gebhart/patrepeval huggingface dataset:
Erf2, a Novel Gene Product That Affects the Localization and Palmitoylation of Ras2 in Saccharomyces cerevisiae (1999)

Plasma membrane localization of Ras requires posttranslational addition of farnesyl and palmitoyl lipid moieties to a C-terminal CaaX motif (C is cysteine, a is any aliphatic residue, X is the carboxy terminal residue). To better understand the relationship between posttranslational processing and the subcellular localization of Ras, a yeast genetic screen was undertaken based on the loss of function of a palmitoylation-dependent RAS2 allele. Mutations were identified in an uncharacterized open reading frame (YLR246w) that we have designated ERF2 and a previously described suppressor of hyperactive Ras, SHR5. ERF2 encodes a 41-kDa protein with four predicted transmembrane (TM) segments and a motif consisting of the amino acids Asp-His-His-Cys (DHHC) within a cysteine-rich domain (CRD), called DHHC-CRD. Mutations within the DHHC-CRD abolish Erf2 function. Subcellular fractionation and immunolocalization experiments reveal that Erf2 tagged with a triply iterated hemagglutinin epitope is an integral membrane protein that colocalizes with the yeast endoplasmic reticulum marker Kar2. Strains lacking ERF2 are viable, but they have a synthetic growth defect in the absence of RAS2 and partially suppress the heat shock sensitivity resulting from expression of the hyperactive RAS2(V19) allele. Ras2 proteins expressed in an erf2Delta strain have a reduced level of palmitoylation and are partially mislocalized to the vacuole. Based on these observations, we propose that Erf2 is a component of a previously uncharacterized Ras subcellular localization pathway. Putative members of an Erf2 family of proteins have been uncovered in yeast, plant, worm, insect, and mammalian genome databases, suggesting that Erf2 plays a role in Ras localization in all eucaryotes.
Relationship between nasal absorption and physicochemical properties of quaternary ammonium compounds. (1992)

The present study was undertaken to investigate the in situ nasal absorption of a series of tetraethylammonium chloride-related aliphatic quaternary ammonium compounds in rats and its relationship with their physicochemical properties (molecular weight and partition coefficient). All of the ten quaternary ammonium compounds examined were found to be absorbed through the nasal mucosa of rats. The nasal absorption rates of ethyltrimethyl-ammonium iodide and tetraethylammonium chloride, with the lowest molecular weight, were the highest, and those of tetra-n-butylammonium chloride and tetra-n-propylammonium bromide, with high molecular weight, were much lower. Thus, there was a tendency that the nasal absorption rates of quaternary ammonium compounds in rats decreased with an increase in their molecular weight. A physicochemical study has shown that there was a linear relationship between the molecular weight of the ten quaternary ammonium compounds and their partition coefficient, thereby suggesting an increase in lipophilicity with the molecular weight. In addition, there was a good correlation between the extent of the nasal absorption of the quaternary ammonium compounds studied and their molecular weight or partition coefficient. These data suggest that there is a reciprocal relationship between the membrane transport of quaternary ammonium compounds in the nasal mucosa and their lipophilic character. In conclusion, it seems likely that quaternary ammonium compounds are predominantly absorbed from the nasal mucosa of the rat through waterfilled channels or pores rather than through the lipid membrane.
Transcutaneous measurement of renal function in conscious mice (2012)

Determination of glomerular filtration rate (GFR) in conscious mice is cumbersome for the experimenter and stressful for the animals. Here we report on a simple new technique allowing the transcutaneous measurement of GFR in conscious mice. This approach extends our previously developed technique for rats to mice. The technique relies on a miniaturized device equipped with an internal memory that permits the transcutaneous measurement of the elimination kinetics of the fluorescent renal marker FITC-sinistrin. This device is described and validated compared with FITC-sinistrin plasma clearance in healthy, unilaterally nephrectomized and pcy mice. In summary, we describe a technique allowing the measurement of renal function in freely moving mice independent of blood or urine sampling as well as of laboratory assays.
Genetic algorithm against cancer. (2006)

We present an evolutionary approach to the search for effective vaccination schedules using mathematical computerized model as a fitness evaluator. Our study is based on our previous model that simulates the Cancer - Immune System competition activated by a tumor vaccine. The model reproduces pre-clinical results obtained for an immunoprevention cancer vaccine (Triplex) for mammary carcinoma on HER-2/neu mice. A complete prevention of mammary carcinoma was obtained in vivo using a Chronic vaccination schedule. Our genetic algorithm found complete immunoprevention with a much lighter vaccination schedule. The number of injections required is roughly one third of those used in Chronic schedule.
Enhanced Partial Expansion A* (2014)

When solving instances of problem domains that feature a large branching factor, A* may generate a large number of nodes whose cost is greater than the cost of the optimal solution. We designate such nodes as surplus. Generating surplus nodes and adding them to the OPEN list may dominate both time and memory of the search. A recently introduced variant of A* called Partial Expansion A* (PEA*) deals with the memory aspect of this problem. When expanding a node n, PEA* generates all of its children and puts into OPEN only the children with f = f (n). n is re-inserted in the OPEN list with the f -cost of the best discarded child. This guarantees that surplus nodes are not inserted into OPEN. In this paper, we present a novel variant of A* called Enhanced Partial Expansion A* (EPEA*) that advances the idea of PEA* to address the time aspect. Given a priori domain- and heuristic- specific knowledge, EPEA* generates only the nodes with f = f(n). Although EPEA* is not always applicable or practical, we study several variants of EPEA*, which make it applicable to a large number of domains and heuristics. In particular, the ideas of EPEA* are applicable to IDA* and to the domains where pattern databases are traditionally used. Experimental studies show significant improvements in run-time and memory performance for several standard benchmark applications. We provide several theoretical studies to facilitate an understanding of the new algorithm.
IMPACT OF 10 SESSIONS OF WHOLE BODY CRYOSTIMULATION ON AEROBIC AND ANAEROBIC CAPACITY AND ON SELECTED BLOOD COUNT PARAMETERS (2012)

The systemic effect of low temperature suggests that sessions in a cryogenic chamber might improve athletes' capacity as a standard element of training. Therefore the authors decided to evaluate the impact of 10 sessions of whole body cryostimulation (WBCT) on aerobic and anaerobic efficiency as well as on selected blood count parameters. The study group included 32 volunteers - 16 women and 16 men. The volunteers underwent 10 sessions of WBCT in a cryogenic chamber. Blood samples (RBC, WBC, PLT, HGB, HCT) were taken, and aerobic and anaerobic efficiency and lactate concentration in capillary blood were measured before the first session and one day after the last one. No significant differences were observed in values of aerobic capacity after 10 sessions of WBCT. There was a rising trend in men and a declining trend in women. The lactate concentration did not differ significantly before and after WBCT. A slight rise in aerobic and anaerobic threshold was observed in men, while in women the values slightly fell. The Wingate test showed no significant differences in results before and after cryostimulation. Only the TOBT was significantly shorter in men (6.12±1.49 vs 3.79±1.14 s). The WBCT sessions resulted in a significant rise of the haematological parameters both in women and men, excluding HCT, which showed a statistically insignificant rise. Ten sessions of whole body cryostimulation did not affect aerobic or anaerobic capacity in the tested group, although it improved the blood count parameters.
A new wireless system for decentralised measurement of physiological parameters from shake flasks (2006)

The here introduced wireless system can read parallel sensor data over long distances from shake flasks that are under vigorous shaking in cultivation rooms or closed incubators. The presented technology allows centralised monitoring of decentralised targets. It is useful for the monitoring of pH and dissolved oxygen in shake flask cultures. It is not limited to standard sensors, but can be easily adopted to new types of sensors and measurement places (e.g., new sensor points in large-scale bioreactors).
A Hybridization Model for the Plasmon Response of Complex Nanostructures (2003)

We present a simple and intuitive picture, an electromagnetic analog of molecular orbital theory, that describes the plasmon response of complex nanostructures of arbitrary shape. Our model can be understood as the interaction or "hybridization" of elementary plasmons supported by nanostructures of elementary geometries. As an example, the approach is applied to the important case of a four-layer concentric nanoshell, where the hybridization of the plasmons of the inner and outer nanoshells determines the resonant frequencies of the multilayer nanostructure.
α‐Hydroxy Acids in Enantioselective Syntheses (1997)

Attention synthetic chemist! Chiral alpha-hydroxy acids available from nature's chiral pool serve as starting materials in a wide variety of enantioselective conversions leading to commercially important products. This monograph, a stimulating source of ideas and an essential reference work for research chemists, focuses on the well-known lactic, mandelic, malic, and tartaric acids. Well-chosen examples show how chiral centers inherent in these simple compounds can be used to control the introduction of further stereogenic centers. Readers can directly apply new transformations in their own work since reaction conditions are given in handy tables.
Life Stress, Genes, and Depression: Multiple Pathways Lead to Increased Risk and New Opportunities for Intervention (2004)

Major depression is a common, severe, chronic, and often life-threatening illness. There is a growing appreciation that, far from being a disease with purely psychological manifestations, major depression is a systemic disease with deleterious effects on multiple organ systems. Stressful life events have a substantial causal association with depression, and there is now compelling evidence that even early life stress constitutes a major risk factor for the subsequent development of depression. The emerging evidence suggests that the combination of genetics, early life stress, and ongoing stress may ultimately determine individual responsiveness to stress and the vulnerability to psychiatric disorders, such as depression. It is likely that genetic factors and life stress contribute not only to neurochemical alterations, but also to the impairments of cellular plasticity and resilience observed in depression. Recent preclinical and clinical studies have shown that signaling pathways involved in regulating cell plasticity and resilience are long-term targets for the actions of antidepressant agents. Agents capable of reversing the hypothesized impairments of cellular resilience, reductions in brain volume, and cell death or atrophy in depression have the potential of becoming new therapeutic classes of antidepressant drugs. Novel cellular targets include agents targeting neurotrophic pathways, glucocorticoid signaling, phosphodiesterase activity, and glutamatergic throughput. The future development of treatments that more directly target molecules in critical CNS (central nervous system) signaling pathways that regulate cellular plasticity thus hold promise as novel, improved long-term treatments for major depression.
Treating common warts - options and evidence. (2010)

Many common warts will resolve spontaneously but others are recalcitrant and often require ongoing treatment beyond first line measures. Without definite guidelines for treating recalcitrant warts, it is important for the general practitioner to consider the available evidence for efficacy and contraindication of the various treatment options.
Estimation of airway obstruction using oximeter plethysmograph waveform data (2005)

The findings suggest that mathematic interpretation of plethysmograph waveform data may estimate the severity of airway obstruction and be of clinical utility in objective assessment of patients with obstructive airway diseases.
Rapid and specific targeting of monoclonal antibody A33 to a colon cancer xenograft in nude mice. (1998)

Monoclonal antibody (mAb) A33 detects a glycoprotein homogeneously expressed by > 95% of human colon cancers and by normal colon cells. The A33 antigen is not secreted or shed and after mAb A33 binds to antigen on the cell membrane, a fraction of membrane-bound mAb A33 is internalized into endosomes. Phase I 131I-mAb A33 biodistribution studies have shown consistent, specific tumor-targeting, and phase I radioimmunotherapy trials with 131I- or 125I-mAb A33 have demonstrated antitumor effects. Here we describe a nude mouse model that was established using a human colon cancer cell line, SW1222, which grows as a relatively hypovascular, invasive heterotransplant when injected i.m. Peak uptake of 131I-labeled or 111In-chelated mAb A33 was observed at 48-96 h, with a mean of 34% (SE +/- 5.0) and 46.7% (SE +/- 1.7) injected dose per gram of tumor tissue, respectively. 111In-mAb A33 was retained in tumor tissue longer than halide radioimmunoconjugates. The specificity of antibody localization was assessed using a control antibody (tumor uptake and pharmacokinetics), a control tumor, corrections for vascular antibody blood-pooling in tumor tissue, and blocking of radiolabeled mAb A33 localization by pretreating mice with excess unlabeled mAb A33. These experiments demonstrate that mAb A33 localization in tumor was specific, and they emphasize the unexpected rapidity with which the antibody localizes. Our conclusions were confirmed by immunohistochemical techniques which allowed direct visualization of localization and distribution of the humanized version of mAb A33 in tumor tissue. Furthermore, antibody doses approximating tumor-saturating doses demonstrated that a homogeneous distribution of antibody in tumor is possible. This model will be valuable for studies focusing on general physiologic aspects of antibody-to-tumor cell localization and critical as a guide to the evaluation of various A33 antibody constructs and combinations with other therapies for the treatment of colon cancer.
Somatic Gene Therapy (2018)

Preface, W.F. Anderson. Overview, I.M. Verma. Human Hematopoietic Cells for Gene Therapy, R. Jurecic and J.W. Belmont. Somatic Gene Therapy for Severe Combined Immune Deficiency (SCID), K.I. Weinberg and D.B. Kohn. Fibroblast Cell Biology and Gene Therapy, D.A. Treco, M. Heartlein, and R.F. Selden Hepatic Gene Therapy, F.D. Ledley. Epidermal Keratinocytes: Opportunities and Applications in Somatic Cell Gene Therapy, B.J. Aneskievich, A.G. Letai, and E. Fuchs. Endothelial Cells: Endothelium as a Target Organ for Somatic Gene Therapy, L.M. Messina and J.C. Stanley. Gene Therapy by Myoblast-Mediated Gene Transfer, K. Kurachi and S.-N. Yao. Gene Delivery to Neurons of the Adult Mammalian Nervous System Using Herpes and Adenovirus Vectors, J.K. Andersen and X.O. Breakefield. Implantation of Genetically-Modified Cells in the Brain, J. Ray, L.J. Fisher, and F.H. Gage. Direct Gene Transfer In Vivo, H. Herweijer, J.D. Fritz, J.E. Hagstrom, and J.A. Wolff. Nonautologous Somatic Gene Therapy, P.L. Chang. Current Gene Marking and Gene Therapy Protocols for Human Bone Marrow Transplantation, M.K. Brenner. Gene Therapy for Brain Tumors, K.W. Culver, J. Van Gilder, T. Carlstrom, M. Prados, and C.J. Link, Jr. Gene Therapy for Adult Cancers: Advance in Immunologic Approaches Using Cytokines, H. Tahara and M.T. Lotze.
Autoimmune Thyroid Disease: Developments in Our Understanding (1984)

THIS REVIEW of autoimmune thyroid disease will highlight the recent advances made in understanding the control of the autoimmune process particularly at pathogenetic and therapeutic levels. Many novel techniques have recently been applied to the investigation of thyroid autoimmunity although the results obtained have not always clarified the overall picture. These new methodologies are discussed and attention is also focused upon experimental thyroiditis produced in a variety of animals. We believe that these models have been neglected somewhat by clinically oriented investigators. Yet their use originally led to the foundation of autoimmune concepts, and experimental thyroiditis continues to provide major insights into the possible etiology and pathogenesis of the human counterpart. Before discussing thyroid disease in detail however, it is worth considering the current themes in autoimmunity in general.
“Stemness” Does Not Explain the Repair of Many Tissues by Mesenchymal Stem/Multipotent Stromal Cells (MSCs) (2007)

There has recently been an explosion of interest in adult stem/progenitor cells that have the potential to repair tissues, with over 3,000 citations to publications (PubMed) and numerous announcements of clinical trials in which the cells are used to treat individuals with a broad range of diseases. At the same time, the data present a paradox-the cells originally attracted attention because of their stem-cell-like properties, but the cells frequently repair injured tissues without much evidence of either engraftment or differentiation.
A Cross-National Comparison of Victims of Crime: Victim Surveys of Twelve Countries (1993)

Comparison of national crime surveys must be made very cautiously because of differences in sampling, methodology and content. In this report methodological differences between the United States' National Crime Survey and victimization surveys of other countries are examined and survey estimates of victimization are adjusted. It is found that U.S. rates of assault/threat, robbery, and burglary are not extraordinarily higher than those of other eleven other countries or regions. However, U.S. levels of gun use are much higher and U.S. levels of both gun and non-gun lethal violence (using Killias, 1990) far exceed those of other industrialized societies.
Prediction of the Coding Sequences of Unidentified Human Genes. II. The Coding Sequences of 40 New Genes (KIAA0041-KIAA0080) Deduced by Analysis of cDNA Clones from Human Cell Line KG-1 (1994)

By applying the protocol previously established, we isolated and sequenced full-length cDNA clones longer than 2 kb from cDNA library of human immature myeloid cell line KG-1, and the coding sequences of 40 new genes were predicted. A computer search of the sequences indicated that 29 genes contained sequences with similarities to reported genes in the GenBank/EMBL databases. Significant transmembrane domains were identified in 9 genes, 5 of which harbored multiple hydrophobic regions. Protein motifs that matched those in the PROSITE motif database were identified in 13 genes. In terms of sequence similarities and protein motifs, 5 genes were related to transcriptional factors. Repetitive sequences were found in the 3'-untranslated region of 8 genes. Northern hybridization demonstrated that the expression of 9 genes was tissue-specific, while the remaining 31 genes were expressed ubiquitously. It was also noted that 17 genes yielded different sizes of bands possibly due to either alternative splicing or alternative initiation. The chromosomal location of these genes has been determined.
Basics of cancer gene therapy. (1997)

Gene therapy is a rapidly evolving concept for the therapy of different forms of cancer. A number of phase-I clinical trials have recently been initiated world wide. This review discusses the technical concepts underlying the protocols currently coming into clinics. Two tools essentially constitute such concepts, the vector for efficient transfer and expression of the transgene in the cancer cell, and the therapeutic gene. The most advanced vectors ready for clinical use are the retrovirus- and adenovirus-derived vectors. The application of a broad spectrum of therapeutic genes can be classified into gene replacement of replace e.g. mutated tumor suppressor genes, gene addition to increase immunogenicity by cytokine genes or introduce prodrug genes for suicide induction and, thirdly, targeted affection of gene expression by antisense oligonucleotides or expression of ribozymes e.g. directed against oncogene sequences. Cancer gene therapy holds great promise to become an important addition to the multimodality in the therapy of some forms of cancer.
Benzonorphan Related Compounds. XV. A Versatile Method for the Synthesis of Heteromorphans (1980)

From 2 -b e n z o y l -S m e t h y l -6 0 x 0 -2 -a z a h i c y c l o [?.?.I] nonane-7carboxylate the preparation of 5-methyl substituted pyrazolo [3,4-f] -, pyrido[2,3-f]-, and indola[2,3-~morphans is descrihed.~eterornorphnn~ synthesis usually implies the acid-induced final cyclization of a 2-(heteraarylmethy1)tetrahydropyridine.It means that the carbocyclic ring f g sed to the aromatic heterocycle is formed in the last stage of the synthesis.By 1 1 this procedure thien~-~-', benro[b]thieno-a, indo10[2,3-f]-~'", pyrldo[3,zf]-, and pyrrola[3,2-flmorphansl have been prepared in the last years.I CH3 HETEROMORPHAN Nevertheless, this approach to heteromorphans has some limitations: a) Those deriving from the inaccessibility o f certain starting products in the case of some hcterocyclcs.Thus, it is not possible to obtain indolylmethyl-, pyrrg lylmethyl-and furfurylmagnesium12 halides, required far the preparation of type I systems through condensation with a pyridinium salt and furthcr reduction of the ry 13 sulting dihydrapyridine (drewc route) .b) It is not applicable to systems which arc sensitive to the strong acid medium required in the cyclization, such as far 2-(furylmethy1)tetrahydropyridines 14,15 Also cyclizations on indale 3-position fail b e c a u s e of its protanation in the r e a c -
Effect of galactose and glucose on the exopolysaccharide production and the activities of biosynthetic enzymes in Lactobacillus casei CRL 87 (2001)

Knowledge of the effect of the sugar source on EPS production and the activities of biosynthetic enzymes provides information about the mechanisms of regulation of the synthesis of EPS which can contribute to improving polymer production.
Microfluidic Air-Liquid Cavity Acoustic Transducers for On-Chip Integration of Sample Preparation and Sample Detection (2010)

A simple low-cost yet versatile microtechnology platform is demonstrated as capable of performing a variety of microfluidic actuation functions including on-chip pumping, mixing, cell/particle sorting, and sample extraction. This technology termed air-liquid cavity acoustic transducers (ALCATs) uses trapped air bubbles as the functional elements. When an external acoustic energy source is applied to the device, the trapped bubbles oscillate, generating acoustic streaming within the fluid. By controlling their relative position and angle with the liquid channel/chamber, the ALCAT can push away or pull in the surrounding liquid contents and its contained particulates. In this report, we provide a general introduction of the ALCAT microtechnology platform and its application to enhancing biomolecular assays.
Female donors and transfusion‐related acute lung injury (2010)

Our data support the notion that plasma from female donors is associated with an increased risk of TRALI, while RBCs from female donors are not.