gebhart/patrepeval huggingface dataset:
Light-Activated Immobilization of Biomolecules to Agarose Hydrogels for Controlled Cellular Response (2004)

We describe a new method of synthesizing photolabile hydrogel materials for convenient photoimmobilization of biomolecules on surfaces or in 3-D matrixes. Dissolved agarose was modified with photolabile S-(2-nitrobenzyl)cysteine (S-NBC) via 1,1'-carbonyldiimidazole (CDI) activation of primary hydroxyl groups. S-NBC-modified agarose remained soluble and gelable with up to 5% S-NBC substitution, yet gelation was slower and the elastic modulus of the resulting gel was lower than those of unmodified agarose. Irradiating S-NBC-grafted agarose resulted in the loss of the protecting 2-nitrobenzyl groups, thereby exposing free sulfhydryl groups for biomolecular coupling. When appropriately activated with sulfhydryl-reactive groups, either peptides or proteins were effectively immobilized to the photoirradiated hydrogel matrixes, with the irradiation energy dose (i.e., irradiation time) used to control the amount of biomolecule immobilization. When the GRGDS peptide was immobilized on agarose, it was shown to be cell-adhesive and to promote neurite outgrowth from primary, embryonic chick dorsal root ganglion neurons. The immobilized GRGDS surface ligand concentration affected the cellular response: neurite length and density increased with GRGDS surface concentration at low adhesion ligand concentration and then plateaued at higher GRGDS concentration. Grafting 2-nitrobenzyl-protected compounds to hydrogel materials is useful for creating new photolabile hydrogel substrates for light-activated functional group generation and biomolecular immobilization.
MOS buried load logic (1980)

A MOS buried logic technique using buried JFET loads with a gate delay of 0.34ns and a power delay product of 0.17pJ will be reported. Development has been applied to a 4-stage binary counter operating with a maximum toggle of 72.4MHz.
An Efficient Synthesis of 2,4-Substituted [1,8]Naphthyridines from 3-(2-Amino-5-methylpyridin-3-yl)-1-arylprop-2-yn-1-ones (2002)

3-(2-Amino-5-methylpyridin-3-yl)-1-arylprop-2-yn-1-ones 2, readily available through Pd-catalyzed carbonylative coupling of 5-methyl-3-[2-(trimethylsilyl)ethynyl]pyridine-2-ylamine (1) with aryl iodides in the presence of carbon monoxide, undergo a domino conjugate addition/annulation reaction to give 4-heterosubstituted 2-aryl[1,8]naphthyridines 3 in high yields.
Heterogeneous stream processing for disaster detection and alarming (2014)

We present a novel approach for event recognition in massive streams of heterogeneous data driven by privacy policies and big data event processing. New technologies in mobile computing combined with sensing infrastructures distributed in a city or country are generating massive, poly-structured spatio-temporal data. With a view on emergencies and disasters these various data sources enable early response and offer situative insights when integrated in an on-line incident recognition system. Our hereby presented system architecture integrates multi-faceted sensing and distributed event detection to identify, label and increase confidence in detected incidents. A higher flexibility than existing event detection approaches is achieved by combination of the data streams at a round table. At the round table the data flow adjusts itself during execution of the real-time detection system. This offers more robustness in case streams appear or disappear. The developed architecture is used in nation-wide and city-level incident recognition scenarios.
Radiation‐induced alterations of fracture healing biomechanics (1984)

The effects of irradiation on the normal temporal progression of the physical properties of healing fractures were studied in a rat model. Fractures were surgically produced in the femur, stabilized with an intramedullary pin, and irradiated. One group of rats was exposed to 2,500 rads in divided doses over 2 weeks, beginning 3 days after fracture, and compared to a control group with fractures which were not irradiated. Animals were sacrificed at periodic intervals and the bones were tested to failure in torsion. The torque, stiffness, and energy increased and the angle decreased for the nonirradiated specimens in the expected fashion. This progression was deleteriously altered in the irradiated femurs.
Unleashing meiotic crossovers in hybrid plants (2017)

Meiotic crossovers shuffle parental genetic information, providing novel combinations of alleles on which natural or artificial selection can act. However, crossover events are relatively rare, typically one to three exchange points per chromosome pair. Recent work has identified three pathways limiting meiotic crossovers in <i>Arabidopsis thaliana</i> that rely on the activity of FANCM [Crismani W, et al. (2012) <i>Science</i> 336:1588-1590], RECQ4 [Séguéla-Arnaud M, et al. (2015) <i>Proc Natl Acad Sci USA</i> 112:4713-4718], and FIGL1 [Girard C, et al. (2015) <i>PLoS Genet</i> 11:e1005369]. Here we analyzed recombination in plants in which one, two, or all three of these pathways were disrupted in both pure line and hybrid contexts. The greatest effect was observed when combining <i>recq4</i> and <i>figl1</i> mutations, which increased the hybrid genetic map length from 389 to 3,037 cM. This corresponds to an unprecedented 7.8-fold increase in crossover frequency. Disrupting the three pathways did not further increase recombination, suggesting that some upper limit had been reached. The increase in crossovers is not uniform along chromosomes and rises from centromere to telomere. Finally, although in wild type recombination is much higher in male meiosis than in female meiosis (490 cM vs. 290 cM), female recombination is higher than male recombination in <i>recq4 figl1</i> (3,200 cM vs. 2,720 cM), suggesting that the factors that make wild-type female meiosis less recombinogenic than male wild-type meiosis do not apply in the mutant context. The massive increase in recombination observed in <i>recq4 figl1</i> hybrids opens the possibility of manipulating recombination to enhance plant breeding efficiency.
Blind source extraction based on a linear predictor (2007)

A rigorous analysis of the blind source extraction (BSE) approach based on a linear predictor is provided. It is shown that by minimising the mean squared prediction error (MSPE), as originally proposed, it is only possible to reach a solution subject to an arbitrary orthogonal transformation. To remove this ambiguity, a new cost function based on the normalised MSPE is introduced which by design provides a unique solution to this class of BSE problems. Depending on whether the pre-whitening operation is required or not, a novel class of BSE algorithms are derived and approaches with both fixed and adaptive linear predictor coefficients are considered. The proposed algorithms are justified by both the analysis and simulation results.
Factors Influencing the Long-Term Behavior of Extracellular Matrix-Derived Scaffolds for Musculoskeletal Soft Tissue Repair (2012)

Musculoskeletal connective tissues such as tendon, ligament, and cartilage possess a limited ability for self-repair. Tissue engineering seeks to use combinations of cells, bioactive molecules, and biomaterials to develop new treatment options for the repair or replacement of damaged tissues. The use of native extracellular matrix as scaffold material for tissue engineering has become increasingly attractive because such tissues can not only provide structural support, but also regulate cell behavior. Although demineralized bone matrix has long been recognized for its osteoinductive abilities, recent studies have identified the ability of cartilage and tendon extracellular matrices to stimulate the differentiation of mesenchymal or adipose-derived adult stem cells toward chondrogenic or tenogenic lineages, respectively. This review discusses the motivation for fabricating scaffolds from musculoskeletal tissues, the in vitro and in vivo efficacy of these tissue-derived scaffolds, and various processing techniques such as decellularization or cross-linking that can mitigate immunogenic responses, moderate the degradation profile, and enhance the mechanical properties of these constructs following long-term implantation in vivo.
Prevalence of Eating Disorders And Menstrual Ir- regularities Among Female Football Players (2017)

Purpose: In the present study the occurrence of eating disorders (EDs) and menstrual  dysfunctions  (MDs)  was  examined  among  physically  inactive women (C) and elite female football players (FP). Methods: ED was investigated by EDI and SCOFF-test. MD was measured by questions on menstrual history.  Results: Although there were a few participants in both groups who reached the  cut-off  scores  in  ‘Drive  for Thinness’  and  ‘Body  Dissatisfaction’  sub- scales of EDI, there were no significant differences between the rates. None of the participants passed the critical limit in the ’Bulimia’ subscale. There was no significant difference between the average scores of the first three subscales of EDI in the two groups. The next five subscales of EDI mea- sure  psychopathology  commonly  associated  with,  but  not  unique  to,  ED. We could observe significant difference only between the average score of ‘Interpersonal  Distrust’  subscale.  Depending  on  the  SCOFF-test  we  could not observe any significant difference between the incidences of EDs in the groups. In the FP group the age of menarche was significantly older. Less FPs had oligomenorrhea, but there was no significant difference between the rates of secondary amenorrhea. The common incidence of EDs and MDs was the same in both groups.
Information processing in buried pipeline leak detection system (2005)

Detecting leak noises of buried pipelines is the most effective method of pinpointing a leak or leaks in buried pipelines. However, the acquired leak signals are usually blurred with ambient noises and therefore they have low signal-to-noise ratio. It is essential to use appropriate information processing scheme in order to acquire the leak signatures. The sensors are positioned on either side of the suspected leak position. By estimating the time delay between the two sensor signals, the leak can be localized. However the features of leak noise vary with the materials, sizes and inbuilt conditions of pipes. It is difficult to predetermine the spectral knowledge of a leak noise. The spectral knowledge is a prerequisite for the commonly used generalized correlation method to get the time delay estimation between the sensor signals. Here, the LMS adaptive filter is used to determine the time delay. As leak noise is stationary, the mean response of the LMS adaptive filter can converge to the discrete Winner filter and be peaked at the delay. This way, the estimation is adaptive and does not depend on either the spectrum of leak noise or the spectra of ambient noises. In practice, bursting interferences are inevitable where detection operates. The bursting interferences produce nonstationary characteristics in a signal and in turn result in diverging of the adaptive filtering process. The Wavelet decomposition and thresholding is deployed to remove the bursting interferences and recover the stationary behaviors.
Application of Microarrays for Deciphering the Structure and Function of the Human Glycome (2013)

Glycan structures were defined historically using multiple methods to determine composition, sequence, linkage, and anomericity of component monosaccharides. Such approaches have been replaced by more sensitive MS methods to profile or predict glycan structures, but these methods are limited in their ability to completely define glycan structures. Glycan-binding proteins, including lectins and antibodies, have been found to have exquisite binding specificities that can provide information about glycan structures. Here, we show glycan-binding proteins can be used along with MS to help define glycan linkages and other determinants in unknown glycans printed as shotgun glycan microarrays.
Structured Light in Sunlight (2013)

Strong ambient illumination severely degrades the performance of structured light based techniques. This is especially true in outdoor scenarios, where the structured light sources have to compete with sunlight, whose power is often 2-5 orders of magnitude larger than the projected light. In this paper, we propose the concept of light concentration to overcome strong ambient illumination. Our key observation is that given a fixed light (power) budget, it is always better to allocate it sequentially in several portions of the scene, as compared to spreading it over the entire scene at once. For a desired level of accuracy, we show that by distributing light appropriately, the proposed approach requires 1-2 orders lower acquisition time than existing approaches. Our approach is illumination-adaptive as the optimal light distribution is determined based on a measurement of the ambient illumination level. Since current light sources have a fixed light distribution, we have built a prototype light source that supports flexible light distribution by controlling the scanning speed of a laser scanner. We show several high quality 3D scanning results in a wide range of outdoor scenarios. The proposed approach will benefit 3D vision systems that need to operate outdoors under extreme ambient illumination levels on a limited time and power budget.
Intrinsically stable light source at telecom wavelengths (2013)

We present a highly stable light source at telecom wavelengths, based on a short erbium doped fiber. The high stability arises from the high inversion of the Er3+ ion population. This source is developed to work as a stable reference in radiometric applications and is useful in any application where high stability and/or a large bandwidth are necessary. The achieved long-term stability is 10 ppm.
Polar codes for partial response channels (2013)

We describe an error-correcting system that combines polar codes with turbo equalization for partial response channels. The successive cancellation decoder, originally proposed by Arikan for polar codes, does not produce the soft outputs needed for turbo processing. The belief propagation decoder, on the other hand, requires many iterations and has high computational complexity. In this paper, we propose a soft-input soft-output variant of the successive cancellation decoder that produces the soft information required for turbo architectures, while keeping the computational complexity low. Numerical results show that the proposed decoder performs better than the hard-output successive cancellation decoder and the belief propagation decoder in the context of turbo equalization. The proposed decoder achieves this performance gain with lower complexity compared to belief propagation and maximum-likelihood decoders. Additionally, we prove that Arikan's successive cancellation decoder is a fast-polarizing instance of our soft-input soft-output successive cancellation decoder.
Regulation of connexin 43-mediated gap junctional intercellular communication by Ca2+ in mouse epidermal cells is controlled by E-cadherin. (1991)

Gap junctional intercellular communication (GJIC) of cultured mouse epidermal cells is mediated by a gap junction protein, connexin 43, and is dependent on the calcium concentration in the medium, with higher GJIC in a high-calcium (1.2 mM) medium. In several mouse epidermal cell lines, we found a good correlation between the level of GJIC and that of immunohistochemical staining of E-cadherin, a calcium-dependent cell adhesion molecule, at cell-cell contact areas. The variant cell line P3/22 showed both low GJIC and E-cadherin protein expression in low- and high-Ca2+ media. P3/22 cells showed very low E-cadherin mRNA expression. To test directly whether E-cadherin is involved in the Ca(2+)-dependent regulation of GJIC, we transfected the E-cadherin expression vector into P3/22 cells and obtained several stable clones which expressed high levels of E-cadherin mRNA. All transfectants expressed E-cadherin molecules at cell-cell contact areas in a calcium-dependent manner. GJIC was also observed in these transfectants and was calcium dependent. These results suggest that Ca(2+)-dependent regulation of GJIC in mouse epidermal cells is directly controlled by a calcium-dependent cell adhesion molecule, E-cadherin. Furthermore, several lines of evidence suggest that GJIC control by E-cadherin involves posttranslational regulation (assembly and/or function) of the gap junction protein connexin 43.
Multiple Cytokines Stimulate Hepatic Lipid Synthesis<i>in Vivo</i>* (1989)

We have previously shown that administration of tumor necrosis factor-alpha (TNF alpha) to intact rats results in an acute (within 60-120 min) stimulation of hepatic fatty acid synthesis, which persists for an extended period. Hepatic cholesterol synthesis is also stimulated by 16-17 h after TNF alpha treatment. We now demonstrate, using intact mice, that stimulation of hepatic lipid synthesis is not solely the property of the cytokine TNF alpha. Incorporation of 3H2O into fatty acids in the liver was increased 60-120 min and 16-17 h after the administration of TNF beta, interleukin-1 (IL-1), and interferon-alpha (IFN alpha). TNF alpha, IL-1, and IFN alpha all rapidly stimulate hepatic fatty acid synthesis (within 0-30 min), with the peak occurring at 60-120 min. The half-maximal doses of TNF alpha (200 ng) and IL-1 (20 ng) that stimulate hepatic fatty acid synthesis are similar to those that induce fever, a well recognized biological effect of these cytokines. Additionally, hepatic cholesterol synthesis was increased 16-17 h after TNF beta, IL-1, and IFN gamma treatment. The present study demonstrates that multiple cytokines from different cell types which act through different receptors can stimulate hepatic fatty acid and cholesterol synthesis. Previous studies have shown that multiple cytokines can inhibit the synthesis and storage of fat in cultured adipose cells. Taken together, these data indicate that multiple signals to perturb lipid metabolism may be produced as a consequence of an immunological or inflammatory response.
Complement Activation Occurs on Subendothelial Extracellular Matrix In Vitro and Is Initiated by Retraction or Removal of Overlying Endothelial Cells (1998)

Vascular endothelium is continuously exposed to plasma complement, which could generate a potent proinflammatory signal if activated on the vascular wall. Normal endothelium, however, expresses an anti-inflammatory phenotype, which includes resistance to complement fixation. As activated endothelium converts to a proinflammatory phenotype, we investigated the effect of cytokines on endothelial susceptibility to complement fixation. Cytokine-treated HUVEC were exposed to human serum as a source of complement, and C3 deposition was quantified. IL-1beta and TNF-alpha in combination with IFN-gamma markedly increased endothelial C3 deposition; however, immunofluorescence microscopy revealed that the endothelial cells had retracted, and that bound C3 was concentrated not on cells but in areas of exposed subendothelial extracellular matrix (ECM). Studies with cell-free ECM indicated that complement activation required only ECM exposure and was independent of cellular activation. C3 deposition on ECM was reproduced by reconstituting the alternative pathway, which generated a stable C3 convertase on ECM, but not on endothelial cells. C3b and iC3b were identified on ECM exposed to purified alternative pathway components and serum, respectively. In conditions associated with endothelial disruption, exposure of subendothelial ECM could induce complement fixation and contribute to inflammation and vascular damage.
Multi-cellular natural killer (NK) cell clusters enhance NK cell activation through localizing IL-2 within the cluster (2017)

Multi-cellular cluster formation of natural killer (NK) cells occurs during in vivo priming and potentiates their activation to IL-2. However, the precise mechanism underlying this synergy within NK cell clusters remains unclear. We employed lymphocyte-laden microwell technologies to modulate contact-mediated multi-cellular interactions among activating NK cells and to quantitatively assess the molecular events occurring in multi-cellular clusters of NK cells. NK cells in social microwells, which allow cell-to-cell contact, exhibited significantly higher levels of IL-2 receptor (IL-2R) signaling compared with those in lonesome microwells, which prevent intercellular contact. Further, CD25, an IL-2R α chain, and lytic granules of NK cells in social microwells were polarized toward MTOC. Live cell imaging of lytic granules revealed their dynamic and prolonged polarization toward neighboring NK cells without degranulation. These results suggest that IL-2 bound on CD25 of one NK cells triggered IL-2 signaling of neighboring NK cells. These results were further corroborated by findings that CD25-KO NK cells exhibited lower proliferation than WT NK cells, and when mixed with WT NK cells, underwent significantly higher level of proliferation. These data highlights the existence of IL-2 trans-presentation between NK cells in the local microenvironment where the availability of IL-2 is limited.
The Process of Microbial Translocation (1990)

The process of microbial translocation was studied using Candida albicans, Escherichia coli, or endotoxin instilled into Thiry-Vella loops of thermally injured guinea pigs and rats. Translocation of C. albicans occurred by direct penetration of enterocytes by a unique process different from classical phagocytosis. Translocation between enterocytes was not observed. Internalization was associated with a disturbance of the plasma membrane and brush border, but most internalized organisms were not surrounded by a plasma membrane. Passage of the candida into the lamina propria appeared to be associated with disruption of the basal membrane with extrusion of cytoplasm of the cell and candida. Organisms in the lamina propria were commonly phagocytized by macrophages but also were found free in lymphatics and blood vessels. Translocation of E. coli and endotoxin also occurred directly through enterocytes rather than between them, but translocated endotoxin diffused through the lamina propria and muscular wall of the bowel wall by passing between rather than through the myocytes. These descriptive phenomena provide new insight into the role of the enterocyte and intestinal immune cells in the translocation process.
Sensitive and specific discrimination of pathogenic and nonpathogenic Escherichia coli using Raman spectroscopy—a comparison of two multivariate analysis techniques (2013)

The determination of bacterial identity at the strain level is still a complex and time-consuming endeavor. In this study, visible wavelength spontaneous Raman spectroscopy has been used for the discrimination of four closely related Escherichia coli strains: pathogenic enterohemorrhagic E. coli O157:H7 and non-pathogenic E. coli C, E. coli Hfr K-12, and E. coli HF4714. Raman spectra from 600 to 2000 cm(-1) were analyzed with two multivariate chemometric techniques, principal component-discriminant function analysis and partial least squares-discriminant analysis, to determine optimal parameters for the discrimination of pathogenic E. coli from the non-pathogenic strains. Spectral preprocessing techniques such as smoothing with windows of various sizes and differentiation were investigated. The sensitivity and specificity of both techniques was in excess of 95%, determined by external testing of the chemometric models. This study suggests that spontaneous Raman spectroscopy with visible wavelength excitation is potentially useful for the rapid identification and classification of clinically-relevant bacteria at the strain level.