gebhart/patrepeval huggingface dataset:
Introduction (1994)

Fourteen years have passed since the Shah of Iran was deposed. This event marked the beginning of the political transformation of Iran which, in the intervening time, seems to have been completed. A republican constitution has been adopted, clerical rule has been established and institutionalised, and the succession process has been swiftly and painlessly effected.
HLA-DR3 molecules can bind peptides carrying two alternative specific submotifs. (1994)

Three different HLA-DR3-specific peptide binding motifs have been proposed. These motifs shared a major hydrophobic anchor at the N-terminus, but differed in the C-terminal anchor residues. In the present study, the structural requirements for peptide binding to HLA-DR3 were examined in further detail by using quantitative HLA-DR3-specific binding assays and sets of single substitution analogues of DR3 binding peptides (Lol pollen amino acids 171-190 and sperm whale myoglobin amino acids 132-151). We found that the requirements for binding to HLA-DR3 vary among different DR3 binding peptides; the absence of an anchor or the presence of only a weak anchor residue at either position n or n + 3 can be compensated for by the presence of a strong, positively charged anchor residue at position n + 5. These results explain several of the previously reported differences between DR3-specific peptide binding motifs. To evaluate the predictive value of the thus-refined motif, the DR3 binding capacity of an overlapping set of peptides, spanning the entire sequence of the 65-kDa heat shock protein of Mycobacterium tuberculosis was investigated and correlated with the occurrence of the different DR3 motifs. A strong correlation was found between the presence of the refined DR3 motif and peptide binding to purified HLA-DR3 molecules.
Identification and light‐induced expression of a novel gene of NADPH‐protochlorophyllide oxidoreductase isoform in Arabidopsis thaliana (2000)

In Arabidopsis thaliana , we identified a novel gene of a NADPH‐protochlorophyllide oxidoreductase (POR) isoform, which catalyzes the light‐dependent protochlorophyllide a reduction in the chlorophyll (Chl) biosynthetic pathway. The deduced amino acid sequence of the novel POR isoform (PORC) showed significant identities (∼75%) with the previously isolated two POR isoforms of A. thaliana . Contrasting with these POR isoforms, the PORC transcript increased in etiolated seedlings by illumination, and was dominantly expressed in immature and mature tissues. The present results demonstrated that Chl biosynthesis and chloroplast biogenesis in A. thaliana are controlled by three POR isoforms, which are differentially controlled by light and development.
An Exploratory Study of the Current State of Career Development for Project Managers in the IT and Other Industries (2014)

Critical to project success and job satisfaction of project managers is effective Human Resource Management (HRM). The temporary nature of projects has changed the traditional career paths for project managers and the way project-oriented companies prioritize their motivation tactics. By conducting a survey to explore a general pattern of employers' HRM practices in different industries regarding the project management career, this paper presents the fact that most employers prefer on-job training to organizational career path in motivating and retaining project manager and that there is no difference between IT industry and other industries in terms of the extent of use of on-job training and the organizational career path. These findings contribute to an in-depth understanding of the project management career path and suggest that project managers be proactive in adjusting to change in the workplace by being more autonomous in their career development decisions based on the larger work environment.
Endothelial protein C receptor (CD201) explicitly identifies hematopoietic stem cells in murine bone marrow (2005)

The hematopoietic stem cell (HSC) is a unique cell type found in bone marrow, which has the capacity for both self-renewal and differentiation into all blood lineages. The identification of genes expressed specifically in HSCs may help identify gene products vital to the control of self-renewal and/or differentiation, as well as antigens capable of forming the basis for improved methods of stem cell isolation. In previous studies, we identified a number of genes that appeared to be differentially expressed in murine bone marrow-derived HSCs, using microarray technology. We report here that one of those genes, encoding the murine endothelial protein C receptor (EPCR), is expressed at high levels within the bone marrow in HSCs. Bone marrow cells isolated on the basis of EPCR expression alone are highly enriched for hematopoietic reconstitution activity, showing levels of engraftment in vivo comparable to that of stem cells purified using the most effective conventional methods. Moreover, evaluation of cell populations first enriched for stem cell activity by conventional methods and subsequently fractionated on the basis of EPCR expression indicates that stem cell activity is always associated with EPCR-expressing cells. Based on our findings, we believe EPCR represents the first known marker that 'explicitly' identifies hematopoietic stem cells within murine bone marrow.
Engraftment and long-term expression of human fetal hemopoietic stem cells in sheep following transplantation in utero. (1992)

Hemopoietic stem cells from human fetal liver were transplanted in utero into preimmune fetal sheep (48-54 days of gestation). The fate of donor cells was followed using karyotype analysis, by immunofluorescence labeling with anti-CD antibodies, and by fluorescent in situ hybridization using human-specific DNA probes. Engraftment occurred in 13 of 33 recipients. Of five live born sheep that exhibited chimerism, all expressed human cells in the marrow, whereas three expressed them in blood as well. Engraftment was multilineage (erythroid, myeloid, and lymphoid) and human hemopoietic progenitors (multipotent colony-forming units, colony-forming units-granulocyte, macrophage, and erythroid burst-forming units) capable of forming colonies in vitro were detected in all five lambs for greater than 2 yr. These progenitors responded to human-specific growth factors both in vitro and in vivo. Thus the administration of recombinant human IL-3 and granulocyte macrophage-colony-stimulating factor to chimeric sheep resulted in a 2.1-3.4-fold increase in the relative expression of donor (human) cells. These results demonstrate that the permissive environment of the preimmune fetal sheep provides suitable conditions for the engraftment and long-term multilineage expression of human hemopoietic stem cells in a large animal model. In this model, donor human cells appear to retain certain phenotypic and functional characteristics that can be used to manipulate the size of donor cell pool.
Reactive oxygen species initiate luminal but not basal cell death in cultured human mammary alveolar structures: a potential regulator of involution (2011)

Post-lactational involution of the mammary gland is initiated within days of weaning. Clearing of cells occurs by apoptosis of the milk-secreting luminal cells in the alveoli and through stromal tissue remodeling to return the gland almost completely to its pre-pregnant state. The pathways that specifically target involution of the luminal cells in the alveoli but not the basal and ductal cells are poorly understood. In this study we show in cultured human mammary alveolar structures that the involution process is initiated by fresh media withdrawal, and is characterized by cellular oxidative stress, expression of activated macrophage marker CD68 and finally complete clearing of the luminal but not basal epithelial layer. This process can be simulated by ectopic addition of reactive oxygen species (ROS) in cultures without media withdrawal. Cells isolated from post-involution alveoli were enriched for the CD49f(+) mammary stem cell (MaSC) phenotype and were able to reproduce a complete alveolar structure in subcultures without any significant loss in viability. We propose that the ROS produced by accumulated milk breakdown post-weaning may be the mechanism underlying the selective involution of secretory alveolar luminal cells, and that our culture model represents an useful means to investigate this and other mechanisms further.
Wiederholungen und Einführung in Mathematica (1995)

Wir wollen Mathematica bei einer Veranschaulichung von Beobachtungsdaten kennenlernen. Grafische Darstellungen sind oft besser als Tabellen von Zahlen geeignet, um einen ersten Eindruck von der vorliegenden Situation zu bekommen und um Ideen zur Auswertung zu finden. Wir kommen auf diese Weise schnell zu ersten Ergebnissen. Das Programmsystem verwendet intern Methoden aus unterschiedlichen Gebieten der Mathematik. Auf Grundideen dazu gehen wir später ein. Es ist unser Konzept, möglichst weitreichende Anwendungen zu erhalten, indem wir wesentliche Teile der Berechnungen durch den Computer durchführen lassen. Diese „black box — Behandlung“ hat ihre Grenzen, nämlich zum Beispiel dann, wenn der Anwender einschätzen muß, ob im Computerprogramm verwendete Voraussetzungen in ausreichend guter Näherung biologisch gerechtfertigt sind. Auf derartige Fragen der Modellbildung werden wir an vielen Stellen des Buches zurückkommen Beim Übertragen biologischer Mechanismen in mathematische Modelle muß einerseits ganz wesentlich das biologische Verständnis einfließen, andererseits sollten auch Möglichkeiten und Grenzen der weiteren mathematischen Behandlung berücksichtigt werden. Das ist erfahrungsgemäß nur möglich, wenn durch Biologen und Mediziner auf der einen Seite und Mathematiker auf der anderen Seite ein ausreichend langer gemeinsamer Weg gegangen werden kann. Aus dieser Sicht wurden die mathematischen Ideen für die folgenden Kapitel ausgewählt.
Bakken Lecture: The brain, the heart, and therapeutic hypothermia (2009)

Therapeutic hypothermia in acute resuscitation medicine has a long history, but its currently recommended use dates back to work in the mid-1960s by the late Dr. Peter Safar and colleagues. Compared with normothermia, mild therapeutic hypothermia, induced right after restoration of spontaneous circulation in comatose survivors of cardiac arrest, leads to 1 additional patient with intact neurological outcome for every 6 patients treated. Demonstrating benefit from therapeutic hypothermia in other acute neurological insults, such as traumatic brain injury, has been more difficult. Current research to optimize the benefits of mild therapeutic hypothermia in cardiac arrest is focused on hypothermia's profound effects on drug metabolism, determining the best anesthetics and sedatives to use with cooling, and identifying compounds that may promote induction of hypothermia or create a poikilothermic state. Future applications of therapeutic hypothermia may include induction of emergency preservation and resuscitation to buy time for damage-control surgery in patients with exsanguination cardiac arrest.
Increased Bone Formation and Bone Mass Induced by Sclerostin Antibody Is Not Affected by Pretreatment or Cotreatment with Alendronate in Osteopenic, Ovariectomized Rats (2011)

Clinical studies have revealed a blunting of the bone anabolic effects of parathyroid hormone treatment in osteoporotic patients in the setting of pre- or cotreatment with the antiresorptive agent alendronate (ALN). Sclerostin monoclonal antibody (Scl-Ab) is currently under clinical investigation as a new potential anabolic therapy for postmenopausal osteoporosis. The purpose of these experiments was to examine the influence of pretreatment or cotreatment with ALN on the bone anabolic actions of Scl-Ab in ovariectomized (OVX) rats. Ten-month-old osteopenic OVX rats were treated with ALN or vehicle for 6 wk, before the start of Scl-Ab treatment. ALN-pretreated OVX rats were switched to Scl-Ab alone or to a combination of ALN and Scl-Ab for another 6 wk. Vehicle-pretreated OVX rats were switched to Scl-Ab or continued on vehicle to serve as controls. Scl-Ab treatment increased areal bone mineral density, volumetric bone mineral density, trabecular and cortical bone mass, and bone strength similarly in OVX rats pretreated with ALN or vehicle. Serum osteocalcin and bone formation rate on trabecular, endocortical, and periosteal surfaces responded similarly to Scl-Ab in ALN or vehicle-pretreated OVX rats. Furthermore, cotreatment with ALN did not have significant effects on the increased bone formation, bone mass, and bone strength induced by Scl-Ab in the OVX rats that were pretreated with ALN. These results indicate that the increases in bone formation, bone mass, and bone strength with Scl-Ab treatment were not affected by pre- or cotreatment with ALN in OVX rats with established osteopenia.
Prebiotic Galactooligosaccharides Reduce Adherence of EnteropathogenicEscherichia colito Tissue Culture Cells (2006)

Prebiotic oligosaccharides are thought to provide beneficial effects in the gastrointestinal tract of humans and animals by stimulating growth of selected members of the intestinal microflora. Another means by which prebiotic oligosaccharides may confer health benefits is via their antiadhesive activity. Specifically, these oligosaccharides may directly inhibit infections by enteric pathogens due to their ability to act as structural mimics of the pathogen binding sites that coat the surface of gastrointestinal epithelial cells. In this study, the ability of commercial prebiotics to inhibit attachment of microcolony-forming enteropathogenic Escherichia coli (EPEC) was investigated. The adherence of EPEC strain E2348/69 on HEp-2 and Caco-2 cells, in the presence of fructooligosaccharides, inulin, galactooligosaccharides (GOS), lactulose, and raffinose was determined by cultural enumeration and microscopy. Purified GOS exhibited the greatest adherence inhibition on both HEp-2 and Caco-2 cells, reducing the adherence of EPEC by 65 and 70%, respectively. In addition, the average number of bacteria per microcolony was significantly reduced from 14 to 4 when GOS was present. Adherence inhibition by GOS was dose dependent, reaching a maximum at 16 mg/ml. When GOS was added to adhered EPEC cells, no displacement was observed. The expression of BfpA, a bundle-forming-pilus protein involved in localized adherence, was not affected by GOS, indicating that adherence inhibition was not due to the absence of this adherence factor. In addition, GOS did not affect autoaggregation. These observations suggest that some prebiotic oligosaccharides may have antiadhesive activity and directly inhibit the adherence of pathogens to the host epithelial cell surface.
An Approach to the Control of Massive Hemorrhage in Cyclophosphamide-Induced Cystitis by Intravenous Vasopressin: A Case Report (1978)

Massive bleeding owing to cyclophosphamide-induced hemorrhagic cystitis was not affected by intravesical instillation of 4 per cent formalin or 1 per cent silver nitrate. After initiation of a continuous systemic infusion of vasopressin hematuria and transfusion requirements diminished markedly. Adverse reactions were mild. Intravenous vasopressin was a safe and effective means to control temporarily life-threatening hemorrhagic cystitis.
Germline 657del5 mutation in the NBS1 gene in breast cancer patients (2003)

In this report the proportion of consecutive and familial breast cancer cases harboring the 657del5 of exon 6 of the NBS1 gene was determined to assess whether it is associated with the increased risk of breast cancer development. The study consisted of 3 groups of patients: a series of consecutive 150 patients with histologically confirmed breast cancer, diagnosed under the age of 50 in the city of Szczecin; a series of 80 breast cancer patients with a family history of breast cancer in their first-degree relatives; and a series of 530 consecutive individuals without the diagnosis of breast cancer selected at random by family doctors from the city of Szczecin. Molecular examination included allele-specific PCR assay for the common Slavic NBS1 mutation (657del5), LOH analysis using denucleotide CA repeat microsatellite markers, haplotype analysis and sequencing. The NBS1 founder mutation was detected in 2 of 150 (1.3%) consecutive breast cancer cases diagnosed under the age of 50 years; in 3 of 80 familial breast cancer cases (3.7%); and in 3 of 530 individuals (0.6%) from the general population. Examination of tumor DNA from patients with the NBS1 mutation (groups A and B) revealed loss of heterozygosity (LOH) in all cases. Additional haplotype analysis revealed that allelic loss affects specifically wild-type alleles. The majority of probands with breast cancer and the NBS1 mutation had a positive family history of breast cancer in their first-degree relatives. It appears that the 657del5 mutation in exon 6 of the NBS1 gene is responsible for the occurrence of a small but significant proportion of familial breast cancer patients.
OVID: design and implementation of a video-object database system (1993)

A video-object data model and the design and implementation of a prototype video-object database system named OVID based on the model are described. Notable features of the video-object data model are a mechanism to share common descriptional data among video-objects, called interval-inclusion based inheritance, and operations to composite video-objects. The OVID system offers a browsing/inspection tool called VideoChart, and adhoc query facility called VideoSQL, and a video-object definition tool.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
The BF Identity-Based Encryption System (2006)

We briefly review the notion of cyclic group equipped with a bilinear map, or pairing. In this note, we focus exclusively on symmetric pairings that support a cryptographic hashing operation directly into the bilinear group (these pairings are also called of type 1). These objects can be instantiated using the modified Weil or Tate pairing on certain algebraic curves over finite fields, that include families of supersingular elliptic curves of large characteristic. We refer the reader to the Boneh-Franklin paper [BF03] and some specialized treatises [BSS99] for details.
Simplifying long short-term memory acoustic models for fast training and decoding (2016)

On acoustic modeling, recurrent neural networks (RNNs) using Long Short-Term Memory (LSTM) units have recently been shown to outperform deep neural networks (DNNs) models. This paper focuses on resolving two challenges faced by LSTM models: high model complexity and poor decoding efficiency. Motivated by our analysis of the gates activation and function, we present two LSTM simplifications: deriving input gates from forget gates, and removing recurrent inputs from output gates. To accelerate decoding of LSTMs, we propose to apply frame skipping during training, and frame skipping and posterior copying (FSPC) during decoding. In the experiments, model simplifications reduce the size of LSTM models by 26%, resulting in a simpler model structure. Meanwhile, the application of FSPC speeds up model computation by 2 times during LSTM decoding. All these improvements are achieved at the cost of 1% WER degradation.
Compartmentalization of Lipopolysaccharide Production Correlates with Clinical Presentation in Meningococcal Disease (1992)

Lipopolysaccharide (LPS, endotoxin) was quantified in plasma and cerebrospinal fluid (CSF) collected simultaneously from patients with systemic meningococcal disease. High levels (median, 3800 ng/L; range, 750-14,000) were present in plasma and low levels (median, 40 ng/L; range, less than 25-165) in CSF of patients with fulminant septicemia. Conversely, high levels (median, 2500 ng/L; range, less than 25-500,000) in CSF and low or undetectable levels (median, less than 25 ng/L; range, less than 25-210) in plasma were associated with meningitis without septic shock. Levels of LPS were significantly correlated with protein levels in CSF (r = .50, P = .01) and inversely correlated with the ratio of glucose in CSF to that in blood (r = -.62, P = .0005). LPS level in CSF greater than 800 ng/L was significantly associated with greater than or equal to 10(9) leukocytes/L, protein levels greater than 0.5 g/L, and a glucose ratio less than 0.5. Thus, quantification of LPS levels in the plasma and CSF in systemic meningococcal disease is a better predictor of pathophysiologic events than is demonstrating the presence of live bacteria as in conventional culture.
Codon selection in yeast. (1982)

Extreme codon bias is seen for the Saccharomyces cerevisiae genes for the fermentative alcohol dehydrogenase isozyme I (ADH-I) and glyceraldehyde-3-phosphate dehydrogenase. Over 98% of the 1004 amino acid residues analyzed by DNA sequencing are coded for by a select 25 of the 61 possible coding triplets. These preferred codons tend to be highly homologous to the anticodons of the major yeast isoacceptor tRNA species. Codons which necessitate site by side GC base pairs between the codons and the tRNA anticodons are always avoided whenever possible. Codons containing 100% G, C, A, U, GC, or AU are also avoided. This provides for approximately equivalent codon-anticodon binding energies for all preferred triplets. All sequenced yeast genes show a distinct preference for these same 25 codons. The degree of preference varies from greater than 90% for glyceraldehyde-3-phosphate dehydrogenase and ADH-I to less than 20% for iso-2 cytochrome c. The degree of bias for these 25 preferred triplets in each gene is correlated with the level of its mRNA in the cytoplasm. Genes which are strongly expressed are more biased than genes with a lower level of expression. A similar phenomenon is observed in the codon preferences of highly expressed genes in Escherichia coli. High levels of gene expression are well correlated with high levels of codon bias toward 22 of the 61 coding triplets. As in yeast, these preferred codons are highly complementary to the major cellular isoacceptor tRNA species. In at least four cases (Ala, Arg, Leu, and Val), these preferred E. coli codons are incompatible with the preferred yeast codons.
High Frequency of Submicroscopic Hemizygous Deletion Is a Major Mechanism of Loss of Expression ofPTENin Uveal Melanoma (2005)

This is the first demonstration that PTEN is a tumor suppressor involved in uveal melanoma pathogenesis and may be associated with clinical outcome. Our data also suggest that submicroscopic deletion, but not large deletions, is the major mechanism of loss of PTEN expression in uveal melanomas.