gebhart/patrepeval huggingface dataset:
Characterization of the Physical Interaction between Estrogen Receptor α and JUN Proteins (2001)

Activated estrogen receptor alpha (ERalpha) modulates transcription triggered by the transcription factor activator protein-1 (AP-1), which consists of Jun-Jun homodimers and Jun-Fos heterodimers. Previous studies have demonstrated that the interference occurs without binding of ERalpha to DNA but probably results from protein.protein interactions. However, involvement of a direct interaction between ERalpha and AP-1 is still debated. Using glutathione S-transferase pull-down assays, we demonstrated that ERalpha bound directly to c-Jun and JunB but not to FOS family members, in a ligand-independent manner. The interaction could occur when c-Jun was bound onto DNA, as shown in a protein-protein-DNA assay. It implicated the C-terminal part of c-Jun and amino acids 259-302 present in the ERalpha hinge domain. ERalpha but not an ERalpha mutant deleted of amino acids 250-303 (ER241G), also associated with c-Jun in intact cells, in the presence of estradiol, as shown by two-hybrid and coimmunoprecipitation assays. We also show that ERalpha, c-Jun, and the p160 coactivator GRIP1 can form a multiprotein complex in vitro and in intact cells and that the ERalpha.c-Jun interaction could be crucial for the stability of this complex. VP16-ERalpha and c-Jun, which both interact with GRIP1, had synergistic effect on GAL4-GRIP1-induced transcription in the presence of estradiol, and this synergistic effect was not observed with the ERalpha mutant VP16-ER241G or when c-Fos, which bound GRIP1 but not ERalpha, was used instead of c-Jun. Finally, ER241G was inefficient for regulation of AP-1 activity, and an ERalpha truncation mutant encompassing the hinge domain had a dominant negative effect on ERalpha action. These results altogether demonstrate that ERalpha can bind to c-Jun in vitro and in intact cells and that this interaction, by stabilizing a multiprotein complex containing p160 coactivator, is likely to be involved in estradiol regulation of AP-1 responses.
Size dependency variation in lattice parameter and valency states in nanocrystalline cerium oxide (2005)

A correlation between the particle size and the lattice parameter has been established in nanocerium oxide particles (3–30nm). The variation in the lattice parameter is attributed to the lattice strain induced by the introduction of Ce3+ due to the formation of oxygen vacancies. Lattice strain was observed to decrease with an increase in the particle size. Ce3+ ions concentration increased from 17% to 44% with the reduction in the particle size.
Advanced glycation end products accumulate in the reproductive tract of men with diabetes (2009)

Light microscopic studies comparing sperm parameters show little association between diabetes and male fertility. However, with the introduction of new analytical techniques, evidence is now emerging of previously undetectable effects of diabetes on sperm function. Specifically, a recent study has found a significantly higher sperm nuclear DNA fragmentation in diabetic men. As advanced glycation end products (AGEs) are important instigators of oxidative stress and cell dysfunction in numerous diabetic complications, we hypothesized that these compounds could also be present in the male reproductive tract. The presence and localization of the most prominent AGE, carboxymethyl-lysine (CML), in the human testis, epididymis and sperm was determined by immunohistochemistry. Parallel ELISA and Western blot analyses were performed to ascertain the amount of CML in seminal plasma and sperm from 13 diabetic and nine non-diabetic subjects. CML immunoreactivity was found throughout the seminiferous epithelium, the nuclei of spermatogonia and spermatocytes, in the basal and principle cells cytoplasm and nuclei of the caput epididymis and on most sperm tails, mid pieces and all cytoplasmic droplets. The acrosomal cap, especially the equatorial band, was prominently stained in diabetic samples only. The amount of CML was significantly higher (p = 0.004) in sperm from non-diabetic men. Considering the known detrimental actions of AGEs in other organs, the presence, location and quantity of CML, particularly the increased expression found in diabetic men, suggest that these compounds may play a hitherto unrecognized role in male infertility.
Cetuximab+FOLFIRI as first-line treatment for metastatic colorectal CA (2004)

3513 Background: Cetuximab is an IgG1 monoclonal antibody targeting the EGFR. In irinotecan-refractory metastatic CRC and in first-line therapy trials cetuximab has shown to be active (ASCO 2002, 2003). This phase II trial evaluates the safety and efficacy of cetuximab combined with a FOLFIRI regimen as first-line treatment for pts with EGFR-expressing metastatic CRC. Methods: Cetuximab was given at an initial dose of 400 mg/m2, then 250 mg/m2 i.v. weekly. FOLFIRI was administered every 2 weeks: Irinotecan 180 mg/m2, FA 400 mg/m2 and 5-FU 300 mg/m2 bolus plus infusion of 2,000 mg/m2/46h (low dose group, LD) or 400 mg/m2 bolus plus infusion of 2,400 mg/m2/46h (high dose group, HD). Dose limiting toxicity (DLT) was defined as neutropenia/leukopenia, thrombopenia, alk. phosphatase, bilirubin, ASAT, ALAT or skin toxicity > grade (Gd) 3; neutropenia with fever/infection, anemia, diarrhea, mucositis, creatinine, or any treatment-related organ toxicity > Gd 2 during the first 3 cycles. Results: The first 23 pts were evaluated for DLT, 10 in LD, 13 in HD group. Median age was 66 years (36–76) and median KPS was 90 (60–100). No DLT occurred in the LD group, but 3 DLT in the HD (diarrhea Gd 3, allergy Gd 3, neutropenia Gd 4). 22 pts were evaluable for efficacy: PR 10 (46%, C.I., 25–66%), SD 9 (41%), PD 3 (14%). 7 pts underwent secondary surgery of metastases. So far, median TTP was 10.9 months. To allow a better estimate of safety and efficacy for a planned phase III trial, further 29 patients were enrolled in the HD group that has demonstrated an acceptable safety profile. Safety analysis in the HD group was based on 42 pts. The most frequent grade 3/4 adverse events were diarrhea 14.3%, neutropenia 11.9%, rash, 11.9%, and nausea/vomiting 9.5%. Frequency of acne-like rash of grade 1/2/3/4 was 28.6/26.2/4.8/0 %. 5 pts were still on treatment at the time of abstract submission. Conclusion: The combination of cetuximab with FOLFIRI is safe and feasible in pts with EGFR-expressing metastatic CRC and is clearly active. Author Disclosure Employment or Leadership Consultant or Advisory Stock Ownership Honoraria Research Funding Expert Testimony Other Remuneration Merck KGaA Merck KGaA Merck KGaA Merck KGaA Merck KGaA
Processing of point cloud data from ToF camera for the localisation of ground-based crop (2012)

This paper describes an approach that analyses point cloud information from a Time-of-Flight (ToF) camera to identify the location of foremost spring onions along the crop bed, for the intention of robotic manipulation. The process uses a combination of 2D image processing on the amplitude data, as well as depth analysis on the point cloud information, extracted from the camera to locate the desired object. Whilst the experimental results demonstrated the robustness of this approach, further testing is required to determine the ability of system to cope with different scenarios that exists in the naturally varying environment. Finally, it is important to validate the accuracy of the system in the physical world by integrating the localization algorithm to a robotic manipulation system.
Risk factors associated with alterations in carotid intima—media thickness in hypertension (1998)

Analysis of baseline data from the ELSA has shown that there is an extremely marked prevalence of carotid artery wall alterations among mild-to-moderate, middle-aged hypertensive patients. In addition to age, systolic blood pressure and pulse pressure, particularly if they are accurately measured by ambulatory monitoring, play a major role, somewhat greater than those of sex, low-density lipoprotein cholesterol concentration and smoking, in influencing intima-media thickness.
Collection-oriented languages (1991)

The authors outline, compare, and contrast the collections and operations found in many collection-oriented languages by putting them into a common framework. In the process, many problems that can occur in specifying such languages are elucidated. These languages are ideal for use with massively parallel machines, even though many of them were developed before parallelism. Some extended examples of collection operations in several languages are given. A taxonomy of collections is introduced. Issues examined include the type of elements a collection can contain, whether a collection must be homogeneously typed, and the ordering among the elements of a collection. The apply-to-each form in collection-oriented languages is examined. This form applies a function to each element of a collection. Issues treated include whether the extension of a function over the elements is explicit or implicit and how the extension is applied to functions with multiple arguments. A variety of languages (including APL, SETL, CM-Lisp, Paralation Lisp, and Fortran 90) are critically compared.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Isolation and characterization of an anti-peptide monoclonal antibody to human erythropoietin. (1985)

A site-specific monoclonal antibody to human erythropoietin has been developed. It is secreted by a hybridoma cell line derived from the fusion of murine myeloma cells with the splenocytes of a mouse that had been immunized with a 26-residue synthetic peptide antigen homologous to the amino-terminal sequence of the hormone. The antibody binds specifically to peptide, 125I-erythropoietin, and biologically active erythropoietin. The equilibrium dissociation constants of the antibody-erythropoietin and the antibody-peptide interactions are identical, Kd = 6.7 X 10(-9) M, suggesting strong conformational similarity or identity of the epitope as expressed on the peptide and the hormone. Immune complexes formed between the antibody and either human or rat erythropoietin exhibit full biologic activity. However, the antibody does not recognize the baboon, sheep, or canine hormones, indicating antigenic differences or structural variation among these erythropoietins. These results indicate that the amino-terminal region of erythropoietin is not involved in receptor binding. Furthermore, they form a basis for the study of the structure and function of the hormone using anti-peptide antibodies.
Discrete Steps in Binding and Signaling of Interleukin-8 with Its Receptor (1996)

The mechanisms by which chemokines bind and signal through their receptors are complex and poorly understood. In the present study, we sought to dissect these processes and to map important functional domains of the two CXC chemokine (interleukin-8) receptors, CXCR1 (formally IL-8RA) and CXCR2 (formally IL-8RB), using blocking monoclonal antibodies (mAbs) to the receptors and a series of chimeras between CXCR1 and CXCR2. A panel of specific mAbs against CXCR1 or CXCR2, generated by immunizing mice with transfectants expressing either receptor, were shown to effectively block IL-8- and/or growth-related oncogene alpha (GROalpha) -mediated ligand binding, chemotaxis, elastase release, and VCAM-1 binding in CXCR1 and CXCR2 transfectants and/or human neutrophils. Of particular interest was an anti-CXCR1 mAb, 7D9, that inhibited chemotaxis, elastase release, and VCAM-1 binding but had no detectable effects on ligand binding. The epitopes of these blocking mAbs were mapped by using a series of CXCR1/2 chimera transfectants and synthetic peptides. Most of the anti-CXCR1 antibodies, except 7D9, mapped to the amino acid sequence WDFDDL (CXCR1 residues 10-15), and all the anti-CXCR2 antibodies mapped to the amino acid sequence FEDFW (CXCR2 residues 6-10). The epitope of mAb 7D9 mainly involved a region within the first 45 residues of CXCR1, and it appeared to be conformation-sensitive. These results support a model in which the binding and signaling of IL-8 with its receptor occur in at least two discrete steps involving distinct domains of the receptor. This model is consistent with the notion that discrete conformational changes of the receptor secondary to ligand binding are required to trigger various biological responses. Moreover, the ligand binding and chemotaxis properties of each CXCR1/2 chimeric receptor to IL-8 and GROalpha were determined. It was found that each is distinct in its ability to confer ligand binding and chemotactic response to IL-8 and GROalpha, and two conclusions could be made. 1) The N-terminal segment of CXCR1 is a dominant determinant of receptor subtype selectivity, consistent with previous studies using rabbit/human CXCR1/2 chimeras; and 2) the specificity determinant for GROalpha binding in CXCR2 involves sequences in the N terminus, distal to the first 15 residues, as well as other parts of the receptor.
Sequence-specific cleavage of RNA by Type II restriction enzymes (2010)

The ability of 223 Type II restriction endonucleases to hydrolyze RNA-DNA heteroduplex oligonucleotide substrates was assessed. Despite the significant topological and sequence asymmetry introduced when one strand of a DNA duplex is substituted by RNA we find that six restriction enzymes (AvaII, AvrII, BanI, HaeIII, HinfI and TaqI), exclusively of the Type IIP class that recognize palindromic or interrupted-palindromic DNA sequences, catalyze robust and specific cleavage of both RNA and DNA strands of such a substrate. Time-course analyses indicate that some endonucleases hydrolyze phosphodiester bonds in both strands simultaneously whereas others appear to catalyze sequential reactions in which either the DNA or RNA product accumulates more rapidly. Such strand-specific variation in cleavage susceptibility is both significant (up to orders of magnitude difference) and somewhat sequence dependent, notably in relation to the presence or absence of uracil residues in the RNA strand. Hybridization to DNA oligonucleotides that contain endonuclease recognition sites can be used to achieve targeted hydrolysis of extended RNA substrates produced by in vitro transcription. The ability to 'restrict' an RNA-DNA hybrid, albeit with a limited number of restriction endonucleases, provides a method whereby individual RNA molecules can be targeted for site-specific cleavage in vitro.
1910–2010: How infrastructure grew our nation (2010)

One hundred years ago this year, South Africa was established by an Act of Union. That Act gave us the shape and the texture that defined us as a nation. And it is wonderful that, despite all the exclusions and discriminations since May 1910, we have survived intact as a state and still live within those same, unchanged borders. While articles in the daily press earlier this year discussed political and governance aspects of how far we have travelled as a nation over the last 100 years, Kevin Wall in this article reflects on infrastructure development and service delivery over the last century.
Influences of mRNA secondary structure on initiation by eukaryotic ribosomes. (1986)

Oligonucleotides designed to create hairpin structures were inserted upstream from the ATG initiator codon in several plasmids that encode preproinsulin, and the effects on translation were monitored in COS cells transfected by the vectors. Creation of a hairpin (delta G = -30 kcal/mol) that directly involves the ATG triplet at the start of the preproinsulin coding sequence does not reduce the yield of proinsulin. However, a more stable stem-and-loop structure (delta G = -50 kcal/mol) reduces the proinsulin yield by 85-95%. The stable hairpin inhibits even when it occurs at the midpoint of the 5' untranslated sequence and thus involves neither the cap nor the ATG codon. Presumably the migrating 40S ribosomal subunit can melt moderately stable duplexes but stalls at structures (delta G = -50 kcal/mol) that resist unfolding. Other experiments argue against the idea that sequestering the 5'-proximal ATG codon in a hairpin structure might allow it to be skipped by ribosomes in favor of an exposed ATG triplet farther downstream: when the primary sequence around the first ATG triplet is favorable for initiation, no translation from a downstream site can be detected, irrespective of whether the first ATG codon is single-stranded or base-paired.
Regeneration of long-distance peripheral nerve defects after delayed reconstruction in healthy and diabetic rats is supported by immunomodulatory chitosan nerve guides (2017)

No considerable differences appear for the delayed nerve regeneration process related to healthy and diabetic conditions. Currently available chitosan nerve grafts do not support delayed nerve regeneration to the same extent as they do after immediate nerve reconstruction. The immunomodulatory characteristics of the biomaterial may, however, be crucial for their regeneration supportive effects.
Wood Hydrolysis and Hydrolyzate Detoxification for Subsequent Xylitol Production (2000)

A great deal of work has been done during the last decade to develop alternative processes for the integral utilization and revaluation of vegetable biomass. Hardwoods (in particular Eucalyptus globulus) were demonstrated to be of particular interest, because of their rapid growth as well as of the excellent quality of the wood pulp that can be obtained. Today only the cellulose fraction is used for paper production from wood pulp, whereas the lignin and hemicellulose fractions are burnt to produce heat or wasted. This process could be performed in a more profitable way by fractionating the woody material into these fractions and separately using them in different processes.
Structural elucidation of two capsular polysaccharides from one strain of Bacteroides fragilis using high-resolution NMR spectroscopy (1992)

The capsule of Bacteroides fragilis is unusual in that it consists of two distinct capsular polysaccharides. Using a combination of high-resolution NMR spectroscopy, theoretical calculations, and as few chemical procedures as required, the structure of both polysaccharide antigens (polysaccharides A and B) was elucidated. Using the above procedures, it was possible to obtain the complete structures using minimal quantities of polysaccharides A and B (8 and 5 mg, respectively). Only small amounts of each subjected to chemical analysis were not recoverable. Polysaccharide A is composed of the following repeating unit: [----3)alpha-D-AATp(1----4)[beta-D-Galf(1----3)]alpha-D- GalpNAc(1----3)beta-D-Galp(1----], where AAT is 2-acetamido-4-amino-2,4,6-trideoxygalactose. A pyruvate substituent having the R configuration spans O-4 and O-6 of the beta-D-galactopyranosyl residue. Polysaccharide B is composed of the following repeating unit: [----4)alpha-L-QuipNAc(1----3)beta-D-QuipNAc(1----4)[alpha-L - Fucp(1----2)beta-D-GalpA(1----3)beta-D-GlcpNAc(1----3)]alpha -D-Galp(1----]. A 2-aminoethylphosphonate substituent is situated on O-4 of the N-acetyl-beta-D-glucopyranosyl residue.
Adaptive e-mail intention finding mechanism based on e-mail words social networks (2007)

Through the rapid evaluation of spam, no fully successful solution for filtering spam has been found. However, the spammers still spread spam by using the same intentions such as advertising and phishing. In this investigation, we propose a mechanism of E-mail Words Social Network (EWSN) for profiling users' intentions related to interesting and uninteresting e-mails. An EWSN is constructed from the information in an individual user's mailbox, and expands e-mail information from the World Wide Web (WWW) via the search engine. Based on the web information and association rules among the words, words and relations are expanded as a words' social network. Via the EWSN, both interested and uninterested EWSNs can be constructed to analyze user intentions. Additionally, an efficiency detection mechanism based on the EWSN is proposed to classify e-mails. Finally, the adaptation algorithm of artificial immune system is applied to EWSN, which is thus adapted to follow the user's confirmed classification results. The experimental results indicate that the proposed system is very helpful for classifying spam e-mails by analyzing senders' intentions. Some ideas for analyzing interested nature of people, and profiling their backgrounds, are also presented.
Comparison of GH, IGF-I, and testosterone with mRNA of receptors and myostatin in skeletal muscle in older men (2001)

Growth hormone (GH), insulin-like growth factor I (IGF-I), and testosterone (T) are important mediators of muscle protein synthesis, and thus muscle mass, all of which decline with age. We hypothesized that circulating hormones would be related to the transcriptional levels of their respective receptors and that this expression would be negatively related to expression of the myostatin gene. We therefore determined content of mRNA transcripts (by RT-PCR) for GH receptor (GHR), IGF-I, androgen receptor (AR), and myostatin in skeletal muscle biopsy samples from 27 healthy men >65 yr of age. There were no significant relationships between age, lean body mass, or percent body fat and transcript levels of GHR, IGF-I, AR, or myostatin. Moreover, there were no significant correlations of serum GH, IGF-I, or T with their corresponding target mRNA levels (GHR, intramuscular IGF-I, or AR) in skeletal muscle. However, GHR was negatively correlated (r = -0.60, P = 0.001) with myostatin mRNA levels. The lack of apparent relationships of muscle transcripts with their respective ligands in healthy older adults suggests that age-related deficits in both GH and T may lead to an increase in myostatin expression and a disassociation in autocrine IGF-I effects on muscle protein synthesis, both of which could contribute to age-related sarcopenia.
Electrical Stimulation Promotes Regeneration of Defective Peripheral Nerves after Delayed Repair Intervals Lasting under One Month (2014)

Electrical stimulation does not continue to promote nerve regeneration after long delays in nerve repair. The effective interval for nerve regeneration after delayed repair was found to be less than 1 month. The mechanism seemed to be related to the expression of nerve growth factors and regeneration environment in the distal nerves.
Antibody engineering by codon-based mutagenesis in a filamentous phage vector system (1992)

A novel codon-based mutagenesis procedure is described that allows rapid and efficient modification of antibody amino acid sequences expressed as F(ab) fragments in M13. The procedure succeeded in generating a library of mutations in the complementarity-determining regions of chimeric L6, an antibody against a tumor-associated Ag. A set of anti-Id antibodies (anti-Id 1, 3, and 7) that bind near the L6 Ag-binding site served as model Ag. The goal was to select mutant antibody sequences that altered the L6 reactivity with the anti-Id in subtle ways, i.e., to eliminate the binding to one anti-Id while preserving other reactivities or to identify mutants with increased binding. A high frequency of variant M13 phage clones exhibiting altered specificity for the anti-Id were identified. Codon-based mutagenesis in conjunction with the M13 antibody expression and screening system should provide an efficient and general approach for redirecting the specificity and potentially improving the affinity of antibodies in vitro.