gebhart/patrepeval huggingface dataset:
A library for light-weight information-flow security in haskell (2008)

Protecting confidentiality of data has become increasingly important for computing systems. Information-flow techniques have been developed over the years to achieve that purpose, leading to special-purpose languages that guarantee information-flow security in programs. However, rather than producing a new language from scratch, information-flow security can also be provided as a library. This has been done previously in Haskell using the arrow framework. In this paper, we show that arrows are not necessary to design such libraries and that a less general notion, namely monads, is sufficient to achieve the same goals. We present a monadic library to provide information-flow security for Haskell programs. The library introduces mechanisms to protect confidentiality of data for pure computations, that we then easily, and modularly, extend to include dealing with side-effects. We also present combinators to dynamically enforce different declassification policies when release of information is required in a controlled manner. It is possible to enforce policies related to what, by whom, and when information is released or a combination of them. The well-known concept of monads together with the light-weight characteristic of our approach makes the library suitable to build applications where confidentiality of data is an issue.
Inositol 1,4,5-trisphosphate-induced Ca2+ signalling is involved in estradiol-induced breast cancer epithelial cell growth (2010)

Altogether, our results are in favour of a role of IICS in MCF-7 cell growth, and we hypothesize that the regulation of IP3R3 expression by E2 is involved in this effect.
Retroviral Mediated Gene Transfer of the Fanconi Anemia Complementation Group C Gene to Hematopoietic Progenitors of Group C Patients. National Institutes of Health, Bethesda, Maryland (1997)

Fanconi Anemia (FA) is a rare genetic disorder characterized by progress pancytopenia, congenial abnormalities, and a predisposition to malignancy. Therapy is currently limited to allogeneic marrow transplantation; patients lacking a suitable donor usually die from aplasia or acute leukemia. Recently, mutation in a novel gene named FACC (Fanconi anemia C-complementing) has been identified as causing one type of FA. FACC mutations, which introduce splicing errors or stop codons, have been identified in approximately 15% of FA patients. We have recently been successful in functional complementation of four FA cell lines using retroviral vectors to transfer a copy of the normal FACC gene. We also analyzed the ability of our viral vectors to functionally correct hematopoietic progenitor cells from a patient bearing a splice donor mutation. As for the lymphoid cell lines, these CD34-enriched cells were extremely sensitive to MMC. After infection of these progenitor cells with viral vectors bearing normal FACC, the progenitors gave rise to increased numbers of colonies both in the absence and presence of up to 5nM MMC, whereas control cells were completely destroyed by 1nM MMC. In summary, we have demonstrated that: (1) retroviral vectors can be engineered to transfer a normal FACC gene to FA(C) lymphoid cell lines and primary hematopoietic cells; (2) introduction of a normal FACC gene into CD34+ progenitors markedly enhances their growth in the absence and presence of MMC. This study is designed to determine whether hematopoietic progenitors transduced with the normal FACC gene can be reinfused safely into FA(C) patients. CD34+ cells obtained from G-CSF mobilized peripheral blood will be transduced ex vivo over a 72-hour period in the presence of IL-3, IL-6, and Stem Cell Factor with the FACC retroviral vector. These transduced cells will be reinfused into FA(C) patients. Patients will be monitored for toxicities as well as evidence of successful gene transfer and expression. The procedure will be repeated up to a total of 4 times with each treatment 2-4 months apart. Theoretically, these rescued stem cells should have a selective growth advantage within the hypoplastic FA marrow environment in vivo.
Expression of Preproinsulin-2 Gene Shapes the Immune Response to Preproinsulin in Normal Mice (2004)

Deciphering mechanisms involved in failure of self tolerance to preproinsulin-2 is a key issue in type 1 diabetes. We used nonautoimmune 129SV/Pas mice lacking preproinsulin-2 to study the immune response to preproinsulin-2. In these mice, a T cell response was detected after immunization with several preproinsulin-2 peptides and confirmed by generating hybridomas. Activation of some of these hybridomas by wild-type (wt) islet cells or recombinant murine proinsulin-2 demonstrated that two epitopes can be generated from the naturally expressed protein. Although T cells from wt mice responded to preproinsulin-2 peptides, we could not detect a response to the naturally processed epitopes in these mice. Moreover, after immunization with recombinant whole proinsulin-2, a T cell response was detected in preproinsulin-2-deficient but not in wt mice. This suggests that islet preproinsulin-2-autoreactive T cells are functionally eliminated in wt mice. We used a transplantation model to evaluate the relevance of reactivity to preproinsulin-2 in vivo. Wild-type preproinsulin-2-expressing islets transplanted in preproinsulin-2-deficient mice elicited a mononuclear cell infiltration and insulin Abs. Graft infiltration was further increased by immunization with preproinsulin-2 peptides. Preproinsulin-2 expression thus shapes the immune response and prevents self reactivity to the islet. Moreover, islet preproinsulin-2 primes an immune response to preproinsulin-2 in deficient mice.
Transactional coherence and consistency: simplifying parallel hardware and software (2004)

Transactional coherence and consistency (TCC) simplifies parallel hardware and software design by eliminating the need for conventional cache coherence and consistency models and letting programmers parallelize a wide range of applications with a simple, lock-free transactional model. TCC eases both parallel programming and parallel architecture design by relying on programmer-defined transactions as the basic unit of parallel work, communication, memory coherence, and memory consistency
The significance ofDemodex folliculorumdensity in rosacea (1998)

Rosacea is a disease of multifactorial origin, and individual properties may modify the severity of the inflammatory response to Demodex. We suggest that a certain mite density is not an appropriate criterion in the diagnosis of the disease; nevertheless, large numbers of D. folliculorum may have an important role in the pathogenesis of rosacea, together with other triggering factors.
ADAM15 Supports Prostate Cancer Metastasis by Modulating Tumor Cell–Endothelial Cell Interaction (2008)

Abstract Using human tumor and cDNA microarray technology, we have recently shown that the ADAM15 disintegrin is significantly overexpressed during the metastatic progression of human prostate cancer. In the current study, we used lentiviral-based short hairpin RNA (shRNA) technology to down-regulate ADAM15 in the metastatic prostate cancer cell line, PC-3. ADAM15 down-regulation dramatically attenuated many of the malignant characteristics of PC-3 cells in vitro and prevented the s.c. growth of PC-3 cells in severe combined immunodeficient (SCID) mice. By inhibiting the expression of ADAM15 in PC-3 cells, we showed decreased cell migration and adhesion to specific extracellular matrix proteins. This was accompanied by a reduction in the cleavage of N-cadherin by ADAM15 at the cell surface. Fluorescence-activated cell sorting analysis revealed reduced cell surface expression of the metastasis-associated proteins αv integrin and CD44. Furthermore, matrix metalloproteinase 9 secretion and activity were abrogated in response to ADAM15 reduction. In an in vitro model of vascular invasion, loss of ADAM15 reduced PC-3 adhesion to, and migration through, vascular endothelial cell monolayers. Using an SCID mouse model of human prostate cancer metastasis, we found that the loss of ADAM15 significantly attenuated the metastatic spread of PC-3 cells to bone. Taken together, these data strongly support a functional role for ADAM15 in prostate tumor cell interaction with vascular endothelium and the metastatic progression of human prostate cancer. [Cancer Res 2008;68(4):1092–9]
[Preparation of liposomes using the phase reversal method without sonication]. (1985)

A simple procedure for preparation of liposomes based on the phase reversal method but differing from the original technique by the absence of ultrasonic treatment, has been developed. Using this method, the effects of NaCl concentration used for the preparation of liposomes from a mixture of neutral and charged lipids, on the inner liposome volume were studied. The experimental data suggest that NaCl concentration may be regarded as a basic criterion determining the size of liposomes in many routine techniques used for the preparation of liposomes from a mixture of neutral and charged lipids.
4. Brave new worlds (2006)

In 1482, a new edition of Ptolemy's Geography was published. This transformed 15th-century perceptions of the shape and size of the earth. ‘Brave new worlds’ shows how Ptolemy's Geography provided the template to be used by 15th- and 16th-century voyages of trade and discovery culminating in the discovery of America, which went on to shape today's ideas on the modern world. The discovery of America revolutionized Renaissance Europe's world picture. It was partly responsible for defining Europe's change from a medieval world to a more modern one. It also brought to the surface a fear of the new and unknown which battled with a desire for wealth.
Influence of mineral content and composition on graylevels in backscattered electron images of bone (1993)

To determine the meaning of graylevels in backscattered electron (BSE) images of actual bone tissues, the influence of mineral content and mineral composition on BSE image graylevels was studied using chick bone tissue representing a broad age range. These tissues were analyzed for BSE image graylevels, Ca/P molar ratios, mineral composition mineral content (v/v), ash fraction (w/w), and density (g/cm3). Linear regression analyses showed that the weighted mean graylevels (WMGLs) in BSE images were positively correlated to ash fraction (r2 = 0.711), mineral content (r2 = 0.720), and density (r2 = 0.843). Although the Ca/P ratio increased from 1.65 in embryos to 1.80 in 2-year olds, the compositional changes corresponding to this Ca/P molar ratio were estimated to produce a relatively minor (< 4.0%) change in BSE image graylevel. These results demonstrate that graylevels in BSE images of actual bone tissue can be attributed to mineral content and density, but only as a coincidence of their association with atomic number.
surface layers and their applications (2005)

Surface (S-) layers are crystalline arrays of proteinaceous subunits present as the outermost component of cell wall in several species of the genus Lactobacillus, as well as in many other bacteria and Archaea. Despite the high similarity of the amino acid composition of all known S-layer proteins, the overall sequence similarity is, however, surprisingly small even between the Lactobacillus S-layer proteins. In addition, the typical characteristics of Lactobacillus S-layer proteins, distinguishing them from other S-layer proteins, are small size and high-predicted pI value. Several lactobacilli possess multiple S-layer protein genes, which can be differentially or simultaneously expressed. To date, the characterized functions of Lactobacillus S-layers are involved in mediating adhesion to different host tissues. A few applications for the S-layer proteins of lactobacilli already exist, including their use as antigen delivery vehicles.
P-selectin blockade does not impair leukocyte host defense against bacterial peritonitis and soft tissue infection in rabbits. (1993)

Adhesion molecules are responsible for PMN-endothelial cell interactions involved in both PMN-mediated endothelial injury (e.g., after ischemia-reperfusion injury) and PMN-mediated host defense against bacterial infection. Inhibition of PMN-endothelial adherence with CD18 and P-selectin mAb has been shown to ameliorate the tissue injury resulting from ischemia and reperfusion under a variety of experimental conditions. However, interference with PMN function may result in an increased risk of bacterial infection. Previous investigations suggest that CD18 blockade can lead to increased infectious risk. Little is known of the infectious risks associated with selectin blockade. We report the effects of P-selectin blockade (using mAb PB1.3) on bacteria-induced PMN emigration into the peritoneum and subcutaneous (s.c.) tissue in rabbits. Leukocyte and PMN emigration into the peritoneum 4 h after inoculation with 10 ml of 10(9) CFU/ml Escherichia coli was significant in saline-treated animals, and not different in animals pretreated with mAb PB1.3. Similarly, the incidence and severity of abscess formation 7 days after s.c. inoculation with Staphylococcus aureus (10(7), 10(8), or 10(9) CFU) was not increased in rabbits pretreated with mAb PB1.3 compared to saline. PMN emigration to the s.c. S. aureus was also similar in both saline and mAb PB1.3-treated animals, as determined by light microscopy. We conclude that P-selectin blockade with mAb PB1.3: 1) does not interfere with acute, E. coli-induced PMN emigration into the peritoneum, 2) does not increase the incidence or severity of S. aureus abscess formation in s.c. tissue, and 3) interferes less with PMN antibacterial host defense mechanisms than inhibition of CD18-mediated PMN adherence.
Characterization of High-light-responsive Promoters of the psaAB Genes in Synechocystis sp. PCC 6803 (2006)

In cyanobacteria, transcription of genes encoding subunits of PSI is tightly repressed under high-light conditions. To elucidate the molecular mechanism, we examined the promoter architecture of the psaAB genes encoding reaction center subunits of PSI in a cyanobacterium Synechocystis sp. PCC 6803. Primer extension analysis showed the existence of two promoters, P1 and P2, both of which are responsible for the light intensity-dependent transcription of the psaAB genes. Deletion analysis of the upstream region of psaAB fused to bacterial luciferase reporter genes (luxAB) indicated that the light response of these promoters is achieved in a totally different manner. The cis-element required for the light response of P1, designated as PE1, was located just upstream of the -35 element of P1 and was comprised of AT-rich sequence showing significant homology to the upstream promoter (UP)-element often found in strong bacterial promoters. PE1 activated P1 under low-light conditions, and the down-regulation of P1 was achieved by rapid inactivation of PE1 upon the shift to high-light conditions. On the other hand, the cis-element required for the light response of P2, designated as HNE2, was located upstream of the P1 region, far from the basal promoter of P2. The down-regulation of P2 seemed to be attained through the negative regulation by HNE2 activated only under high-light conditions. DNA gel mobility shift assays showed that at least five regions in psaAB promoters were responsible for the binding of putative regulatory protein factors.
A comparison of the neurotrophic activities of the flavonoid fisetin and some of its derivatives (2006)

Neurotrophic factors promote the development, maintenance and regeneration of nerve cells. Classical neurotrophic factors are proteins and thus not well-suited for therapeutic purposes. Recently, we showed that specific flavonoids such as fisetin (3, 7, 3', 4' tetrahydroxyflavone) promote the differentiation of nerve cells in culture through the activation of extracellular signal-regulated kinase (ERK) suggesting that flavonoids could substitute for neurotrophic factors. It has also been shown that fisetin promotes nerve cell survival following exposure to toxic oxidative insults. To determine whether or not this is unique to fisetin, a series of related compounds were assayed for neurotrophic activities. Many of these related compounds also promote nerve cell differentiation and are neuroprotective against toxic oxidative insults. However, the mechanisms underlying these neurotrophic effects differ among the compounds.
Syndecan-1 expression in malignant mesothelioma: correlation with cell differentiation, WT1 expression, and clinical outcome (1998)

Syndecan-1 binds basic fibroblast growth factor (bFGF), modulates neovascularization, plays a role in epithelial differentiation and is up-regulated by WT1. Malignant mesothelioma of the pleura is one of the most aggressive tumours known and expresses high levels of angiogenic growth factors. This study has analysed syndecan-1 expression in mesothelioma tumours and cell lines by immunohistochemistry and immunoblotting, using anti-syndecan-1 antibody directed against the core protein, and has examined its relation to morphology, bFGF, WT1, and intra-tumoural microvascular density (IMD). Shedding of syndecan-1 in the conditioned medium of mesothelioma cell lines was detected in variable amounts. These studies indicate that (1) there is no correlation of syndecan-1 with either bFGF expression or IMD in mesotheliomas in vivo; (2) syndecan-1 is strongly expressed in the epithelial type of mesothelioma and in the epithelial component of biphasic mesotheliomas and the expression is reduced or lost in sarcomatoid differentiation; together with the finding that (3) syndecan-1 correlates with WT1 immuno-expression, this suggests that syndecan-1 might relate to the differentiation state of mesothelial/mesothelioma cells; and (4) syndecan-1-positive tumours are associated with a longer survival (p = 0.02) than mesotheliomas with no or little syndecan-1 expression, on univariate analysis. These findings therefore indicate that syndecan-1 can be an important prognostic indicator in mesotheliomas and its loss may be important in the epithelial-mesenchymal transformation of mesothelioma cells.
Error Frequencies of Picornavirus RNA Polymerases: Evolutionary Implications for Virus Populations (2014)

This chapter examines key features of the three main stages in virus evolution with examples drawn from several virus groups. It then reviews specific results with picornaviruses, as well as implications of high mutation rates and quasispecies dynamics for this important and diverse group of pathogens. With the levels of heterogeneity and viral load often seen in infected individuals, RNA virus populations include potentially all possible single mutants and decreasing amounts of multiple mutants. There are probably many routes to drug resistance, including amino acid replacements in the wall of the pocket preventing accommodation of the drug into the pocket (termed "exclusion" mutants), and replacements elsewhere in the capsid that affect viral uncoating. Resistant mutants display decreased affinity for the drug or increased affinity for the receptor, and often show low fitness values relative to their parental counterparts. Studies with picornaviral RNA-dependent RNA polymerases (replicases) face limitations derived from the difficulties in obtaining purified enzymes capable of sustaining multiple rounds of template-dependent copying. Viral quasispecies show features of complex adaptive systems such as mobilization of minority components (individual genomes from the mutant spectrum) in response to external stimuli. New developments in biochemistry and structural biology, and a deeper understanding of the principles governing viral evolution can now be combined to produce practical developments following an extensive (and necessary) accumulation of results from basic research.
The efficacy of acupressure to prevent nausea and vomiting in post‐operative patients (2002)

In view of the total absence of side-effects in acupressure, its application is worthy of use. This study confirmed the effectiveness of acupressure in preventing post-operative nausea and vomiting.
Microfluidic droplet platform for ultrahigh-throughput single-cell screening of biodiversity (2017)

Ultrahigh-throughput screening (uHTS) techniques can identify unique functionality from millions of variants. To mimic the natural selection mechanisms that occur by compartmentalization in vivo, we developed a technique based on single-cell encapsulation in droplets of a monodisperse microfluidic double water-in-oil-in-water emulsion (MDE). Biocompatible MDE enables in-droplet cultivation of different living species. The combination of droplet-generating machinery with FACS followed by next-generation sequencing and liquid chromatography-mass spectrometry analysis of the secretomes of encapsulated organisms yielded detailed genotype/phenotype descriptions. This platform was probed with uHTS for biocatalysts anchored to yeast with enrichment close to the theoretically calculated limit and cell-to-cell interactions. MDE-FACS allowed the identification of human butyrylcholinesterase mutants that undergo self-reactivation after inhibition by the organophosphorus agent paraoxon. The versatility of the platform allowed the identification of bacteria, including slow-growing oral microbiota species that suppress the growth of a common pathogen, <i>Staphylococcus aureus</i>, and predicted which genera were associated with inhibitory activity.
Small nucleolar RNA interference in Trypanosoma brucei: mechanism and utilization for elucidating the function of snoRNAs (2010)

Expression of dsRNA complementary to small nucleolar RNAs (snoRNAs) in Trypanosoma brucei results in snoRNA silencing, termed snoRNAi. Here, we demonstrate that snoRNAi requires the nuclear TbDCL2 protein, but not TbDCL1, which is involved in RNA interference (RNAi) in the cytoplasm. snoRNAi depends on Argonaute1 (Slicer), and on TbDCL2, suggesting that snoRNA dicing and slicing takes place in the nucleus, and further suggesting that AGO1 is active in nuclear silencing. snoRNAi was next utilized to elucidate the function of an abundant snoRNA, TB11Cs2C2 (92 nt), present in a cluster together with the spliced leader associated RNA (SLA1) and snR30, which are both H/ACA RNAs with special nuclear functions. Using AMT-UV cross-linking and RNaseH cleavage, we provide evidence for the interaction of TB11Cs2C2 with the small rRNAs, srRNA-2 and srRNA-6, which are part of the large subunit (LSU) rRNA. snoRNAi of TB11Cs2C2 resulted in defects in generating srRNA-2 and LSUβ rRNA. This is the first snoRNA described so far to engage in trypanosome-specific processing events.
[Rate of decomposition of keratinous material used by various organisms]. (1984)

Keratinous materials such as feather, horn and nail are resistant to enzymatic degradation because they contain about 11-12 % cystine. However these materials can be used as a substrate by certain microorganisms. In this experiment 3 bacteria with different keratinous activities isolated from beforehand have been grown on ground feather. These microorganisms have rapidly used and as a result decomposed more than 60 % of the substrate in the first 3 days. But the amount of microbiological mass which has grown on the substrate is not high.
Fast organic thin-film transistor circuits (1999)

We have fabricated organic thin-film transistors and integrated circuits using pentacene as the active material. Devices were fabricated on glass substrates using low-temperature ion-beam sputtered silicon dioxide as the gate dielectric and a double-layer photoresist process to isolate devices. These transistors have carrier mobility near 0.5 cm <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sup> /V-s and on/off current ratio larger than 10/sup 7/. Using a level-shifting design that allows circuits to operate over a wide range of threshold voltages, we have fabricated ring oscillators with propagation delay below 75 μs per stage, limited by the level-shifting circuitry. When driven directly, inverters without level shifting show submicrosecond rise and fall time constants.