gebhart/patrepeval huggingface dataset:
Food chains, small‐scale food enterprises and rural development: Illustrations from Ireland (1999)

Abstract The indigenous agri‐food sector in the Republic of Ireland has evolved to a stage where Irish companies are firmly implicated in a competitive European and global marketplace. Considerable restructuring of the sector has taken place, the central features of which are identified. One of the consequences has been a shift in the location of food industry employment to the more rural areas. Food chains and related state actions are described under three main product categories: agri‐industrial, organic and speciality foods. Small‐scale rural enterprises in the latter two categories form the main focus of the paper. Qualitative data from a study of these enterprises are used to discuss their recent growth and their production and marketing patterns, as well as their significance for rural development. They face particular problems in selling their products in a limited domestic market and in a context where more powerful interests are striving for greater efficiencies in food supply chains. The issues are analysed and producer options interpreted in terms of two general models: ‘incorporation’ into the dominant capital‐driven and globalizing market systems, or ‘adaptation’ by adhering to more localized and self‐controlled supply chains.
Complete Freund's adjuvant immunization prolongs survival in experimental prion disease in mice (2002)

We recently reported that immunization of mice with certain self-prion protein peptides induced specific T-cell and B-cell immune responses; importantly, this immunization was associated with a decrease in the number of protease-resistant PrP(Sc) particles recoverable in a transplanted, scrapie-infected syngeneic tumor. The present study was carried out to determine whether immunization with the immunogenic PrP peptides might influence the natural history of experimental scrapie in mice. We immunized C57BL/6 mice with self-prion peptides in complete Freund's adjuvant (CFA) or with CFA alone as a control and then infected the mice with mouse-adapted scrapie by injection either intraperitoneally or intracerebrally. We report here that immunization with CFA, irrespective of whether prion peptides were present in the inoculum, resulted in marked prolongation of survival of the mice, whether the challenge was intracerebral or intraperitoneal. Mice in the immunized and control groups that died contained equivalent amounts of PrP(Sc). Thus, CFA immunization has a therapeutic effect in experimental scrapie in mice, possibly by reducing the rate of PrP(Sc) accumulation in the brain.
Polyinosinic-polycytidylic acid complexed with poly-L-lysine and carboxymethylcellulose in combination with interleukin 2 in patients with cancer: clinical and immunological effects. (1992)

We have performed a phase IB study of polyinosinic-polycytidylic acid complexed with poly-L-lysine and carboxymethylcellulose (poly-ICLC) in combination with interleukin 2 (IL-2) in 25 patients with a variety of cancers. Patients received weekly or biweekly poly-ICLC by i.m. injection, at doses ranging from 0.01 to 1.0 mg/m2, for 1 month. This was followed by 2 months of outpatient therapy with biweekly i.m. poly-ICLC in combination with IL-2 (3 x 10(6) units/m2) given i.v. by 24-h continuous infusion twice weekly, using a portable infusion pump. No objective tumor responses were observed. Toxicity was moderate at all poly-ICLC doses tested and increased only slightly following the addition of IL-2. No increases in peripheral blood natural killer (NK) activity were observed after treatment with poly-ICLC alone. However, high dose poly-ICLC (greater than or equal to 0.3 mg/m2) in combination with IL-2 resulted in NK activity greater than that seen using the same dose of IL-2 in combination with lower poly-ICLC doses. Increases in the number and percentage of CD56+ cells were evident only after initiation of IL-2 therapy and were unaffected by the poly-ICLC dose. In the majority of patients, these increases were preferentially associated with the subset of CD56+ cells coexpressing CD8, while the CD56+/CD16+ population was elevated to a lesser extent. Moderate increases in serum neopterin levels and 2',5'-oligoadenylate synthetase activity in peripheral blood mononuclear cells were noted at 72 h following initial treatment with 1.0 mg/m2 poly-ICLC. No induction of alpha or gamma interferon was detected. This study shows that the addition of poly-ICLC to a well tolerated IL-2 regimen can significantly enhance NK activity. Poly-ICLC can be used to enhance IL-2-induced NK lytic activity without increases in the dose and, therefore, the toxicity of IL-2 treatment.
SemKey: A Semantic Collaborative Tagging System (2007)

By analysing the current structure and the usage patterns of collaborative tagging systems, we can find out many important aspects which still need to be improved. Problems related to synonymy, polysemy, dierent lexical forms, mispelling errors or alternate spellings, dierent levels of precision and dierent kinds of tag-to-resource association cause inconsistencies and reduce the eciency of content search and the eectiveness of the tag space structuring and organization. They are mainly caused by the lack of semantic information inclusion in the tagging process. We propose a new way to describe resources: the semantic tagging. It allows user to state semantic assertions: each of them expresses a defined characteristic of a resource associating it with a concept. We present SemKey, a semantic collaborative tagging system, describing its global architecture and functioning along with the most relevant organizational issues faced. We explore the adequacy of the support oered by the entries of Wikipedia and WordNet in order to access to and reference concepts.
Radretumab Radioimmunotherapy in Patients with Brain Metastasis: A 124I-L19SIP Dosimetric PET Study (2013)

Radioimmunotherapy (RIT) with (131)I-labeled L19SIP (radretumab; a small immunoprotein format antibody directed against the ED-B domain of fibronectin; ∼ 80 kDa molecular weight) has been investigated in several clinical trials. Here, we describe the use of immuno-PET imaging with iodine-124 ((124)I)-labeled L19SIP to predict doses delivered to tumor lesions and healthy organs by a subsequent radretumab RIT in patients with brain metastases from solid cancer. Bone marrow doses were evaluated both during the diagnostic phase and posttherapy, measuring activities in blood (germanium detector) and whole body (lanthanum bromide detector). Expected doses for radretumab administration (4,107 MBq/m(2)) were calculated from data obtained after administration of an average of 167 MBq (124)I-L19SIP to 6 patients. To assess lesion average doses, the positron emission tomography (PET) scanner was calibrated for the use of (124)I with an International Electrotechnical Commission (IEC) Body Phantom and recovery coefficients were calculated. The average dose to bone red marrow was 0.21 Gy/GBq, with high correlation between provisional and actual posttherapy doses. Although the fraction of injected activity in normal organs was similar in different patients, the antibody uptake in the neoplastic lesions varied by as much as a factor of 60. Immuno-PET with (124)I-labeled L19SIP offers significant advantages over conventional (131)I imaging, in particular accuracy of dosimetric results. Furthermore, the study indicates that antibody uptake can be highly variable even in different lesions of the same patient and that immuno-PET procedures may guide product development with armed antibodies.
Prostaglandin E2Stimulates Insulin-Like Growth Factor I Synthesis in Osteoblast-Enriched Cultures from Fetal Rat Bone* (1991)

Prostaglandin E2 (PGE2) affects both bone resorption and formation, but its mechanism of action remains unclear. PGE2 is known to elevate intracellular cAMP levels in a variety of culture systems. Agents that increase cAMP in primary osteoblast-enriched (Ob) cultures enhance the synthesis of skeletal insulin-like growth factor I (IGF-I), a potent anabolic factor for bone. A 5 min exposure to PGE2 at 0.01-1 microM enhanced cAMP synthesis in Ob cultures by 8- to 54-fold, and within 6 h produced up to a 3- fold increase in steady state prepro-IGF-I transcripts. The stimulatory effect of PGE2 on IGF-I messenger RNA was first evident within 4 h of treatment and remained elevated for at least 24 h. Furthermore, 0.01-1 microM PGE2 increased immunoreactive IGF-I polypeptide accumulation by 1.9- to 4.7-fold. In contrast PGE2 did not elevate steady state IGF-II mRNA or polypeptide levels within this time frame. Although PTH increase cAMP, intracellular calcium, and PGE2 production by bone cells, our previous studies indicate that the stimulatory effect of PTH on IGF-I production is cAMP, but not calcium dependent. Inhibition of PGE2 synthesis by exposure to indomethacin did not alter basal or PTH-stimulated IGF-I levels, substantiating that the effect of PTH on IGF-I is not PGE2 dependent. These studies indicate that PGE2 production, a feature common to many agents that enhance bone resorption, could contribute to the coupling of bone resorption and new bone formation, by way of its ability to increase cAMP and, consequently, IGF-I synthesis by the osteoblast.
Impact of the lysine‐188 and aspartic acid‐189 inversion on activity of trypsin (1999)

The impact of the charge rearrangement on the specificity of trypsin was tested by an inversion of sequence K188D/D189K maintaining the integrity of the charges of the substrate binding pocket when switching their polarity. In native trypsin, aspartate 189 situated at the bottom of the primary substrate binding pocket interacts with arginine and lysine side chains of the substrate. The kinetic parameters of the wild-type trypsin and K188D/D189K mutant were determined with synthetic tetrapeptide substrates. Compared with trypsin, the mutant K188D/D189K exhibits a 1.5- to 6-fold increase in the Km for the substrates containing arginine and lysine, respectively. This mutant shows a approximately 30-fold decrease of its k(cat) and its second-order rate constant k(cat)/Km decreases approximately 40- and 150-fold for substrates containing arginine and lysine, respectively. Hence, trypsin K188D/D189K displays a large increase in preference for arginine over lysine.
High Peak Brightness Polymer Light-Emitting Diodes (1998)

Laser action is currently limited by device efficiency, rather than peak current density, is one conclusion drawn from this investigation of optically pumped light-emitting diodes (LEDs) made of conjugated polymers. The structure of the LEDs has been optimized to allow high current operation using short drive pulses. Unexpectedly high current densities and high luminous efficiencies at these current densities allow a high peak brightness of 5 × 106 cd/m2; see also the cover of this issue. The implications of these results for the fabrication of injection lasers are discussed.
Use of systemic agents in the treatment of acne vulgaris. (2000)

Effective treatment of acne vulgaris can prevent emotional and physical scarring. Therapy varies according to the severity of the disease. Topical medication is generally adequate in clearing comedonal acne, while inflammatory acne usually requires the addition of oral medication. Systemic antibiotics are used most frequently and can be highly effective. Newer formulations of combined oral contraceptives are also helpful in modulating sebum production in the female patient. Severe nodulocystic acne that does not respond to topical retinoids and systemic antibiotics may be treated with isotretinoin. However, the side effect profile of this medication is extensive, and physicians should be well-versed in its potential adverse effects.
Staphylococcus aureus Pneumonia in Hamsters with Elastase-Induced Emphysema--the Virulence Enhancing Activity of Mucin (1988)

Staphylococcus aureus pneumonia was studied in hamsters with elastase-induced emphysema and in saline-treated controls. Emphysematous animals cleared endotracheally administered inocula of S. aureus in saline as rapidly as controls. After infection with S. aureus in 1% mucin, emphysematous animals had impaired clearance compared with controls; after infection with S. aureus in 5% mucin, emphysematous animals had decreased survival at 96 hr compared to controls (6/24 vs 15/24, P less than 0.01 Fisher's exact test). Bronchoalveolar lavage of uninfected elastase-treated hamsters yielded twice as many cells per animal as uninfected controls (P less than 0.0001, paired t test), and the cells contained a higher percentage of polymorphonuclear leukocytes (37.8% vs 3.8%, P less than 0.0001). Lavage cells from both groups of animals were equally efficient per cell at killing opsonized S. aureus in an in vitro bactericidal assay. Hamsters with elastase-induced emphysema were resistant to infection with S. aureus alone despite marked structural abnormalities in the lung, possibly due in part to increased numbers of resident phagocytic cells. After infection with S. aureus in mucin as a virulence enhancing factor emphysematous animals had impaired clearance and decreased survival compared to controls.
Wider or Deeper: Revisiting the ResNet Model for Visual Recognition (2016)

The trend towards increasingly deep neural networks has been driven by a general observation that increasing depth increases the performance of a network. Recently, however, evidence has been amassing that simply increasing depth may not be the best way to increase performance, particularly given other limitations. Investigations into deep residual networks have also suggested that they may not in fact be operating as a single deep network, but rather as an ensemble of many relatively shallow networks. We examine these issues, and in doing so arrive at a new interpretation of the unravelled view of deep residual networks which explains some of the behaviours that have been observed experimentally. As a result, we are able to derive a new, shallower, architecture of residual networks which significantly outperforms much deeper models such as ResNet-200 on the ImageNet classification dataset. We also show that this performance is transferable to other problem domains by developing a semantic segmentation approach which outperforms the state-of-the-art by a remarkable margin on datasets including PASCAL VOC, PASCAL Context, and Cityscapes. The architecture that we propose thus outperforms its comparators, including very deep ResNets, and yet is more efficient in memory use and sometimes also in training time. The code and models are available at https://github.com/itijyou/ademxapp
Gene expression fingerprinting for human hereditary hemorrhagic telangiectasia (2007)

Hereditary hemorrhagic telangiectasia (HHT) or Osler-Weber-Rendu syndrome is an autosomal dominant vascular disorder characterized by telangiectases and internal arteriovenous malformations. It is caused by mutations in elements of the transforming growth factor-beta (TGF-beta) receptor complex: endoglin, a co-receptor, responsible for HHT1, or ALK1 (activin receptor-like kinase 1), a type I receptor leading to HHT2. Recently, we have established cultures of HHT endothelial cells, primary targets of the disease. These cells showed deficient TGF-beta signaling and angiogenesis, representing a useful human model to study the molecular mechanism of this disease. To understand the pathogenic mechanism underlying HHT, we have used total RNA probes to compare HHT versus non-HHT cells by expression microarrays. This work represents a systematic study to identify target genes affected in HHT cells. Given the similarity of symptoms in HHT1 and HHT2, special interest has been put on the identification of common targets for both HHT types. As a result, 277 downregulated and 63 upregulated genes were identified in HHT versus control cells. These genes are involved in biological processes relevant to the HHT pathology, such as angiogenesis, cytoskeleton, cell migration, proliferation and NO synthesis. The type of misregulated genes found in HHT endothelial cells lead us to propose a model of HHT pathogenesis, opening new perspectives to understand this disorder. Moreover, as the disease is originated by mutations in proteins of the TGF-beta receptor complex, these results may be useful to find out targets of the TGF-beta pathway in endothelium.
Reversal of Hepatic Fibrosis — Fact or Fantasy? (2006)

The prospect of reversing hepatic fibrosis has generated great interest now that basic science advances are being translated into promising new antifibrotic therapies. It is appropriate to recognize both the historical advances that created the framework for these successes, and the important role that Hepatology has played in disseminating them. A sense of urgency underlies this effort as the epidemics of HCV and NASH are becoming associated with advancing fibrosis. To maintain progress and minimize confusion among investigators and clinicians it is essential to standardize terms referring to fibrosis 'reversal' and 'regression.' There must also be rapid optimization of non-invasive markers of fibrosis to relieve this current bottleneck to conducting clinical trials. Progress in identifying genetic determinants of fibrosis could further refine patient selection for clinical trials and shorten their duration, as well as unearthing new directions of scientific inquiry. Realistic expectations for successful anti-fibrotic therapies reflect solid evidence of fibrosis regression in patients treated effectively for viral liver disease, as well as growing clarity in the understanding mechanisms of extracellular matrix production and degradation. The paradigms of stellate cell activation and apoptosis remain valuable frameworks for understanding pathways of hepatic fibrogenesis and fibrosis regression, respectively. Continued progress is essential in order to identify the determinants and dynamics of fibrosis reversibility, to discover additional targets for anti-fibrotic therapy, and to develop customized multi-drug regimens. These advances are sure to be captured in the next 25 years by Hepatology , and to profoundly impact the prognosis of patients with chronic liver disease.
Involvement of CD44 in leukocyte trafficking at the blood-retinal barrier (2002)

In the present study, we investigated the involvement of CD44 in leukocyte trafficking in vivo at the blood-retinal barrier using experimental autoimmune uveoretinitis (EAU) as a model system. Leukocyte trafficking was evaluated using adoptive transfer of calcein-AM (C-AM)-labeled spleen cells harvested from syngeneic mice at prepeak severity of EAU to mice at a similar stage of disease. CD44 and its ligand hyaluronan were up-regulated in the eye during EAU. CD44-positive leukocytes were found sticking in the retinal venules and postcapillary venules but not in the retinal arterioles nor in mesenteric vessels. Preincubation of in vitro C-AM-labeled leukocytes with anti-CD44 monoclonal antibodies (mAb; IM7) or high molecular weight hyaluronic acid (HA) before transfer significantly suppressed leukocyte rolling but not sticking in retinal venules and also reduced cell infiltration in the retinal parenchyma. Administration of the HA-specific enzyme hyaluronidase to mice before cell transfer also reduced leukocyte infiltration, suggesting that CD44-HA interactions are involved in leukocyte recruitment in EAU. This was further supported by the observation that disease severity was reduced by administration of anti-CD44 mAb (IM7) at the early leukocyte-infiltration stage. Further studies also indicated that CD44 activation was associated with increased levels of apoptosis, and this may also be in part responsible for the reduction in disease severity. These findings demonstrate that CD44 is directly involved in leukocyte-endothelial interaction in vivo and influence the trafficking of primed leukocytes to the retina and their overall survival.
Relevance of Mitochondrial Genetics and Metabolism in Cancer Development (2013)

Cancer cells are characterized in general by a decrease of mitochondrial respiration and oxidative phosphorylation, together with a strong enhancement of glycolysis, the so-called Warburg effect. The decrease of mitochondrial activity in cancer cells may have multiple reasons, related either to the input of reducing equivalents to the electron transfer chain or to direct alterations of the mitochondrial respiratory complexes. In some cases, the depression of respiratory activity is clearly the consequence of disruptive mitochondrial DNA (mtDNA) mutations and leads as a consequence to enhanced generation of reactive oxygen species (ROS). By acting both as mutagens and cellular mitogens, ROS may contribute directly to cancer progression. On the basis of our experimental evidence, we suggest a deep implication of the supercomplex organization of the respiratory chain as a missing link between oxidative stress, energy failure, and tumorigenesis. We speculate that under conditions of oxidative stress, a dissociation of mitochondrial supercomplexes occurs, with destabilization of complex I and secondary enhanced generation of ROS, thus leading to a vicious circle amplifying mitochondrial dysfunction. An excellent model to dissect the role of pathogenic, disassembling mtDNA mutations in tumor progression and their contribution to the metabolic reprogramming of cancer cells (glycolysis vs. respiration) is provided by an often underdiagnosed subset of tumors, namely, the oncocytomas, characterized by disruptive mutations of mtDNA, especially of complex I subunits. Such mutations almost completely abolish complex I activity, which slows down the Krebs cycle, favoring a high ratio of α-ketoglutarate/succinate and consequent destabilization of hypoxia inducible factor 1α (HIF1α). On the other hand, if complex I is partially defective, the levels of NAD(+) may be sufficient to implement the Krebs cycle with higher levels of intermediates that stabilize HIF1α, thus favoring tumor malignancy. The threshold model we propose, based on the population-like dynamics of mitochondrial genetics (heteroplasmy vs. homoplasmy), implies that below threshold complex I is present and functioning correctly, thus favoring tumor growth, whereas above threshold, when complex I is not assembled, tumor growth is arrested. We have therefore termed "oncojanus" the mtDNA genes whose disruptive mutations have such a double-edged effect.
TWO CHROMOSOMAL GENES REQUIRED FOR KILLING EXPRESSION IN KILLER STRAINS OF SACCHAROMYCES CEREVISIAE (1976)

The killer character of yeast is determined by a 1.4 X 10(6) molecular weight double-stranded RNA plasmid and at least 12 chromosomal genes. Wild-type strains of yeast that carry this plasmid (killers) secret a toxin which is lethal only to strains not carrying this plasmid (sensitives).--We have isolated 28 independent recessive chromosomal mutants of a killer strain that have lost the ability to secrete an active toxin but remain resistant to the effects of the toxin and continue to carry the complete cytoplasmic killer genome. These mutants define two complementation groups, kex1 and kex2. Kex1 is located on chromosome VII between ade5 and lys5. Kex2 is located on chromosome XIV, but it does not show meiotic linkage to any gene previously located on this chromosome.--When the killer plasmid of kex1 or kex2 strains is eliminated by curing with heat or cycloheximide, the strains become sensitive to killing. The mutant phenotype reappears among the meiotic segregants in a cross with a normal killer. Thus, the kex phenotype does not require an alteration of the killer plasmid.--Kex1 and kex2 strains each contain near-normal levels of the 1.4 x 10(6) molecular weight double-stranded RNA, whose presence is correlated with the presence of the killer genome.