gebhart/patrepeval huggingface dataset:
Flocks, herds and schools: A distributed behavioral model (1987)

The aggregate motion of a flock of birds, a herd of land animals, or a school of fish is a beautiful and familiar part of the natural world. But this type of complex motion is rarely seen in computer animation. This paper explores an approach based on simulation as an alternative to scripting the paths of each bird individually. The simulated flock is an elaboration of a particle systems, with the simulated birds being the particles. The aggregate motion of the simulated flock is created by a distributed behavioral model much like that at work in a natural flock; the birds choose their own course. Each simulated bird is implemented as an independent actor that navigates according to its local perception of the dynamic environment, the laws of simulated physics that rule its motion, and a set of behaviors programmed into it by the "animator." The aggregate motion of the simulated flock is the result of the dense interaction of the relatively simple behaviors of the individual simulated birds.
Future vaccines against emerging encephalitides (2004)

The vaccine strategies available for control of emerging encephalitides range in a continuum from traditional approaches to those utilizing new technologies. In this report, we explore the use of live attenuated vaccines where the attenuating mutations have been selected in a rational way to improve attenuation without sacrificing effectiveness. A strategy for paired lethal and resuscitating mutations is presented that will greatly reduce the possibility of reversion to virulence. Finally, we describe an example of a vaccine vector system that could be rapidly adapted for use against these virus diseases as they emerge.
Robust Real-Time Visual Odometry with a Single Camera and an IMU (2011)

The increasing demand for real-time high-precision Visual Odometry systems as part of navigation and localization tasks has recently been driving research towards more versatile and scalable solutions.In this paper, we present a novel framework for combining the merits of inertial and visual data from a monocular camera to accumulate estimates of local motion incrementally and reliably reconstruct the trajectory traversed.We demonstrate the robustness and efficiency of our methodology in a scenario with challenging camera dynamics, and present a comprehensive evaluation against ground-truth data.
Biological applications of colloidal nanocrystals (2003)

Due to their interesting properties, research on colloidal nanocrystals has moved in the last few years from fundamental research to first applications in materials science and life sciences. In this review some recent biological applications of colloidal nanocrystals are discussed, without going into biological or chemical details. First, the properties of colloidal nanocrystals and how they can be synthesized are described. Second, the conjugation of nanocrystals with biological molecules is discussed. And third, three different biological applications are introduced: (i) the arrangement of nanocrystal–oligonucleotide conjugates using molecular scaffolds such as single-stranded DNA, (ii) the use of nanocrystal–protein conjugates as fluorescent probes for cellular imaging, and (iii) a motility assay based on the uptake of nanocrystals by living cells.
Analysis of Genome Plasticity in Pathogenic and Commensal Escherichia coli Isolates by Use of DNA Arrays (2003)

Genomes of prokaryotes differ significantly in size and DNA composition. Escherichia coli is considered a model organism to analyze the processes involved in bacterial genome evolution, as the species comprises numerous pathogenic and commensal variants. Pathogenic and nonpathogenic E. coli strains differ in the presence and absence of additional DNA elements contributing to specific virulence traits and also in the presence and absence of additional genetic information. To analyze the genetic diversity of pathogenic and commensal E. coli isolates, a whole-genome approach was applied. Using DNA arrays, the presence of all translatable open reading frames (ORFs) of nonpathogenic E. coli K-12 strain MG1655 was investigated in 26 E. coli isolates, including various extraintestinal and intestinal pathogenic E. coli isolates, 3 pathogenicity island deletion mutants, and commensal and laboratory strains. Additionally, the presence of virulence-associated genes of E. coli was determined using a DNA "pathoarray" developed in our laboratory. The frequency and distributional pattern of genomic variations vary widely in different E. coli strains. Up to 10% of the E. coli K-12-specific ORFs were not detectable in the genomes of the different strains. DNA sequences described for extraintestinal or intestinal pathogenic E. coli are more frequently detectable in isolates of the same origin than in other pathotypes. Several genes coding for virulence or fitness factors are also present in commensal E. coli isolates. Based on these results, the conserved E. coli core genome is estimated to consist of at least 3,100 translatable ORFs. The absence of K-12-specific ORFs was detectable in all chromosomal regions. These data demonstrate the great genome heterogeneity and genetic diversity among E. coli strains and underline the fact that both the acquisition and deletion of DNA elements are important processes involved in the evolution of prokaryotes.
Feasibility of Using Autologous Transplantation to Evaluate Hematopoietic Stem Cell-Based Gene Therapy Strategies in Transgenic Mouse Models of Human Disease (2002)

Histoincompatibility between murine donors and recipients of bone marrow (BM) transplants reduces engraftment, and this compromises assessment of hematopoietic stem cells (HSCs) in certain transgenic mice. To study HSCs in the S+S-Antilles mouse model of human sickle cell disease (SCD), we developed an autotransplant protocol. Initial experiments showed no differences between S+S-Antilles mice and normal C57BL/6 (+/+) mice in their radiosensitivity or baseline hematopoietic progenitor numbers. The kinetics of red blood cell (RBC) replacement post-transplant in +/+ recipients of mixtures of transgenic and +/+ BM cells also showed no competitive advantage of the +/+ cells. BM cells were then aspirated from mice 4 days after 5-fluorouracil treatment, transduced with a green fluorescent protein (GFP)-encoding retrovirus, and transplanted into the same recipients that, just before transplant, were irradiated with 800 cGy. We subsequently detected high levels of GFP(+) RBCs (21-79%) and white blood cells (WBCs; 35-88%) in the blood for 11 months and showed that transduced HSCs regenerated in the primary mice also repopulated secondary mice. These findings provide a generally applicable protocol for performing autotransplants in mice and forecast the potential utility of this approach in assessing HSC-based gene therapy protocols in transgenic mouse models of many human diseases.
β-catenin plays a key role in metastasis of human hepatocellular carcinoma (2011)

Currently, there are no diagnostic or metastatic markers that can be used in early diagnosis and treatment of human hepatocellular carcinoma (HCC). The aim of this study was to find a molecular marker that regulated migration and metastasis in HCC. We analyzed the gene expression of β-catenin, c-Myc and IL-8 in human HCC tissue by RT-PCR and immunohistochemistry and analyzed five variously differentiated HCC cell lines by Western blotting and migration and invasion assays to find markers for HCC diagnosis and HCC metastasis. mRNA expression of β-catenin was significantly higher in the tumor area compared to the non-tumor area and was more abundant in specimens of late-stage HCC. Immunohistochemistry revealed that the translocation of β-catenin into the nucleus was closely correlated with IL-8 protein levels and tumor stage. Similarly, the level of expression and nuclear translocation of β-catenin was greater in HA22T cells with high proliferative activity than in HCC cell lines with low proliferative activity (PLC, Hep3B, HepG2). Knockdown of the β-catenin gene with β-catenin antisense oligonucleotides resulted in inhibition of cell migration and invasion of HA22T cells. Taken together, these results suggest that β-catenin may be a suitable diagnostic marker of metastasis in human HCC.
A role for B cells in the development of T cell helper function in a malaria infection in mice (1998)

B cell knockout mice are unable to clear a primary erythrocytic infection of Plasmodium chabaudi chabaudi. However, the early acute infection is controlled to some extent, giving rise to a chronic relapsing parasitemia that can be reduced either by drug treatment or by adoptive transfer of B cells. Similar to mice rendered B-cell deficient by lifelong treatment with anti-mu antibodies, B cell knockout mice (muMT) retain a predominant CD4+ Th1-like response to malarial antigens throughout a primary infection. This contrasts with the response seen in control C57BL/6 mice in which the CD4+ T-cell response has switched to that characteristic of Th2 cells at the later stages of infection, manifesting efficient help for specific antibodies in vitro and interleukin 4 production. Both chloroquine and adoptive transfer of immune B cells reduced parasite load. However, the adoptive transfer of B cells resulted in a Th2 response in recipient muMT mice, as indicated by a relative increase in the precursor frequency of helper cells for antibody production. These data support the idea that B cells play a role in the regulation of CD4+ T subset responses.
Small‐Molecule Stabilization of Protein–Protein Interactions: An Underestimated Concept in Drug Discovery? (2012)

The modulation of protein-protein interactions (PPIs) has been recognized as one of the most challenging tasks in drug discovery. While their systematic development has long been considered as intractable, this view has changed over the last years, with the first drug candidates undergoing clinical studies. To date, the vast majority of PPI modulators are interaction inhibitors. However, in many biological contexts a prolonged lifespan of a PPI might be desirable, calling for the complementary approach of PPI stabilization. In fact, nature offers impressive examples of this concept and some PPI-stabilizing natural products have already found application as important drugs. Moreover, directed small-molecule stabilization has recently been demonstrated. Therefore, it is time to take a closer look at the constructive side of modulating PPIs.
The release of adenosine and inosine from canine subcutaneous adipose tissue by nerve stimulation and noradrenaline. (1981)

1. Plasma and adipose tissue purine nucleosides were assayed by reversed phase high-performance liquid chromatography after purification of the samples on phenylboronate affinity gel. 2. The adenosine content of unstimulated subcutaneous adipose tissue was close to 1 n-mole/g. The concentrations of adenosine and inosine in canine arterial plasma were 0.26 +/- 0.03 and 0.16 +/- 0.03 microM, respectively. In venous plasma from the canine subcutaneous adipose tissue the corresponding values were 0.32 +/- 0.04 and 0.28 +/- 0.06 microM under basal conditions. The arterio-venous concentration difference of adenosine was linearly dependent upon the arterial adenosine concentration. At arterial concentrations below 0.3 microM there was a net production of adenosine; above 0.3 microM there was a net extraction of approximately 77% of the adenosine. Adenosine was extensively eliminated in blood. The major part of this elimination could be accounted for by metabolism to inosine, hypoxanthine and uric acid. 3. Following sympathetic nerve stimulation (4 Hz for 20 min) the rate of adenosine outflow from adipose tissue increased from 0.33 +/- 0.22 to a peak value of 1.2 +/- 0.26 n-mole/min. This corresponds to a net release of 8.7 +/- 3.0 n-mole/100 g tissue. Inosine outflow rose from 0.64 +/- 0.37 to 5.3 +/- 1.4 n-mole/min, corresponding to a net release of 24.6 4/- 8.7 n-mole/100 g. Nerve stimulation also increased the release of [3H]purines from [3H]adenine pre-labelled adipose tissue. The fractional release increased 15-fold after stimulation. The radioactivity was mainly in the form of hypoxanthine, inosine and uric acid while adenosine was a minor component. When metabolism in blood was inhibited by dipyridamole and an adenosine deaminase inhibitor nerve-stimulation-induced release of [3H]purines was mainly in the form of adenosine. 4. Noradrenaline injection also induced a release of radioactive purines and of inosine. On the other hand, the outflow of endogenous adenosine was very small. 5. The present results demonstrate that under basal conditions adenosine is present in arterial and venous canine plasma. The free extracellular tissue level may be similar to the basal arterial adenosine concentration. Sympathetic nerve stimulation and noradrenaline induces a marked release of adenosine which is rapidly metabolized in the tissue and blood stream to inosine, hypoxanthine and uric acid. In adipose tissue the levels of adenosine reached after adrenergic stimulation appear high enough to be of physiological relevance.
[History of the development and functional description of the Nucleus cochlear implant]. (1994)

For deaf children and adults who derive no significant benefit from conventional hearing aids the cochlear implant (CI) has become a clinically accepted alternative. More than 7,000 people worldwide, including over 2,000 children, have received the 22 channel Nucleus Mini System during the last decade. The functional principle of the CI is the translation of acoustic sound signals into electrical impulses for direct stimulation of the hearing nerve. The middle ear and the damaged sensory organ of the inner ear are completely bypassed. The function of the healthy ear is replaced by a microphone, an electronic speech processor, and stimulation electrodes. Approximately two thirds of the postlingually deafened CI users achieve open set speech understanding without lipreading through the Nucleus implant. The Nucleus system is a programmable digital device and is continuously being improved in terms of both performance and ease of use. It is the only CI system with FDA approval for use in both adults and children from 2 years of age. Over 100 European clinics in more than 20 countries are carrying out successful CI programs with the Nucleus device in compliance with strict pre- and postsurgical diagnostic and rehabilitative guidelines. In Austria it was introduced to the Landeskrankenanstalten Salzburg in 1992. A successful program, including specialized rehabilitation, is carried on in close cooperation with the world's largest Cochlear Implant Center in Hannover, Germany.
Detecting and resolving packet filter conflicts (2002)

Packet filters are rules for classifying packets based on their header fields. Packet classification is essential to routers supporting services such as quality of service (QoS), virtual private networks (VPNs), and firewalls. A filter conflict occurs when two or more filters overlap, creating an ambiguity in packet classification. Current techniques for resolving filter conflicts are based on prioritizing conflicting filters, and choosing the higher priority filter. We show that such ordering does not always work. Instead, we propose a new scheme for conflict resolution, which is based on the idea of adding resolve filters. Our main results are algorithms for detecting and resolving conflicts in a filter database. We have tried our algorithm on 3 existing firewall databases, and have found conflicts, which are potential security holes, in each of them.
Smoking and age related macular degeneration: the number of pack years of cigarette smoking is a major determinant of risk for both geographic atrophy and choroidal neovascularisation (2005)

The authors have demonstrated a strong association between the risk of both GA and CNV and pack years of cigarette smoking. This provides support for a causal relation between smoking and AMD. They also show an increased risk for AMD in non-smokers exposed to passive smoking. Stopping smoking appears to reduce the risk of developing AMD.
Comparison of electron-density measurements made using a Langmuir probe and microwave interferometer in the Gaseous Electronics Conference reference reactor (1993)

A Langmuir probe and a microwave interferometer have been combined to measure the electron density of argon glow discharges in the Gaseous Electronics Conference reference reactor [Bull. Am. Phys. Soc. 36, 207 (1991)]. The two techniques indicate the same charge density at 100 mTorr to within 30%. This 30% difference is easily explained by the experimental peculiarities. While the predicted charge densities obtained from the two techniques track one another as the applied rf voltage is varied at constant pressure, they do not track one another as the pressure is varied at constant rf voltage. In fact, the charge densities predicted from the Langmuir probe using Laframboise’s theory (Tech. Rep. 100, Univ. Toronto Inst. Aerospace Study, 1966) are factors of 2 and 4 times lower than those from the interferometer at 250 and 500 mTorr, respectively. It appears that the probe alters the charge density in its vicinity when the probe radius becomes greater than the ion mean free path. The interferometer has also been used to investigate the macroscopic perturbation of the plasma electron density caused by the Langmuir probe. It was found that presence of the probe in a radio-frequency discharge does not appreciably alter the electron density measured by the interferometer at a set rf voltage irrespective of the potential placed upon it. This was not the case for dc discharges in the same apparatus where the volume-averaged electron density could be depleted by as much as 70% when the probe was biased even a few volts above plasma potential.
Biofilms and Chronic Infections (2008)

be made and acted on, a response reflected in the current move to increase US medical school capacity. Given the time required to train competent physicians and the growing reliance on other nations to provide physicians, it would seem in the national interest to err on the side of expanding US medical schools. The alternative is to risk the devastating effects of a physician shortage—effects almost certain to be felt most acutely by those in the greatest need—that would require many years to reverse.
Activation of the 92-kDa Gelatinase by Stromelysin and 4-Aminophenylmercuric Acetate (1995)

The matrix metalloproteinase 92-kDa gelatinase is a major product of inflammatory cells. Macrophages synthesize and secrete this proteinase as a proenzyme in association with tissue inhibitor of metalloproteinases (TIMP) (92TIMP), whereas neutrophils store and release it from secondary granules as a TIMP-free proenzyme (92TIMP-free). Metalloproteinase proenzymes can be activated in vitro by a variety of agents, including organomercurials and proteinases, resulting in loss of an 8-10-kDa NH2-terminal domain which disrupts the interaction of a conserved cysteine residue with the catalytic zinc molecule. We report that the activation and processing of 92-kDa gelatinase differs depending on its association with TIMP and the nature of the activating agent. We observed that 92TIMP undergoes classic activation to 82 kDa by stromelysin, whereas exposure to 4-aminophenylmercuric acetate (APMA) results in a final product of 83 kDa that still contains the "prodomain" cysteine. Association with TIMP appears to stabilize the COOH-terminal domain, whereas 92TIMP-free is converted by APMA to a final product of 67 kDa lacking the COOH-terminal portion. In the continued presence of APMA, which maintains cysteine-zinc disruption, the 67-kDa species is at least as active as the classic 82 kDa. In contrast, activation of 92TIMP-free by stromelysin initially generates the 82-kDa form which is followed by final conversion to a 50-kDa species that lacks the catalytic domain of the parent molecule. Therefore, although stromelysin activation of 92TIMP-free is initially efficient, the active 82-kDa form is short-lived and is replaced by an inactive 50-kDa product. This complex pattern of activation of the 92-kDa gelatinase may serve to restrict its proteolytic capacity following exposure to stromelysin and may serve to regulate proteinase activity in vivo.
Surface modification of poly(dimethylsiloxane) microchannels (2003)

This review looks at the efforts that are being made to modify the surface of poly(dimethylsiloxane) (PDMS) microchannels, in order to enhance applicability in the field of microfluidics. Many surface modifications of PDMS have been performed for electrophoretic separations, but new modifications are being done for emerging applications such as heterogeneous immunoassays and cell-based bioassays. These new modification techniques are powerful because they impart biospecificity to the microchannel surfaces and reduce protein adsorption. Most of these applications require the use of aqueous or polar solvents, which makes surface modification a very important topic.
Resonant Enhancement of Tunneling Magnetoresistance in Double-Barrier Magnetic Heterostructures (2002)

We show that spin-dependent resonant tunneling can dramatically enhance tunneling magnetoresistance. We consider double-barrier structures comprising a semiconductor quantum well between two insulating barriers and two ferromagnetic electrodes. By tuning the width of the quantum well, the lowest resonant level can be moved into the energy interval where the density of states for minority spins is zero. This leads to a great enhancement of the magnetoresistance, which exhibits a strong maximum as a function of the quantum well width. We demonstrate that magnetoresistance exceeding 800% is achievable in GaMnAs/AlAs/GaAs/AlAs/GaMnAs double-barrier structures.
Proliferative and secretory activity in human breast during natural and artificial menstrual cycles. (1988)

Events of cell proliferation have been assessed by thymidine labeling index (TLI) in morphologically normal breast lobules from women of reproductive age. TLI is higher during the second half of the menstrual cycle both in women with natural menstrual cycles and in those with artificial cycles due to oral contraceptive (OC) use. TLI varies between 0.04% and 5.7% and declines with increasing age. There is no difference in mean TLI between OC users and nonusers if correction is made for the difference in age distribution between these two groups. Immunohistochemical detection of immunoglobulin A (IgA), secretory component (SC), and alpha-lactalbumin shows more frequent positive staining during artificial than natural menstrual cycles, and positive staining tends to be associated with higher TLI values. No significant variation in staining with cycle phase is detected in natural or artificial cycles. These results show that breast tissue does not resemble endometrium in the relationships that exist between proliferation, secretion, and menstrual cycle phase.