gebhart/patrepeval huggingface dataset:
Plant Retrotransposons (1999)

Retrotransposons are mobile genetic elements that transpose through reverse transcription of an RNA intermediate. Retrotransposons are ubiquitous in plants and play a major role in plant gene and genome evolution. In many cases, retrotransposons comprise over 50% of nuclear DNA content, a situation that can arise in just a few million years. Plant retrotransposons are structurally and functionally similar to the retrotransposons and retroviruses that are found in other eukaryotic organisms. However, there are important differences in the genomic organization of retrotransposons in plants compared to some other eukaryotes, including their often-high copy numbers, their extensively heterogeneous populations, and their chromosomal dispersion patterns. Recent studies are providing valuable insights into the mechanisms involved in regulating the expression and transposition of retrotransposons. This review describes the structure, genomic organization, expression, regulation, and evolution of retrotransposons, and discusses both their contributions to plant genome evolution and their use as genetic tools in plant biology.
Regeneration across cold preserved peripheral nerve allografts (1999)

The feasibility of peripheral nerve allograft pretreatment utilizing cold storage (5 degrees C in the University of Wisconsin Cold Storage Solution) or freeze-thawing to prevent rejection was investigated. Regeneration across cold-stored (3 or 5 weeks) or freeze-thawed (FT), 3.0-cm sciatic nerve allografts were compared to fresh auto- and allografts in an inbred rat model. At 16-week post-engraftment, only FT allografts appeared similar to autografts on gross inspection; FT grafts were neither shrunken nor adherent to the surrounding tissue as seen in the other allograft groups. Qualitatively, the pattern of regeneration in the graft segments of the fresh allograft and to a lesser extent of pretreated allografts was inferior to that of autografts as evidenced by a disruption in the perineurium, more extrafascicular axons, smaller and fewer myelinated axons, increased intrafascicular collagen deposition, and the persistence of perineurial cell compartmentation and perivascular infiltrates. Distal to these grafts, the regeneration became more homogenous between groups, although areas of ongoing Wallerian degeneration, new regeneration as well as compartmentation, were more prevalent in fresh and pretreated allografts. Although the number of myelinated fibres was equivalent to autografts, the fibre diameters, the number of large diameter fibres, and the G-ratio were significantly decreased in the allograft groups, which, in part, accounted for the significant decrease in conduction velocity in the 3-week stored and fresh allograft, and the slight decrease in the 5-week stored and FT allograft groups. There was a small return in the Sciatic Function Index towards normal, but no consistent differences between groups were found. Prolonged cold storage and freeze-thawing of nerve allografts resulted in regeneration that was better than fresh allografts, but inferior to autografts. With the concomitant use of host immunosuppression or other immunotherapies, these storage techniques can provide a means of transporting nerve allografts between medical centres and for converting urgent into elective procedures.
Renin-angiotensin system-regulating aminopeptidases in tumor growth of rat C6 gliomas implanted at the subcutaneous region. (2012)

Although gliomas are heterogeneous tissues, angiotensin peptides are involved in this model of tumor growth and their role could be analyzed through their corresponding regulatory proteolytic enzymes.
The level of ADAM12-S in maternal serum is an early first-trimester marker of fetal trisomy 18 (2005)

A reduced concentration of ADAM12-S in maternal serum is a promising marker for foetal trisomy 18, as well as for DS.
The Minor Histocompatibility Antigen HA-1: A Diallelic Gene with a Single Amino Acid Polymorphism (1998)

The minor histocompatibility antigen (mHag) HA-1 is the only known mHag for which mismatching is correlated with the development of severe graft versus host disease (GvHD) after human leukocyte antigen-identical bone marrow transplantation. HA-1 was found to be a nonapeptide derived from an allele of the KIAA0223 gene. The HA-1-negative allelic counterpart encoded by KIAA0223 had one amino acid difference from HA-1. Family analysis with HA-1 allele-specific polymerase chain reaction showed an exact correlation between this allelic polymorphism and the HA-1 phenotype. HA-1 allele typing of donor and recipient should improve donor selection and allow the determination of bone marrow transplantation recipients with high risk for HA-1-induced GvHD development.
Synthesis and Characterization of Photocurable Elastomers from Poly(glycerol-co-sebacate) (2007)

Elastomeric networks are increasingly being investigated for a variety of biomedical applications including drug delivery and tissue engineering. However, in some cases, their preparation requires the use of harsh processing conditions (e.g., high temperature), which limits their biomedical application. Herein, we demonstrate the ability to form elastomeric networks from poly(glycerol-co-sebacate) acrylate (PGSA) under mild conditions while preserving a wide range of physical properties. These networks presented a Young's modulus between 0.05 and 1.38 MPa, an ultimate strength from 0.05 to 0.50 Mpa, and elongation at break between 42% and 189% strain, by varying the degree of acrylation (DA) of PGSA. The in vitro enzymatic and hydrolytic degradation of the polymer networks was dependent on the DA. The copolymerization of poly(ethylene glycol) diacrylate with PGSA allowed for an additional control of mechanical properties and swelling ratios in an aqueous environment, as well as enzymatic and hydrolytic degradation. Photocured PGSA networks demonstrated in vitro biocompatibility as judged by sufficient human primary cell adherence and subsequent proliferation into a confluent monolayer. These photocurable degradable elastomers could have potential application for the encapsulation of temperature-sensitive factors and cells for tissue engineering.
Mature monocytic cells enter tissues and engraft (1998)

The goal of this study was to identify the circulating cell that is the immediate precursor of tissue macrophages. ROSA 26 marrow mononuclear cells (containing the beta-geo transgene that encodes beta-galactosidase and neomycin resistance activities) were cultured in the presence of macrophage colony-stimulating factor and flt3 Ligand for 6 days to generate monocytic cells at all stages of maturation. Expanded monocyte cells (EMC), the immature (ER-MP12(+)) and more mature (ER-MP20(+)) subpopulations, were transplanted into irradiated B6/129 F2 mice. beta-gal staining of tissue sections from animals 15 min after transplantation demonstrated that the donor cells landed randomly. By 3 h, donor cells in lung and liver were more frequent in animals transplanted with ER-MP20(+) (more mature) EMC than in animals transplanted with unseparated EMC or fresh marrow mononuclear cells, a pattern that persisted at 3 and 7 days. At 3 days, donor cells were found in spleen, liver, lung, and brain (rarely) as clusters as well as individual cells. By 7 and 14 days, the clusters had increased in size, and the cells expressed the macrophage antigen F4/80, suggesting that further replication and differentiation had occurred. PCR for the neogene was used to quantitate the amount of donor DNA in tissues from transplanted animals and confirmed that ER-MP20(+) EMC preferentially engrafted. These data demonstrate that a mature monocytic cell gives rise to tissue macrophages. Because these cells can be expanded and manipulated in vitro, they may be a suitable target population for gene therapy of lysosomal storage diseases.
Evolution of Cancer Pharmacological Treatments at the Turn of the Third Millennium (2018)

The medical history of cancer began millennia ago. Historical findings of patients with cancer date back to ancient Egyptian and Greek civilizations, where this disease was predominantly treated with radical surgery and cautery that were often ineffective, leading to the death of patients. Over the centuries, important discoveries allowed to identify the biological and pathological features of tumors, without however contributing to the development of effective therapeutic approaches until the end of the 1800s, when the discovery of X-rays and their use for the treatment of tumors provided the first modern therapeutic approach in medical oncology. However, a real breakthrough took place after the Second World War, with the discovery of cytotoxic antitumor drugs and the birth of chemotherapy for the treatment of various hematological and solid tumors. Starting from this epochal turning point, there has been an exponential growth of studies concerning the use of new drugs for cancer treatment. The second fundamental breakthrough in the field of oncology and pharmacology took place at the beginning of the '80s, thanks to molecular and cellular biology studies that allowed the development of specific drugs for some molecular targets involved in neoplastic processes, giving rise to targeted therapy. Both chemotherapy and target therapy have significantly improved the survival and quality of life of cancer patients inducing sometimes complete tumor remission. Subsequently, at the turn of the third millennium, thanks to genetic engineering studies, there was a further advancement of clinical oncology and pharmacology with the introduction of monoclonal antibodies and immune checkpoint inhibitors for the treatment of advanced or metastatic tumors, for which no effective treatment was available before. Today, cancer research is always aimed at the study and development of new therapeutic approaches for cancer treatment. Currently, several researchers are focused on the development of cell therapies, anti-tumor vaccines, and new biotechnological drugs that have already shown promising results in preclinical studies, therefore, in the near future, we will certainly assist to a new revolution in the field of medical oncology.
Optical image analysis using fractal techniques (1993)

Using an optical technique, we classified images of natural terrain based on their fractal dimension. We calculated the fractal dimension from an optically generated power spectrum obtained with a magneto-optic spatial light modulator (SLM). By using the fractal dimension to classify images of natural terrain, our post processing was simpler that when a ring-wedge detector was used.
Multiple glycoproteins synthesized by the smallest RNA segment (S10) of bluetongue virus (1992)

The genome of bluetongue virus, an orbivirus, consists of 10 double-stranded RNAs, each encoding at least one polypeptide. The smallest RNA segment (S10) encodes two minor nonstructural proteins, NS3 and NS3A, the structures and functions of which are not understood. We have expressed these two proteins in mammalian cells by using the T7 cytoplasmic transient expression system. Using a deletion mutant (lacking the first AUG initiation codon), we have demonstrated that the second initiation codon is used to initiate the synthesis of NS3A protein and that the two initiation codons are responsible for the synthesis not only of NS3 and NS3A but also of high-molecular-weight forms of both proteins. These higher-molecular-weight forms (GNS3 and GNS3A) are glycosylated. We have also demonstrated that the carbohydrate chains of GNS3 and GNS3A could be further modified by heterogeneous extension to polylactosaminoglycan forms. The glycosylated and nonglycosylated forms are found in similar intracellular locations in the Golgi complex. In the presence of cycloheximide, NS3 and NS3A immunofluorescence staining was pronounced in the Golgi complex, confirming that NS3 and NS3A are competent for transport to the Golgi apparatus after synthesis. We conclude that S10 gene products are integral membrane glycoproteins.
Three Uses for Springs in Legged Locomotion (1990)

Running animals and robots can save energy and reduce unwanted heat production by bouncing along on springs, using the principle of the pogo stick. (The principal springs in animals are tendons.) They can make further energy savings by using return springs to halt the legs at the end of each foward or backward swing and start them swinging the other way. The forces at impact of feet with the ground can be moderated by compliant foot pads, which can improve road holding by preventing "chatter" (vibrations in which the foot repeatedly leaves and returns to the ground before settling). Animals use springs in all three ways but there seems to be a need for more use of springs in legged robots, especially in robots designed to run fast.
Mutants of the Escherichia coli heat-labile enterotoxin with reduced ADP-ribosylation activity or no activity retain the immunogenic properties of the native holotoxin (1996)

The Escherichia coli heat-labile enterotoxin (LT) is a potent inducer of mucosal immune responses. In a previous study (L. DeHaan, W. R. Verweij, M. Holtrop, E. Agsteribbe, and J. Wilschut, Vaccine 14:620-626, 1996), we have shown that efficient induction of an LTB-specific mucosal immune response by LT requires the presence of the LTA chain, suggesting a possible role of the enzymatic activity of LTA in the induction of these responses. In the present study, we generated LT mutants with altered ADP-ribosylation activities and evaluated their immunogenicity upon intranasal administration to mice. The results demonstrate that the mucosal immunogenicity of LT is not dependent on its ADP-ribosylation activity.
Extrapleural Pneumonectomy in the Multimodality Therapy of Malignant Pleural Mesothelioma (1996)

Extrapleural pneumonectomy with adjuvant therapy is appropriate treatment for selected patients with malignant mesothelioma selected using a revised staging system.
Nonessential active site residues modulate selenosubtilisin's kinetic mechanism (1995)

Selenosubtilisin, a semisynthetic enzyme produced by chemical modification of subtilisin's catalytic serine, mimics the antioxidant enzyme glutathione peroxidase, catalyzing the reduction of hydroperoxides by 3-carboxy-4-nitrobenzenethiol. In analogy with the unmodified protease, selenosubtilisins derived from distantly related subtilisin templates exhibit significantly different kinetic properties. Selenosubtilisin BPN' not only is less active than the previously studied Carlsberg selenoenzyme but exhibits sequential rather than ping-pong kinetics, indicating the formation of a ternary complex between enzyme, thiol, and peroxide prior to product release. Experiments with subtilisin E and the BPN' Y217L variant show that the observed differences in kinetic mechanism and chemical efficiency can be attributed largely to amino acid substitutions in the enzyme's S1 and S1' binding sites, respectively. These contributions appear to be roughly additive, and a BPN' triple mutant (E156S/G169A/Y217L) has properties that closely approximate those of selenosubtilisin Carlsberg. The kinetic mechanism of selenosubtilisin can thus be controlled by limited mutagenesis of several active site residues not directly involved in the redox chemistry.
Human cyclin-dependent kinase-activating kinase exists in three distinct complexes. (1996)

Transcription factor IIH (TFIIH) is a multisubunit complex required for transcription and for DNA nucleotide excision repair. TFIIH possesses three enzymatic activities: (i) an ATP-dependent DNA helicase, (ii) a DNA-dependent ATPase, and (iii) a kinase with specificity for the carboxyl-terminal domain of RNA polymerase II. The kinase activity was recently identified as the cdk (cyclin-dependent kinase) activating kinase, CAK, composed of cdk7, cyclin H, and MAT-1. Here we report the isolation and characterization of three distinct CAK-containing complexes from HeLa nuclear extracts: CAK, a novel CAK-ERCC2 complex, and TFIIH. CAK-ERCC2 can efficiently associate with core-TFIIH to reconstitute holo-TFIIH transcription activity. We present evidence proposing a critical role for ERCC2 in mediating the association of CAK with core TFIIH subunits.
Mapping of IgE Binding Regions in the Major Rat Urinary Protein, α2u-Globulin, Using Overlapping Peptides (1999)

Exposure to laboratory animals poses a hazard for development of occupational allergy. Identification of antigenic determinants of allergenic proteins may be valuable for immunotherapeutic purposes. Overlapping peptides of the major allergen in rat urine, Rat n 1.02, corresponding to the protein alpha2u-globulin were synthesised on solid support and screened simultaneously to locate IgE binding linear epitopes using a simple modified ELISA procedure. Thirty-nine peptides were synthesised, each 8 amino acids long with 4 amino acids overlaps. Sera from fifteen rat-sensitized subjects were analyzed and as controls sera from 7 non-rat-sensitized individuals were used. In general low binding and a great individual variation between sera from rat allergic individuals were seen. Some peptides were more frequently recognized by IgE antibodies in sera from rat allergics. These peptides were mainly clustered towards the N-terminal and C-terminal parts of the protein. Taken together our data suggest the existence of linear IgE binding epitopes in the rat urine allergen, Rat n 1.02. However, the role of these sequences in the allergic reaction needs further investigation.
Negative Average Preference Utilitarianism (2012)

For many philosophers working in the area of Population Ethics, it seems that either they have to confront the Repugnant Conclusion (where they are forced to the conclusion of creating massive amounts of lives barely worth living), or they have to confront the Non-Identity Problem (where no one is seemingly harmed as their existence is dependent on the “harmful” event that took place). To them it seems there is no escape, they either have to face one problem or the other. However, there is a way around this, allowing us to escape the Repugnant Conclusion, by using what I will call Negative Average Preference Utilitarianism (NAPU) – which though similar to anti-frustrationism, has some important differences in practice. Current “positive” forms of utilitarianism have struggled to deal with the Repugnant Conclusion, as their theory actually entails this conclusion; however, it seems that a form of Negative Average Preference Utilitarianism (NAPU) easily escapes this dilemma (it never even arises within it).
Simplex crossover and linkage learning in real-coded GAs (2001)

In this paper, we propose a method of linkage identification in real-coded GAs with simplex crossover (SPX) and evaluate it using test functions.
The role of the B7 costimulatory pathway in experimental cold ischemia/reperfusion injury. (1997)

Ischemia/reperfusion injury associated with organ retrieval and storage influences the development of chronic graft dysfunction, the major clinical problem in solid organ transplantation. The potential role of mononuclear cells (T cells and monocyte/macrophages) in this type of injury is unknown. Inbred male Lewis rats were uninephrectomized and the left kidney perfused in situ with 10 ml of iced University of Wisconsin solution. Immunohistological studies showed mononuclear cell infiltration of the ischemic organs associated with the upregulation of MHC class II antigen expression. Reverse transcriptase-PCR indicated that T cell associated cytokines and monocyte/macrophage activation markers/products are upregulated early after the ischemic insult. B7 expression occurred within 24 h and peaked at 3 d. Plasma creatinine levels rose transiently with complete recovery of renal function by 5 d. Animals began to develop progressive proteinuria after 8-12 wk, indicative of the long-term functional consequences of early ischemia/reperfusion injury. Blockade of T cell CD28-B7 costimulation with CTLA4Ig resulted in significant inhibition of T cell and macrophage infiltration and activation in situ. Treated animals did not exhibit transient renal dysfunction, nor developed proteinuria over time. This is the first demonstration that blocking T cell costimulatory activation in the absence of alloantigen can prevent the early and late consequences of ischemia/reperfusion injury.
Stromal-derived factor 1–induced megakaryocyte migration and platelet production is dependent on matrix metalloproteinases (2000)

Despite the discovery of thrombopoietin (TPO) and its contribution to megakaryocytopoiesis, the exact mechanisms and sites of platelet production are unknown. It has been shown that mature megakaryocytes (MKs) functionally express the stromal-derived factor 1 (SDF-1) receptor, CXCR4. SDF-1–induced migration of mature MKs through endothelial cell layers results in increased platelet production. Because the migration of polyploid MKs from the bone marrow microenvironment requires remodeling of the perivascular extracellular matrix, it was hypothesized that mature polyploid MKs may express matrix metalloproteinases (MMPs), facilitating their exit into the bone marrow extravascular space. In this report, it is demonstrated that SDF-1 induces the expression and release of gelatinase B (MMP-9) by purified mature polyploid human MKs and an adeno-CXCR4–infected megakaryocytic cell line. Neutralizing antibody to MMP-9, but not MMP-2, blocked SDF-1–induced migration of MKs through reconstituted basement membrane, suggesting that expression of MMP-9 is critical for MK migration. Incubation of mature MKs with a synthetic MMP inhibitor, 5-phenyl-1,10-phenanthrolene, resulted in the inhibition of platelet formation, suggesting that the expression of MMPs is not only critical for megakaryocyte migration but also for subsequent platelet release. Confirming these results, adeno-SDF-1 injection into normal mice resulted in increased platelet counts, a process that could be blocked by a synthetic MMP inhibitor. These results suggest mobilization of MKs involves sequential expression and activation of chemokine receptors such as CXCR4, MMP-9, followed by transendothelial migration. MMP inhibitors may have potential use in the treatment of thrombotic and myeloproliferative disorders.
The packing of α-helices: simple coiled-coils (1953)

It is shown in this paper by Crick that when -helices of the same sense pack together they will probably do so about 20° away from parallel. For very long chains this may lead to a coiled-coil. The two simplest models - the two-strand rope and the three-strand rope - are described, and used to illustrate the diffraction theory already developed. It is shown that they would give a diffuse -pattern. Possible examples of these models are briefly discussed.
A visual user interface for map information retrieval based on semantic significance (1988)

User-interface facilities of a map information system HI-MAP that provide visual feedback to the user are presented. The facilities include semantic panning and zooming, overlaying of thematic maps, etc., and are available through an interactive menu system. HI-MAP retrieves map elements in a specified region on the basis of their relevance and their categorical classification. It has a data structure that includes logical and physical hierarchies for the management of semantic relationships and graphic map elements. The software for implementing these facilities is well modularized, and a variety of interfacing modes can be realized by simple communication between modules. The system contributes toward a reduction of the difficulties in obtaining what is really required from databases.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Hydrogen-bonding cyclodiphosphazanes: superior effects of 3,5-(CF3)2-substitution in anion-recognition and counter-ion catalysis (2018)

Syntheses, X-ray characterization and employment of new cyclodiphosph(<sc>v</sc>)azane hydrogen-bonding catalysts in experimental and computational anion recognition and the <italic>N</italic>-acyl-Mannich reaction.