gebhart/patrepeval huggingface dataset:
Photoinduced Plasticity in Cross-Linked Polymers (2005)

Chemically cross-linked polymers are inherently limited by stresses that are introduced by post-gelation volume changes during polymerization. It is also difficult to change a cross-linked polymer's shape without a corresponding loss of material properties or substantial stress development. We demonstrate a cross-linked polymer that, upon exposure to light, exhibits stress and/or strain relaxation without any concomitant change in material properties. This result is achieved by introducing radicals via photocleavage of residual photoinitiator in the polymer matrix, which then diffuse via addition-fragmentation chain transfer of midchain functional groups. These processes lead to photoinduced plasticity, actuation, and equilibrium shape changes without residual stress. Such polymeric materials are critical to the development of microdevices, biomaterials, and polymeric coatings.
Dermatological aspects of angiogenesis (2002)

Neovascularization is vital for the growth of tumours, providing a lifeline for sustenance and waste disposal. Tumour vessels can grow by sprouting, intussusception or by incorporating bone marrow-derived endothelial precursor cells into growing vessels. Recent advances in vascular biology have identified some key factors that control vascular growth, and have led to the hypothesis that in normal tissues vascular quiescence is maintained by the dominant influence of endogenous angiogenesis inhibitors over angiogenic stimuli. In contrast, increased secretion of angiogenic factors and the down-regulation of endogenous angiogenesis inhibitors induce tumour angiogenesis. Vascular quiescence in the skin seems to be primarily maintained by a balance between the endogenous angiogenesis inhibitors thrombospondin 1 and thrombospondin 2 and the potent proangiogenic factor vascular endothelial growth factor A. Inhibiting tumour growth by controlling angiogenesis is an intriguing approach with great potential for the treatment of vascular tumours such as haemangioma, Kaposi's sarcoma and solid cutaneous tumours such as squamous cell carcinoma, melanoma and basal cell carcinoma. In this review, the role of angiogenesis and more recent topics such as lymphangiogenesis in cutaneous tumour growth, invasion and metastasis will be discussed.
Primitives for the manipulation of general subdivisions and the computation of Voronoi (1985)

The following problem is discussed: given n points in the plane (the sites) and an arbitrary query point q , find the site that is closest to q . This problem can be solved by constructing the Voronoi diagram of the griven sites and then locating the query point inone of its regions. Two algorithms are given, one that constructs the Voronoi diagram in O ( n log n ) time, and another that inserts a new sit on O(n) time. Both are based on the use of the Voronoi dual, or Delaunay triangulation, and are simple enough to be of practical value. the simplicity of both algorithms can be attributed to the separation of the geometrical and topological aspects of the problem and to the use of two simple but powerful primitives, a geometric predicate and an operator for manipulating the topology of the diagram. The topology is represented by a new data structure for generalized diagrams, that is, embeddings of graphs in two-dimensional manifolds. This structure represents simultaneously an embedding, its dual, and its mirror image. Furthermore, just two operators are sufficients for building and modifying arbitrary diagrams.
Cell‐Penetrating Homochiral Cyclic Peptides as Nuclear‐Targeting Molecular Transporters (2011)

Going round in circles: Amphipathic L-cyclic peptides facilitate the cellular uptake of fluorescently labeled lamivudine and a phosphopeptide. A corresponding fluorescently labeled conjugate F-[W5R4K] showed a highly efficient translocation in the nucleus of colon adenocarcinoma, breast carcinoma, and human ovarian adenocarcinoma (see picture).
실험(實驗), 실습(實習)을 통한 탐구(探究)능력(能力) 평가(評價)(3) (1991)

This is the consecutive study of evaluation of inquiry ability in scientific experiments and practices( I , II ) (Yang et. al., 1989, 1990). Students inquiry ability in experiment of science education is prime concern of science educators, However, studies pertaining to the assessment of inquiry ability in experiments of science courses are scarce. This study was designed to analyze and to assess basic element of inquiry ability revealed in experiments which should be thought in science education of secondary schools, fifty objective items were constructed and administered to 200 9th-grade students. On the basis of data obtained from traditional item analysis, 25 items were selected. Using varimax rotation, five factors were identified as basic elements of the inquiry ability in experiments. They are abilities of identifying problems (Factor 1), planning experiments (Factor 2), conducting experiments (Factor 3), interpreting results (Factor 4) and formulating generalization(Factor 5). When subscale scores of five factors were linearly transfer to T-score, scores on subscale 1 and 4 were significantly higher than those on subscale 2, 3, and 5. For boys scores on subscale 1 and 4 were higher than those on subscale 2, 3, and 4, while for girls scores on subscale 1, 3, and 4 were higher than those on subscale 2 and 5. Especially, scores on subscale 2 were significantly lower than those on subscale 1, 3, 4, and 5.
In Vitro and In Vivo Correlates of Hybrid Tumor Resistance<xref ref-type="fn" rid="FN2">2</xref> (1987)

Tumorigenicity of 2 sublines, TU1 and TM5, of the C.B6-H-2dm4 (dm4) mouse tumor, TDM4, was tested in dm4 and F1 hybrid mice (from crosses of dm4 with a variety of other strains) to determine the genetics of hybrid resistance to these 2 tumor sublines. Resistance to TU1 was associated with at least 3 genes and required heterozygosity in the H-2D region, with secondary effects attributable to H-2K genes and non-H-2 genes. Resistance to TM5, however, did not require H-2D region heterozygosity, whereas H-2K and non-H-2 genes appeared to have significant effects. For evaluation of possible mechanisms for hybrid resistance, 4 assay systems were used. Comparison of natural killer cell activity in dm4 and various hybrid mice revealed no consistent activity against either TU1 or TM5. Little correlation was seen between resistance and generation of strong T-lymphocyte proliferative responses to the sublines. Likewise, cytotoxic T-lymphocyte (CTL) activity, particularly against TU1, was not associated with increased resistance. In contrast, delayed-type hypersensitivity (DTH) was consistently greater in hybrids with increased resistance to either subline. These results suggest a strong association between DTH responsiveness and hybrid resistance. Furthermore, the association, in some hybrids, of CTL activity with resistance to the TM5 subline, but not to TU1, may mean that different sublines of the same tumor can induce different sets of immune responses.
Localization, trafficking, and temperature-dependence of the Aequorea green fluorescent protein in cultured vertebrate cells. (1995)

The localization, trafficking, and fluorescence of Aequorea green fluorescent protein (GFP) in cultured vertebrate cells transiently transfected with GFP cDNA were studied. Fluorescence of GFP in UV light was found to be strongest when cells were incubated at 30 degrees C but was barely visible at an incubation temperature of 37 degrees C. COS-1 cells, primary chicken embryonic retina cells, and carp epithelial cells were fluorescently labeled under these conditions. GFP was distributed uniformly throughout the cytoplasm and nucleus independent of cell type examined. When GFP was fused to PML protooncogene product, fluorescence was detected in a unique nuclear organelle pattern indistinguishable from that of PML protein, showing the potential use of GFP as a fluorescent tag. To analyze both function and intracellular trafficking of proteins fused to GFP, a GFP-human glucocorticoid receptor fusion construct was prepared. The GFP-human glucocorticoid receptor efficiently transactivated the mouse mammary tumor virus promoter in response to dexamethasone at 30 degrees C but not at 37 degrees C, indicating that temperature is important, even for function of the GFP fusion protein. The dexamethasone-induced translocation of GFP-human glucocorticoid receptor from cytoplasm to nucleus was complete within 15 min; the translocation could be monitored in a single living cell in real time.
Rapid lysis technique for mycobacterial species (1987)

The lysis of mycobacterial cells typically has been difficult and time-consuming. We report a method for the physical rupture of Mycobacterium paratuberculosis and several other members of the family Mycobacteriaceae using a Mini-Beadbeater cell disrupter (Biospec Products; Bartlesville, Okla.) and zirconium beads, a process which yields DNA and RNA of high molecular weight and in greater quantity than that obtained by rupture in a Ribi pressure cell.
Humanized Single Domain Antibodies Neutralize SARS-CoV-2 by Targeting Spike Receptor Binding Domain (2020)

Abstract Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has spread across more than 200 countries and regions, leading to an unprecedented medical burden and live lost. SARS-CoV-2 specific antivirals or prophylactic vaccines are not available. Neutralizing antibodies provide efficient blockade for viral infection and are a promising category of biological therapies. Using SARS-CoV-2 spike RBD as a bait, we have discovered a panel of humanized single domain antibodies (sdAbs). These sdAbs revealed binding kinetics with the equilibrium dissociation constant (KD) of 0.7~33 nM. The monomeric sdAbs showed half maximal inhibitory concentration (IC 50 ) of 0.003~0.3 μg/mL in pseudotyped particle neutralization assay, and 0.23~0.50 μg/mL in authentic SARS-CoV-2 neutralization assay. Competitive ligand-binding data suggested that the sdAbs either completely blocked or significantly inhibited the association between SARS-CoV-2 RBD and viral entry receptor ACE2. Finally, we showed that fusion of the human IgG1 Fc to sdAbs improved their neutralization activity by tens of times. These results reveal the novel SARS-CoV-2 RBD targeting sdAbs and pave a road for antibody drug development.
The Max b-HLH-LZ Can Transduce into Cells and Inhibit c-Myc Transcriptional Activities (2012)

The inhibition of the functions of c-Myc (endogenous and oncogenic) was recently shown to provide a spectacular therapeutic index in cancer mouse models, with complete tumor regression and minimal side-effects in normal tissues. This was achieved by the systemic and conditional expression of omomyc, the cDNA of a designed mutant of the b-HLH-LZ of c-Myc named Omomyc. The overall mode of action of Omomyc consists in the sequestration of Max and the concomitant competition of the Omomyc/Max complex with the endogenous c-Myc/Max heterodimer. This leads to the inhibition of the transactivation of Myc target genes involved in proliferation and metabolism. While this body of work has provided extraordinary insights to guide the future development of new cancer therapies that target c-Myc, Omomyc itself is not a therapeutic agent. In this context, we sought to exploit the use of a b-HLH-LZ to inhibit c-Myc in a cancer cell line in a more direct fashion. We demonstrate that the b-HLH-LZ domain of Max (Max*) behaves as a bona fide protein transduction domain (PTD) that can efficiently transduce across cellular membrane via through endocytosis and translocate to the nucleus. In addition, we show that the treatment of HeLa cells with Max* leads to a reduction of metabolism and proliferation rate. Accordingly, we observe a decrease of the population of HeLa cells in S phase, an accumulation in G1/G0 and the induction of apoptosis. In agreement with these phenotypic changes, we show by q-RT-PCR that the treatment of HeLa cells with Max* leads to the activation of the transcription c-Myc repressed genes as well as the repression of the expression of c-Myc activated genes. In addition to the novel discovery that the Max b-HLH-LZ is a PTD, our findings open up new avenues and strategies for the direct inhibition of c-Myc with b-HLH-LZ analogs.
The application of CD71 and Hoechst33258 to staining method for sorting fetal nucleated red blood cells in the peripheral blood of pregnant women. (2000)

CD71 and HO258 double-staining method could exclude mature erythrocytes, thrombocytes and reticulocytes and this improve NRBCs' specific label and sorting purity.
Increasing Hydrophobicity or Disulfide Bridging at the Factor VIII A1 and C2 Domain Interface Enhances Procofactor Stability (2011)

Factor VIII (FVIII) consists of a heavy (A1A2B domains) and light chain (A3C1C2 domains), whereas the contiguous A1A2 domains are separate subunits in the cofactor, FVIIIa. FVIII x-ray structures show close contacts between A1 and C2 domains. To explore the role of this region in FVIII(a) stability, we generated a variant containing a disulfide bond between A1 and C2 domains by mutating Arg-121 and Leu-2302 to Cys (R121C/L2302C) and a second variant with a bulkier hydrophobic group (A108I) to better occupy a cavity between A1 and C2 domains. Disulfide bonding in the R121C/L2302C variant was >90% efficient as judged by Western blots. Binding affinity between the A108I A1 and A3C1C2 subunits was increased ∼3.7-fold in the variant as compared with WT as judged by changes in fluorescence of acrylodan-labeled A1 subunits. FVIII thermal and chemical stability were monitored following rates of loss of FVIII activity at 57 °C or in guanidinium by factor Xa generation assays. The rate of decay of FVIIIa activity was monitored at 23 °C following activation by thrombin. Both R121C/L2302C and A108I variants showed up to ∼4-fold increases in thermal stability but minimal improvements in chemical stability. The purified A1 subunit of A108I reconstituted with the A3C1C2 subunit showed an ∼4.6-fold increase in thermal stability, whereas reconstitution of the variant A1 with a truncated A3C1 subunit showed similar stability values as compared with WT A1. Together, these results suggest that altering contacts at this A1-C2 junction by covalent modification or increasing hydrophobicity increases inter-chain affinity and functionally enhances FVIII stability.
Etiological agents of mastitis in dairy cows on a farm in the West Pomeranian region [Poland] (2008)

Four hundred milk samples were collected from cows. In 78 samples (19.50%) an in - crease of somatic cells was detected employing the California Mastitis Test (CMT). Therefore, those milk samples were plated (0.1 mL) onto bacteriological and mycological media. Cultures were incubated at 37 °C and 20 °C for 24h to 72h. Biochemical features of bacteria and fungi were determined in API tests and/or on liquid O-F Medium. The presence of coagulase in Staphylo - coccus spp. was investigated by tube test using rabbit plasma. For identification of C. albicans the germ tubes test was conducted. Based on microbiological investigation and increase of so - matic cells, mastitis was confirmed in all cows, whose milk was selected for further research. The presence of bacteria was confirmed in 64.10% of samples, bacteria and yeast in 34.62% and yeast alone in 1.28%. Sixteen bacterial species were isolated: Staphylococcus spp. (5 species ), Enterobacteriaceae (5 species) , Streptococcus spp. (4 species ), Bacillus cereus and Pseudomonas aeruginosa . Among yeasts, 15 species were identified: Candida spp. (9 species ), Blastoschizomyces capitatum , Dipodascus ingens , Geotrichum candidum , Trichosporon asahii , Saccharomyces cere - visiae , Torulopsis conglobata . The most frequent isolated yeasts were Candida spp., mainly C. guilliermondii (6 strains), C. kefyr (4 strains) and C. butyri (4 strains). The most frequent iso - lated bacteria were Staphylococcus spp. (37 strains), Streptococcus spp. (28 strains) and Enter - obacteriaceae (23 strains).
Aptamer Selection by High-Throughput Sequencing and Informatic Analysis (2011)

Traditional methods for selecting aptamers require multiple rounds of selection and optimization in order to identify aptamers that bind with high affinity to their targets. Here we describe an assay that requires only one round of positive selection followed by high-throughput DNA sequencing and informatic analysis in order to select high-affinity aptamers. The assay is flexible, requires less hands on time, and can be used by laboratories with minimal expertise in aptamer biology to quickly select high-affinity aptamers to a target of interest. This assay has been utilized to successfully identify aptamers that bind to thrombin with dissociation constants in the nanomolar range.
Hidden technical debt in Machine learning systems (2015)

Machine learning offers a fantastically powerful toolkit for building useful complex prediction systems quickly. This paper argues it is dangerous to think of these quick wins as coming for free. Using the software engineering framework of technical debt, we find it is common to incur massive ongoing maintenance costs in real-world ML systems. We explore several ML-specific risk factors to account for in system design. These include boundary erosion, entanglement, hidden feedback loops, undeclared consumers, data dependencies, configuration issues, changes in the external world, and a variety of system-level anti-patterns.
N,N‘-Linked Oligoureas as Foldamers: Chain Length Requirements for Helix Formation in Protic Solvent Investigated by Circular Dichroism, NMR Spectroscopy, and Molecular Dynamics (2005)

N,N'-linked oligoureas with proteinogenic side chains are peptide backbone mimetics belonging to the gamma-peptide lineage. In pyridine, heptamer 4 adopts a stable helical fold reminiscent of the 2.6(14) helical structure proposed for gamma-peptide foldamers. In the present study, we have used a combination of CD and NMR spectroscopies to correlate far-UV chiroptical properties and conformational preferences of oligoureas as a function of chain length from tetramer to nonamer. Both the intensity of the CD spectra and NMR chemical shift differences between alphaCH2 diastereotopic protons experienced a marked increase for oligomers between four and seven residues. No major change in CD spectra occurred between seven and nine residues, thus suggesting that seven residues could be the minimum length required for stabilizing a dominant conformation. Unexpectedly, in-depth NMR conformational investigation of heptamer 4 in CD3OH revealed that the 2.5 helix probably coexists with partially (un)folded conformations and that Z-E urea isomerization occurs, to some degree, along the backbone. Removing unfavorable electrostatic interactions at the amino terminal end of 4 and adding one H-bond acceptor by acylation with alkyl isocyanate (4 --> 7) was found to reinforce the 2.5 helical population. The stability of the 2.5 helical fold in MeOH is further discussed in light of unrestrained molecular dynamics (MD) simulation. Taken together, these new data provide additional insight into the folding propensity of oligoureas in protic solvent and should be of practical value for the design of helical bioactive oligoureas.
The unfolding clinical spectrum of POLG mutations (2009)

The clinical features of the patient are the most important features to select putative POLG mutation carriers and not the presence of mtDNA deletions or OXPHOS (oxidative phosphorylation) activity. The authors conclude that POLG mutations are an important cause of heterogeneous mitochondrial pathology and that more accurate genotype-phenotype correlations allow a more rapid genetic diagnosis and improved prognosis for mutation carriers.
Identification of surface-exposed linear B-cell epitopes of the nonfimbrial adhesin CS31A of Escherichia coli by using overlapping peptides and antipeptide antibodies (1996)

As a first step toward the design of an epitope vaccine, by using the nonfimbrial adhesin CS31A of Escherichia coli as a carrier, a low-resolution topological and epitope map of the CS31A subunit was developed by using solid-phase peptide synthesis and polyclonal rabbit antibodies raised against both native and denatured proteins. Peptides constituting antigenic epitopes on the major subunit (ClpG) of the multimeric CS31A antigen were identified by examining the binding of the antibodies to 249 overlapping nonapeptides covering the amino acid sequence of ClpG. With antibodies raised against denatured ClpG subunit, seven major epitope regions, corresponding to residues 10 to 18, 45 to 58, 88 to 107, 148 to 172, 187 to 196, 212 to 219, and 235 to 241, were located. Most of the epitopes were hydrophilic and were located in variable regions, residing largely in loop regions at the boundaries of secondary structural elements of ClpG. In contrast, antibodies raised against native CS31A antigen reacted only with the peptide AVNPNA (positions 179 to 184), demonstrating that this peptide was the only linear B-cell epitope of the native protein. The different immunogenic profiles of native CS31A antigen and denatured ClpG indicated that the denaturation process resulted in marked conformational changes in the protein, which could expose epitopes hidden or absent in native CS31A. To identify the surface-exposed epitopes, nine peptides covering the dominant antigenic regions of ClpG were synthesized and used to prepare site-specific antibodies. Antipeptide antibodies were tested, in a competitive enzyme-linked immunosorbent assay (ELISA), for cross-reactivity with native CS31A and denatured ClpG subunit. Four of these antipeptide antibodies bound to the native protein in an accessibility ELISA, indicating that residues 44 to 56, 174 to 190, 185 to 199, and 235 to 249 were surface exposed on CS31A. These data indicate that an immunodominant surface-exposed linear epitope was present in the region from positions 179 to 184 of ClpG in the native CS31A antigen on intact bacterial cells and suggest that the four surface-exposed epitopes constitute potential sites for insertions or substitutions with heterologous peptides.
The Cornell program synthesizer (1981)

Programs are not text; they are hierarchical compositions of computational structures and should be edited, executed, and debugged in an environment that consistently acknowledges and reinforces this viewpoint. The Cornell Program Synthesizer demands a structural perspective at all stages of program development. Its separate features are unified by a common foundation: a grammar for the programming language. Its full-screen derivation-tree editor and syntax-directed diagnostic interpreter combine to make the Synthesizer a powerful and responsive interactive programming tool.