gebhart/patrepeval huggingface dataset:
Novel blood group H glycolipid antigens exclusively expressed in blood group A and AB erythrocytes (type 3 chain H). II. Differential conversion of different H substrates by A1 and A2 enzymes, and type 3 chain H expression in relation to secretor status. (1986)

The novel A-associated H antigen (type 3 chain H), described in the accompanying paper (Clausen, H., Levery, S.B., Kannagi, R., and Hakomori, S. (1986) J. Biol. Chem. 261, 1380-1387), as well as globo-H were found to be present in greater quantity in A2 erythrocytes than in A1 erythrocytes. A1 erythrocytes contain the repetitive A epitope (type 3 chain A) (Clausen, H., Levery, S.B., Nudelman, E., Tsuchiya, S., and Hakomori, S. (1985) Proc. Natl. Acad. Sci. U. S. A. 82, 1199-1203), which is defined by A1-specific monoclonal antibody TH-1, in addition to globo-A. The ability of alpha-GalNAc transferase from A1 and A2 serum to catalyze the conversion of type 2 chain H, type 3 chain H, and globo-H to type 2 chain A, type 3 chain A, and globo-A, respectively, was compared. The conversion to type 3 chain A and globo-A occurred to a minimal degree in the presence of the A2 enzyme as compared with the A1 enzyme, particularly at low substrate concentration. Although a lower conversion from type 2 chain H to type 2 chain A was also observed in the presence of the A2 enzyme than in the presence of the A1 enzyme, the conversion of type 2 chain H to type 2 chain A was less restricted than the type 3 chain conversion catalyzed by the A2 enzyme, particularly at low substrate concentration. The conversion from globo-H to globo-A was essentially absent in the presence of the A2 enzyme. Since the expression of type 1 chain H in erythrocytes is dependent on secretor status, the distribution of type 3 chain H and globo-H in erythrocytes from secretors and non-secretors was compared. These antigens appeared to be present in the same quantity in erythrocytes of secretors and nonsecretors.
Activated Signal Transducer and Activator of Transcription (STAT) 3 (2004)

Constitutive activation of the Janus-activated kinase/signal transducer and activator of transcription (STAT) pathway promotes the proliferation and survival of cancer cells in culture and is associated with various cancers, including those of the ovary. We found that constitutively activated STAT3 levels correlated with aggressive clinical behavior of ovarian carcinoma specimens. Furthermore, inhibition of STAT3 reduced the motility of ovarian cancer cells in vitro. Surprisingly, we found that activated STAT3 localized not only to nuclei but also to focal adhesions in these cells. Activated STAT3 coimmunoprecipitated with phosphorylated paxillin and focal adhesion kinase and required paxillin and Src for its localization to focal adhesions. These results suggest that Janus-activated kinase/STAT signaling may contribute to ovarian cancer cell invasiveness.
Molecular photovoltaics that mimic photosynthesis (2001)

Abstract Learning from the concepts used by green plants, we have developed a photovoltaic cell based on molecular light absorbers and mesoporous electrodes. The sensitized nanocrystalline injection solar cell employs organic dyes or transition-metal complexes for spectral sensitization of oxide semiconductors, such as TiO2, ZnO, SnO2, and Nb2O5. Mesoporous films of these materials are contacted with redox electrolytes, amorphous organic hole conductors, or conducting polymers, as well as inorganic semiconductors. Light harvesting occurs efficiently over the whole visible and near-IR range due to the very large internal surface area of the films. Judicious molecular engineering allows the photoinduced charge separation to occur quantitatively within femtoseconds. The certified overall power conversion efficiency of the new solar cell for standard air mass 1.5 solar radiation stands presently between 10 and 11. The lecture will highlight recent progress in the development of solar cells for practical use. Advancement in the understanding of the factors that govern photovoltaic performance, as well as improvement of cell components to increase further its conversion efficiency will be discussed.
Measuring the activity of BioBrick promoters using an in vivo reference standard (2009)

Relative activity measurements based on an in vivoreference standard enables improved measurement of promoter activity given variation in measurement conditions and instruments. These improvements are sufficient to begin to support the measurement of promoter activities across many laboratories. Additional in vivo reference standards for other types of biological functions would seem likely to have similar utility, and could thus improve research on the design, production, and reuse of standard biological parts.
Relationship Between Thyroid Autoimmunity and Yersinia Enterocolitica Antibodies (2002)

It has previously been proposed that subclinical Yersinia enterocolitica infection may play a role in autoimmune thyroid disease (AITD). In this study, we investigated the relationship between the thyroid autoantibodies and the antibodies that produced against different serotypes of Y. enterocolitica. A total of 215 subjects were included into the study (65 newly diagnosed Graves' disease [GD], 57 Hashimoto's thyroiditis [HT], 53 nontoxic diffuse goiter [NTDG], and 40 subjects for control group [CG]). Thyroid receptor antibodies (TRAb), thyroid and agglutinating antibodies against Y. enterocolitica serotype O:3, O:5, O:8, O:9 were measured in the blood samples. The highest incidence of Y. enterocolitica antibody positivity was measured in GD (53.8% for O:3, 29.2% for O:5, 44.6% for O:8, and 40% for O:9) and followed by HT. In patients with GD, TRAb levels were also higher than in patients with HT, NTDG, and CG. There was no difference between NTDG and CG in respect to the titer levels and the positivity of both TRAb and Y. enterocolitica antibodies. There was also a weak linear correlation between TRAb level and the titer of antibodies against Y. enterocolitica antigens. It can be concluded that Y. enterocolitica infection may play a role in etiology of GD in Turkey.
Partially-parallel LDPC decoder based on high-efficiency message-passing algorithm (2006)

This paper proposes a partially-parallel LDPC decoder based on a high-efficiency message-passing algorithm. Our proposed partially-parallel LDPC decoder performs the column operations for bit nodes in conjunction with the row operations for check nodes. Bit functional unit with pipeline architecture in our LDPC decoder allows us to perform column operations for every bit node connected to each of check nodes which are updated by the row operations in parallel. Our proposed LDPC decoder improves the tuning when the column operations are performed, accordingly it improves the message-passing efficiency within the limited number of iterations for decoding. We implemented the proposed partially-parallel LDPC decoder on an FPGA, and simulated its decoding performance. Practical simulation shows that our proposed LDPC decoder reduces the number of iterations for decoding, and it improves the bit error performance with a small hardware overhead.
Two different approaches for developing immunometric assays of haptens (1996)

To improve immunoassays of small haptens, we developed two different approaches for their measurement in a non-competitive format. We first devised two-site immunometric assays for small peptides (8-11 amino acids) by selecting two sets of antibodies specifically directed against C- and N-terminal moieties of the peptides. In each case, assay sensitivity improved substantially over that of the corresponding competitive assays. More interestingly, all of these new immunometric assays were much more specific than the competitive assays. In a second approach, we developed a new procedure, solid-phase-immobilized epitope immunoassay (SPIE-IA), in which a single monoclonal antibody uses the same epitope for capture and tracer binding and the hapten is covalently cross-linked to solid-phase proteins. To date, SPIE-IA have been successfully applied to the determination of haptens bearing primary amino groups, including substance P, thyroxine, leukotriene C4, endothelin, and angiotensin II. In each case, assay sensitivity was significantly improved.
Regulation of neuropeptide Y (NPY) binding by guanine nucleotides in the rat cerebral cortex (1984)

In the presence of GTP, GDP, GMPP(NH)P, GMPP(CH2)P, GMPP(S)P but not in the presence of GMP, cGMP or ATP, the high affinity binding of neuropeptide Y (NPY) was reduced in a dose-dependent manner. GTP (0.1 mM) diminished the maximal binding capacity for 125I-labelled NPY by 40% without any change in the equilibrium dissociation constant of the receptor 125I-labelled NPY complex.
Preparation of colloidal silver dispersions by the polyol process (1997)

In a previous paper (J. Mater. Chem., 1996, 6, 573), we reported that colloidal silver dispersions can be synthezised by the polyol process, using an ethylene glycol–polyvinylpyrolidone (PVP) solution to reduce silver nitrate under precise temperature conditions. Quasi-spherical particles with a narrow size distribution were obtained. Low precursor and PVP concentrations, in contrast to high silver nitrate concentrations, were found to yield monodisperse systems with an average particle size of 15 to 21 nm. To understand the particle formation mechanism, the evolution of particle size and shape during the reaction was monitored by TEM and UV absorption spectroscopy techniques. An Ostwald ripening mechanism is proposed to account for the formation of the silver particles, even though the variation of temperature with time is not ideal for a complete mechanistic understanding.
Immunohistochemistry-Based Consensus Molecular Subtypes as a Prognostic and Predictive Biomarker for Adjuvant Chemotherapy in Patients with Stage II Colorectal Cancer (2020)

For stage II colorectal cancer (CRC), the efficacy of adjuvant chemotherapy remains controversial, in that its minimal benefit (no more than 5% on average) is considered not worth the toxic effects of the drugs. There are still no effective prognostic and predictive biomarkers. This study showed that consensus molecular subtype (CMS) status is a predictive marker for adjuvant chemotherapy efficacy. Patients with left-sided tumors of CMS2/3 subtype have survival benefit by receiving adjuvant chemotherapy, which will aid in personalized treatment for stage II CRCs. Moreover, this test of CMS based on immunohistochemistry is cheap, not time consuming, and easily conducted in the laboratories of most hospitals.
Particle assembly and Vpr expression in human immunodeficiency virus type 1-infected cells demonstrated by immunoelectron microscopy (1994)

The 96 amino acid viral protein R (Vpr) of human immunodeficiency virus type 1 (HIV-1) was detected during virus assembly in intracellular vacuoles and at the plasma membrane on peripheral blood mononuclear cells. In both immature and mature virus particles, Vpr was located immediately beneath the viral envelope, colocalizing with the core structural protein, Gag p24. Vpr was present in intracellular HIV-1 wild-type virions at 50% of the level found in extracellular HIV-1 particles. Cells infected with HIV-1 strains with C-terminal truncations of Vpr manifested a different pattern of Vpr expression. A mutant with an alteration of amino acids 79 to 85 exhibited a 23% reduction in total levels of Vpr expression, but a marked accumulation of Vpr in intracellular rather than extracellular virions. A mutant with the last 17 amino acids of Vpr deleted expressed only 10% of wild-type levels of Vpr. These observations indicate that Vpr is incorporated into virions from the cytoplasmic aspect of either the vacuolar or plasma membrane. Furthermore, the proportion of Vpr on intracellular compared to extracellular virions is affected by a specific locus within the protein.
Problematic social situations and international institutions: on the use of game theory in international politics (1993)

binding the concepts of game theory more closely to the international relations concepts under investigation.In section three, different procedures for assessing actor preferences independent of the outcome to be explained are reviewed.Finally, section four very briefly reports on an attempt of applying this approach.
Genetic and physiological characterization of a Rhizobium etli mutant strain unable to synthesize poly-beta-hydroxybutyrate (1996)

Rhizobium etli accumulates poly-beta-hydroxybutyrate (PHB) in symbiosis and in free life. PHB is a reserve material that serves as a carbon and/or electron sink when optimal growth conditions are not met. It has been suggested that in symbiosis PHB can prolong nitrogen fixation until the last stages of seed development, but experiments to test this proposition have not been done until now. To address these questions in a direct way, we constructed an R. etli PHB-negative mutant by the insertion of an Omega-Km interposon within the PHB synthase structural gene (phaC). The identification and sequence of the R. etli phaC gene are also reported here. Physiological studies showed that the PHB-negative mutant strain was unable to synthesize PHB and excreted more lactate, acetate, pyruvate, beta-hydroxybutyrate, fumarate, and malate than the wild-type strain. The NAD+/NADH ratio in the mutant strain was lower than that in the parent strain. The oxidative capacity of the PHB-negative mutant was reduced. Accordingly, the ability to grow in minimal medium supplemented with glucose or pyruvate was severely diminished in the mutant strain. We propose that in free life PHB synthesis sequesters reductive power, allowing the tricarboxylic acid cycle to proceed under conditions in which oxygen is a limiting factor. In symbiosis with Phaseolus vulgaris, the PHB-negative mutant induced nodules that prolonged the capacity to fix nitrogen.
Etomidate vs. propofol to carry out suspension laryngoscopies. (1991)

Patients about to undergo a suspension laryngoscopy were randomly assigned to one of two groups (n = 10). They were given either etomidate 1 mg kg-1 followed by 1 mg kg-1 h-1, or propofol 2.5 mg kg-1 followed by 9 mg kg-1 h-1. Alfentanil 10 micrograms kg-1 was given to provide analgesia with a further half dose if necessary. Duration of apnoea, quality of anaesthesia, times between stopping hypnotic administration and the moment when the patients opened their eyes, gave their name, date of birth and the day's date were noted. Heart rate, blood pressures, respiratory frequency and blood gases were noted before induction, before suspension and when hypnotic infusion was stopped. Clinical tolerance was good, the duration of surgery, apnoea and quality of anaesthesia were the same for both groups. Blood pressure was less depressed by etomidate, but ventilatory frequency was higher. Recovery was significantly faster after propofol. Propofol is recommended for patients who require good post-operative cooperation (chronic obstructive pulmonary disease) and etomidate for those who are haemodynamically compromised.
The Study of Interleukin-17 Level in Vernal Keratoconjunctivitis Disease and its Relationship between Symptom and Sign Severity (2016)

Interleukin-17 has a role in the pathogenesis of VKC and also has been proven in the former studies.
CasA mediates Cas3-catalyzed target degradation during CRISPR RNA-guided interference (2014)

In bacteria, the clustered regularly interspaced short palindromic repeats (CRISPR)-associated (Cas) DNA-targeting complex Cascade (CRISPR-associated complex for antiviral defense) uses CRISPR RNA (crRNA) guides to bind complementary DNA targets at sites adjacent to a trinucleotide signature sequence called the protospacer adjacent motif (PAM). The Cascade complex then recruits Cas3, a nuclease-helicase that catalyzes unwinding and cleavage of foreign double-stranded DNA (dsDNA) bearing a sequence matching that of the crRNA. Cascade comprises the CasA-E proteins and one crRNA, forming a structure that binds and unwinds dsDNA to form an R loop in which the target strand of the DNA base pairs with the 32-nt RNA guide sequence. Single-particle electron microscopy reconstructions of dsDNA-bound Cascade with and without Cas3 reveal that Cascade positions the PAM-proximal end of the DNA duplex at the CasA subunit and near the site of Cas3 association. The finding that the DNA target and Cas3 colocalize with CasA implicates this subunit in a key target-validation step during DNA interference. We show biochemically that base pairing of the PAM region is unnecessary for target binding but critical for Cas3-mediated degradation. In addition, the L1 loop of CasA, previously implicated in PAM recognition, is essential for Cas3 activation following target binding by Cascade. Together, these data show that the CasA subunit of Cascade functions as an essential partner of Cas3 by recognizing DNA target sites and positioning Cas3 adjacent to the PAM to ensure cleavage.
Prolonged disease-free period in patients with advanced epithelial ovarian cancer after adoptive transfer of tumor-infiltrating lymphocytes. (1995)

Thirteen patients with epithelial ovarian cancer, who did not show any detectable lesion after cisplatin-containing chemotherapy following primary operation, were treated with adoptive transfer of tumor-infiltrating lymphocytes (TIL group). Eleven patients with almost equivalent conditions of disease, who were treated with only chemotherapy following primary operation, served as a control group. The median time of follow-up was 36 (range, 23-44) months in the TIL group and 33 (range, 14-48) months in the control group. The estimated 3-year overall survival rate of disease-free patients in the TIL group and in the control group was 100% and 67.5%, respectively. A significant difference was noticed between the overall survival rate of the TIL group and the control group (P < 0.01). Furthermore, the estimated 3-year disease-free survival rate of the patients in the TIL group and in the control group was 82.1% and 54.5%, respectively. The disease-free survival rate of patients in the TIL group and in the control group was significantly different (P < 0.05). These results suggest that the adoptive transfer of TILs after all chemotherapy has been finished might be one promising method to achieve complete cure of advanced epithelial ovarian cancer.
Quantitative analysis of gene suppression in integrated retrovirus vectors. (1986)

Previously, we described a retrovirus vector that contained two genes: a 5' gene under transcriptional control of the viral long terminal repeat and a 3' gene under transcriptional control of the herpes simplex virus thymidine kinase promoter. By using a biological assay, we found that expression of the 5' gene is suppressed when there was selection for the 3' gene and expression of the 3' gene is suppressed when there is selection for the 5' gene (M. Emerman and H. M. Temin, Cell 39:459-467, 1984). In the present study, we replaced the thymidine kinase promoter with stronger promoters, and we measured expression of the genes in the retrovirus vectors by enzyme activity and RNA analysis. We found that all of the vectors displayed gene suppression when analyzed biochemically, although not when analyzed biologically. The suppressed genes produced about 10 to 50% as much product as when they were selected. The amount of suppression depended on whether the suppressed gene was 5' or 3' to the selected gene and from which promoter the suppressed gene was transcribed. The amount of suppression correlated with a decrease in the amount of steady-state RNA transcribed from the suppressed gene's promoter.
Biocompatibility, Biodistribution, and Drug‐Delivery Efficiency of Mesoporous Silica Nanoparticles for Cancer Therapy in Animals (2010)

Mesoporous silica nanoparticles (MSNs) are a promising material for drug delivery. In this Full Paper, MSNs are first shown to be well tolerated, as demonstrated by serological, hematological, and histopathological examinations of blood samples and mouse tissues after MSN injection. Biodistribution studies using human cancer xenografts are carried out with in vivo imaging and fluorescent microscopy imaging, as well as with inductively coupled plasma mass spectroscopy. The results show that MSNs preferentially accumulate in tumors. Finally, the drug-delivery capability of MSNs is demonstrated by following tumor growth in mice treated with camptothecin-loaded MSNs. These results indicate that MSNs are biocompatible, preferentially accumulate in tumors, and effectively deliver drugs to the tumors and suppress tumor growth.
Improved Protocols for the Illumina Genome Analyzer Sequencing System (2009)

In this unit, we describe a set of improvements we have made to the standard Illumina Genome Analyzer protocols to make the sequencing process more reliable in a high-throughput environment, reduce amplification bias, narrow the distribution of insert sizes, and reliably obtain high yields of data.
Canonical Wnts function as potent regulators of osteogenesis by human mesenchymal stem cells (2009)

Genetic evidence indicates that Wnt signaling is critically involved in bone homeostasis. In this study, we investigated the functions of canonical Wnts on differentiation of adult multipotent human mesenchymal stem cells (hMSCs) in vitro and in vivo. We observe differential sensitivities of hMSCs to Wnt inhibition of osteogenesis versus adipogenesis, which favors osteoblastic commitment under binary in vitro differentiation conditions. Wnt inhibition of osteogenesis is associated with decreased expression of osteoblastic transcription factors and inhibition of c-Jun N-terminal kinase and p38 mitogen-activated protein kinase activation, which are involved in osteogenic differentiation. An hMSC subpopulation exhibits high endogenous Wnt signaling, the inhibition of which enhances osteogenic and adipogenic differentiation in vitro. In an in vivo bone formation model, high levels of Wnt signaling inhibit de novo bone formation by hMSCs. However, hMSCs with exogenous expression of Wnt1 but not stabilized beta-catenin markedly stimulate bone formation by naive hMSCs, arguing for an important role of a canonical Wnt gradient in hMSC osteogenesis in vivo.
Neuropilin-1 Mediates Divergent R-Smad Signaling and the Myofibroblast Phenotype (2010)

The transforming growth factor-beta (TGF-β) superfamily is one of the most diversified cell signaling pathways and regulates many physiological and pathological processes. Recently, neuropilin-1 (NRP-1) was reported to bind and activate the latent form of TGF-β1 (LAP-TGF-β1). We investigated the role of NRP-1 on Smad signaling in stromal fibroblasts upon TGF-β stimulation. Elimination of NRP-1 in stromal fibroblast cell lines increases Smad1/5 phosphorylation and downstream responses as evidenced by up-regulation of inhibitor of differentiation (Id-1). Conversely, NRP-1 loss decreases Smad2/3 phosphorylation and its responses as shown by down-regulation of α-smooth muscle actin (α-SMA) and also cells exhibit more quiescent phenotypes and growth arrest. Moreover, we also observed that NRP-1 expression is increased during the culture activation of hepatic stellate cells (HSCs), a liver resident fibroblast. Taken together, our data suggest that NRP-1 functions as a key determinant of the diverse responses downstream of TGF-β1 that are mediated by distinct Smad proteins and promotes myofibroblast phenotype.
Orientations of theBacteroides fragilisCapsular Polysaccharide Biosynthesis Locus Promoters during Symbiosis and Infection (2010)

Orientations of the seven invertible polysaccharide biosynthesis locus promoters of Bacteroides fragilis were determined from bacteria grown in vitro, from feces of monoassociated and complex colonized mice, and from B. fragilis-induced murine abscesses. Bacteria grown in vivo have greater variability in orientation of polysaccharide locus promoters than culture-grown organisms.