gebhart/patrepeval huggingface dataset:
Immunohistochemical study of Fas, Fas ligand and interleukin‐1β converting enzyme expression in human prostatic cancer (1998)

Objective To determine the cellular expression of Fas, Fas ligand and interleukin‐1β converting enzyme (ICE) in prostatic cancer. Patients and methods Specimens of prostate were obtained from 21 patients (mean age 66 years, sd 5) undergoing radical prostatectomy for prostatic cancer. Nine of the 21 patients had received endocrine therapy before surgery. Specimens were also obtained from 10 patients with benign prostatic hypertrophy (BPH) and during autopsy from 10 patients who had died from hormone‐unresponsive prostate cancer. Paraffin‐embedded sections were cut from the specimens and stained immunohistochemically to detect Fas, Fas ligand and ICE. Results Fas was expressed in all 21 of the cancer specimens while Fas ligand was detected in none and ICE was expressed in 11. The difference between the expression of Fas and ICE was significant ( P &lt;0.001). ICE was expressed in nine of 12 patients who were untreated before surgery and in two of nine treated with endocrine therapy ( P &lt;0.05). Fas expression was detected in the specimens from all 10 patients with BPH and in all 10 autopsy specimens; the expression tended to be more marked than that in specimens from total prostatectomy ( P &lt;0.1). Conclusion The expression of ICE was weaker than that of Fas in the total prostatectomy specimens, suggesting a possible interruption of the apoptotic signalling pathway. Prostates with BPH and hormone‐unresponsive cancer therefore showed no appreciable change in Fas expression when compared with total prostatectomy samples.
Annual Incidence of Alzheimer Disease in the United States Projected to the Years 2000 Through 2050 (2001)

Alzheimer disease will affect increasing numbers of people as baby boomers (persons born between 1946 and 1964) age. This work reports projections of the incidence of Alzheimer disease(AD) that will occur among older Americans in the future. Education adjusted age-specific incidence rates of clinically diagnosed probable AD were obtained from stratified random samples of residents 65 years of age and older in a geographically defined community. These rates were applied to U.S. Census Bureau projections of the total U.S. population by age and sex to estimate the number of people newly affected each year. The annual number of incident cases is expected to more than double by the midpoint of the twenty-first century: from 377,000 (95% confidence interval = 159,000-595,000) in 1995 to 959,000 (95% confidence interval = 140,000-1,778,000) in 2050. The proportion of new onset cases who are age 85 or older will increase from 40% in 1995 to 62% in 2050 when the youngest of the baby boomers will attain that age. Without progress in preventing or delaying onset of Alzheimer disease, both the number of people with Alzheimer disease and the proportion of the total population affected will increase substantially.
Ubiquitin-activating enzyme. Mechanism and role in protein-ubiquitin conjugation. (1982)

Energy-dependent proteolysis in rabbit reticulocyte lysates has an absolute requirement for both ATP and ubiquitin that is believed due to the ATP-dependent covalent conjugation of ubiquitin (Ub) to substrate proteins as a signal event. Recently the enzyme responsible for activation of ubiquitin has been purified to near homogeneity by covalent affinity chromatography. In the present work we demonstrate that the enzyme catalyzes the net reaction (formula: see text); in which both an enzyme-bound COOH-terminal ubiquitin thiolester and a COOH-terminal ubiquitin adenylate are formed. The complex is sufficiently stable to be isolated by exclusion chromatography and contains ubiquitin/AMP in a ratio of 2. The presence of two forms of covalently linked ubiquitin provides a rationale for the observation of both ubiquitin-dependent ATP:PPi and ATP:AMP exchange. Selective derivatization of the thiol site with iodoacetamide results in a modified enzyme capable of catalyzing only ATP:PPi exchange and in forming only ubiquitin adenylate. Derivatization of the thiol site prevents conjugate formation in a reconstituted system, demonstrating that the ubiquitin thiolester is the proximal donor for subsequent conjugate formation. A three-step mechanism is proposed for ubiquitin activation by the enzyme prior to conjugation.
[HIV-1 resistance in the Yamal region and the comparison of mutation frequency with various score values]. (2010)

The amino acid sequence of the known strain HXB-2 belonging to subtype B is used as a reference strain matrix to determine HIV genotypic resistance by the sequencing technique. However, numerous studies have ascertained that HIV non-B subtypes have been widely accepted in Russia. The authors' data show that the significance of low score mutations in the Russian populations of HIV-1 is yet to be explained, unquestionably, arouses great scientific interest, and calls for further study.
MARA - A Mobile Augmented Reality-Based Virtual Assistant (2007)

High-end mobile devices are becoming increasing popular in every day life. Augmented reality (AR) builds on this trend by combining mobile computing with connectivity and location-awareness. In doing so, AR can provide a very rich user experience. In this paper we discuss the approach and development of an AR-based personal assistant, combining the familiar interface of a human person with the functionality of a location-aware digital information system. The paper discusses the main components of the system, including the anthropomorphic user interface as well as the results of an initial prototype evaluation.
The PINHEAD/ZWILLE gene acts pleiotropically in Arabidopsis development and has overlapping functions with the ARGONAUTE1 gene (1999)

Several lines of evidence indicate that the adaxial leaf domain possesses a unique competence to form shoot apical meristems. Factors required for this competence are expected to cause a defect in shoot apical meristem formation when inactivated and to be expressed or active preferentially in the adaxial leaf domain. PINHEAD, a member of a family of proteins that includes the translation factor eIF2C, is required for reliable formation of primary and axillary shoot apical meristems. In addition to high-level expression in the vasculature, we find that low-level PINHEAD expression defines a novel domain of positional identity in the plant. This domain consists of adaxial leaf primordia and the meristem. These findings suggest that the PINHEAD gene product may be a component of a hypothetical meristem forming competence factor. We also describe defects in floral organ number and shape, as well as aberrant embryo and ovule development associated with pinhead mutants, thus elaborating on the role of PINHEAD in Arabidopsis development. In addition, we find that embryos doubly mutant for PINHEAD and ARGONAUTE1, a related, ubiquitously expressed family member, fail to progress to bilateral symmetry and do not accumulate the SHOOT MERISTEMLESS protein. Therefore PINHEAD and ARGONAUTE1 together act to allow wild-type growth and gene expression patterns during embryogenesis.
Role of the TCR binding region of the HLA class I α 2 domain in regulation of cell adhesion and proliferation (1996)

In addition to Ag presentation for T cell surveillance, MHC molecules have been implicated in mediating regulatory signals. We have assessed biologic responses following engagement of the TCR accessible region of the HLA class I alpha 2 domain. mAbs directed to this domain specifically induced cell aggregation of normal hematopoietic and leukemic cells. The functional consequences were unique since other mAbs reactive with HLA class I residues outside the TCR binding domain did not induce cell aggregation. The adhesion response required ATP, mRNA, protein, and actin synthesis and did not depend on LFA-1/ICAM interactions. Cell aggregation was also induced when all but four of the intracytoplasmic residues of the class I molecule were deleted, indicating that transduction of signals leading to cell adhesion does not require this portion of the molecule. mAbs directed to HLA class I alpha 2 amino acid residues within the TCR binding domain were also able to inhibit proliferation of normal mitogen-stimulated T cells. Growth inhibition correlated with down-regulated expression of CD25, CD28, and CD95, suggesting that reduced transduction of costimulatory signals is involved. Although HLA class I signals inducing cell aggregation required engagement of positions within the TCR binding region, growth inhibitory signals could be generated through positions both within and adjacent to this domain. Taken together, engagement of specific positions within the TCR binding domain of the class I alpha 2 helix results in active cellular responses. Thus, this region may be directly involved in signal transduction following CTL recognition of target cells.
Complete genome sequence of the probiotic lactic acid bacteriumLactobacillus acidophilusNCFM (2005)

Lactobacillus acidophilus NCFM is a probiotic bacterium that has been produced commercially since 1972. The complete genome is 1,993,564 nt and devoid of plasmids. The average GC content is 34.71% with 1,864 predicted ORFs, of which 72.5% were functionally classified. Nine phage-related integrases were predicted, but no complete prophages were found. However, three unique regions designated as potential autonomous units (PAUs) were identified. These units resemble a unique structure and bear characteristics of both plasmids and phages. Analysis of the three PAUs revealed the presence of two R/M systems and a prophage maintenance system killer protein. A spacers interspersed direct repeat locus containing 32 nearly perfect 29-bp repeats was discovered and may provide a unique molecular signature for this organism. In silico analyses predicted 17 transposase genes and a chromosomal locus for lactacin B, a class II bacteriocin. Several mucus- and fibronectin-binding proteins, implicated in adhesion to human intestinal cells, were also identified. Gene clusters for transport of a diverse group of carbohydrates, including fructooligosaccharides and raffinose, were present and often accompanied by transcriptional regulators of the lacI family. For protein degradation and peptide utilization, the organism encoded 20 putative peptidases, homologs for PrtP and PrtM, and two complete oligopeptide transport systems. Nine two-component regulatory systems were predicted, some associated with determinants implicated in bacteriocin production and acid tolerance. Collectively, these features within the genome sequence of L. acidophilus are likely to contribute to the organisms' gastric survival and promote interactions with the intestinal mucosa and microbiota.
INSTRUMENTAL MEASURES OF BITE FORCES ASSOCIATED WITH CRISP PRODUCTS (2006)

ABSTRACT The usefulness of a bite force apparatus for measuring bite forces generated while biting extruded crisp snacks was assessed. Snacks were produced using a twin‐screw extruder, and their textural properties were modified by equilibrating to water activities ranging from 0.11 to 0.44. Maximum force to bite, stress, duration and area under the bite force curve were analyzed and compared to perceived sensory crispness, hardness, brittleness and sound duration evaluated by eight individuals. Maximum bite force and stress were significantly related to hardness, brittleness and crispness showing for the first time, and the relationship between sensory crispness of extruded crisp products and hardness was measured intraorally.
Complications of Carbon Dioxide Laser Resurfacing. An Evaluation of 500 Patients (1998)

Cutaneous CO2 laser resurfacing is a relatively safe procedure with a low complication profile. Proper laser treatment protocol and postoperative management is important in reducing side effects and complications.
cAMP control of Mg2+ homeostasis in heart and liver cells. (1992)

The increase of intracellular cAMP level in intact myocytes and hepatocytes induced by beta-adrenergic stimulation or by forskolin or permeant cyclic AMP analogues induces a sizeable Mg2+ efflux from the cells. Approximately 10-15% of total cell Mg2+ is mobilized over 5-8 min stimulation. The addition of cAMP to digitonin-permeabilized hepatocytes also mobilizes Mg2+ from intracellular compartment(s). Furthermore, cAMP stimulates a major Mg2+ extrusion from isolated rat liver mitochondria, indicating this compartment as the main source of Mg2+ mobilization in liver cells.
Synthesis of 5'-C-Methyl-D-allo- & L-Talo-ribonucleoside 3'-O-Phosphoramidites & Their Incorporation into Hammerhead Ribozymes (1995)

Abstract 5′-C-Methyl-D-allo & L-talo-ribonucleoside 3′-O-phosphoramidites were prepared from L-rhamnose in 13 and 15 steps respectively. Incorporation of L-talo residues in the hammerhead ribozyme and the resulting activity and stability of the modified ribozymes is described.
Basic fibroblast growth factor expressed in Bacillus subtilis BS224 (2002)

To make a kind of nonpathogenic Bacillus subtilis BS224 with the antibacterial characteristics to express and secret basic fibroblast growth factor (bFGF) so that it has both antibacterial and accelerating wound healing nature. We constructed an integrative vector with the α-amylase promoter and signal sequence coding region obtained by PCR from the chromosome of an α-amylase hyperproducing strain, and the synthesized gnt (gluconate) terminator, and the 3^sequence of α-amylase gene inserting into plasmid pHV32. The bFGF cDNA was inserted into the vector. BS224 was transformed by protoplast transformation. The transformants were screened by chloromycetin resistance and they were verified to integrate at the amy locus of BS224 by α-amylase secretion analysis and Southern hybridization. Basic fibrobast growth factor expression was tested by Western immunoblot analysis.
Optimum Collection and Storage Conditions for Ghrelin Measurements: Octanoyl Modification of Ghrelin Is Rapidly Hydrolyzed to Desacyl Ghrelin in Blood Samples (2004)

Ghrelin is an acylated peptide with growth-hormone-releasing activity (1). It was first isolated from rat and human stomach during the search for an endogenous ligand to the “orphan” G-protein-coupled receptor, growth hormone secretagogue receptor (2). The peptide contains 28 amino acids, and n-octanoylation of the Ser-3 hydroxyl group is necessary for biological activity. Most studies have focused on the somatotropic and orexigenic roles of ghrelin; therefore, little is known about the kinetics of this peptide. Because the ester bond is both chemically and enzymatically unstable, elimination of the octanoyl modification of ghrelin can occur during storage, handling, and/or dissolution in culture medium (3). Because of increased interest in ghrelin measurements, a standardized method of sample collection is required.

In the present study, which focused on the active form of ghrelin, we investigated the effects of anticoagulants and storage conditions on ghrelin stability. To distinguish the active form of ghrelin, we established two ghrelin-specific RIAs; N-RIA recognizes the N-terminal, octanoyl-modified portion of the peptide, whereas C-RIA recognizes the C-terminal portion. Thus, the value determined by N-RIA specifically measures active ghrelin, whereas the value determined by C-RIA gives the total ghrelin immunoreactivity, including both active and desacyl ghrelin (4)(5)(6). The minimum detectable quantities in the N- and C-RIAs were 5.0 and 50 pmol/L, respectively. The respective intra- and interassay CV were 3% and 6% for the N-RIA and 6% and 9% for the C-RIA (n = 8 assays). Data are reported as the mean (SD). Comparisons of the time course of ghrelin concentrations between subgroups were made by two-way ANOVA for repeated measures, followed by the Scheffe test. P <0.05 was considered statistically significant.

All blood samples were taken from three healthy male volunteers who gave written informed consent. Blood was taken from the forearm vein and immediately …
Motion Matters: Secretory Granule Motion Adjacent to the Plasma Membrane and Exocytosis (2006)

Total internal reflection fluorescence microscopy was used to monitor changes in individual granule motions related to the secretory response in chromaffin cells. Because the motions of granules are very small (tens of nanometers), instrumental noise in the quantitation of granule motion was taken into account. ATP and Ca2+, both of which prime secretion before fusion, also affect granule motion. Removal of ATP in permeabilized cells causes average granule motion to decrease. Nicotinic stimulation causes a calcium-dependent increase in average granule motion. This effect is more pronounced for granules that undergo exocytosis than for those that do not. Fusion is not preceded by a reduction in mobility. Granules sometimes move 100 nm or more up to and within a tenth of a second before fusion. Thus, the jittering motion of granules adjacent to the plasma membrane is regulated by factors that regulate secretion and may play a role in secretion. Motion continues until shortly before fusion, suggesting that interaction of granule and plasma membrane proteins is transient. Disruption of actin dynamics did not significantly alter granule motion.
Bone Marrow Stem Cells and Genotoxicity Studies in These Cells: Review (2016)

Kök hücreler; uzun süre bölünebilme, kendini yenileme ve farklılaşma özellikleri nedeni ile kimyasal maddelerin insan üzerindeki olası toksik etkilerinin değerlendirilmesinde alternatif bir çalışma alanı hâline gelmiştir. Kemik iliği, hematopoietik ve mezenkimal kök hücreleri tedavisindeki kullanımlarının yanı sıra ilaç geliştirme ve toksikolojik analizler açısından da önemli bir yere sahiptir. Çeşitli kemik iliği hastalıklarının mekanizmalarının anlaşılması, kimyasal maddelerin toksik etkilerinin belirlenmesi ve ilaç etkinliğinin uygun mikroçevrelerde incelenmesi amacıyla hematopoietik ve mezenkimal kök hücrelerde gerçekleştirilmiş çok sayıda genotoksisite çalışması bulunmaktadır. Hematopoietik kök hücrelerde yapılmış çalışmalarda çoğunlukla, katekol ve kinon gibi metabolitleri aracılığıyla hematopoietik dokulara zarar verdiği bilinen benzenin toksik etkileri incelenmiştir. Bu çalışmalarda, DNA hasarı ve apoptoz belirteci genlerin ekspresyonlarında artış olduğu ve p53/p21 hiperaktivasyonunun DNA hasar mekanizmasından sorumlu olduğu belirlenmiştir. Kemoterapide kullanılan melfalan ve Sisplatinin hematopoietik kök hücrelerdeki etkileri incelendiğinde, CD34+ hücrelerinde CD34- hücrelerine kıyasla daha fazla DNA tek zincir kırıkları gözlenmiştir. Hücre kültür ortamının etkileri mezenkimal kök hücreleri kullanılan çalışmalarda incelenmiş, geç dönem pasajlarında artan atipik ve apoptotik hücreler, DNA bütünlüğünün korunmasında kültür koşullarının önemini göstermiştir. Mezenkimal kök hücrelerinde yapılan diğer çalışmalarda, demir oksit nanopartikülleri ve kobalt çinko ferrit nanopartikülleri DNA hasarına yol açar iken SiO2 nanopartikülleri sitotoksik ve genotoksik etkiler göstermiştir. Ancak, kök hücrelerle gerçekleştirilen az sayıda genotoksisite çalışması bulunmaktadır. Genotoksik maddelerin sebep olduğu DNA hasar mekanizmalarının aydınlatılması ve kemik iliği kök hücrelerinin toksikoloji alanındaki in vitro/in vivo yöntemlere geçerli ve güvenilir alternatif olabilmesi için ileri çalışmalara ihtiyaç vardır.
BMN 673, a Novel and Highly Potent PARP1/2 Inhibitor for the Treatment of Human Cancers with DNA Repair Deficiency (2013)

BMN 673 is currently in early-phase clinical development and represents a promising PARP1/2 inhibitor with potentially advantageous features in its drug class.
Distributed computing in practice: the Condor experience (2005)

Abstract Since 1984, the Condor project has enabled ordinary users to do extraordinary computing. Today, the project continues to explore the social and technical problems of cooperative computing on scales ranging from the desktop to the world‐wide computational Grid. In this paper, we provide the history and philosophy of the Condor project and describe how it has interacted with other projects and evolved along with the field of distributed computing. We outline the core components of the Condor system and describe how the technology of computing must correspond to social structures. Throughout, we reflect on the lessons of experience and chart the course travelled by research ideas as they grow into production systems. Copyright © 2005 John Wiley &amp; Sons, Ltd.
Adaptation of beef cattle to high-concentrate diets: Performance and ruminal metabolism1 (2006)

The diet adaptation period is widely considered a critical period of time in which nutritional management practices can promote or impair subsequent performance and health. Performance studies indicate that adapting feedlot cattle with incremental increases in dietary concentrate, from approximately 55 to 90% of diet DM, in 14 d or less, while allowing ad libitum access to the diet, generally results in reduced performance during adaptation or over the entire feeding period. However, the number of cattle involved in these studies does not allow insight into the frequencies of metabolic disorders associated with the management practices tested. Adapting cattle by restricting the quantity of higher-concentrate diets offered shows promise for improving production efficiency, but further development is needed for application in commercial feedlots. Evidence suggests considerable diversity in the ability of animals to cope with ingested cereal grain, and indicates that diet adaptation procedures should affect the frequency of health-impaired or low-performing cattle in a pen. Individuals that seem to effectively regulate voluntary feed intake during adaptation generally display a steady increase in DMI as dietary concentrate is increased. These data also highlight a seemingly counterproductive, repeating cycle of overconsumption, followed by a pronounced reduction in ruminal pH, by cattle that appear to cope less favorably with grain adaptation. At least a portion of this diversity may relate to the maintenance of protozoal populations. Increases in amylolytic bacteria seemed to follow the increment of additional concentrate. Protozoa were most numerous when the diet contained approximately 60% concentrate, and lactate-utilizing bacteria increased more markedly when the diet contained more than approximately 70% concentrate. Available in vivo data suggest that the number of lactate-utilizing bacteria may reach a plateau for a given diet composition after 2 to 7 d, but thorough assessments of the time course of events using modern techniques are lacking. Further research is needed to characterize how the quantity and frequency of increases in cereal grain consumption, reflective of industry practices, impact microbial dynamics, and to identify the biological features that allow certain animals to adapt more readily to high-concentrate diets.