gebhart/patrepeval huggingface dataset:
Structure of the capsular polysaccharide antigen of type IV group B Streptococcus (1989)

The native polysaccharide antigen isolated from type IV group B Streptococcus contains D-galactose, D-glucose, 2-acetamido-2-deoxy-D-glucose, and sialic acid in the molar ratio 2:2:1:1 and is composed of the following repeating unit:[Formula: see text]The structural analysis of this antigen was based on results obtained from methylation analysis, partial hydrolysis, nitrous acid deamination, and nuclear magnetic resonance spectroscopic techniques. Keywords: capsular polysaccharide, high resolution NMR spectroscopy, group B Streptococcus, polysaccharide structure, polysaccharide degradation.
Insulin-like growth factor-binding protein-3 is partially responsible for high-serum-induced apoptosis in PC-3 prostate cancer cells (1999)

Cells are known to undergo apoptosis when cultured in high serum concentrations. However, the serum factors responsible for this induction of apoptosis have not been identified. The IGF-binding protein-3 (IGFBP-3), a negative growth regulator, is found at concentrations of 5 microgram/ml in serum. We have recently demonstrated that IGFBP-3 induces apoptosis in PC-3 cells, a prostate cancer cell line, at a concentration of 500 ng/ml. In this communication, we demonstrate the role of IGFBP-3 as one of the apoptosis-inducing agents in high serum concentrations. Treatment of PC-3 cells with increasing concentrations (40% to 90%) of intact human serum (HS) resulted in a dose-dependent decrease in cell growth. Valinomycin, an ionophore, was used as a positive control to measure the induction of apoptosis by serum treatment in PC-3 cells. Treatment with 90% serum showed significant suppression of growth (P<0.001) compared with the effect of 10% serum. Treatment with increasing concentrations of HS (40% to 90%) resulted in a dose-dependent increase in apoptosis. Treatment with 90% HS showed a 10-fold increase in apoptotic index compared with cells treated with 10% HS. Treatment of PC-3 cells with IGFs and IGFBP-3-depleted 90% human sera (depleted serum=DS) demonstrated significantly lower levels of apoptosis (50% reduction in the effect of 90% HS) suggesting a role of IGFBP-3 in inducing apoptosis in high serum concentration. Furthermore, treatment with DS supplemented with recombinant IGFBP-3 (500 ng/ml) brought the apoptotic index down close to the level of apoptosis induced by 90% intact serum treatment (P<0.001). However, DS supplemented with physiological concentrations of IGFs (500 ng/ml) showed only partial recovery of cell survival demonstrated by 90% DS. This data indicates that IGFBP-3 is one of the factors in serum that is responsible for high-serum-induced apoptosis.
Bispecific antibody‐mediated lysis of primary cultures of ovarian carcinoma cells using multiple target antigens (1999)

We have shown previously that a bispecific antibody (BsAb) directed against both germ-cell alkaline phosphatase (GCAP) and the CD3 complex on mouse T cells could effectively eliminate GCAP-positive tumor cells in vivo using an immunocompetent mouse model. However, some GCAP-negative tumor cells were still able to grow, suggesting that BsAb therapy, when used in a clinical setting, could benefit from targeting several tumor markers to prevent outgrowth of tumor cells lacking a targeted marker. To test this hypothesis, we developed an in vitro model based on primary human ovarian carcinoma (OC) cultures and BsAbs directed against human T cells and several tumor markers [placental alkaline phosphatase (PLAP), GCAP, folate-binding protein (FBP) and CA19.9]. OC cells, isolated from primary tumors, were co-cultured with human peripheral blood mononuclear cells in the presence or absence of various concentrations of BsAbs against PLAP/GCAP, FBP and CA19.9 administered separately or in combination. Results derived from 18 primary OC samples showed that the combination treatment was better than or equally effective as the best single BsAB treatment in 60% of cases. Sometimes targeting FBP, PLAP/GCAP or CA19.9 alone was superior to targeting all simultaneously. Combining each BsAb with a low dose of IL-2 was always beneficial. These results indicate that before using a specific BsAb in the clinic, it is important to determine the optimal BsAb for each patient using this in vitro assay on cells from the removed tumor mass. Int. J. Cancer 83:270–277, 1999. © 1999 Wiley-Liss, Inc.
Location and function of voltage‐sensitive conductances in retinal rods of the salamander, Ambystoma tigrinum. (1984)

The functional role and spatial location of voltage-sensitive conductances that modify the light-evoked electrical signals were studied in retinal rods of the tiger salamander. An isolated rod was drawn into a suction electrode for recording membrane current and impaled with an intracellular electrode for recording membrane potential and passing current. A bright flash gave a rapid initial hyperpolarization that relaxed to a smaller plateau. Simultaneously the dark current of the outer segment was shut off with the time course of a rounded step function. This characteristic difference between the wave forms demonstrates that the voltage relaxation does not result from reopening of light-sensitive channels. The voltage relaxation in (2) did not require light or interruption of the dark current, as the wave form was duplicated by suddenly switching off a depolarizing current injected during steady saturating light. This is explained if the relaxation depends purely on voltage-sensitive conductances. The voltage response to a dim flash reached its peak value before the current response. The voltage wave form was predicted assuming that the recorded photo-current drove a linear high-pass filter with parameters derived from analysis of the voltage response to injection of a current step. When the intracellular voltage was changed by current injection the slope resistance of the outer segment slowly declined to a lower level, indicating that the outer segment contains a voltage-sensitive conductance. When a current step was injected in bright steady light, the current recorded from the outer segment consisted of a capacity component proportional to dV/dt and a small extracellular leakage current but no detectable ionic current. This supports other evidence indicating that light-sensitive channels comprise the main or exclusive ionic conductance of the outer segment. The behaviour in (5) is explained if the light-sensitive channels themselves are slowly opened by hyperpolarization and closed by depolarization. Analysis of the current-injection experiments suggests that most of the high-pass filtering in a rod results from the action of voltage-sensitive conductances located in the inner segment. Addition of 10 mM-CsCl to the Ringer solution abolished the relaxation in the voltage response to a bright flash but left intact the high-pass filtering of small signals. This would be explained by a selective block of one of two sets of voltage-sensitive channels in the inner segment or by a voltage-sensitive block of one kind of channel.
Development of Fluoroimmunoassays for the Determination of Individual or Combined Levels of Procainamide and N-Acetylprocainamide in Serum (1982)

A fluoroimmunoassay has been developed for the simultaneous determination of serum levels of procainamide and its active metabolite N-acetylprocainamide. It employs procainamide linked through its aromatic amino group to fluorescein isothiocyanate as tracer and an antiserum raised against procainamide conjugated to human thyroglobulin through the same position. Separation is rapidly and simply achieved by covalently linking the antiserum to magnetisable microparticles and use of a magnet. Specific magnetisable particle fluorimmunoassays were also developed for procainamide and for N-acetylprocainamide by the use of suitable immunogens and fluorescein-labelled tracers. That for procainamide uses an antiserum raised to a procainamide-enzyme conjugate and fluorescein-labelled p-aminobenzoic acid while the fluoroimmunoassay for N-acetylprocainamide employs an antiserum against a N-acetylprocainamide-enzyme conjugate and fluorescein-labelled p-acetamidobenzoic acid.
Introduction (2011)

Witnessing firsthand the ways drama activity puts their students’ imaginations to work, these teachers experienced drama’s value as a powerful teaching and learning strategy that invites students of all ages to move collaboratively inside classroom content, human issues, and significant events.
Stimulated natural killer cells secrete factors with chemotactic activity, including NAP‐1/IL‐8, which supports VLA‐4‐ and VLA‐5‐mediated migration of T lymphocytes (1994)

In vivo, natural killer (NK) cells dominate among the early invading cells in allografts and virus-infected tissues, and they are followed later by an influx of T cells. The same sequence of events was seen in our modified Boyden chamber assay. The migration of both CD3+/CD4+ and CD3+/CD8+ cells through fibronectin-coated filters increased after co-culture with NK cells. The migratory response to a soluble factor from NK cells supernatants was predominantly chemotactic rather than chemokinetic. Endogenous NK cells, purified in the presence of human serum albumin, did not induce T cell chemotaxis, but NK cells which were purified in the presence of 10% fetal calf serum (FCS), or which were activated in the absence of FCS with 10(-4) M histamine, with 300 IU/ml interleukin (IL)-2, or with a combination of 10 IU/ml IL-2 and 10 micrograms/ml CD16 monoclonal antibody increased T cell migration by 30-70%. Both the random and chemotactic migration were dependent on fibronectin receptors VLA-4 and VLA-5 on T cells. About 60% of the chemotactic was neutralized by NAP-1/IL-8 polyclonal antibody. Northern blot analysis revealed IL-8 mRNA expression in highly purified, stimulated NK cells; dimeric IL-8 protein secreted by NK cells was detected by immunoblotting, and, in immunofluorescence staining IL-8 was visualized in NK cells. These observations suggest that NK cells, early invaders in the foci of injury, participate in the initiation of a specific immune response by facilitating T cell recruitment.
Fumigant Nematicides Registered for Vegetable Crop Use in Florida (2013)

This 3-page fact sheet lists of multispectrum fumigant nematicides currently registered for use on different Florida crops (Table 1); their maximum rates and specific details for field application (Table 2); and a generalized summary of maximum use rate and relative effectiveness of various soil fumigants for nematode, soilborne disease, and weed control in Florida (Table 3). Written by J. W. Noling and published by the UF Department of Entomology and Nematology, January 2013.&#x0D; http://edis.ifas.ufl.edu/in980
ADP Receptors of Platelets and their Inhibition (2001)

ADP plays a crucial role in haemostasis and thrombosis and its receptors are potential targets for antithrombotic drugs. Two G-protein coupled P2 receptors contribute to platelet aggregation: the P2Y1 receptor initiates aggregation through mobilisation of calcium stores, while the more recently identified P2Y12 receptor coupled to adenylyl cyclase inhibition is essential for a full aggregation response to ADP and the stabilisation of aggregates. The latter is defective in certain patients with a selective congenital deficiency of aggregation to ADP. It is also the target of the antithrombotic drug clopidogrel and of ATP analogues and other compounds currently under evaluation. In addition, the P2X1 ionotropic receptor is present in platelets but its role is not yet completely known. Studies in P2Y1 knock-out mice and experimental thrombosis models using selective P2Y1 antagonists have shown that the P2Y1 receptor, like the P2Y12 receptor, is a potential target for new antithrombotic drugs.
Cumulative and discrete similarity analysis of electrostatic potentials and fields (1993)

Abstract A new index suitable for computing molecular similarity based upon the similarity of molecular properties such as electrostatic potentials or electrostatic fields is presented in two forms. For one form of the present index, general conditions are established for which a linear measure of similarity is obtained. An illustrative example is provided in which the electrostatic field and electrostatic potential of guanine obtained from different wave functions are compared. © 1993 John Wiley &amp; Sons, Inc.
Increased Persistent Sodium Currents in Rat Entorhinal Cortex Layer V Neurons in a Post–Status Epilepticus Model of Temporal Lobe Epilepsy (2003)

Summary: Purpose: Spontaneous seizures in rats emerge several weeks after induction of status epilepticus with pharmacologic treatment or electrical stimulation, providing an animal model for human temporal lobe epilepsy. In this study, we investigated whether status epilepticus caused changes in the function of voltage‐gated sodium channels in entorhinal cortex layer V neurons, a cellular group important for the genesis of limbic seizures. Methods: We induced status epilepticus in rats, by using lithium‐pilocarpine, and then 2–12 weeks later, used whole‐cell voltage‐clamp to examine voltage‐activated sodium currents of acutely dissociated layer V neurons. Results: Transient sodium currents of entorhinal cortex layer V neurons isolated from 9‐ to 12‐week post–status epilepticus rats were similar to currents in age‐matched controls; however, low‐threshold persistent sodium currents were significantly larger. This increase in persistent activity was not seen 2–3 weeks after pilocarpine treatment; thus it occurred after a delay comparable to the delay in the appearance of spontaneous seizures. Conclusions: Increased persistent currents are expected to accentuate neuronal excitability and thus may contribute to the genesis of spontaneous seizures after status epilepticus.
Tape-Arabidopsis Sandwich - a simpler Arabidopsis protoplast isolation method (2009)

The protoplasts generated by this new Tape-Arabidopsis Sandwich method are suitable for the same range of research applications as those that use the current method, but require less operator skill, equipment and time.
Solving the find-path problem by good representation of free space (1983)

Free space is represented as a union of (possibly overlapping) generalized cones. An algorithm is presented which efficiently finds good collision-free paths for convex polygonal bodies through space littered with obstacle polygons. The paths are good in the sense that the distance of closest approach to an obstacle over the path is usually far from minimal over the class of topologically equivalent collision-free paths. The algorithm is based on characterizing the volume swept by a body as it is translated and rotated as a generalized cone, and determining under what conditions one generalized cone is a subset of another.
Inverted duplication pattern in anaphase bridges confirms the breakage-fusion-bridge (BFB) cycle model for 11q13 amplification (2007)

The homogeneously staining region (hsr) involving chromosome band 11q13 includes amplified genes from this chromosome segment and carries a relatively poor prognosis in oral squamous cell carcinomas (OSCC), with shorter time to recurrence and reduced overall survival. We previously identified an inverted duplication pattern of genes within the 11q13 hsr in OSCC cells, supporting a breakage-fusion-bridge (BFB) cycle model for gene amplification. To validate our hypothesis that 11q13 gene amplification in OSCC occurs via BFB cycles, we carried out fluorescence in situ hybridization (FISH) using probes for band 11q13 on 29 OSCC cell lines. We demonstrate that all OSCC cell lines with 11q13 amplification express a significantly higher frequency of anaphase bridges containing 11q13 sequences compared to cell lines without amplification, providing further experimental evidence that 11q13 gene amplification in OSCC cells occurs via BFB cycles. Elucidation of mechanisms responsible for initiating and promoting gene amplification provides opportunities to identify new biomarkers to aid in the diagnosis and prognosis of oral cancer, and may be useful for developing novel therapeutic strategies for patients with OSCC.
A Mutation in Plasma Platelet-Activating Factor Acetylhydrolase (Val 279 →Phe) is a Genetic Risk Factor for Stroke (1997)

These results suggest that plasma PAF acetylhydrolase deficiency may be a risk factor for stroke. This may explain the relatively high prevalence of stroke in Japan, as the mutation is more common among Japanese than Caucasians.
Intraarticular Injections with Methylprednisolone Acetate Reduce Osteoarthritic Lesions in Parallel with Chondrocyte Stromelysin Synthesis in Experimental Osteoarthritis (1994)

These findings provide additional evidence for the protective effect of corticosteroid injections on OA lesions, and indicate that the effect of this drug may be mediated through the suppression of stromelysin synthesis.
Fluorescence-activated cell sorting of mouse-human hybrid cells aids in locating the gene for the Leu 7 (HNK-1) antigen to human chromosome 11. (1983)

Leu 7 (HNK-1) is a membrane antigen expressed on human natural killer cells and some other lymphoid cells. Starting with two clones of mouse-human hybrid lymphoid cells that had 1.6% and 35% Leu 7-positive cells, respectively, we viably sorted Leu 7-positive and -negative cells using a fluorescence-activated cell sorter (FACS). Short-term progeny of the sorted cells were then karyotyped. Chromosome 11 was the only human chromosome that was absent from the Leu 7-negative population and present in nearly all of the progeny of the Leu 7-positive selected cells. Thus, we assigned the Leu 7 gene to chromosome 11.
The prognostic value of anti-cyclic citrullinated peptide antibody in patients with recent-onset rheumatoid arthritis (2000)

Our data show that in almost 70% of RA patients, anti-CCP antibody is present at the early stages of disease. Anti-CCP-positive patients developed significantly more severe radiologic damage than patients who were anti-CCP negative, although in multiple regression analysis the additional predictive value was rather moderate.
Aligning sequence reads, clone sequences and assembly con*gs with BWA-MEM (2014)

Presented in April, 2013.
An interaction between the mammalian DNA repair protein XRCC1 and DNA ligase III. (1994)

XRCC1, the human gene that fully corrects the Chinese hamster ovary DNA repair mutant EM9, encodes a protein involved in the rejoining of DNA single-strand breaks that arise following treatment with alkylating agents or ionizing radiation. In this study, a cDNA minigene encoding oligohistidine-tagged XRCC1 was constructed to facilitate affinity purification of the recombinant protein. This construct, designated pcD2EHX, fully corrected the EM9 phenotype of high sister chromatid exchange, indicating that the histidine tag was not detrimental to XRCC1 activity. Affinity chromatography of extract from EM9 cells transfected with pcD2EHX resulted in the copurification of histidine-tagged XRCC1 and DNA ligase III activity. Neither XRCC1 or DNA ligase III activity was purified during affinity chromatography of extract from EM9 cells transfected with pcD2EX, a cDNA minigene that encodes untagged XRCC1, or extract from wild-type AA8 or untransfected EM9 cells. The copurification of DNA ligase III activity with histidine-tagged XRCC1 suggests that the two proteins are present in the cell as a complex. Furthermore, DNA ligase III activity was present at lower levels in EM9 cells than in AA8 cells and was returned to normal levels in EM9 cells transfected with pcD2EHX or pcD2EX. These findings indicate that XRCC1 is required for normal levels of DNA ligase III activity, and they implicate a major role for this DNA ligase in DNA base excision repair in mammalian cells.
Electronic Structure of Bis(imino)pyridine Iron Dichloride, Monochloride, and Neutral Ligand Complexes:  A Combined Structural, Spectroscopic, and Computational Study (2006)

The electronic structure of a family of bis(imino)pyridine iron dihalide, monohalide, and neutral ligand compounds has been investigated by spectroscopic and computational methods. The metrical parameters combined with Mössbauer spectroscopic and magnetic data for ((i)PrPDI)FeCl(2) ((i)PrPDI = 2,6-(2,6-(i)Pr(2)C(6)H(3)N=CMe)(2)C(5)H(3)N) established a high-spin ferrous center ligated by a neutral bis(imino)pyridine ligand. Comparing these data to those for the single electron reduction product, ((i)PrPDI)FeCl, again demonstrated a high-spin ferrous ion, but in this case the S(Fe) = 2 metal center is antiferromagnetically coupled to a ligand-centered radical (S(L) = (1)/(2)), accounting for the experimentally observed S = (3)/(2) ground state. Continued reduction to ((i)PrPDI)FeL(n) (L = N(2), n = 1,2; CO, n = 2; 4-(N,N-dimethylamino)pyridine, n = 1) resulted in a doubly reduced bis(imino)pyridine diradical, preserving the ferrous ion. Both the computational and the experimental data for the N,N-(dimethylamino)pyridine compound demonstrate nearly isoenergetic singlet (S(L) = 0) and triplet (S(L) = 1) forms of the bis(imino)pyridine dianion. In both spin states, the iron is intermediate spin (S(Fe) = 1) ferrous. Experimentally, the compound has a spin singlet ground state (S = 0) due to antiferromagnetic coupling of iron and the ligand triplet state. Mixing of the singlet diradical excited state with the triplet ground state of the ligand via spin-orbit coupling results in temperature-independent paramagnetism and accounts for the large dispersion in (1)H NMR chemical shifts observed for the in-plane protons on the chelate. Overall, these studies establish that reduction of ((i)PrPDI)FeCl(2) with alkali metal or borohydride reagents results in sequential electron transfers to the conjugated pi-system of the ligand rather than to the metal center.
Synthesis and Biological Properties of Insulin−Deoxycholic Acid Chemical Conjugates (2005)

Bile acids have been considered very useful in the preparation of new pharmaceuticals, and more recently in the preparation of peptide and protein drugs because of their natural chemical and biological properties. In this study, we modified recombinant human insulin by covalently attaching deoxycholic acid (DOCA) derivatives in order to synthesize orally active insulin analogues. DOCA derivatives, namely succinimido deoxycholate and succinimido bisdeoxycholyl-L-lysine were prepared and site specifically conjugated at Lys(B29) of insulin. The resultant insulin conjugates, [N(B29)-deoxycholyl] insulin (Ins-DOCA) and [N(B29)-bisdeoxycholyl-L-lysil] insulin (Ins-bisDOCA), were studied for their chemical, structural, and biological properties. Their chemical properties were determined by HPLC, MALDI-TOF mass spectroscopy, and dynamic light scattering. Lipophilicity and self-aggregation behavior of insulin conjugates were enhanced with increasing number of labeled bile acid. The far-ultraviolet region of circular dichroism spectra showed no significant change of the tertiary structure of insulin in aqueous solution due to conjugation. Competitive insulin binding assay with HepG2 cells revealed that monosubstituted insulin conjugates still retained high binding affinity to the insulin receptor. When the insulin conjugates were intravenously administered (0.33 IU/kg) to streptozotocin (STZ)-induced diabetic rats, the conjugates showed sustained biological activity for a longer period with the similar lowest blood glucose level (glucose nadir), compared to native insulin. In further studies, the resulting new insulin conjugates will be investigated for their oral efficiency as a long-acting insulin formulation for the treatment of diabetic patients.