gebhart/patrepeval huggingface dataset:
Transgenic cereal (tritordeum) plants obtained at high efficiency by microprojectile bombardment of inflorescence tissue (1994)

Transgenic cereal plants expressing the beta-glucuronidase (uidA) and neomycin phosphotransferase (neo) genes were obtained via microprojectile bombardment of immature inflorescence tissue of tritordeum (the fertile Hordeum x Triticum amphiploid, HchHchAABB). A total of 17 independent transgenic plants were recovered from 32 bombardments (on average four inflorescences per shot). Of the bombardment and culture parameters tested, explant preculture had the most influence on stable transformation frequency. The uidA and neo genes were supplied on two separate plasmids (co-transformation) and 88% of the transgenic plants recovered expressed both genes. Southern analysis confirmed the results of histochemical GUS and NPT II assays. Transgenic plants were grown to maturity and flowered and set seed. Pollen from four T0 GUS+ plants analysed showed GUS activity and T1 seedlings derived from one of the transgenic plants showed a segregation of 2.75:1 (GUS+:GUS-) for uidA gene activity.
Evaluation of NIH consensus criteria for classification of late acute and chronic GVHD (2009)

Historically, graft-versus-host disease (GVHD) beyond 100 days after hematopoietic cell transplantation (HCT) was called chronic GVHD, even if the clinical manifestations were indistinguishable from acute GVHD. In 2005, the National Institutes of Health (NIH) sponsored a consensus conference that proposed new criteria for diagnosis and classification of chronic GVHD for clinical trials. According to the consensus criteria, clinical manifestations rather than time after transplantation should be used in clinical trials to distinguish chronic GVHD from late acute GVHD, which includes persistent, recurrent, or late-onset acute GVHD. We evaluated major outcomes according to the presence or absence of NIH criteria for chronic GVHD in a retrospective study of 740 patients diagnosed with historically defined chronic GVHD after allogeneic HCT between 1994 and 2000. The presence or absence of NIH criteria for chronic GVHD showed no statistically significant association with survival, risks of nonrelapse mortality or recurrent malignancy, or duration of systemic treatment. Antecedent late acute GVHD was associated with an increased risk of nonrelapse mortality and prolonged treatment among patients with NIH chronic GVHD. Our results support the consensus recommendation that, with appropriate stratification, clinical trials can include patients with late acute GVHD as well as those with NIH chronic GVHD.
Rev1 is a base excision repair enzyme with 5′-deoxyribose phosphate lyase activity (2016)

Rev1 is a member of the Y-family of DNA polymerases and is known for its deoxycytidyl transferase activity that incorporates dCMP into DNA and its ability to function as a scaffold factor for other Y-family polymerases in translesion bypass events. Rev1 also is involved in mutagenic processes during somatic hypermutation of immunoglobulin genes. In light of the mutation pattern consistent with dCMP insertion observed earlier in mouse fibroblast cells treated with a base excision repair-inducing agent, we questioned whether Rev1 could also be involved in base excision repair (BER). Here, we uncovered a weak 5'-deoxyribose phosphate (5'-dRP) lyase activity in mouse Rev1 and demonstrated the enzyme can mediate BER in vitro The full-length Rev1 protein and its catalytic core domain are similar in their ability to support BER in vitro The dRP lyase activity in both of these proteins was confirmed by NaBH<sub>4</sub> reduction of the Schiff base intermediate and kinetics studies. Limited proteolysis, mass spectrometry and deletion analysis localized the dRP lyase active site to the C-terminal segment of Rev1's catalytic core domain. These results suggest that Rev1 could serve as a backup polymerase in BER and could potentially contribute to AID-initiated antibody diversification through this activity.
Mechanisms of eukaryotic DNA double strand break repair (2006)

For all cells, a DNA double strand break (DSB) is a dangerous lesion that can have profound consequences for the genome. If a DSB is encountered during mitosis, chromosomal separation may be adversely affected. Alternatively, during S phase a DSB may cause replication fork stalling or collapse. Improperly repaired DSBs can result in chromosomal rearrangements, senescence or activation of apoptotic pathways. Cells have developed sophisticated recombination pathways to metabolize and repair DSBs quickly as well as the capacity to differentiate physiologically occurring breaks from life threatening lesions. The two major pathways of recombination repair are known as non-homologous end-joining (NHEJ) and homologous recombination (HR). In this review, we will discuss the detection, response, and repair of DSBs in eukaryotes.
Network Management: A Practical Perspective (1993)

How do you effectively manage today's complex computer networks? Network Management provides system managers with complete yet accessible answers to that question. This edition continues to explore the information available and provides the insight and knowledge needed to evaluate network management tools and applications.
Insertions in the anticodon loop of tRNA1Gln(sufG) and tRNALys promote quadruplet decoding of CAAA (2002)

Base insertion mutations in the anticodons of two different Escherichia coli tRNAs have been isolated that allow suppression of a series of +1 frameshift mutations. Insertion of a U between positions 34 and 35 of tRNAGln1 or addition of a G between positions 36 and 37 of tRNA(Lys) expand the anticodons of both tRNAs similarly to 3'-GUUU(-5') and allow decoding of complementary 5'-CAAA(-3') quadruplets. Analysis of the suppressed mRNA sequences suggests that suppression occurs by pairing of the expanded anticodons to all four bases of the complementary, quadruplet codon. The tRNA Gln mutants are identical to the sufG class of frameshift suppressors isolated both in Salmonella enterica serovar Typhimurium and E. coli by Kohno and Roth and previously thought to affect tRNA(Lys).
The Evolving Erythrocyte: Red Blood Cells as Modulators of Innate Immunity (2018)

The field of red cell biology is undergoing a quiet revolution. Long assumed to be inert oxygen carriers, RBCs are emerging as important modulators of the innate immune response. Erythrocytes bind and scavenge chemokines, nucleic acids, and pathogens in circulation. Depending on the conditions of the microenvironment, erythrocytes may either promote immune activation or maintain immune quiescence. We examine erythrocyte immune function through a comparative and evolutionary lens, as this framework may offer perspective into newly recognized roles of human RBCs. Next, we review the known immune roles of human RBCs and discuss their activity in the context of sepsis where erythrocyte function may prove important to disease pathogenesis. Given the limited success of immunomodulatory therapies in treating inflammatory diseases, we propose that the immunologic function of RBCs provides an understudied and potentially rich area of research that may yield novel insights into mechanisms of immune regulation.
Cell for Simultaneous Synchrotron Radiation X-ray and Electrochemical Corrosion Measurements on Cultural Heritage Metals and Other Materials (2006)

We describe the construction of an electrochemical cell of the Bragg type suitable for in situ synchrotron X-ray measurements on rough, heterogeneous metals such as cultural heritage alloys and simulants with corroding or passivated surfaces. The cell features a working electrode, which may be moved under remote control from a position close to an X-ray window to full immersion in the electrolyte. A pocket of electrolyte in contact with the bulk can be maintained on the working electrode surface at all times. Its thickness (typically 100-200 microm) can be controlled by adjusting the working electrode position and, independently, altering the conformation of the X-ray window with hydrostatic pressure. Alternatively, the electrode may be lowered into the bulk of the electrolyte. Early results from the cell showing a time-resolved study of the reduction of nantokite to cuprite in sodium sesquicarbonate, accompanied by corrosion potential measurements obtained in parallel, are presented here.
ATLaS: A Native Extension of SQL for Data Mining (2003)

A lack of power and extensibility in their query languages has seriously limited the generality of DBMSs and hampered their ability to support data mining applications. Thus, there is a pressing need for more general mechanisms for extending DBMSs to support efficiently database-centric data mining appliacations. To satisfy this need, we propose a new extensibility mechanism for SQL-compliant DBMSs, and demonstrate its power in supporting decision support applications. The key extension is the ability of defining new table functions and aggregate functions in SQL—rather than in external procedural languages as Object-Relational (O-R) DBMSs currently do. This simple extension turns SQL into a powerful language for decision-support applications, including ROLAPs, time-series queries, stream-oriented processing, and data mining functions. First, we discuss the use of ATLaS for data mining applications, and then the architecture and techniques used in its realization.
Electrochemical and megavolt treatment of rat tumours. (1994)

In a series of experiments, an electrolytic method of tumour destruction has been developed. When tested clinically, no tumour has been totally destroyed but substantial necroses have been achieved. To make the electrolytic method more effective it can favourably be combined with radiotherapy. This has been done experimentally with good results. It is likely that the intense inflammation around the chemical destruction creates a radio-sensitising effect.
The utilization of sterols by insects (1964)

The experimental data discussed in this review are fragmentary and frequently fail, in a most tantalizing fashion, to allow of precise interpretation. For reasons that are indicated, a shadow of uncertainty hangs over several of the nutritional data discussed. The problems inherent in working with the small amounts of material available from insects' tissues have also contributed to the difficulties of interpretation, and even when an unambiguous experimental result is obtained, it may well be hazardous to generalize from one or two species to all members of the class, which, after all, is the largest in the animal kingdom.Nevertheless, it is becoming clear that the sterols play a role in insect physiology that seems remarkably similar to that of cholesterol in the mammal. It is evident that both “structural” and metabolic functions are fulfilled, and there is evidence for the existence of mechanisms for the excretion of sterols and their metabolites. If the latter are excretory forms of physiologically active substances, it seems clear that some metabolites other than ecdysone must be involved, since polar derivatives of cholesterol have been detected in the tissues of adult insects in which, presumably, the prothoracic glands have degenerated and ecdysone is no longer secreted.Studies of the distribution and dynamic state of the tissue sterols of insects show that the sterols per se have diverse roles within the tissues, which for convenience may be described as “structural.” Many species of insects can modify the sterols of their diet and presumably such modifications serve to provide a structure that is more appropriate to one or all of the insect's requirements. It is not entirely clear whether phytosterols must always be converted to some extent to cholesterol, but one must conclude from the data available that species differ widely in the extent to which they carry out such conversions. This suggests that while there is probably a basic unity among all species with respect to the types of multimolecular structures into which the sterols are incorporated, there are species differences in the detailed structure of the immediate environment of the sterol molecule. A rewarding aspect of future research in this field may well be the analysis of the relationship between sterols of different structures and the other lipid molecules with which they are associated in the cells of different species. Such studies may shed new light on the manner in which sterols contribute to the stability of subcellular structures.It is almost certain that with the structure of ecdysone finally established as that of a steroid and its biogenesis from cholesterol demonstrated, there will be increasing interest in the functions of sterols and steroids in insects. It is hoped that this review shows that there is an emergent body of coherent biochemical and physiological information to serve as a basis for future work.
New Strategies of Screening and Treatment for Sleep Apnea Syndrome. (1998)

The prevalence of sleep apnea syndrome (SAS) is approximately 7.5% in Japanese adults aged 18-68 years old. SAS is characterized by repeated episodes of apnea, especially obstructive apnea, during sleep. Severe SAS has life-threatening complications such as pulmonary hypertension, arrhythmias, right heart failure or brain damage, which could be caused by hypoxemia and/or hypercapnia. Upper airway relaxation is responsible for the obstruction during apnea, and an increase in the activities of the upper airway muscles dilates and stiffens the upper airway wall. Maintaining the activities of the upper airway muscles may contribute to keeping the airway patent. Submental electrical stimulation of the upper airway muscles would be a novel treatment method for obstructive apnea.
Sulfate incorporation by articular chondrocytes in monolayer culture (1970)

Abstract Articular chondrocytes in primary monolayers or subcultures synthesize sulfated macromolecules, presumably mucopolysaccharides. Intracellular 35 SO 4 incorporation by postnatal rabbit chondrocytes reached a steady level by 24 hr of incubation; the nondialyzable extracellular (centrifuged medium + trypsin digest) counts increased over 72 hr, when they were up to 100 times the intracellular value. Cell for cell, radiosulfate counts in each fraction were higher in chondrocytes than fibroblasts. Data from a 3‐year‐old rabbit were comparable to those from recently weaned animals. Secretion of sulfated mucopolysaccharide was also found in cultures of adult human and bovine articular chondrocytes. Although Ham's F12 medium is advantageous in establishing a primary culture of chondrocytes, sulfate incorporation was greater when Dulbecco‐Eagle medium, with or without supplemental L‐proline, was used for subcultures. Ascorbic acid (5 mg/100 ml) added to an already confluent monolayer had no consistent effect.
Insights into Ligand Binding and Catalysis of a Central Step in NAD+ Synthesis (2001)

Nicotinamide mononucleotide adenylyltransferase (NMNATase) catalyzes the linking of NMN(+) or NaMN(+) with ATP, which in all organisms is one of the common step in the synthesis of the ubiquitous coenzyme NAD(+), via both de novo and salvage biosynthetic pathways. The structure of Methanobacterium thermoautotrophicum NMNATase determined using multiwavelength anomalous dispersion phasing revealed a nucleotide-binding fold common to nucleotidyltransferase proteins. An NAD(+) molecule and a sulfate ion were bound in the active site allowing the identification of residues involved in product binding. In addition, the role of the conserved (16)HXGH(19) active site motif in catalysis was probed by mutagenic, enzymatic and crystallographic techniques, including the characterization of an NMN(+)/SO4(2-) complex of mutant H19A NMNATase.
Retroviral Integrase: Then and Now (2015)

The retroviral integrases are virally encoded, specialized recombinases that catalyze the insertion of viral DNA into the host cell's DNA, a process that is essential for virus propagation. We have learned a great deal since the existence of an integrated form of retroviral DNA (the provirus) was first proposed by Howard Temin in 1964. Initial studies focused on the genetics and biochemistry of avian and murine virus DNA integration, but the pace of discovery increased substantially with advances in technology, and an influx of investigators focused on the human immunodeficiency virus. We begin with a brief account of the scientific landscape in which some of the earliest discoveries were made, and summarize research that led to our current understanding of the biochemistry of integration. A more detailed account of recent analyses of integrase structure follows, as they have provided valuable insights into enzyme function and raised important new questions.
Improving the Accuracy and Reliability of Remote System-Calibration-Free Eye-Gaze Tracking (2009)

Remote eye-gaze tracking provides a means for nonintrusive tracking of the point-of-gaze (POG) of a user. For application as a user interface for the disabled, a remote system that is noncontact, reliable, and permits head motion is very desirable. The system-calibration-free pupil-corneal reflection (P-CR) vector technique for POG estimation is a popular method due to its simplicity, however, accuracy has been shown to be degraded with head displacement. Model-based POG-estimation methods were developed, which improve system accuracy during head displacement, however, these methods require complex system calibration in addition to user calibration. In this paper, the use of multiple corneal reflections and point-pattern matching allows for a scaling correction of the P-CR vector for head displacements as well as an improvement in system robustness to corneal reflection distortion, leading to improved POG-estimation accuracy. To demonstrate the improvement in performance, the enhanced multiple corneal reflection P-CR method is compared to the monocular and binocular accuracy of the traditional single corneal reflection P-CR method, and a model-based method of POG estimation for various head displacements.
Acceleration of muscle regeneration by local injection of muscle‐specific microRNAs in rat skeletal muscle injury model (2009)

MicroRNA (miRNA)s are a class of non-coding RNAs that regulate gene expression post-transcriptionally. Muscle-specific miRNA, miRNA (miR)-1, miR-133 and miR-206 play a crucial role in the regulation of muscle development and homeostasis. Muscle injuries are a common musculoskeletal disorder, and the most effective treatment has not been established yet. The purpose of this study was to demonstrate that a local injection of double-stranded (ds) miR-1, miR-133 and 206 can accelerate muscle regeneration in a rat skeletal muscle injury model. After the laceration of the rat tibialis anterior muscle, ds miR-1, 133 and 206 mixture mediated atelocollagen was injected into the injured site. The control group was injected with control siRNA. At 1 week after injury, an injection of miRNAs could enhance muscle regeneration morphologically and physiologically, and prevent fibrosis effectively compared to the control siRNA. Administration of exogenous miR-1, 133 and 206 can induce expression of myogenic markers, MyoD1, myogenin and Pax7 in mRNA and expression in the protein level at 3 and 7 days after injury. The combination of miR-1, 133 and 206 can promote myotube differentiation, and the expression of MyoD1, myogenin and Pax7 were up-regulated in C2C12 cells in vitro. Local injection of miR-1, 133 and 206 could be a novel therapeutic strategy in the treatment of skeletal muscle injury.
In search of a function for the TIS21/PC3/BTG1/TOB family (2001)

The Btg family of anti-proliferative gene products includes Pc 3/Tis 21/Btg 2, Btg 1, Tob, Tob2, Ana/Btg3, Pc3k and others. These proteins are characterized by similarities in their amino-terminal region: the Btg1 homology domain. However, the pleiotropic nature of these family proteins has been observed and no common physiological function among family members was suggested from the history of their identification. Recent progress in the search for Btg family functions has come from the analysis of cell regulation and of cell differentiation. It is now emerging that every member of this family has a potential to regulate cell growth. We would like to propose here to use a nomenclature APRO as a new term for the family.
Mutant ras epitopes as targets for cancer vaccines. (1996)

The ras p21 proto-oncogenes (ie, K-ras, H-ras, N-ras) encode a family of proteins vital to cellular signaling and function. Point mutations in these genes have been found in a wide diversity of human cancers, suggesting a strong association in the development of the malignant phenotype. Although the precise mechanisms leading to tumorigenesis are not fully understood, it has been proposed that point mutations in the ras p21 proto-oncogenes contribute to the transformation process through constitutive transduction of growth-promoting signals. These oncoproteins are distinct from normal ras p21 in both DNA and protein sequences at specific sites, typically positions 12, 13, 59, or 61. A large frequency of human cancers harbor point mutations in the ras gene at codon 12, where the normal Gly residue is substituted with either a Val, Asp or Cys residue. From an immunologic perspective, these "neo-determinants" may now represent unique and highly specific epitopes for T cell (CD4+ and/or CD8+) recognition in cancer immunotherapy. Evaluation of point-mutated ras as a T-cell epitope could be determined biologically with short synthetic peptides that precisely mimic those altered sites. Several laboratories have established approaches in both murine and human systems to evaluate the point-mutated ras p21 oncogene product as a potential tumor-specific target and characterization of the resulting cellular immune responses. It has been demonstrated that (1) active immunization of mice with the appropriate mutant protein or peptides leads to the production of cytotoxic CD4+ (Th1 subtype) or CD8+ T lymphocytes, which mediate MHC-restricted, antigen-specific lysis of tumor cells in vitro bearing endogenous mutant ras epitopes; and (2) in vitro stimulation of human lymphocytes from some normal individuals or carcinoma patients with mutant ras peptides results in the expansion of CD4+ and CD8+ precursors, which may exhibit cytotoxicity against autologous or MHC-matched, antigen-bearing target cells. Taken collectively, these preclinical findings provide the rationale for the development of potential immunotherapies directed against point-mutated ras oncogene products.
Evolution and Development of the Silicone Suction Socket (3S) for Below-Knee Prostheses (1989)

Fillauer, Carlton E. C.P.O; Pritham, Charles H. C.P.O; Fillauer, Karl D. C.P.O Author Information