gebhart/patrepeval huggingface dataset:
Enhanced Pedon Horizonation Using Portable X-ray Fluorescence Spectrometry (2012)

Soil pedons are commonly differentiated into a succession of horizons based on observable differences in soil color, texture, structure, or other characteristics, which are essentially associated with or determined by the chemical composition of soil materials. Portable X-ray fluorescence spectrometry (PXRF), which provides scanning results in ∼60 to 90 s, offers a rapid means of quantifying elemental concentrations in the soil. This research evaluated the use of PXRF on 10 soil pedons in Louisiana for enhanced identification of soil horizons based on differences in elemental concentrations. Three quantifiable measures, difference of clay contents (DC), difference of laboratory analysis results (DLA), and difference of PXRF elemental concentrations (DE), were established based on principal component analysis for evaluating PXRF for soil horizonation. The results showed the variations of PXRF elemental concentrations (DE) in the pedons matched with described horizons better than those of laboratory (DLA) or clay (DC) measures in terms of horizon uniqueness. Furthermore, the PXRF scans conducted under field, lab, or monolith conditions achieved almost the same results. This will allow the use of PXRF as a means of discreetly differentiating elemental differences in archived monoliths with implications for adjustments to their taxonomic classification and land use recommendations. In summary, PXRF was shown to be an effective tool for enhanced soil horizon differentiation on alluvial soils in Louisiana.
Direct preparation of organically modified MCM-type materials. Preparation and characterisation of aminopropyl–MCM and 2-cyanoethyl–MCM (1996)

D. J. Macquarrie, Chem. Commun., 1996, 1961 DOI: 10.1039/CC9960001961
Expression of ACC oxidase promoter—GUS fusions in tomato and Nicotiana plumbaginifolia regulated by developmental and environmental stimuli (1997)

The enzyme ACC oxidase, catalysing the last step in the biosynthesis of the plant hormone ethylene, is encoded by a small multigene family in tomato, comprising three members, LEACO1, LEACO2 and LEACO3. LEACO1 is the major gene expressed during ripening, leaf senescence, and wounding (Barry et al., 1996). To investigate the transcriptional regulation of ACC oxidase gene expression, chimeric fusions between the beta-glucuronidase reporter gene and 97 bp of 5' UTR plus 124, 396 and 1825 bp, respectively, of 5' untranscribed LEACO1 sequence were constructed and introduced into Lycopersicon esculentum (Mill cv. Ailsa Craig) and Nicotiana plumbaginifolia. Analysis of transgenic tomatoes indicated that the region containing nucleotides -124 to +97 of the LEACO1 gene is sufficient to confer a marked increase in GUS activity during fruit ripening, albeit at very low levels. Fusion of 396 and 1825 bp of LEACO1 upstream sequence resulted in strong and specific induction of GUS expression in situations known to be accompanied by enhanced ethylene production. Reporter gene expression was similar to that of the endogenous LEACO1 gene, with major increases especially during fruit ripening, senescence and abscission of leaves and, to a lesser extent, of flowers. Analysis of transgenic N. plumbaginifolia plants confirmed the pattern of LEACO1 promoter activity detected in tomato leaves and flowers. Reporter gene expression was also induced following wounding, treatment with ethylene, and pathogen infection. Histochemical analysis illustrated localized GUS activity in the pericarp of ripening fruit, abscission zones of senescent petioles and unfertilized flowers, and at wound sites. These results demonstrate that ACC oxidase is regulated at the transcriptional level in a wide range of cell types at different developmental stages and in response to several external stimuli.
The autosomal recessive juvenile Parkinson disease gene product, parkin, interacts with and ubiquitinates synaptotagmin XI (2003)

Inactivating mutations of the gene encoding parkin are responsible for some forms of autosomal recessive juvenile Parkinson disease. Parkin is a ubiquitin ligase that ubiquitinates misfolded proteins targeted for the proteasome-dependent protein degradation pathway. Using the yeast two-hybrid system and co-immunoprecipitation methods, we identified synaptotagmin XI as a protein that interacts with parkin. Parkin binds to the C2A and C2B domains of synaptotagmin XI resulting in the polyubiquitination of synaptotagmin XI. Truncated and missense mutated parkins reduce parkin-sytXI binding affinity and ubiquitination. Parkin-mediated ubiquitination also enhances the turnover of sytXI. In sporadic PD brain sections, sytXI was found in the core of the Lewy bodies. Since synaptotagmin XI is a member of the synaptotagmin family that is well characterized in their importance for vesicle formation and docking, the interaction with this protein suggests a role for parkin in the regulation of the synaptic vesicle pool and in vesicle release. Loss of parkin could thus affect multiple proteins controlling vesicle pools, docking and release and explain the deficits in dopaminergic function seen in patients with parkin mutations.
Clinical Use of Cooled Radiofrequency Ablation (2008)

Irrigated (cooled) radiofrequency (RF) ablation has become our primary ablation tool for treating atrial fibrillation, macroreentrant atrial tachycardias, and scar-related ventricular tachycardias. As with any technology that increases ablation lesion size, there is the potential for increased risk. The methods described are a cautious approach to power titration that considers the risks of excessive heating and the lesion size needed for a particular site. Future methods of assessing lesion creation will hopefully refine energy titration to improve safety and efficacy of cooled RF ablation.
Organoids recapitulate organs? (2018)

The gastrointestinal (GI) tract is a complex organ system derived from a simple hollow long tube generated in early human development. The GI tract is developed by a series of complex mutual interactions among several types of cells derived from all three germ layers during development (1).
Activation of β-Catenin in Dendritic Cells Regulates Immunity Versus Tolerance in the Intestine (2010)

Dendritic cells (DCs) play a vital role in initiating robust immunity against pathogens as well as maintaining immunological tolerance to self antigens. However, the intracellular signaling networks that program DCs to become tolerogenic remain unknown. We report here that the Wnt-beta-catenin signaling in intestinal dendritic cells regulates the balance between inflammatory versus regulatory responses in the gut. beta-catenin in intestinal dendritic cells was required for the expression of anti-inflammatory mediators such as retinoic acid-metabolizing enzymes, interleukin-10, and transforming growth factor-beta, and the stimulation of regulatory T cell induction while suppressing inflammatory effector T cells. Furthermore, ablation of beta-catenin expression in DCs enhanced inflammatory responses and disease in a mouse model of inflammatory bowel disease. Thus, beta-catenin signaling programs DCs to a tolerogenic state, limiting the inflammatory response.
The Dendritic Box: Shape-Selective Liberation of Encapsulated Guests (1995)

No abstract.
Two‐year follow up of women randomised to medical management or transcervical resection of the endometrium for heavy menstrual loss: clinical and quality of life outcomes (1999)

Objective To assess clinical status and changes in health related quality of life after two years in women randomised to medical management or transcervical resection of the endometrium (TCRE) for treatment of heavy menstrual loss. Design Two‐year follow up using postal questionnaires and operative databank review. Setting Gynaecology department of a large UK teaching hospital. Participants Women who had joined a randomised comparison of medical treatment with TCRE for heavy menstrual loss two years previously. Main outcome measures Women's satisfaction with treatment, gynaecological symptoms, changes in health related quality of life, and additional treatments received at two years. Results Women allocated medical treatment were significantly less likely to be totally or generally satisfied (57% vs 79%, difference −22%, 95% CI −36, −9%), to find their management acceptable (77% vS 93%. difference −16%, 95% CI −26, A%) , or to recommend their allocated treatment (24% vs 78%, difference −54%, 95% CI −61, −33%). In the medical cohort 59% of women had undergone TCRE, hysterectomy or both, whereas 17% in the TCRE cohort had undergone further surgery. Bleeding and pain scores were similar in the groups and highly significantly better than at recruitment. Short Form‐36 health survey scores were significantly improved from baseline for five of the eight health scores in the medical arm, and seven in the TCRE arm. Conclusions The results at two years consolidate the findings and conclusions based on the four‐month follow up data. A policy of early TCRE is effective and safe and does not result in an increase in hysterectomies. It should not be routinely withheld in an effort to try alternative medical therapies.
The case for polyvalent cancer vaccines that induce antibodies (2002)

Antibodies are ideally suited for eradicating pathogens from the bloodstream and early tissue invasion. With regard to cancer cells, passively administered and vaccine induced antibodies have accomplished this, eliminating circulating tumor cells and systemic or intraperitoneal micrometastases in a variety of preclinical models. A series of cancer cell-surface differentiation antigens have now been identified and synthesized. Antibodies against each can be induced in most vaccinated patients using keyhole limpet hemocyanin conjugate vaccines with a potent immunological adjuvant. Polyvalent vaccines may be required due to tumor cell heterogenely, heterogeneity of the human immune response and the correlation between overall antibody titer against tumor cells and antibody effector mechanisms. Trials testing the clinical impact of these polyvalent vaccines in the adjuvant setting are planned for the near future.
Metabolic effects of short‐chain ceramide and glucosylceramide on sphingolipids and protein kinase C (1992)

Recent studies have identified a potential role for glucosylceramide (GlcCer) in growth promotion and hormonal signalling. In an effort to demonstrate a growth-promoting activity of GlcCer, we prepared a GlcCer having a short-chain acid (octanoyl), in the belief that this glycolipid could be absorbed more readily and more uniformly by cultured cells. By using a mixture of two specific lecithins, dioleoylglycerophosphocholine and 1-stearoyl-2-palmitoylglycerophosphocholine, we were able to prepare dispersions containing a high molar proportion of the GlcCer and the related ceramide, octanoyl sphingosine. Unexpectedly, both sphingolipids inhibited protein and DNA synthesis in Madin-Darby canine kidney cells and produced large increases in the levels of the natural lipids, GlcCer, ceramide, free sphingosine, and an amine that may be glucosylsphingosine (GlcSph). Decreases were seen in the level of sphingomyelin and the proportion of protein kinase C in the cell membranes. The level of lactosylceramide was diminished by octanoyl GlcCer but elevated considerably by octanoyl sphingosine. Diacylglycerols were increased by the lecithins in the liposomes, but the exogenous sphingolipids had no effect. Octanoyl sphingosine labeled in the sphingoid base yielded labeled GlcCer and sphingomyelin labeled in both long-chain and very-long-chain fatty acid families, as well as the octanoyl version. The two families of ceramides, however, had relatively little radioactivity. Some of these changes are attributed to rapid hydrolysis of the added lipids with the formation, particularly from the ceramide, of sphingosine and its anabolic metabolite, GlcSph. Several observations support the idea that the octanoyl sphingosine inhibited the phosphocholinetransferase that synthesizes sphingomyelin while the octanoyl GlcCer inhibited GlcCer beta-glucosidase and GlcCer galactosyltransferase. The use of unnatural short-chain lipids in the study of cell growth and other phenomena may result in unexpected changes in related metabolites and the findings from such experiments should therefore be interpreted cautiously.
Immunization with human papillomavirus type 16 (HPV16) oncoprotein-loaded dendritic cells as well as protein in adjuvant induces MHC class I-restricted protection to HPV16-induced tumor cells. (1998)

Human papillomavirus (HPV) E6 and E7 oncoproteins are attractive targets for T-cell-based immunotherapy of cervical cancer. In this study, we demonstrate that dendritic cells (DCs) pulsed with HPV16 E7 protein are not only recognized in vitro by E7-specific CTLs but also elicit E7-specific CTL responses in vivo, associated with protection against a challenge with syngeneic HPV16-induced tumor cells. Vaccination with soluble E7 protein in incomplete Freund's adjuvant likewise induces E7-specific CTL responses associated with tumor protection. The presence of HPV16 E7-specific CTLs in vivo and the observation that depletion of CD8+ cells completely abolishes tumor protection demonstrate that CTLs are the major effector cells in mediating antitumor activity. The in vivo involvement of DCs in the activation of protective CTLs is suggested by the surface display of E7 peptide-loaded MHC class I molecules on these cells after E7 protein immunization. These data show that HPV16 E7 protein-pulsed DCs, as well as the administration of E7 protein antigen in adjuvant, can effectively stimulate tumor-specific MHC class I-restricted CD8+ T-cell-mediated protective immunity to HPV16-induced cancers.
The inhibition of bacterial growth by hypochlorous acid. Possible role in the bactericidal activity of phagocytes (1988)

The 'respiratory burst' of phagocytes such as neutrophils generates superoxide which forms H2O2 by dismutation. H2O2 and Cl- ions serve as substrates for the enzyme myeloperoxidase to generate hypochlorous acid (HOCl). HOCl is thought to play an important role in bacterial killing, but its mechanism of action is not well characterized. Furthermore, although many studies in vitro have shown HOCl to be a damaging oxidant with little or no specificity (particularly at high concentrations), bacteria which have been ingested by phagocytes appear to experience a rapid and selective inhibition of cell division. Bacterial membrane disruption, protein degradation, and inhibition of protein synthesis, do not seem to occur in the early phases of phagocyte action. We have now found that low concentrations of HOCl exert a rapid and selective inhibition of bacterial growth and cell division, which can be blocked by taurine or amino acids. Only 20 microM-HOCl was required for 50% inhibition of bacterial growth (5 x 10(8) Escherichia coli/ml), and 50 microM-HOCl completely inhibited cell division (colony formation). These effects were apparent within 5 min of HOCl exposure, and were not reversed by extensive washings. DNA synthesis (incorporation of [3H]-thymidine) was significantly affected by even a 1 min exposure to 50 microM-HOCl, and decreased by as much as 96% after 5 min. In contrast, bacterial membrane disruption and extensive protein degradation/fragmentation (release of acid-soluble counts from [3H]leucine-labelled cells) were not observed at concentrations below 5 mM-HOCl. Protein synthesis (incorporation of [3H]leucine) was only inhibited by 10-30% following 5 min exposure to 50 microM-HOCl, although longer exposure produced more marked reductions (80% after 30 min). Neutrophils deficient in myeloperoxidase cannot convert H2O2 to HOCl, yet can kill bacteria. We have found that H2O2 is only 6% as effective as HOCl in inhibiting E. coli growth and cell division (0.34 mM-H2O2 required for 50% inhibition of colony formation), and taurine or amino acids do not block this effect. Our results are consistent with a rapid and selective inhibition of bacterial cell division by HOCl in phagocytes. H2O2 may substitute for HOCl in myeloperoxidase deficiency, but by a different mechanism and at a greater metabolic cost.
Noninvasive Photonic-Crystal Material for Sensing Glucose in Tears (2004)

Most noninvasive (NI) methods for the determination of glucose either detect a small specific glucose signal or measure the effect of glucose on a tissue optical property (1)(2). A recent review identified the three main issues in NI glucose measurements as specificity, compartmentalization of glucose values, and calibration (1). This editorial discusses a photonic crystal method (3), with respect to these issues.

Asher’s group have developed a novel photonic sensing material that responds to glucose concentrations via diffraction of visible light. Polymerized crystalline colloidal arrays (PCCAs) are periodic crystalline lattices of polystyrene microspheres polymerized within thin hydrogel films (3)(4)(5)(6)(7). The arrays are brightly colored and act as diffraction gratings for white light according to the Bragg diffraction equation (4)(5): \batchmode \documentclass[fleqn,10pt,legalpaper]{article} \usepackage{amssymb} \usepackage{amsfonts} \usepackage{amsmath} \pagestyle{empty} \begin{document} \[{\Delta}{\lambda} {=} \frac{n {\times} d}{\mathrm{sin}{\Theta}}\] \end{document} In Eq. 1, n is the refractive index of the system (medium, hydrogel, and colloids), d is the spacing between the diffracting planes, λ is the diffracted wavelength, and Θ is the glancing angle between the incident light and the diffracting planes. A change in electric charge in the PCCAs resulting from binding of molecular or ionic species causes changes the spacing, d , and there is a subsequent wavelength shift, Δλ, of the light reflected off the array.

Asher’s group have constructed a photonic glucose sensor in the form of thin acrylamide PCCA hydrogel films that contain glucose molecular recognition elements (3)(6)(7). Phenylboronic acid derivatives …
Mechanisms and Genes of Cellular Suicide (1995)

Apoptosis is a morphologically distinct form of programmed cell death that plays a major role during development, homeostasis, and in many diseases including cancer, acquired immunodeficiency syndrome, and neurodegenerative disorders. Apoptosis occurs through the activation of a cell-intrinsic suicide program. The basic machinery to carry out apoptosis appears to be present in essentially all mammalian cells at all times, but the activation of the suicide program is regulated by many different signals that originate from both the intracellular and the extracellular milieu. Genetic studies in the nematode Caenorhabditis elegans and in the fruit fly Drosophila melanogaster have led to the isolation of genes that are specifically required for the induction of programmed cell death. At least some components of the apoptotic program have been conserved among worms, insects, and vertebrates.
Enzyme-catalysed synthesis of peptides containing D-amino acids (1986)

J. B. West and C. Wong, J. Chem. Soc., Chem. Commun., 1986, 417 DOI: 10.1039/C39860000417
Antibody Fusion Proteins: Anti-CD22 Recombinant Immunotoxin Moxetumomab Pasudotox (2011)

Recombinant immunotoxins are fusion proteins that contain the cytotoxic portion of a protein toxin fused to the Fv portion of an antibody. The Fv binds to an antigen on a target cell and brings the toxin into the cell interior, where it arrests protein synthesis and initiates the apoptotic cascade. Moxetumomab pasudotox, previously called HA22 or CAT-8015, is a recombinant immunotoxin composed of the Fv fragment of an anti-CD22 monoclonal antibody fused to a 38-kDa fragment of Pseudomonas exotoxin A, called PE38. Moxetumomab pasudotox is an improved, more active form of a predecessor recombinant immunotoxin, BL22 (also called CAT-3888), which produced complete remission in relapsed/refractory hairy cell leukemia (HCL), but it had a <20% response rate in chronic lymphocytic leukemia (CLL) and acute lymphoblastic leukemia (ALL), diseases in which the leukemic cells contain much lower numbers of CD22 target sites. Compared with BL22, moxetumomab pasudotox is up to 50-fold more active on lymphoma cell lines and leukemic cells from patients with CLL and HCL. A phase I trial was recently completed in HCL patients, who achieved response rates similar to those obtained with BL22 but without dose-limiting toxicity. In addition to further testing in HCL, moxetumomab pasudotox is being evaluated in phase I trials in patients with CLL, B-cell lymphomas, and childhood ALL. Moreover, protein engineering is being used to increase its activity, decrease nonspecific side effects, and remove B-cell epitopes.
Prevalent Class I-Restricted T-Cell Response to the Theiler’s Virus Epitope Db:VP2121–130in the Absence of Endogenous CD4 Help, Tumor Necrosis Factor Alpha, Gamma Interferon, Perforin, or Costimulation through CD28 (1999)

C57BL/6 mice mount a cytotoxic T-lymphocyte (CTL) response against the Daniel's strain of Theiler's murine encephalomyelitis virus (TMEV) 7 days after infection and do not develop persistent infection or the demyelinating syndrome similar to multiple sclerosis seen in susceptible mice. The TMEV capsid peptide VP2121-130 sensitizes H-2Db+ target cells for killing by central-nervous-system-infiltrating lymphocytes (CNS-ILs) isolated from C57BL/6 mice infected intracranially. Db:VP2121-130 peptide tetramers were used to stain CD8(+) CNS-ILs, revealing that 50 to 63% of these cells bear receptors specific for VP2121-130 presented in the context of Db. No T cells bearing this specificity were found in the cervical lymph nodes or spleens of TMEV-infected mice. H-2(b) mice lacking CD4, class II, gamma interferon, or CD28 expression are susceptible to persistent virus infection but surprisingly still generate high frequencies of CD8(+), Db:VP2121-130-specific T cells. However, CD4-negative mice generate a lower frequency of Db:VP2121-130-specific T cells than do class II negative or normal H-2(b) animals. Resistant tumor necrosis factor alpha receptor I knockout mice also generate a high frequency of CD8(+) CNS-ILs specific for Db:VP2121-130. Furthermore, normally susceptible FVB mice that express a Db transgene generate Db:VP2121-130-specific CD8(+) CNS-ILs at a frequency similar to that of C57BL/6 mice. These results demonstrate that VP2121-130 presented in the context of Db is an immunodominant epitope in TMEV infection and that the frequency of the VP2121-130-specific CTLs appears to be independent of several key inflammatory mediators and genetic background but is regulated in part by the expression of CD4.
Infinite length hash chains and their applications (2003)

Hash chains are used extensively in various cryptography applications such as one-time passwords, server-supported signatures and micropayments. In this paper, we present a method, called infinite length hash chains to improve the flexibility of this chaining idea by using public-key techniques. One of its distinguishing features is that communication and computation overhead of restarting of the system is avoided For the owner of the chain it is possible to go in either way in the chain at any time without any restriction in the chain length, but others see no difference as the functionality it provides with respect to traditional hash chains. On the other hand the drawback here is the increased computation cost due to public-key operations. Part of our work would be considered as one additional step after traditional one-time passwords in the natural progression from fixed password schemes to challenge-response identification protocols.