gebhart/patrepeval huggingface dataset:
A comparison of constant and variable amplitude command shaping techniques for vibration reduction (2002)

Investigates the characteristics of constant-amplitude input shapers for robust time-optimal maneuvers of flexible structures. Trends in the timing of the shaper impulses are shown as a function of the system damping constant and move distance. The insensitivity to modeling errors, time-optimality, amount of vibration caused during maneuvers, and high frequency excitation of these shapers are then discussed and compared with some variable-amplitude input shapers.
Cidofovir Resistance in Vaccinia Virus Is Linked to Diminished Virulencein Mice (2006)

Cidofovir [(S)-1-(3-hydroxy-2-phosphonylmethoxypropyl)cytosine (HPMPC)] is recognized as a promising drug for the treatment of poxvirus infections, but drug resistance can arise by a mechanism that is poorly understood. We show here that in vitro selection for high levels of resistance to HPMPC produces viruses encoding two substitution mutations in the virus DNA polymerase (E9L) gene. These mutations are located within the regions of the gene encoding the 3'-5' exonuclease (A314T) and polymerase (A684V) catalytic domains. These mutant viruses exhibited cross-resistance to other nucleoside phosphonate drugs, while they remained sensitive to other unrelated DNA polymerase inhibitors. Marker rescue experiments were used to transfer A314T and/or A684V alleles into a vaccinia virus Western Reserve strain. Either mutation alone could confer a drug resistance phenotype, although the degree of resistance was significantly lower than when virus encoded both mutations. The A684V substitution, but not the A314T change, also conferred a spontaneous mutator phenotype. All of the HPMPC-resistant recombinant viruses exhibited reduced virulence in mice, demonstrating that these E9L mutations are inextricably linked to reduced fitness in vivo. HPMPC, at a dose of 50 mg/kg of body weight/day for 5 days, still protected mice against intranasal challenge with the drug-resistant virus with A314T and A684V mutations. Our studies show that proposed drug therapies offer a reasonable likelihood of controlling orthopoxvirus infections, even if the viruses encode drug resistance markers.
Cost-effective computer security: cognitive and associative passwords (2002)

Recall and guessing rates for conventional, cognitive, and word association passwords were compared using 86 Massey University undergraduates. Respondents completed a questionnaire covering all three password types, returning two weeks later for a recall test. Each respondent also nominated a "significant other" (parent, partner, etc.) who tried to guess the respondent's answers. On average, cognitive items produced the highest recall rates (80%) but the guessing rate was also high (39.5%). Word associations produced low guessing rates (7%) but response words were poorly recalled (39%). Nevertheless, both cognitive items and word associations showed sufficient promise as password techniques to warrant further investigation.
The interferons. (1992)

In the 10 years since the interferons (IFN) entered large-scale clinical trials, much has been learned much about their uses as single agents. alpha-IFN, the most widely studied, has shown antitumor and antiviral efficacy against various tumors and tumor-related viruses; it has been approved by the Food and Drug Administration for the treatment of patients with hairy cell leukemia, acquired immune deficiency syndrome-related Kaposi sarcoma, and condylomata acuminata. Although IFN are effective as single agents in certain clinical situations, increasing experience with these cytokines suggests that their greatest therapeutic potential may be in combination with other biologic response-modifying, cytotoxic, or antiviral drugs. Trials combining alpha-IFN with 5-fluorouracil to treat colorectal carcinoma or with zidovudine to treat acquired immune deficiency syndrome have shown the significant impact that IFN administered in conjunction with other carefully selected agents can have. To design the most effective combination regimens, better preclinical models that clarify the mechanisms of action of IFN and define their biochemical interactions with other agents are needed.
Rock fracture mechanics : principles, design, and applications (1992)

Preface. Contents. List of Notations. 1. Introduction. 2. Some Fundamental Aspects of Mechanics. 3. The Griffith Theory and the Evolution of Modern Fracture Mechanics. 4. Linear Elastic Fracture Mechanics and Fracture Initiation Theories. 5. Determination of Stress Intensity Factors. 6. Aspects of Non-linear Elastic Fracture Mechanics. 7. Some Aspects of Statistical Fracture Mechanics. 8. Mode I Fracture Toughness Testing. 9. Mode II and Mixed Mode I-II Fracture Toughness Testing. 10. Interrelationships Between Fracture Toughness, Hardness Index and Physico-Mechanical Properties of Rocks. 11. Fracture Mechanics Applied to Hydraulic Fracture Propagation and In Situ Stress Determinations. 12. Fracture Mechanics Applied to Rock Fragmentation by Cutting Action. 13. Fracture Mechanics Applied to Rock Fragmentation due to Blasting. 14. Fracture Mechanics Applied to Analysis of Rockbursts. 15. Fracture Mechanics Applied to Design and Stability of Rock Slopes Engineering Problems. Appendix: A Compilation of Mode I Fracture Toughness Values of Rocks. References. Supplementary List of Recommended References. Index.
Bone Marrow Stromal Cells: Characterization and Clinical Application (1999)

The bone marrow stroma consists of a heterogeneous population of cells that provide the structural and physiological support for hematopoietic cells. Additionally, the bone marrow stroma contains cells with a stem-cell-like character that allows them to differentiate into bone, cartilage, adipocytes, and hematopoietic supporting tissues. Several experimental approaches have been used to characterize the development and functional nature of these cells in vivo and their differentiating potential in vitro. In vivo, presumptive osteogenic precursors have been identified by morphologic and immunohistochemical methods. In culture, the stromal cells can be separated from hematopoietic cells by their differential adhesion to tissue culture plastic and their prolonged proliferative potential. In cultures generated from single-cell suspensions of marrow, bone marrow stromal cells grow in colonies, each derived from a single precursor cell termed the colony-forming unit-fibroblast. Culture methods have been developed to expand marrow stromal cells derived from human, mouse, and other species. Under appropriate conditions, these cells are capable of forming new bone after in vivo transplantation. Various methods of cultivation and transplantation conditions have been studied and found to have substantial influence on the transplantation outcome. The finding that bone marrow stromal cells can be manipulated in vitro and subsequently form bone in vivo provides a powerful new model system for studying the basic biology of bone and for generating models for therapeutic strategies aimed at regenerating skeletal elements.
Structure of a gene encoding the 1.7 S storage protein, napin, from Brassica napus. (1987)

A rapeseed chromosomal region containing a gene (napA), which encodes the 1.7 S seed storage protein (napin), was isolated in several overlapping recombinant clones from a phage lambda genomic library. Following restriction enzyme mapping of the genomic region, a subclone containing the napA coding region as well as some 1.1 and 1.4 kilobases of DNA from the 5' and 3' regions, respectively, was mapped and sequenced. The gene turned out to lack introns. Southern blotting analyses utilizing a napin cDNA clone as a probe revealed the presence of on the order of 10 napin genes in the rapeseed genome. The major polyadenylated transcript encoded by these genes was shown to be an 850-nucleotide species, the initiation site of which was mapped onto the napA gene. The major initiation site for transcription is located some 33 nucleotides downstream from a sequence perfectly conforming to the consensus sequence of a TATA box. Further analyses of the sequence revealed several features that may be of relevance for the expression of the napin genes.
Exosomes as a Potential Tool for a Specific Delivery of Functional Molecules (2013)

Extracellular membrane vesicles derived from the endosomal compartments and released by the fusion of the multivesicular bodies with the cell membrane are referred as exosomes (Exo) [Van Niel et al., J Biochem 140:13-21, 2006]. They function as mediators of intercellular communication and are employed by the organism in the regulation of systemic and local processes. Meantime, Exo are recognized as an indispensable entity of physiological fluids [Caby et al., Int Immunol 17:879-887, 2005; Lasser et al., J Transl Med 9:9, 2011; Lasser et al., Am J Rhinol Allergy 25:89-93, 2011]. Exo and other types of extracellular vesicles, e.g., exosome-like vesicles [van Niel et al., Gastroenterology 121:337-349, 2001] and microvesicles (MV) [Daveloose et al., Thromb Res 22:195-201, 1981], contain multiple functional molecules including lipids [Vidal et al., J Cell Physiol 140:455-462, 1989]; proteins [Simpson et al., Expert Rev Proteomics 6:267-283, 2009]; mRNA [Valadi et al., Nat Cell Biol 9:654-659, 2007]; DNA [Waldenstrom et al., PLoS One 7:e34653, 2012]; noncoding RNA, e.g., miRNA [Simpson et al., Expert Rev Proteomics 6:267-283, 2009]; and retrotransposon elements [Balaj et al., Nat Commun 2:180, 2011]. Assessment of the biological functions of Exo showed that they deliver specifically their cargo from the donor to recipient cells. Albeit the molecular mechanisms of this process are not fully understood, approaches for the application of Exo and MV as a tool for a cell-specific delivery of signalling molecules were successfully tested in in vitro and in vivo models [Maguire et al., Mol Ther 20:960-971, 2012]. Ovarian cancer cells release Exo, which bind stroma cells as well as donor cancer cells [Escrevente et al., BMC Cancer 11:108, 2011]. Here we describe an experimental approach for the assessment of Exo interaction and uptake by target cells. Methods for the isolation and purification of Exo from cell culture supernatants are included. To allow visualization of vesicle uptake, labelling of Exo with different fluorescent dyes, such as CFSE, PKH, DHPE, and DiOC18, is presented. Finally, we explain qualitative and quantitative analysis of Exo uptake by immunofluorescence and flow cytometry, respectively.
Identification and characterization of novel rare mutations in the planar cell polarity genePRICKLE1in human neural tube defects (2011)

The planar cell polarity (PCP) pathway controls the process of convergent extension (CE) during gastrulation and neural tube closure, and has been implicated in the pathogenesis of neural tube defects (NTDs) in animal models and human cohorts. In this study, we analyzed the role of one core PCP gene PRICKLE1 in these malformations. We screened this gene in 810 unrelated NTD patients and identified seven rare missense heterozygous mutations that were absent in all controls analyzed and predicted to be functionally deleterious using bioinformatics. Functional validation of five PRICKLE1 variants in a zebrafish model demonstrated that one variant, p.Arg682Cys, antagonized the CE phenotype induced by the wild-type zebrafish prickle1a (zpk1a) in a dominant fashion. Our study demonstrates that PRICKLE1 could act as a predisposing factor to human NTDs and further expands our knowledge of the role of PCP genes in the pathogenesis of these malformations.
Homo‐ and Hetero‐Dimeric Complex Formations of the Human Oxytocin Receptor (2004)

Using two different coimmunoprecipitation strategies as well as bioluminescence resonance energy transfer (BRET) techniques, we determined that the human oxytocin receptor forms dimeric and oligomeric complexes in vivo in intact living cells, and that these complexes exist at the cell surface level. Using a BRET-based assay, we found that oligomers can form between oxytocin receptors themselves (homo-oligomers) as well as, with a reduced affinity, between the oxytocin receptor and related members of the vasopressin receptor family (V1a and V2 receptors), but not with the more remotely related bradykinin receptor. The existence of oxytocin receptor oligomers at the level of the cell surface was demonstrated by a coimmunoprecipitation approach involving direct antibody exposure of intact living cells. Furthermore, this approach demonstrated that cell surface oxytocin receptor oligomerization is ligand independent. However, agonist addition led to an apparent rapid decrease in receptor oligomerization, as assessed by the coimmunoprecipitation approach, indicating that agonist exposure may modulate the oligomerization status. It remains to be determined to what extent oxytocin receptor oligomerization impacts on signal transduction.
Positive selection identifies an in vivo role for FimH during urinary tract infection in addition to mannose binding (2009)

FimH, the type 1 pilus adhesin of uropathogenic Escherichia coli (UPEC), contains a receptor-binding domain with an acidic binding pocket specific for mannose. The fim operon, and thus type 1 pilus production, is under transcriptional control via phase variation of an invertible promoter element. FimH is critical during urinary tract infection for mediating colonization and invasion of the bladder epithelium and establishment of intracellular bacterial communities (IBCs). In silico analysis of FimH gene sequences from 279 E. coli strains identified specific amino acids evolving under positive selection outside of its mannose-binding pocket. Mutating two of these residues (A27V/V163A) had no effect on phase variation, pilus assembly, or mannose binding in vitro. However, compared to wild-type, this double mutant strain exhibited a 10,000-fold reduction in mouse bladder colonization 24 h after inoculation and was unable to form IBCs even though it bound normally to mannosylated receptors in the urothelium. In contrast, the single A62S mutation altered phase variation, reducing the proportion of piliated cells, reduced mannose binding 8-fold, and decreased bladder colonization 30-fold in vivo compared to wild-type. A phase-locked ON A62S mutant restored virulence to wild-type levels even though in vitro mannose binding remained impaired. Thus, positive selection analysis of FimH has separated mannose binding from in vivo fitness, suggesting that IBC formation is critical for successful infection of the mammalian bladder, providing support for more general use of in silico positive selection analysis to define the molecular underpinnings of bacterial pathogenesis.
The High-Affinity CXCR4 Antagonist BKT140 Is Safe and Induces a Robust Mobilization of Human CD34+ Cells in Patients with Multiple Myeloma (2013)

When combined with G-CSF, BKT140 is a safe and efficient stem cell mobilizer that enabled the collection of a high number of CD34(+) cells in 1 and 2 aphaeresis procedures, resulting in successful engraftment.
GVSPM for reconstruction in electrical impedance tomography (2003)

We apply the generalized vector sampled pattern matching (GVSPM) method to an inverse parameter problem for the reconstruction of electrical impedance tomography (EIT). Most of the inverse problems are reduced into solving for an ill-posed system of equations whose solution is not uniquely determined. The GVSPM introduced in this paper enables us to select the physically existing solution among possible ones. By applying GVSPM for EIT reconstruction, this point is verified by reliable reconstructed images.
Studies Cast Doubt on Plasticity of Adult Cells (2002)

Opponents of research on human embryos have raised a politically powerful argument against work involving embryonic stem (ES) cells: Such research can be avoided because adult stem cells may offer similar promise. Defying scientific dogma, numerous reports have suggested that adult stem cells can morph into many types of cells, raising hopes that adult cells could eventually be used to treat diseases—without the ethical baggage that accompanies ES cells.
Using symmetry and evolutionary search to minimize sorting networks (2013)

Sorting networks are an interesting class of parallel sorting algorithms with applications in multiprocessor computers and switching networks. They are built by cascading a series of comparison-exchange units called comparators. Minimizing the number of comparators for a given number of inputs is a challenging optimization problem. This paper presents a two-pronged approach called Symmetry and Evolution based Network Sort Optimization (SENSO) that makes it possible to scale the solutions to networks with a larger number of inputs than previously possible. First, it uses the symmetry of the problem to decompose the minimization goal into subgoals that are easier to solve. Second, it minimizes the resulting greedy solutions further by using an evolutionary algorithm to learn the statistical distribution of comparators in minimal networks. The final solutions improve upon half-century of results published in patents, books, and peer-reviewed literature, demonstrating the potential of the SENSO approach for solving difficult combinatorial problems.
The Effects of Electric Currents on ATP Generation, Protein Synthesis, and Membrane Transport in Rat Skin (1982)

Direct electric currents ranging from 10 microA to 1000 microA increase ATP concentrations in the tissue and stimulate amino acid incorporation into the proteins of rat skin. The amino acid transport through the cell membrane, followed by the alpha-aminoisobutyric acid uptake, is stimulated between 100 microA and 750 microA. The stimulatory effects on ATP production and on amino acid transport, apparently mediated by different mechanisms, contribute to the final increased protein synthesizing activity. DNA metabolism followed by thymidine incorporation remains unaffected during the course of current application. The effects on AtP production can be explained by proton movements on the basis of the chemiosmotic theory of Mitchell, while the transport functions are controlled by modification in the electrical gradients across the membranes.
Defining Proximity Relationships in the Tertiary Structure of the Dopamine Transporter (1999)

Recently, we have described a distance constraint in the unknown tertiary structure of the human dopamine transporter (hDAT) by identification of two histidines, His(193) in the second extracellular loop and His(375) at the top of transmembrane (TM) 7, that form two coordinates in an endogenous, high affinity Zn(2+)-binding site. To achieve further insight into the tertiary organization of hDAT, we set out to identify additional residues involved in Zn(2+) binding and subsequently to engineer artificial Zn(2+)-binding sites. Ten aspartic acids and glutamic acids, predicted to be on the extracellular side, were mutated to asparagine and glutamine, respectively. Mutation of Glu(396) (E396Q) at the top of TM 8 increased the IC(50) value for Zn(2+) inhibition of [(3)H]dopamine uptake from 1.1 to 530 microM and eliminated Zn(2+)-induced potentiation of [(3)H]WIN 35,428 binding. These data suggest that Glu(396) is involved in Zn(2+) binding to hDAT. Importantly, Zn(2+) sensitivity was preserved following substitution of Glu(396) with histidine, indicating that the effect of mutating Glu(396) is not an indirect effect because of the removal of a negatively charged residue. The common participation of Glu(396), His(193), and His(375) in binding the small Zn(2+) ion implies their proximity in the unknown tertiary structure of hDAT. The close association between TM 7 and 8 was further established by engineering of a Zn(2+)-binding site between His(375) and a cysteine inserted in position 400 in TM 8. Summarized, our data define an important set of proximity relationships in hDAT that should prove an important template for further exploring the molecular architecture of Na(+)/Cl(-)-dependent neurotransmitter transporters.
Le rire des jésuites (2007)

Consacre a l’etude du mimetisme entre Francais et Amerindiens dans la Nouvelle-France 
des XVIIe - XVIIIe siecles, cet article ne s’interroge pas tant sur les echanges, les transferts 
culturels et les processus d’acculturation qui caracterisent la rencontre – comme en temoigne 
l’adoption par certains colons de la pratique autochtone du tatouage –, que sur la facon 
dont les cultures, avec leurs logiques particulieres, se revelent et s’actualisent en toute 
spontaneite dans des contextes d’interaction exotique. L’attitude du comte de Frontenac 
qui, lors d’une conference a Montreal en 1690, danse et chante la guerre un tomahawk a 
la main parmi ses allies autochtones, est ainsi moins analysee comme une forme d’indianisation que comme le reflexe d’un homme de Cour passe maitre dans l’art de la representation. 
La propension des Amerindiens, dans certains contextes de la rencontre, a mimer les 
manieres, les gestes ou l’esthetique des Francais, est quant a elle distinguee de l’acculturation a proprement parler, et interpretee comme une forme ritualisee et spontanee d’apprehension de l’autre dans sa difference. Imiter les Francais, pour les autochtones, ne reviendrait 
pas a les parodier mais a les adopter, a etablir avec eux, par la mediation du rituel, une 
relation d’homologie et de connivence. Il ne s’agirait pas, au fond, en les mimant, de 
reconnaitre les Francais, mais d’annihiler toute possibilite d’emergence de l’alterite humaine 
et toute amorce d’histoire.
Combined Newborn Screening for Succinylacetone, Amino Acids, and Acylcarnitines in Dried Blood Spots (2008)

The inclusion of SUAC analysis into routine analysis of AC and AA allows for rapid and cost-effective screening for TYR 1 with no tangible risk of false-negative results.
An anti‐inflammatory role for interleukin‐11 in established murine collagen‐induced arthritis (1998)

Interleukin-11 (IL-11) is a cytokine belonging to the IL-6 family which has both pro- and anti-inflammatory potential. Like IL-6 it can diminish tumour necrosis factor-alpha and IL-1 production, and augment immunoglobulin synthesis. We have explored the immunomodulatory effects of IL-11 treatment in mice in a model of inflammatory autoimmune joint disease, collagen-induced arthritis (CIA). Recombinant human IL-11 was administered at various doses to DBA/1 mice after the onset of CIA. IL-11 treatment caused a significant reduction in the clinical severity of established CIA, which was associated with protection from joint damage, as assessed by histology. Although there was a suggestion at high doses of IL-11 that the anticollagen type II (CII) response may have been augmented, there was no statistically significant effect of IL-11 treatment on anti-CII antibody levels. Similarly, the acute-phase reactant serum amyloid P was only elevated in mice receiving very high doses (50-100 microgram/day) of IL-11. Endogenous IL-11 was abundantly produced in synovial membrane cultures derived from CII-immunized mice with active disease, suggesting that, as in rheumatoid arthritis, this cytokine is spontaneously produced in the inflammatory response in CIA. The results presented here demonstrate an anti-arthritic immunoregulatory role for IL-11 in murine CIA, and suggest that IL-11 is a candidate therapeutic molecule for human inflammatory arthritic diseases.