicating that a large fraction of the protein is composed of β turns. A small fraction of PPII in a calcium-bound or anhydrous form (∼1642 cm-1) was also observed in the HA- and CHA-bound proteins, which could play a role in protein−mineral interactions. The conformational changes in PRP1 adsorbed on CHA and HA were similar in nature; however, these changes were greater in the protein bound to HA. Interestingly, these results are in agreement with protein adsorption data that show that less protein is adsorbed onto CHA than onto HA. Our results demonstrate that binding to apatitic mineral surfaces leads to major conformational changes in PRP1, which might reflect the expulsion of water and the formation of protein−mineral and/or protein−protein interactions in the adsorbed layer.
Creation Of Patient Derived AML Xenografts Displaying Distinct Phenotypes and Geneotypes (2013)

Abstract We have recently successfully engrafted leukemic cells from bone marrow of several AML patients into immunocompromised NOD/SCID mice. One of them, AM7577, was reported in the last year ASH1. This model displayed typical aggressive AML disease of M5 subtype, which starts at bone marrow and gradually expand to peripheral (spleen, lymphonode and peripheral blood…). AM7577 also harbors interesting genotypes of mutations for IDH2-R140Q, FLT3-ITD, DNMT3A R882H and NPM1. Our second AML PDX model, AM8096, was established similarly using bone marrow from a recurrent patient with AML-M2 disease. AML8096 displayed similarly aggressive disease and the same 100% mortality, including typical symptoms (BW loss, hunched, inactivity, labored breathing, ruffled coat and eventual mortality) and with abundant leukemic cells in bone, etc. The leukemic cells can serially be passed in mice with 100% take-rate and cause consistent disease (even with &lt; 1e4 cells). This also creates a renewable and potentially unlimited source of leukemia cells. The leukemic cells in mice are identical to those of the original patient leukemic cells (CD45+, CD33+, CD13+, CD123+, and CD19-. However, some aspects of disease presentations are vastly different from that of AM7577. First, the peripheral symptom is significant less characterized by lower leukemic counts in peripheral blood and only slightly enlarged spleen and smaller lymphonode. Second, the leukemic cell morphology is also rather different with AM8096 demonstrating less differentiated phenotype. Third, the genotype, in contrast to AM7577, is wild-types for all the above oncogenes. While we have not identified the likely leukemogenesis driver gene for this model, we are currently performing RNAseq of AM8096, along with AM7577, in order to explore the underlying molecular mechanisms that drive both diseases. In addition, we are also investigating the drug response to standard of care (SOC), as compared to those AM7577. In summary, the two AML models could serve as useful experimental models to investigate the diverse leukemogenesis, including molecular mechanisms by genetic profiling. Ultimately, they can be used to help to identify new treatment strategies for AML. 1. Liu, e.a. A unique leukemia mouse model established from AML patient with IDH2 R140Q and FLT3-ITD mutations among other common AML mutations. ASH-2012 Annual Meeting (2012). Disclosures: Li: Crown Bioscience: Employment. Liu:Crown Bioscience: Employment. An:Crown Bioscience: Employment. Wu:Crown Bioscience: Employment. Cai:Crown Bioscience: Employment. Wery:Crown Bioscience: Employment.
OpenStreetSLAM: Global vehicle localization using OpenStreetMaps (2013)

In this paper we propose an approach for global vehicle localization that combines visual odometry with map information from OpenStreetMaps to provide robust and accurate estimates for the vehicle's position. The main contribution of this work comes from the incorporation of the map data as an additional cue into the observation model of a Monte Carlo Localization framework. The resulting approach is able to compensate for the drift that visual odometry accumulates over time, significantly improving localization quality. As our results indicate, the proposed approach outperforms current state-of-the-art visual odometry approaches, indicating in parallel the potential that map data can bring to the global localization task.
Vacuum field emission from a Si-TaSi2 semiconductor-metal eutectic composite (1991)

We report on measurements of vacuum field emission from ungated field emission cathode arrays fabricated from Si-TaSi2 eutectic composite wafers. The Si-TaSi2 material is an ideal candidate for large area field emission array cathodes due to the large density of TaSi2 fibers incorporated into the Si matrix, the high melting point of the TaSi2 material, the ease with which single-crystal large diameter (2.5 cm) material can be fabricated, and the promise of integrability of the field emission array with conventional Si technology through the use of epitaxial Si layers grown on the cathode backplane.
Tumour-associated antigens CEA, CA125, SCC and TPS in gynaecological cancer. (1998)

Pretreatment values of CEA, CA125, SCC and TPS were measured in 130 women with 1) ovarian carcinoma (n = 25), 2) breast cancer (n = 20), 3) endometrial cancer (n = 14), 4) cervical squamous cell carcinoma (n = 20), 5) cervical adenocarcinoma (n = 9) and 6) benign gynaecological diseases (n = 42) in order to evaluate the usefulness of multiple markers in diagnosing and monitoring patients with gynaecological cancer. Antigen values were significantly higher in the cancer groups than those in the benign one (p < 0.0001). CEA values were significantly elevated in the 2nd and 5th groups, CA125 in the 1st and 5th, SCC in the 4th and 5th, and TPS in the 1st, 2nd and 5th compared to the remaining groups (p < 0.04-p < 0.0001). In advanced stage diseases, significantly higher antigen values, except for SCC, than those in limited tumours were measured (p < 0.05-p < 0.0001). In conclusion, our results suggest that, multiple markers may be more efficient than the use of single markers in accurately identifying malignant from benign gynaecological diseases and in monitoring cancer patients.
The evolution of hydrocarbon pheromone parsimony in ants (Hymenoptera: Formicidae) – interplay of colony odor uniformity and odor idiosyncrasy. A review (2024)

Hydrocarbons are the main lipid constituents on the insect cuticle, and generally provide the insect with a waterproof layer to prevent desiccation. In many insects this class of chemicals has been coopted to serve as pheromones. In social insects, in particular in ants cuticular hydrocarbons (CHCs) have at least two pheromonal functions. They act as recognition cues that facilitate colony insularity, protecting it from parasites or conspecific invasions. Supporting evidence for this function are their extreme complexity, their colony specific composition, and in a few cases also demonstrating elevated or reduced aggression between encountering ants as a function of the label (alien or nestmate) they were painted with. The second function of CHCs is in signaling fertility. In many ant species it was demonstrated that fertile individuals (queens, gamergates, or egg laying workers) have CHC profiles that are distinct from that of their sterile nestmates. This can be expressed as the augmentation of a single or a small subset of the blend components, or differences in the entire blend. The fact that these signals have an abundance of branched alkanes, which lower the break point of cuticular impermeability thus imposing cost on the individual, indicates that these may constitute honest signals. This dual function seems contradictory since nestmate recognition necessitates a uniform colony odor, i.e., uniform CHC composition, whereas fertility signal requires idiosyncrasy since the fertile individual needs to be singled out among the colony members rather than conform to colony odor. A possible resolution is that species that use CHCs for nestmate recognition do not use them as fertility signals and vice versa. I propose an alternative solution whereby workers have variable discrimination thresholds and response to differences in the pheromone blend, large or small, in a contextdependent manner.
Identification and Characterization of Immunoglobulin G in Blood as a Major Inhibitor of Diagnostic PCR (2000)

ABSTRACT A major inhibitor of diagnostic PCR in human plasma was identified and the mechanism of inhibition was characterized. Human blood was divided by centrifugation into buffy coat, plasma, platelets, and erythrocytes. All these blood fractions were found to be highly inhibitory to a standardized PCR mixture containing the thermostable DNA polymerase Ampli Taq Gold. PCR inhibitors in human plasma were purified by chromatographic procedures and were characterized by a process of elimination, so that the PCR-inhibitory effects of plasma fractions were tested after each purification step. The major inhibitor in human plasma, as determined by size-exclusion chromatography, anion-exchange chromatography, and chromatofocusing, was found to be immunoglobulin G (IgG) on the basis of N-terminal amino acid sequencing and electrophoretic analysis of the purified polypeptide. When different concentrations of purified plasma IgG (PIgG) were added to PCR mixtures containing 11 different thermostable DNA polymerases and 1 ng of Listeria monocytogenes DNA as template DNA, the only polymerase that resisted inhibition was rTth . The inhibitory effect was reduced when PIgG was heated at 95°C before it was added to PCR or after the addition of excess nontarget DNA to the PCR mixture. However, heating of PIgG together with target DNA at 95°C was found to block the amplification. Inhibition by PIgG may be due to an interaction with single-stranded DNA, which makes the target DNA unavailable for 10 of the DNA polymerases tested. The results show the danger of using boiling as a method of sample pretreatment or using a hot start prior to PCR. The effect of plasma PCR inhibition could be removed by mixing plasma with DNA-agarose beads prior to amplification, while plasma PCR inhibitors were found to bind to the DNA-agarose beads.
Clinical experience with recombinant factor VIIa (1998)

Recombinant factor VIIa (rFVIIa) represents a major therapeutic advance in the treatment of haemophilia patients with inhibitors. The efficacy and safety of rFVIIa has been extensively studied in over 1900 surgical and non-surgical bleeding episodes in over 400 patients with haemophilia A or B (with or without inhibitors) or acquired haemophilia. Of 103 evaluable surgical bleeding episodes, the response to treatment with rFVIIa was considered to be either excellent or effective in 81%, 86% and 92% of major, minor and dental bleeding episodes, respectively. Treatment has been evaluated in 518 serious bleeding episodes and the response was considered either excellent or effective in 62% of muscle, 80% of ear, nose and throat, 88% of central nervous system, 76% of joint, and 75% of internal or retroperitoneal bleeding episodes. An excellent safety profile has also been demonstrated: of 1957 treatments with rFVIIa, only 16 serious adverse events have been reported that were considered to be possibly, but not necessarily, related to treatment.
AutoDock Vina: Improving the speed and accuracy of docking with a new scoring function, efficient optimization, and multithreading (2009)

AutoDock Vina, a new program for molecular docking and virtual screening, is presented. AutoDock Vina achieves an approximately two orders of magnitude speed-up compared with the molecular docking software previously developed in our lab (AutoDock 4), while also significantly improving the accuracy of the binding mode predictions, judging by our tests on the training set used in AutoDock 4 development. Further speed-up is achieved from parallelism, by using multithreading on multicore machines. AutoDock Vina automatically calculates the grid maps and clusters the results in a way transparent to the user.
Structure-based prediction of insertion-site preferences of transposons into chromosomes (2006)

Mobile genetic elements with the ability to integrate genetic information into chromosomes can cause disease over short periods of time and shape genomes over eons. These elements can be used for functional genomics, gene transfer and human gene therapy. However, their integration-site preferences, which are critically important for these uses, are poorly understood. We analyzed the insertion sites of several transposons and retroviruses to detect patterns of integration that might be useful for prediction of preferred integration sites. Initially we found that a mathematical description of DNAdeformability, called V step , could be used to distinguish preferential integration sites for Sleeping Beauty (SB) transposons into a particular 100 bp region of a plasmid [G.
A Mathematical Model of the Cardiac Chronotropic Response to Exercise (1989)

A mathematical model was developed from data collected from 410 normal subjects in order to describe the normal cardiac Chronotropic response to exercise. Subjects were examined by treadmill testing on either the Bruce protocol (189 patients) or the Chronotropic Assessment Exercise Protocol (CAEP) (221 patients), The CAEP, designed specifically for chronotropic assessment, is structured to collect heart rate data at submaximal as well as peak exercise intensities. Analysis of these subjects, without evidence of medical illness or cardiac medications, found the heart rate response to be a function of exercise intensity, age, resting heart rate, and maximal functional capacity. Heart rate reserve (HRR) was defined as the difference betii'een maximal predicted heart rate (MPHR) and resting heart (HR rest ). Metabolic reserve was defined as the difference between the maximally achieved workload (METS peak ) and the workload at rest (METS rest ). The Bruce and CAEP data provided a statistically linear and identical response of the form y = mx + b. The Bruce equation was %HRR = 0.95 ×%MR + 3.4 and the CAEP equation is %HRR = 0.94 ×%MR + 4.55. The following formula describes the normal predicted heart rate for an individual at some submaximal stage of exercise: HR stage = [(220 ‐ age ‐HR rest ) × (METS stage ‐ 1)/(METS peak ‐ 1)] + HR rest . We conclude that the cardiac chronotropic response can be modeled as a simple linear mathematical function of exercise intensity, age, resting heart rate, and maximal functional capacity, and is independent of type of treadmill exercise protocol in normal subjects.
Efficient Transcript Mapping to Ease the Creation of Document Image Segmentation Ground Truth with Text-Image Alignment (2010)

One of the major issues in document image processing is the efficient creation of ground truth in order to be used for training and evaluation purposes. Since a large number of tools have to be trained and evaluated in realistic circumstances, we need to have a quick and low cost way to create the corresponding ground truth. Moreover, the specific need for having the correct text correlated with the corresponding image area in text line and word level makes the process of ground truth creation a difficult, tedious and costly task. In this paper, we introduce an efficient transcript mapping technique to ease the construction of document image segmentation ground truth that includes text-image alignment. The proposed text line transcript mapping technique is based on Hough transform that is guided by the number of the text lines. Concerning the word segmentation ground truth, a gap classification technique constrained by the number of the words is used. Experimental results prove that using the proposed technique for handwritten documents, the percentage of time saved for ground truth creation and text-image alignment is more than 90%.
Murine thrombosis models (2004)

Due to exciting advances in molecular biology, the laboratory mouse has become an important and frequently used model for studying thrombosis. This article reviews several experimental approaches that have been used to study arterial, venous, and microvascular thrombosis in mice. The advantages and limitations of different models are examined. Related topics of mouse anesthesia, phlebotomy, and in vitro hemostasis testing are also reviewed.
Synthesis of Band-Limited Orthogonal Signals for Multichannel Data Transmission (1966)

This paper presents a principle of orthogonal multiplexing for transmitting a number of data messages simultaneously through a linear band-limited transmission medium at a maximum data rate without interchannel and intersymbol interferences. A general method is given for synthesizing an infinite number of classes of band-limited orthogonal time functions in a limited frequency band. Stated in practical terms, the method permits the synthesis of a large class of practical transmitting filter characteristics for an arbitrarily given amplitude characteristic of the transmission medium. Rectangular-shaped ideal filters are not required. The synthesis procedure is convenient. Furthermore, the amplitude and the phase characteristics of the transmitting filters can be synthesized independently. Adaptive correlation reception can be used for data processing, since the received signals remain orthogonal no matter what the phase distortion is in the transmission medium. The system provides the same signal distance protection against channel noises as if the signals of each channel were transmitted through an independent medium and intersymbol interference in each channel were eliminated by reducing data rate.
Geomorphology – Understanding the Near-surface Impact on Seismic Data (2009)

Surface seismic data are significantly affected by the properties of the near-surface strata. We propose to integrate information extracted from geomorphology into the seismic processing workflow. Topography classification of the elevation and lithology information of satellite imagery allows mapping formation tops, which in turn, provide the basis for 3D near-surface modelling. The lithology class map can be converted into a surface velocity map for the estimation of coherent noise velocities. The 3D geologic model can be converted into an elastic model using standardized velocities. The result is a model of the statics estimates, which can be generated prior to data acquisition. The comparison of the model with refraction statics from data processing reveals that the estimate matches the refraction statics in areas with homogeneous surface lithology. In terrain with heterogeneous surface lithology such as isolated limestone ridges and steep cliffs with rapidly changing lithology, differences are observed, which are yet to be explained.
Protocols for Adaptive Wireless and Mobile Networking (1996)

this article, we give a status report of our current work in the Monarch Project, placing it in the context of broader efforts by the Internet mobile networking community. Our work will enable mobile hosts to communicate with each other and with stationary or wired hosts, transparently making the most efficient use of the best network connectivity available to the mobile host at any time. To this end, the networking protocols must support adaptive operation in a number of ways. For example, host mobility means that protocols must be able to adapt packet routing to reach each mobile host in its current location. In addition, different wireless networks, intended for example for local-area, metropolitan-area, and wide-area use, make different tradeoffs in factors such as bandwidth, latency, error rate, and usage cost, providing different levels of quality of network connection with each wireless networking product or service. Network protocols should be able to adapt to optimize use of the best available network connection for each mobile host at any time. Further, in order to allow higher-layer protocols and applications to adapt to these changes in network connection quality, network protocols should be able to provide information to higher layers when such changes take place. We are experimenting with our protocols in the context of the &amp;quot;Wireless Andrew&amp;quot; infrastructure,currently being built at Carnegie Mellon [10]. The Wireless Andrew infrastructure builds on the current wired network infrastructure on campus, consisting mostly of 10-megabit per second Ethernet equipment. For high-speed wireless access on campus, we are installing an AT&amp;amp;T WaveLAN network covering most of the campus buildings [32]. WaveLAN uses direct-sequence spread spectrum radio in the 900 MHz ISM ba...
State-outcome consistency in smoking relapse crises: A reversal theory approach. (1991)

Previous investigations of smoking relapse crises have found limited within-subject consistency. Several investigators have suggested that greater consistency might be observed if situations were described phenomenologically. Reversal theory provides one phenomenological framework. Two relapse crises from each of 49 ex-smokers were compared, using reversal theory constructs. Maintaining abstinence in both crises was consistently associated with being in serious-minded (telic) and conformist states. Smoking in both crises was consistently associated with being in playful (paratelic) or negativistic states. Crises with different outcomes occurred in different state combinations. The findings suggest that coping strategies should be state-tailored for optimal effectiveness.
<title>Tomographic absorption spectroscopy of combustion gases using tunable infrared diode lasers</title> (1992)

A novel method was developed for tomographic combustion diagnostics using tunable infrared laser absorption spectroscopy. In this method complete spectral profiles are reconstructed rather than at one or a few frequencies. When compared to existing techniques, the new method needs much less prior infonnation about the sample gas and the spectroscopic behavior of the candidate spectral lines. Acklitionally, the new method is much more immune to interference and random noise. The method is demonstrated by CO2 measurements in an axisymmelric flame.