gebhart/patrepeval huggingface dataset:
Weed biomass production and its potential use in pineapple crops in the north coast of Rio Grande do Sul, Brazil. (2009)

The objectives of this work were to identify and quantify the biomass production of weeds in order to improve its control and also to indicate those with potential use in benefit of soil and the pineapple culture. Two experiments were carried out in the field, in one same area, from Aug./97 to Oct./99 and from Mar./05 to Dez./05, at FEPAGRO, Litoral Norte, Maquiné-RS (lat. 29°54’ S, long. 50°19’, alt. 46 m, rain 1659 mm, in a Chernosolo Haplico Ortico typical). In both, the spontaneous plants were identified before planting (Aug./97 and Mar./05) and the weeds at three (Nov./97), five (Aug./05) and nine months later (Dec./05), dates when the biomass was quantified. Influenced by the season of the year, applied treatments and management of the soil and of the culture before the collections, in each date a certain group of species produced more biomass. In Nov./97, 93,4% of the total biomass were produced by Digitaria horizontalis (79,4%), Paspalum notatum (9.8%) and Ageratum conyzoides (4,2%); in Aug./05, 59,0% of the total corresponded to the production of Lolium mulfiflorum (24,6%), Paspalum paniculatum (22,0%) and Hypochoeris brasiliensis (12,4%); in Dec./05, 56,4% of the biomass originated from the productions of Digitaria horizontalis (26,5%), Eragrosfis planna( 15,6%) and Paspalum urvillei (14,3%). In the referred dates, the ten species that produced more biomass accumulated 18,25; 0,42 and 1,28 t/ha, and the five of larger production and that were identified more frequently (D.horizontalis, L. mulfiflorum, C. juncea, D. incanum and V. safiva) have potential to be used in benefit of the soil and of the pineapple crop.&amp;nbsp;
DepthTouch: Using Depth-Sensing Camera to Enable Freehand Interactions On and Above the Interactive Surface (2009)

DepthTouch is an exploratory interactive surface system that combines the benefits of multi-touch-sensitive surface with the ability to interact in the hover space in front of the surface. DepthTouch uses a depth-sensing camera, which reports a range value per pixel in addition to color, to track the 3D position of the user’s head and hand through a transparent vertical display screen (DNP HoloScreen). The camera location behind the screen minimizes situations in which one hand occludes the other and allows for tracking of the user’s interactions on and off the surface by segmentation of range data. We outline our system hardware, the tracking implementation, and 3D interactions enabled. We also discuss feedback from hundreds of preliminary users and implications for future research.
The Janus Kinase Inhibitor, JAB/SOCS-1, Is an Interferon-γ Inducible Gene and Determines the Sensitivity to Interferons (2000)

The Janus family of protein tyrosine kinases (JAKs) and STAT transcription factors regulate cellular processes involved in cell growth, differentiation, and transformation through their association with cytokine receptors. The CIS family of proteins (also referred as the SOCS or SSI family) has been implicated in the regulation of signal transduction by a variety of cytokines. Among them, we have shown that JAB/SOCS-1 is strongly induced by interferon-gamma and forced expression of JAB/SOCS-1I conferred cells interferon resistance. This resistance was caused by inhibition of JAK1 and JAK2 activation in response to IFNgamma. Moreover, recent detailed analysis of JAB/SOCS-1 knockout mice revealed that JAB/SOCS-1 is indeed a "negative feedback regulator" that determine the sensitivity of cells to IFNgamma. Using in vitro mutagensis, we defined a functional structure of JAB/SOCS-1 and proposed a mechanism for how JAB inhibits JAK kinase activity.
Human umbilical cord mesenchymal stem cells: Osteogenesis in vivo as seed cells for bone tissue engineering (2008)

Mesenchymal stem cells (MSCs) are ideal seed cells for bone tissue engineering. However, intrinsic deficiencies exist for the autologous transplantation strategy of constructing artificial bone with MSCs derived from bone marrow of patients. In this study, MSCs-like cells were isolated from human umbilical cords and were expanded in vitro. Flow cytometric analysis revealed that cells from the fourth passage were positive for CD29, CD44, CD71, CD73, CD90, and CD105 whereas they were negative for CD14, CD34, CD45, and CD117. Furthermore, these cells expressed HLA-A, B, C (MHC-I), but not HLA-DP, DQ, DR (MHC-II), or costimulatory molecules such as CD80 and CD86. Following incubation in specific inductive media for 3 weeks, cultured cells were shown to possess potential to differentiate into adipogenic, osteogenic or chondrogenic lineages in vitro. The umbilical cord-derived MSCs (UC-MSCs) were loaded with a biomimetic artificial bone scaffold material before being implanted subcutaneously in the back of Balb/c nude mice for four to twelve weeks. Our results revealed that UC-MSCs loaded with the scaffold displayed capacity of osteogenic differentiation leading to osteogenesis with human origin in vivo. As a readily available source of seed cells for bone tissue engineering, UC-MSCs should have broad application prospects.
Lipopolysaccharides from Distinct Pathogens Induce Different Classes of Immune Responses In Vivo (2001)

The adaptive immune system has evolved distinct responses against different pathogens, but the mechanism(s) by which a particular response is initiated is poorly understood. In this study, we investigated the type of Ag-specific CD4(+) Th and CD8(+) T cell responses elicited in vivo, in response to soluble OVA, coinjected with LPS from two different pathogens. We used Escherichia coli LPS, which signals through Toll-like receptor 4 (TLR4) and LPS from the oral pathogen Porphyromonas gingivalis, which does not appear to require TLR4 for signaling. Coinjections of E. coli LPS + OVA or P. gingivalis LPS + OVA induced similar clonal expansions of OVA-specific CD4(+) and CD8(+) T cells, but strikingly different cytokine profiles. E. coli LPS induced a Th1-like response with abundant IFN-gamma, but little or no IL-4, IL-13, and IL-5. In contrast, P. gingivalis LPS induced Th and T cell responses characterized by significant levels of IL-13, IL-5, and IL-10, but lower levels of IFN-gamma. Consistent with these results, E. coli LPS induced IL-12(p70) in the CD8alpha(+) dendritic cell (DC) subset, while P. gingivalis LPS did not. Both LPS, however, activated the two DC subsets to up-regulate costimulatory molecules and produce IL-6 and TNF-alpha. Interestingly, these LPS appeared to have differences in their ability to signal through TLR4; proliferation of splenocytes and cytokine secretion by splenocytes or DCs from TLR4-deficient C3H/HeJ mice were greatly impaired in response to E. coli LPS, but not P. gingivalis LPS. Therefore, LPS from different bacteria activate DC subsets to produce different cytokines, and induce distinct types of adaptive immunity in vivo.
Synthetic lipid A with endotoxic and related biological activities comparable to those of a natural lipid A from an Escherichia coli re-mutant (1985)

A synthetic compound (506), beta (1-6) D-glucosamine disaccharide 1,4'-bisphosphate, which is acylated at 2'-amino and 3'-hydroxyl groups with (R)-3-dodecanoyloxytetradecanoyl and (R)-3-tetradecanoyloxytetradecanoyl groups, respectively, and has (R)-3-hydroxytetradecanoyl groups at 2-amino and 3-hydroxyl groups, exhibited full endotoxic activities identical to or sometimes stronger than those of a reference lipid A from an Escherichia coli Re-mutant (strain F515). Endotoxic activities tested include pyrogenicity and leukopenia-inducing activity in rabbits, body weight-decreasing toxicity in normal mice, lethal toxicity in galactosamine-sensitized mice and chicken embryos, and the preparation and provocation of the local Shwartzman reaction in rabbits. Compound 406, a synthetic counterpart of a biosynthetic precursor of lipid A molecule, showed by contrast only weak activities in all of the above assay systems except for the lethality in galactosamine-loaded mice. This finding strongly suggests that the presence of acyloxyacyl groups at the C-2' and C-3' positions of the disaccharide backbone is one of the most important determinant structures of the lipid A molecule for exhibition of strong biological activities characteristic of lipopolysaccharide and its lipid A moiety. The activities of the corresponding 4'-monophosphate (compound 504) and 1-monophosphate (505) analogs were considerably less than those of the parent molecule 506 and the reference F515 lipid A. Regarding other biological activities, not only compound 506 but also compounds 504, 505, and 406 showed definite activities, sometimes comparable to those of F515 lipid A and other reference natural products. These are the activation of Tachypleus tridentatus amoebocyte clotting enzyme cascade and human complement via the classical pathway, mitogenic and polyclonal B-cell activation of murine splenocytes, stimulation of peritoneal macrophages in a guinea pig, enhancement of migration of human blood polymorphonuclear leukocytes, and induction of a serum factor that is cytostatic and cytocidal to L-929 cells in Mycobacterium bovis BCG-primed mice. Relative potencies of test synthetic compounds depended on the assay systems and varied from one system to another. Dephospho-compound 503 lacked most of the biological activities that were definitely observed with phosphorylated compounds, probably because of its insolubility. This study demonstrates the successful chemical synthesis of an E. coli-type lipid A.
Design and Decoding of a Serial Concatenated Code Structure based on Quasi-Cyclic LDPC Codes (2006)

In this paper, we introduce a new serially concatenated code structure, based on Quasi-Cyclic (QC) codes. This structure can be viewed as LDPC codes, and benefits from the advantages of structured QC LDPC codes: simple characterization, good performance for moderate code length and efficient implementation. These codes enable different types of decoding algorithms, from classical Belief Propagation to Turbo-Like decoding algorithms. A joint analysis, in terms of complexity, convergence and performance, has been performed to determine the best decoding choice.
Pharmacokinetic considerations in the development of peptide-based imaging agents. (1997)

Pharmacokinetic factors to be considered in the development of peptide-based imaging agents are reviewed. These include size, plasma protein binding, lipophilicity, resistance or susceptibility to proteolysis and radiolabel integrity. These factors are discussed in the context of several examples of thrombus and tumor imaging agents either commercially available or in development.
Autoantibodies in complex regional pain syndrome bind to a differentiation-dependent neuronal surface autoantigen (2009)

Complex regional pain syndrome, which is characterised by pain and trophic disturbances, develops frequently after peripheral limb trauma. There is an increasing evidence of an involvement of the immune system in CRPS, and recently we showed that CRPS patients have autoantibodies against nervous system structures. Therefore we tested the sera of CRPS patients, neuropathy patients and healthy volunteers for surface-binding autoantibodies to primary cultures of autonomic neurons and differentiated neuroblastoma cell lines using flow cytometry. Thirteen of 30 CRPS patients, but none of 30 healthy controls and only one of the 20 neuropathy sera had specific surface binding to autonomic neurons (p<0.001). The majority of the sera reacted with both sympathetic and myenteric plexus neurons. Interestingly, 6/30 CRPS sera showed binding to undifferentiated SH-SY5Y neuroblastoma cells. However, differentiation of SH-SY5Y into a cholinergic phenotype induced a surface antigen, which is recognised by 60% of CRPS sera (18/30), but not by controls (p<0.001). Our data show that about 30-40% of CRPS patients have surface-binding autoantibodies against an inducible autonomic nervous system autoantigen. These data support an autoimmune hypothesis in CRPS patients. Further studies must elucidate origin and function of these autoantibodies in CRPS.
Mutation tracking in circulating tumor DNA predicts relapse in early breast cancer (2015)

The identification of early-stage breast cancer patients at high risk of relapse would allow tailoring of adjuvant therapy approaches. We assessed whether analysis of circulating tumor DNA (ctDNA) in plasma can be used to monitor for minimal residual disease (MRD) in breast cancer. In a prospective cohort of 55 early breast cancer patients receiving neoadjuvant chemotherapy, detection of ctDNA in plasma after completion of apparently curative treatment-either at a single postsurgical time point or with serial follow-up plasma samples-predicted metastatic relapse with high accuracy [hazard ratio, 25.1 (confidence interval, 4.08 to 130.5; log-rank P < 0.0001) or 12.0 (confidence interval, 3.36 to 43.07; log-rank P < 0.0001), respectively]. Mutation tracking in serial samples increased sensitivity for the prediction of relapse, with a median lead time of 7.9 months over clinical relapse. We further demonstrated that targeted capture sequencing analysis of ctDNA could define the genetic events of MRD, and that MRD sequencing predicted the genetic events of the subsequent metastatic relapse more accurately than sequencing of the primary cancer. Mutation tracking can therefore identify early breast cancer patients at high risk of relapse. Subsequent adjuvant therapeutic interventions could be tailored to the genetic events present in the MRD, a therapeutic approach that could in part combat the challenge posed by intratumor genetic heterogeneity.
Metabolic pathway engineering in cotton: Biosynthesis of polyhydroxybutyrate in fiber cells (1996)

Alcaligenes eutrophus genes encoding the enzymes, beta-ketothiolase (phaA), acetoacetyl-CoA reductase (phaB), and polyhydroxyalkanoate synthase (phaC) catalyze the production of aliphatic polyester poly-d-(-)-3-hydroxybutyrate (PHB) from acetyl-CoA. PHB is a thermoplastic polymer that may modify fiber properties when synthesized in cotton. Endogenous beta-ketothiolase activity is present in cotton fibers. Hence cotton was transformed with engineered phaB and phaC genes by particle bombardment, and transgenic plants were selected based on marker gene, beta-glucuronidase (GUS), expression. Fibers of 10 transgenic plants expressed phaB gene, while eight plants expressed both phaB and phaC genes. Electron microscopy examination of fibers expressing both genes indicated the presence of electron-lucent granules in the cytoplasm. High pressure liquid chromatography, gas chromatography, and mass spectrometry evidence suggested that the new polymer produced in transgenic fibers is PHB. Sixty-six percent of the PHB in fibers is in the molecular mass range of 0.6 x 10(6) to 1.8 x 10(6) Da. The presence of PHB granules in transgenic fibers resulted in measurable changes of thermal properties. The fibers exhibited better insulating characteristics. The rate of heat uptake and cooling was slower in transgenic fibers, resulting in higher heat capacity. These data show that metabolic pathway engineering in cotton may enhance fiber properties by incorporating new traits from other genetic sources. This is an important step toward producing new generation fibers for the textile industry.
An Integrated Approach for the Evaluation of Shaly-sands Reservoirs, Offshore Northwest Java (1990)

Abstract Procedures used by ARCO for shaly-sand analysis in the B-field and other areas of the (offshore) Northwest Java Sea of Indonesia are described. Merged overlays with sidewall core data have been used in over 500 out of 900 wells for “quick-look” qualitative analysis. Quantitative shaly-sand analysis is in the stage of development and is being cross-checked using core data. An integrated approach uses computer enhanced high sampling rate logs, Electromagnetic Propagation log results, Formation MicroScanner information. Geochemical log data and a “Textural” parameter derived from the compressional modulus is used to provide an improved estimate of water saturation. This integrated approach gives an estimate of a variable cementation exponent to be used in shaly-sand saturation equations. Analysis is complicated because the shaly-sands contain of both laminar and dispersed clays. Glauconite, siderite and ankerite are also present, and in some areas the sands also contain potassium rich feldspar.
The C‐Glycoside Analogue of the Immunostimulant α‐Galactosylceramide (KRN7000): Synthesis and Striking Enhancement of Activity (2004)

Welche Quelle liefert den besseren Wirkstoff? Das vollsynthetische C-Glycosid 1 (Y=CH2) ist etwa 1000-mal wirksamer gegen Malaria bei Mäusen als das analoge O-Glycosid (Y=O), das sich von einem Naturstoff ableitet und gegen eine Reihe von Krankheiten bemerkenswert gut wirkt. Die Ergebnisse biologischer Assays betonen das Potenzial von C-Glycosiden als Therapeutika. Supporting information for this article is available on the WWW under http://www.wiley-vch.de/contents/jc_2001/2004/z54215_s.pdf or from the author. Please note: The publisher is not responsible for the content or functionality of any supporting information supplied by the authors. Any queries (other than missing content) should be directed to the corresponding author for the article.
The L4F3 antigen is expressed by unipotent and multipotent colony- forming cells but not by their precursors (1986)

Antibody L4F3 is a murine monoclonal antibody that recognizes an antigen expressed on in vitro colony-forming cells, including virtually all CFU-GM, CFU-Meg, BFU-E, and CFU-Mix. In the present study we examined whether cells that do not express the L4F3 antigen include precursors of hematopoietic colony-forming cells. Colony-forming cells were depleted from marrow by treatment with L4F3 and complement. The remaining cells generated CFU-GM, BFU-E, and CFU-Mix when cultured in the presence of irradiated adherent cell layers from long-term marrow cultures. Marrow cells not expressing the L4F3 antigen, which were separated by cell-sorting techniques, were depleted of colony-forming cells but nevertheless generated CFU-GM when cultured over irradiated adherent cell layers. These data suggest that there are marrow precursors that do not express the L4F3 antigen and that give rise to colony-forming cells of multiple types. Negative selection techniques should allow the enrichment of these precursors of colony-forming cells, thereby enabling direct studies of these immature stem cells.
The Therapeutic Potential of Botulinum Toxin (2004)

BACKGROUND Botulinum toxin type A (BTX-A; commercial preparation BOTOX) is most well known for its effect on muscle contraction because of the BTX binding to the presynaptic nerve terminal, inhibiting the release of acetylcholine (ACH). The therapeutic benefit of BTX-A, however, can also be isolated to pain relief alone, suggesting that BTX-A also works through additional modes of action. OBJECTIVE This article provides insight by an experienced physician into four different case reports. Each case demonstrates the therapeutic potential of BTX-A and the possibility of a different mechanism of action for BTX other than the inhibition of ACH release. RESULTS Four patients, each with different symptoms such as relapsing–remitting multiple sclerosis, postherpetic neuralgia, peripheral neuropathy, and severe tingling caused by herniation of cervical vertebrae at the level of C8, were treated with BOTOX, and their symptoms were alleviated. CONCLUSIONS The BTX-A mechanism providing pain relief is hypothesized to be something other than muscle relaxation by inhibiting the release of ACH at the neuromuscular juncture, such as inhibition of the release of substance P or the blocking of autonomic pathways, etc. This article is intended to continue to keep physicians using this substance for dermatologic indications aware of the potential unsuspected effects.
Increased hepatocyte growth factor level in cerebrospinal fluid in Alzheimer's disease (2003)

These results indicate that CSF HGF levels correspond with the white matter damage in AD brain.
Photoinduced Prevention of Tissue Adhesion (1992)

Postoperative tissue adhesion causes retarded wound healing and the need for reoperation; it can even be life threatening. In this report, the authors present prototype materials and performance of newly developed tissue adhesion prevention technology based on photocurable polysaccharides. Polysaccharides used were hyaluronic acid and chondroitin sulfate, both of which were partially derived with photoreactive groups such as cinnamoyl, coumarin, and thymine. Photoreactive hyaluronic acids with low degrees of derivatization were soluble in water. Films of cinnamated hyaluronic acid or an aqueous solution of cinnamated chondroitin sulfate were photocured by ultraviolet irradiation, resulting in water adsorbable films or water swollen gels, respectively. Gelation was due to intermolecular dimerization between cinnamoyl groups. The authors provide two potentially applicable examples: 1) a photocured, water swollen hydrogel film, and 2) a photocurable chondroitin sulfate buffer solution. The authors used hydrogel films to cover the peritoneum after mechanically injuring its surface. Histologic examination showed neither tissue nor cell adhesion, and only a minimal inflammatory response. When tissues were coated with a photocurable chondroitin sulfate solution, the viscous solution was converted to a hydrogel upon ultraviolet irradiation, resulting in in situ tissue covering. Although an optimal molecular design has not yet been found, unique features of mucopolysaccharides (e.g., high water uptake; biodegradability and bioresorbability; and nontoxicity of photodimerizable groups) may result in the development of photoinduced tissue adhesion prevention technology.
Direct and rapid inhibition of factor Xa by otamixaban: A pharmacokinetic and pharmacodynamic investigation in patients with coronary artery disease (2006)

In patients with stable coronary artery disease taking maintenance doses of their usual concomitant medication, otamixaban exerts a rapid onset of anticoagulation and anti-factor Xa activity. Our data provide evidence that further studies are warranted to investigate the safety and efficacy of otamixaban in the target population.
Identification of Enzymes Homologous to Isocitrate Dehydrogenase That Are Involved in Coenzyme B and Leucine Biosynthesis in Methanoarchaea (2000)

Two putative Methanococcus jannaschii isocitrate dehydrogenase genes, MJ1596 and MJ0720, were cloned and overexpressed in Escherichia coli, and their gene products were tested for the ability to catalyze the NAD- and NADP-dependent oxidative decarboxylation of DL-threo-3-isopropylmalic acid, threo-isocitrate, erythro-isocitrate, and homologs of threo-isocitrate. Neither enzyme was found to use any of the isomers of isocitrate as a substrate. The protein product of the MJ1596 gene, designated AksF, catalyzed the NAD-dependent decarboxylation of intermediates in the biosynthesis of 7-mercaptoheptanoic acid, a moiety of methanoarchaeal coenzyme B (7-mercaptoheptanylthreonine phosphate). These intermediates included (-)-threo-isohomocitrate [(-)-threo-1-hydroxy-1,2, 4-butanetricarboxylic acid], (-)-threo-iso(homo)(2)citrate [(-)-threo-1-hydroxy-1,2,5-pentanetricarboxylic acid], and (-)-threo-iso(homo)(3)citrate [(-)-threo-1-hydroxy-1,2, 6-hexanetricarboxylic acid]. The protein product of MJ0720 was found to be alpha-isopropylmalate dehydrogenase (LeuB) and was found to catalyze the NAD-dependent decarboxylation of one isomer of DL-threo-isopropylmalate to 2-ketoisocaproate; thus, it is involved in the biosynthesis of leucine. The AksF enzyme proved to be thermostable, losing only 10% of its enzymatic activity after heating at 100 degrees C for 10 min, whereas the LeuB enzyme lost 50% of its enzymatic activity after heating at 80 degrees C for 10 min.