gebhart/patrepeval huggingface dataset:
Whole-Genome Amplification by Single-Cell Comparative Genomic Hybridization PCR (SCOMP) (2008)

INTRODUCTIONPCR-based whole-genome amplification (WGA) has the goal of generating microgram quantities of genome-representative DNA from picogram or nanogram amounts of starting material. This amplification should introduce little, or ideally no, representational bias. In contrast to other techniques for WGA, PCR-based methods are generally less affected by DNA quality and are more applicable to DNA extracted from various sources (fixed and fresh tissues). Ligation-mediated PCR techniques involve ligating an adaptor sequence onto a "representation" of DNA molecules, generated following enzymatic digestion, random shearing, or chemical cleavage. Single-cell comparative genomic hybridization (SCOMP), described in this protocol, is a form of ligation-mediated PCR that was specifically designed for WGA of extremely limited sources of genomic DNA. The reaction volume is purposely kept to a minimum, and all buffers are optimized to eliminate the need to purify the reaction between steps. In addition, the entire reaction is performed in a single tube. This avoids initial template loss and reduces the risk of PCR contamination. SCOMP begins by converting the genome to a high-complexity representation with a fragment size of <2 kb by digesting with the restriction enzyme MseI. This results in a smear in the range of 100-1500 bp. Following enzyme digestion, adaptors containing specific primer sequences (specific to the restriction enzyme used) are ligated onto the ends of the genomic DNA and amplified in a high-stringency PCR. This results in a smear of PCR products in the range of 100-1500 bp, which can be visualized by agarose gel electrophoresis.
The Science of Photobiology (1974)

Formation of the American Society for Photobiology for meeting the needs of investigators studying the effects of light on man and other organisms is described. The scientific program of the first meeting of the society included discussions of the followiug topics: detrimental effects of excessive exposure to sunlight and artificial uv radiation; repair of uv-induced damage to cells; the roles of light in the human environnnent; photochemistry in photobiology; effects of near uv light; photosynthesis; bioluminescence; light perception without eyes; chronobiology; the ultraviolet world of insects; vision; and solar energy conversion. (HLW)
Planar holographic optical processing devices (2001)

Time-domain optical processing implemented through linear spectral filtering offers unique potential for future high-bandwidth communications systems. One key to realization of this potential is the development of robust, cost-effective, fully integrated filtering devices. A new spectral filtering device concept, derived from the unique properties of index holograms stamped or otherwise written in thin planar waveguide slabs, is described. The holograms that are described provide for high-resolution spectral filtering while at the same time mapping general input spatial waveforms to desired output waveforms.
Extended focused image in microscopy by digital holography (2005)

In microscopy, high magnifications are achievable for investigating micro-objects but the paradigm is that higher is the required magnification, lower is the depth of focus. For an object having a three-dimensional (3D) complex shape only a portion of it appears in good focus to the observer who is essentially looking at a single image plane. Actually, two approaches exist to obtain an extended focused image, both having severe limitations since the first requires mechanical scanning while the other one requires specially designed optics. We demonstrate that an extended focused image of an object can be obtained through digital holography without any mechanical scanning or special optical components. The conceptual novelty of the proposed approach lies in the fact that it is possible to completely exploit the unique feature of DH in extracting all the information content stored in hologram, amplitude and phase, to extend the depth of focus.
A smoothness priors long AR model method for spectral estimation (1985)

A new smoothness priors long AR model method approach is taken to the short data span spectral estimation problem. An autoregressive (AR) model that is relatively long compared to the data length is considered. The smoothness priors are in the form of the integrated squared derivatives of the AR model whitening filter. A smoothness tradeoff parameter or Bayesian hyperparameter balances the tradeoff between the infidelity of the AR model to the data and the infidelity of the model to the smoothness constraint. The critical computation of the likelihood of the hyperparameters of the Bayesian model is realized by a constrained least squares computation. Numerical examples are shown. The results of simulation studies using entropy comparison evaluations of the Bayesian and minimum AIC-AR methods of spectral estimation are also shown.
Mapping of transcription start sites in Saccharomyces cerevisiae using 5′ SAGE (2005)

A minimally addressed area in Saccharomyces cerevisiae research is the mapping of transcription start sites (TSS). Mapping of TSS in S.cerevisiae has the potential to contribute to our understanding of gene regulation, transcription, mRNA stability and aspects of RNA biology. Here, we use 5' SAGE to map 5' TSS in S.cerevisiae. Tags identifying the first 15-17 bases of the transcripts are created, ligated to form ditags, amplified, concatemerized and ligated into a vector to create a library. Each clone sequenced from this library identifies 10-20 TSS. We have identified 13,746 unique, unambiguous sequence tags from 2231 S.cerevisiae genes. TSS identified in this study are consistent with published results, with primer extension results described here, and are consistent with expectations based on previous work on transcription initiation. We have aligned the sequence flanking 4637 TSS to identify the consensus sequence A(A(rich))5NPyA(A/T)NN(A(rich))6, which confirms and expands the previous reported PyA(A/T)Pu consensus pattern. The TSS data allowed the identification of a previously unrecognized gene, uncovered errors in previous annotation, and identified potential regulatory RNAs and upstream open reading frames in 5'-untranslated region.
Critical Contribution of Ox40 Ligand to T Helper Cell Type 2 Differentiation in Experimental Leishmaniasis (2000)

Infection of inbred mouse strains with Leishmania major is a well characterized model for analysis of T helper (Th)1 and Th2 cell development in vivo. In this study, to address the role of costimulatory molecules CD27, CD30, 4-1BB, and OX40, which belong to the tumor necrosis factor receptor superfamily, in the development of Th1 and Th2 cells in vivo, we administered monoclonal antibody (mAb) against their ligands, CD70, CD30 ligand (L), 4-1BBL, and OX40L, to mice infected with L. major. Whereas anti-CD70, anti-CD30L, and anti-4-1BBL mAb exhibited no effect in either susceptible BALB/c or resistant C57BL/6 mice, the administration of anti-OX40L mAb abrogated progressive disease in BALB/c mice. Flow cytometric analysis indicated that OX40 was expressed on CD4(+) T cells and OX40L was expressed on CD11c(+) dendritic cells in the popliteal lymph nodes of L. major-infected BALB/c mice. In vitro stimulation of these CD4(+) T cells showed that anti-OX40L mAb treatment resulted in substantially reduced production of Th2 cytokines. Moreover, this change in cytokine levels was associated with reduced levels of anti-L. major immunoglobulin (Ig)G1 and serum IgE. These results indicate that anti-OX40L mAb abrogated progressive leishmaniasis in BALB/c mice by suppressing the development of Th2 responses, substantiating a critical role of OX40-OX40L interaction in Th2 development in vivo.
Characteristics of a protease inhibitor produced by Prevotella intermedia (1994)

The characterization of a protease inhibitor produced by a strain of Prevotella intermedia is reported in the present study. The protease inhibitor was secreted into the culture medium during the exponential growth phase and was also present in significant amounts in the periplasmic space. The inhibitor was active against a wide variety of proteolytic enzymes, including the trypsin-like activity of Porphyromonas gingivalis. The inhibitory compound, a heat labile protein, was isolated by non-denaturing preparative polyacrylamide gel electrophoresis, using concentrated culture supernatant as starting material. The exact functions and the ecological roles of the protease inhibitor produced by P. intermedia remain to be determined.
Hematopoietic Differentiation of Embryonic Stem Cells: An In Vitro Model to Study Gene Regulation during Megakaryocytopoiesis (1996)

We are interested in the regulation of the tissue specificity of the megakaryocyte-specific platelet glycoprotein IIb gene. The murine embryonic stem (ES) cells are able to differentiate into erythroid, mast and granulomonocytic cells in appropriate culture conditions. Our goal is to optimize the production of myeloid cells including megakaryocytes (MKs) by ES cells. We have found that coculture with MS-5 stromal cells and the presence of a cocktail of hematopoietic growth factors (HGFs) [stem cell factor, interleukin 3 (IL-3), IL-6, IL-11, G-CSF and erythropoietin] had a high synergistic activity on differentiation of ES cells into pure and MK-containing myeloid colonies from day 12 embryoid bodies. Thrombopoietin increased the number of MKs only when added to the HGF cocktail in the presence of MS-5 cells. Interestingly, many MKs exhibited a "hairy" appearance evocative of pseudopodial proplatelet formation. Expression of genes specific for the megakaryocytic lineage, GPIIb, PF4, mpl and GPIIIa, was detected by reverse transcriptase-polymerase chain reaction (RT-PCR) during differentiation of ES cells, and their relative time course was evaluated. This demonstrates that optimized culture conditions for the differentiation of ES cells into the MK lineage provide a useful tool for the study of the regulation of expression of genes during megakaryocytopoiesis. Stem Cells
Systemic cholesterol crystal embolisation with pulmonary involvement: a fatal combination after coronary angiography (2002)

Cholesterol crystal embolisation (CCE) is a rare but serious complication of invasive arterial procedures associated with a high mortality, and is a condition that medical staff undertaking invasive vascular procedures should be aware of. It is manifest as a multisystem disorder commonly involving the kidneys and peripheries, but rarely affecting the lungs. A case of fatal CCE with pulmonary involvement is reported, and similar published case reports are reviewed. The pathogenesis of lung involvement in CCE is unclear, but the combination is reported to be invariably fatal.
Isolation of an asporogenic (<i>spoOA</i>) protective antigen-producing strain of <i>Bacillus anthracis</i> (1999)

We found that Congo red agar allows identification of sporulation-deficient Bacillus anthracis. Using Congo red agar, we isolated an asporogenic derivative of the protective antigen-producing strain B. anthracis delta Sterne-1(pPA102). Polymerase chain reaction and Southern hybridization analyses of DNA from the asporogenic mutant revealed that a deletion was present in spoOA, an essential gene for the initiation of sporulation. The deletion also encompassed the spoIVB homologue and a portion of the recN homologue. The avirulent spoOA strain delta Sterne-1(pPA102)CR4 is suitable for the safe production of protective antigen without endospore contamination of the vaccine production facility.
Clear-Cell Chondrosarcoma (1988)

A case of clear-cell chondrosarcoma occurred in the proximal femur of a 32-year-old man. The tumor was complicated by a focus of myositis ossificans resulting from a previous intralesional biopsy. Histologic findings included an unusual marrow infiltration by the tumor. The patient was treated with wide resection and has no evidence of local recurrence or distant spread of disease 18 months later.
Location sensing and privacy in a context-aware computing environment (2002)

This article presents and evaluates the performance of a location sensing algorithm developed and demonstrated at Carnegie Mellon University. We compare our model with various others based on different architectures and software paradigms. We show comparative results in accuracy, the complexity of training, total power consumption, and suitability to users. Our method reduces training complexity by a factor of eight over previous algorithms, and yields noticeably better accuracy. The algorithm uses less power than previous models, and offers a more secure privacy model.
Neuropsychological and quality of life outcomes 12 months after unilateral thalamic stimulation for essential tremor (2003)

Cognitive, mood, and QoL outcomes after one year of DBS for ET are favourable; there were no overall deleterious effects on cognition, and DBS was accompanied by a significant reduction in anxiety and improvements in quality of life. However, preoperative verbal fluency diminution may predispose to further fluency declines after DBS.
Bovine factor X1 (Stuart factor). Mechanism of activation by a protein from Russell's viper venom (1972)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTBovine factor X1 (Stuart factor). Mechanism of activation by a protein from Russell's viper venomKazuo Fujikawa, Mark E. Legaz, and Earl W. DavieCite this: Biochemistry 1972, 11, 26, 4892–4899Publication Date (Print):December 19, 1972Publication History Published online1 May 2002Published inissue 19 December 1972https://pubs.acs.org/doi/10.1021/bi00776a003https://doi.org/10.1021/bi00776a003research-articleACS PublicationsRequest reuse permissionsArticle Views101Altmetric-Citations128LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-Alertsclose Get e-Alerts
Targeted intracellular delivery of photosensitizers to enhance photodynamic efficiency (2000)

Photodynamic therapy (PDT) is a novel treatment, used mainly for anticancer therapy, that depends on the retention of photosensitizers (PS) in tumour cells and irradiation of the tumour with appropriate wavelength light. Photosensitizers are molecules such as porphyrins and chlorins that, on photoactivation, effect strongly localized oxidative damage within target cells. The PS used for PDT localize in various cytoplasmic membranous structures, but are not found in the most vulnerable intracellular sites for reactive oxygen species, such as the cell nucleus. The experimental approaches discussed in the present paper indicate that it is possible to design highly efficient molecular constructs, PS carriers, with specific modules conferring cell-specific targeting, internalization, escape from intracellular vesicles and targeting to the most vulnerable intracellular compartments, such as the nucleus. Nuclear targeting of these PS-carrying constructs results in enhanced photodynamic activity, maximally about 2500-fold that of free PS. Future work is intended to optimize this approach to the point at which tumour cells can be killed rapidly and efficiently, while minimizing normal cell and tissue damage.
Qualitative modeling and simulation: promise or illusion (1991)

In this panel discussion, questions shall be addressed relating to the potential usefulness of qualitative modeling and simulation. When might qualitative versus quantitative modeling/simulation be justified? What types of qualitative models if any are useful and under which conditions? What can qualitative simulations reveal that quantitative simulations cannot? Under what conditions are combined quantitative/qualitative models feasible/meaningful? In this article, some basic definitions are presented that may serve as a basis for the discussion. After all, we must first agree on some common ground before particular properties can be explored.
Charakteristische Parameter der dielektrischen Relaxationszeit starrer Dipolmolekeln in verdünnter Lösung / Characteristic Parameters of the Dielectric Relaxation Time of Rigid Dipole Molecules in Diluted Solution (1970)

The dielectric relaxation time of rigid polar molecules in dilute solutions is shown to depend exponentially on an effective molecular radius which is independent of the solvent. This relation contains a temperature-dependent structure parameter, the coefficients of which are used to calculate the activation energy and -entropy of the rate process. The resulting entropies are now more satisfying due to a new formulation of the scattering factor. Similarly the viscosity of the solvent and its structure parameters are related by an exponential law. A characteristical length in this relation is a measure of the "hole distance" of the rate process. From both exponential laws follows that the dielectric relaxation time raised to the power of the ratio of effective molecular radius to hole distance is proportional to the viscosity of the solvent
Analysis of the Receptor Binding Domain of Gpa1p, the G α Subunit Involved in the Yeast Pheromone Response Pathway (1997)

The Saccharomyces cerevisiae G protein alpha subunit Gpa1p is involved in the response of both MATa and MAT alpha cells to pheromone. We mutagenized the GPA1 C terminus to characterize the receptor-interacting domain and to investigate the specificity of the interactions with the a- and alpha-factor receptors. The results are discussed with respect to a structural model of the Gpa1p C terminus that was based on the crystal structure of bovine transducin. Some mutants showed phenotypes different than the pheromone response and mating defects expected for mutations that affect receptor interactions, and therefore the mutations may affect other aspects of Gpa1p function. Most of the mutations that resulted in pheromone response and mating defects had similar effects in MATa and MAT alpha cells, suggesting that they affect the interactions with both receptors. Overexpression of the pheromone receptors increased the mating of some of the mutants tested but not the wild-type strain, consistent with defects in mutant Gpa1p-receptor interactions. The regions identified by the mating-defective mutants correlated well with the regions of mammalian G(alpha) subunits implicated in receptor interactions. The strongest mating type-specific effects were seen for mutations to proline and a mutation of a glycine residue predicted to form a C-terminal beta turn. The analogous beta turn in mammalian G(alpha) subunits undergoes a conformational change upon receptor interaction. We propose that the conformation of this region of Gpa1p differs during the interactions with the a- and alpha-factor receptors and that these mating type-specific mutations preclude the orientation necessary for interaction with one of the two receptors.
Precursor Cells in the Subventricular Zone of the Adult Mouse Are Actively Inhibited from Differentiating into Neurons (2000)

The adult mouse subventricular zone (SVZ) contains precursor cells capable of generating new neurons which populate the olfactory bulb. The SVZ precursors, however, appear to be restricted in their capacity to generate neurons in other regions of the brain indicating a tight regulation of their differentiation. We demonstrate in vitro that explants of SVZ are unable to generate neurons from dividing precursors, even though precursors are present and dividing within explant cultures. However, when plated as single cells in fibroblast growth factor-1 or with no growth factor, approximately 1% of harvested cells gave rise to clones containing neurons and astrocytes, indicating that bipotential precursors were present in the explants. Inhibitory effects of cell density were more directly shown by plating freshly isolated SVZ cells, or explant-derived SVZ cells, at increasing cell density. The frequency of neuron-containing wells was found to be greatly reduced at higher cell concentrations: >100 cells/well in the case of explant-derived cells and >500 cells in the case of freshly isolated cells. Thus, it appears that the precursor's ability to generate neurons is actively inhibited by paracrine mechanisms which may be mediated by either cell-cell contact or by short-range factors.
Immunoglobulin VH region genes of the mouse are organized in overlapping clusters (1987)

Restriction fragment length polymorphism has been compared between the Igh loci of C57BL/6 and MOLF/EI (Mus musculus molossinus) mice utilizing probes which detect the C gamma 2b gene and genes from nine VH-gene families. Distinct restriction site patterns were found for the CH genes and for VH families PC7183, Q52 and X24. VH families V31 and J558 showed identical patterns. Mixed patterns of identical and distinct bands were detected in VH families S107, J606, V3660 and VGAM3.8. This indicates that a recombination took place involving the Igh loci of a M. m. molossinus and a progenitor of the C57BL/6 strain. The breakpoint of recombination maps to the chromosomal region carrying VH families S107, J606, VGAM3.8 and V3660. VH families PC7183, Q52 and X24 map 3' to the recombination breakpoint and proximal to the DH-JH-CH region, whereas VH families V31 and J558 accordingly map 5' to the recombination breakpoint and distal to DH-JH-CH. This order of VH families was confirmed by deletion mapping utilizing hybridomas which are haploid either for the Ighb or for the Igha locus. The mapping data indicate that the VH families of the mouse are organized in overlapping clusters. This notion is confirmed by demonstration of the physical linkage of VH genes from families V31 and J558 in the Igha locus.
Donor Human Milk for the High-Risk Infant: Preparation, Safety, and Usage Options in the United States (2016)

The use of donor human milk is increasing for high-risk infants, primarily for infants born weighing <1500 g or those who have severe intestinal disorders. Pasteurized donor milk may be considered in situations in which the supply of maternal milk is insufficient. The use of pasteurized donor milk is safe when appropriate measures are used to screen donors and collect, store, and pasteurize the milk and then distribute it through established human milk banks. The use of nonpasteurized donor milk and other forms of direct, Internet-based, or informal human milk sharing does not involve this level of safety and is not recommended. It is important that health care providers counsel families considering milk sharing about the risks of bacterial or viral contamination of nonpasteurized human milk and about the possibilities of exposure to medications, drugs, or herbs in human milk. Currently, the use of pasteurized donor milk is limited by its availability and affordability. The development of public policy to improve and expand access to pasteurized donor milk, including policies that support improved governmental and private financial support for donor milk banks and the use of donor milk, is important.