gebhart/patrepeval huggingface dataset:
Burnout: Differences Between Professional and Paraprofessional Nursing Staff in Acute Care and Long-Term Care Health Facilities (1988)

In burnout the cumulative effects of a stressful work environment gradually overwhelm the defenses of staff members, forcing them to withdraw psychologically. Understanding the experience of professional and paraprofessional nurses who suffer from burnout requires a close examination of the environments in which they function. We examined differences in nursing burnout by occupational levels (professional versus paraprofessional nurses), type of facility (acute care hospitals versus long-term care facilities), and professional exposure to patients with poor prognosis for survival (high, moderate, low). The sample included 312 nurses who worked in three acute care and seven long-term care health facilities. Multivariate analysis of variance was used to analyze the data. We found paraprofessional nurses significantly higher on two dimensions of burnout (emotional exhaustion and depersonalization) than professional nurses. In addition, paraprofessional nurses perceived less support in their work environments than did professional nurses. Furthermore, nurses working in long-term care facilities experienced emotional exhaustion more frequently than did nurses working in acute care facilities. We present recommendations for practice and future research.
Human dUTP pyrophosphatase: cDNA sequence and potential biological importance of the enzyme. (1992)

Two functional human dUTP pyrophosphatase (dUTPase; EC 3.6.1.23) cDNAs were isolated from a cDNA expression library by genetic complementation in Escherichia coli. These cDNAs differed in size but exhibited a common overlapping DNA sequence. Contained within this sequence was a single long open reading frame sufficient to encode a polypeptide of 141 amino acids with a calculated molecular mass of 16.6 kDa. The amino acid sequence of this protein exhibits 35% identity with the E. coli dUTPase and 53% identity with the Saccharomyces cerevisiae enzyme. The human dUTPase was found to contain five characteristics amino acid sequence motifs that are common to the dUTPases of E. coli, yeast, and herpesviruses and to dUTPase-like sequences encoded by some retrovirus gag and pol genes. A high degree of amino acid sequence identity (greater than 60%) was also observed between the human dUTPase and the putative pseudoproteases of two poxviruses, indicating that these virus proteins are dUTPases. Northern hybridization analysis reveals that dUTPase is encoded by at least two species of poly(A)+ mRNA and possibly a third, smaller species. All of these mRNAs are present in a variety of human tissues but their relative levels vary between tissues. Southern analysis indicates that the dUTPase gene has been conserved to some extent throughout vertebrate evolution; however, the gene may be very large, or its organization somewhat complex in some systems. We suggest that dUTPase may generally perform an essential role in DNA replication and therefore could serve as a target enzyme for the development of chemotherapeutic compounds.
The story of O/sub 2/ (1990)

A complete description of the O/sub 2/ system, an object-oriented database system, is presented. It has the functionality of a DBMS (persistence, disk management, sharing and query language) and of an object-oriented system (complex objects, object identity, encapsulation, typing, inheritance, overriding, extensibility, and completeness). It also includes a set of user interface generation tools and a complete programming environment. O/sub 2/ supports a multilanguage paradigm and a dual mode of operation (development and execution) and it operates on a workstation/server configuration. The system is described as seen from the programmer's point of view and as seen through the programming environment. A complete description of the implementation is given. An evaluation of the prototype performance is also given.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Efficient partitioning of sequences (1995)

We consider the problem of partitioning a sequence of n real numbers into p intervals such that the cost of the most expensive interval, measured with a cost function f is minimized. This problem is of importance for the scheduling of jobs both in parallel and pipelined environments. We develop a straightforward and practical dynamic programming algorithm that solves this problem in time O(p(n-p)), which is an improvement of a factor of log p compared to the previous best algorithm. A number of variants of the problem are also considered.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Directed evolution of a secretory leader for the improved expression of heterologous proteins and full‐length antibodies in Saccharomyces cerevisiae (2009)

Because of its eukaryotic nature, simple fermentation requirements, and pliable genetics, there have been many attempts at improving recombinant protein production in Saccharomyces cerevisiae. These strategies typically involve altering the expression of a native protein thought to be involved in heterologous protein trafficking. Usually, these approaches yield three- to tenfold improvements over wild-type strains and are almost always specific to one type of protein. In this study, a library of mutant alpha mating factor 1 leader peptides (MFalpha1pp) is screened for the enhanced secretion of a single-chain antibody. One of the isolated mutants is shown to enhance the secretion of the scFv up to 16-fold over wild type. These leaders also confer a secretory improvement to two other scFvs as well as two additional, structurally unrelated proteins. Moreover, the improved leader sequences, combined with strain engineering, allow for a 180-fold improvement over previous reports in the secretion of full-length, functional, glycosylated human IgG(1). The production of full-length IgG(1) at milligram per liter titers in a simple, laboratory-scale system will significantly expedite drug discovery and reagent synthesis while reducing antibody cloning, production, and characterization costs.
A Combined Experimental−Computational Investigation of Carbon Dioxide Capture in a Series of Isoreticular Zeolitic Imidazolate Frameworks (2010)

A series of five zeolitic imidazolate frameworks (ZIFs) have been synthesized using zinc(II) acetate and five different 4,5-functionalized imidazole units, namely ZIF-25, -71, -93, -96, and -97. These 3-D porous frameworks have the same underlying topology (RHO) with Brunauer-Emmet-Teller surface areas ranging from 564 to 1110 m(2)/g. The only variation in structure arises from the functional groups that are directed into the pores of these materials, which include -CH(3), -OH, -Cl, -CN, -CHO, and -NH(2); therefore these 3-D frameworks are ideal for the study of the effect of functionality on CO(2) uptake. Experimental results show CO(2) uptake at approximately 800 Torr and 298 K ranging from 0.65 mmol g(-1) in ZIF-71 to 2.18 mmol g(-1) in ZIF-96. Molecular modeling calculations reproduce the pronounced dependence of the equilibrium adsorption on functionalization and suggest that polarizability and symmetry of the functionalization on the imidazolate are key factors leading to high CO(2) uptake.
Comparative allelotype of early and advanced stage non-small cell lung carcinomas (1996)

To identify chromosomal loci of tumor suppressor genes involved in the genesis and progression of non-small cell lung carcinoma (NSCLC), comparative allelotype analysis was performed in 23 stage I primary lung tumors and in 22 metastatic lung tumors to the brain. In total, 84 loci on all 22 autosomal chromosomes were examined for loss of heterozygosity (LOH) by restriction fragment length polymorphism (RFLP) analysis with 40 polymorphic DNA probes and polymerase chain reaction (PCR)-LOH analysis of 44 polymorphic loci. LOH on chromosome arms 3p, 13q, and 17p was detected frequently (> 60%) in both stage I primary lung tumors and brain metastases, whereas the incidence of LOH on chromosome arms 2q, 5q, 9p, 12q, 18q, and 22q was more than 60% only in brain metastases. In particular, the incidence of LOH on chromosome arms 2q, 9p, 18q, and 22q in brain metastases was significantly higher than that in stage I primary lung tumors (P < 0.05). These results indicate that tumor suppressor genes on chromosome arms 3p, 13q, and 17p are involved in the genesis of NSCLC, whereas those on several chromosome arms, especially on 2q, 9p, 18q and 22q, play an important role in the progression of NSCLC.
Quantitative monitoring of the PRAME gene for the detection of minimal residual disease in leukaemia (2001)

PRAME (Preferentially expressed antigen of melanoma) has been previously identified as a melanoma antigen recognized by cytotoxic T cells (CTLs) and found to be expressed in a variety of cancer cells including leukaemic cells. We have screened 98 Japanese patients with leukaemia and lymphoma for expression of the PRAME gene using semiquantitative reverse transcription polymerase chain reaction (RT-PCR). Forty-one patients (42%) showed high levels of PRAME expression. Eight of these patients were then monitored using real-time PCR for a period of 10-37 months. Significant reductions in the PRAME expression were observed in all patients after chemotherapy. An increased expression was detected in the two patients who relapsed, one of which was before cytological diagnosis. These changes were correlated with those of other known genetic markers, such as the bcr-abl gene. Therefore, quantitative monitoring of the PRAME gene using real-time PCR method may be useful for detecting minimal residual disease and to predict subsequent relapse, especially in patients without known genetic markers. In addition, a PRAME-positive leukaemia cell line and fresh leukaemic cells were found to be susceptible to lysis by PRAME-specific CTLs established from a patient with melanoma, suggesting that the PRAME peptide can also be a target leukaemia antigen for T cells.
Curing Dental Resins and Composites by Photopolymerization (2000)

Photopolymerization has become an integral component of the practice of dentistry. A better appreciation of the photopolymerization process as well as its potential and limitations may aid the dentist in the delivery of both esthetic and restorative dental care.
Complement and Fc Function Are Required for Optimal Antibody Prophylaxis againstPneumocystis cariniiPneumonia (2005)

Pneumocystis carinii is an opportunistic fungal pathogen that causes P. carinii pneumonia (PCP) in the immunocompromised host. We investigated the role of antibody Fc-mediated function in passive prophylaxis against the development of PCP in SCID mice. By comparison of anti-mouse P. carinii immunoglobulin G1 monoclonal antibody (MAb) 4F11(G1) and its F(ab')2 derivative in an intranasal immunoprophylaxis model, we determined that Fc-mediated function is required for maximum effect of this antibody. Comparison of efficacy of antibody prophylaxis in SCID mice depleted of complement to that in nondepleted mice demonstrated that complement fixation by MAb 4F11(G1) is also necessary for optimal effect of passively administered antibody, although residual protection was observed in complement-depleted SCID mice. The necessity of complement for optimal PCP prophylaxis by MAb 4F11(G1) suggests that complement may play a role in antibody-mediated protection against development of PCP.
HOW TO USE THE GERMAN ENIGMA CIPHER MACHINE: A PHOTOGRAPHIC ESSAY (1983)

(1983). HOW TO USE THE GERMAN ENIGMA CIPHER MACHINE: A PHOTOGRAPHIC ESSAY. Cryptologia: Vol. 7, No. 4, pp. 291-296.
An algorithm for finding signals of unknown length in DNA sequences (2001)

Pattern discovery in unaligned DNA sequences is a challenging problem in both computer science and molecular biology. Several different methods and techniques have been proposed so far, but in most of the cases signals in DNA sequences are very complicated and avoid detection. Exact exhaustive methods can solve the problem only for short signals with a limited number of mutations. In this work, we extend exhaustive enumeration also to longer patterns. More in detail, the basic version of algorithm presented in this paper, given as input a set of sequences and an error ratio epsilon < 1, finds all patterns that occur in at least q sequences of the set with at most epsilonm mutations, where m is the length of the pattern. The only restriction is imposed on the location of mutations along the signal. That is, a valid occurrence of a pattern can present at most [epsiloni] mismatches in the first i nucleotides, and so on. However, we show how the algorithm can be used also when no assumption can be made on the position of mutations. In this case, it is also possible to have an estimate of the probability of finding a signal according to the signal length, the error ratio, and the input parameters. Finally, we discuss some significance measures that can be used to sort the patterns output by the algorithm.
Regulation of dimethyl-fumarate toxicity by proteasome inhibitors (2014)

The present studies examined the biology of the multiple sclerosis drug dimethyl-fumarate (DMF) or its in vivo breakdown product and active metabolite mono-methyl-fumarate (MMF), alone or in combination with proteasome inhibitors, in primary human glioblastoma (GBM) cells. MMF enhanced velcade and carfilzomib toxicity in multiple primary GBM isolates. Similar data were obtained in breast and colon cancer cells. MMF reduced the invasiveness of GBM cells, and enhanced the toxicity of ionizing radiation and temozolomide. MMF killed freshly isolated activated microglia which was associated with reduced IL-6, TGFβ and TNFα production. The combination of MMF and the multiple sclerosis drug Gilenya further reduced both GBM and activated microglia viability and cytokine production. Over-expression of c-FLIP-s or BCL(-)XL protected GBM cells from MMF and velcade toxicity. MMF and velcade increased plasma membrane localization of CD95, and knock down of CD95 or FADD blocked the drug interaction. The drug combination inactivated AKT, ERK1/2 and mTOR. Molecular inhibition of AKT/ERK/mTOR signaling enhanced drug combination toxicity whereas molecular activation of these pathways suppressed killing. MMF and velcade increased the levels of autophagosomes and autolysosomes and knock down of ATG5 or Beclin1 protected cells. Inhibition of the eIF2α/ATF4 arm or the IRE1α/XBP1 arm of the ER stress response enhanced drug combination lethality. This was associated with greater production of reactive oxygen species and quenching of ROS suppressed cell killing.
Transfer Printing Techniques for Materials Assembly and Micro/Nanodevice Fabrication (2012)

Transfer printing represents a set of techniques for deterministic assembly of micro-and nanomaterials into spatially organized, functional arrangements with two and three-dimensional layouts. Such processes provide versatile routes not only to test structures and vehicles for scientific studies but also to high-performance, heterogeneously integrated functional systems, including those in flexible electronics, three-dimensional and/or curvilinear optoelectronics, and bio-integrated sensing and therapeutic devices. This article summarizes recent advances in a variety of transfer printing techniques, ranging from the mechanics and materials aspects that govern their operation to engineering features of their use in systems with varying levels of complexity. A concluding section presents perspectives on opportunities for basic and applied research, and on emerging use of these methods in high throughput, industrial-scale manufacturing.
A Self‐Correcting Inking Strategy for Cantilever Arrays Addressed by an Inkjet Printer and Used for Dip‐Pen Nanolithography (2008)

The challenge of multiplexing in dip-pen nanolithography with 1D and 2D cantilever arrays is addressed through an inkjet-printing-enabled method for inking pens in an array with different chemical reagents. A new surface-modification strategy directs the ink droplets to the tips of the cantilevers. This method provides control over the inking process and marks a major step towards high-throughput, multiplexed, nanoscale patterning of soft matter.
A comparative gene-expression analysis of CD34+ hematopoietic stem and progenitor cells grown in static and stirred culture systems (2006)

Static and stirred culture systems are widely used to expand hematopoietic cells, but differential culture performances are observed between these systems. We hypothesize that these differential culture outcomes are caused by the physiological responses of CD34(+) hematopoietic stem and progenitor cells (HSPCs) to the different physical microenvironments created in these culture devices. To understand the genetic changes provoked by culture microenvironments, the gene expression profiling of CD34(+) HSPCs grown in static and stirred culture systems was compared using SMART-PCR and cDNA arrays. The results revealed that 103 and 99 genes were significantly expressed in CD34(+) cells from static and stirred systems, respectively. Of those, 91 have similar levels of expression, while 12 show differential transcription levels. These differentially expressed genes are mainly involved in anti-oxidation, DNA repair, apoptosis, and chemotactic activity. A quantitative molecular understanding of the influences of growth microenvironments on transcriptional events in CD34(+) HSPCs should give new insights into optimizing culture strategies to produce hematopoietic cells.
CodeBERT: A Pre-Trained Model for Programming and Natural Languages (2020)

We present CodeBERT, a bimodal pre-trained model for programming language (PL) and nat-ural language (NL). CodeBERT learns general-purpose representations that support downstream NL-PL applications such as natural language codesearch, code documentation generation, etc. We develop CodeBERT with Transformer-based neural architecture, and train it with a hybrid objective function that incorporates the pre-training task of replaced token detection, which is to detect plausible alternatives sampled from generators. This enables us to utilize both bimodal data of NL-PL pairs and unimodal data, where the former provides input tokens for model training while the latter helps to learn better generators. We evaluate CodeBERT on two NL-PL applications by fine-tuning model parameters. Results show that CodeBERT achieves state-of-the-art performance on both natural language code search and code documentation generation tasks. Furthermore, to investigate what type of knowledge is learned in CodeBERT, we construct a dataset for NL-PL probing, and evaluate in a zero-shot setting where parameters of pre-trained models are fixed. Results show that CodeBERT performs better than previous pre-trained models on NL-PL probing.
Two-color ratio-coding of chromosome targets in fluorescence in situ hybridization: Quantitative analysis and reproducibility (1997)

Ratio coding in fluorescence in situ hybridizations has the potential to identify more DNA and RNA targets simultaneously using fewer fluorescent labels than other multi-color techniques. Ratio coding uses hybridization probes containing different proportions of two or more distinguishable labels to stain each target. In order to better define the limits of ratio coding applied to chromosome detection, we have 1) examined methods of processing electronic images of ratio-coded hybridizations to increase our ability to visually and quantitatively distinguish different stained targets and 2) examined the reproducibility of target identification. A number of hybridizations were performed using eight ratios of two fluorescent labels to identify whole chromosomes in metaphase spreads, and using five ratios of two labels on repetitive sequence probes to identify chromosomes in metaphase spreads and interphase nuclei. Greater visual discrimination was afforded by color composite images which expanded the color range across the entire visual spectrum. Quantitative ratio measurements on 25 metaphase spreads predicted that eight different chromosomes can be identified simultaneously with 96% accuracy using whole chromosome probes. Analysis of a smaller data set predicted that six different chromosomes can be identified with 97% accuracy using repetitive sequence probes.
Recruitment of ZipA to the Septal Ring of Escherichia coli Is Dependent on FtsZ and Independent of FtsA (1999)

Cell division in prokaryotes is mediated by the septal ring. In Escherichia coli, this organelle consists of several essential division proteins, including FtsZ, FtsA, and ZipA. To gain more insight into how the structure is assembled, we studied the interdependence of FtsZ, FtsA, and ZipA localization using both immunofluorescence and Gfp tagging techniques. To this end, we constructed a set of strains allowing us to determine the cellular location of each of these three proteins in cells from which one of the other two had been specifically depleted. Our results show that ZipA fails to accumulate in a ring shape in the absence of FtsZ. Conversely, depletion of ZipA does not abolish formation of FtsZ rings but leads to a significant reduction in the number of rings per unit of cell mass. In addition, ZipA does not appear to require FtsA for assembly into the septal ring and vice versa. It is suggested that septal ring formation starts by assembly of the FtsZ ring, after which ZipA and FtsA join this structure in a mutually independent fashion through direct interactions with the FtsZ protein.
Molecular cloning of rat homologues of the Drosophila melanogaster dunce cAMP phosphodiesterase: evidence for a family of genes. (1989)

To study the structure and function of cyclic nucleotide phosphodiesterases (PDEs) involved in mammalian gametogenesis, a rat testis cDNA library was screened at low stringency with a cDNA clone coding for the Drosophila melanogaster dunce-encoded PDE as a probe. This screening resulted in the isolation of two groups of cDNA clones, differing in their nucleotide sequences (ratPDE1 and ratPDE2). In the rat testis, RNA transcripts corresponding to both groups of clones were expressed predominantly in germ cells. Additional screenings of a Sertoli cell cDNA library with a ratPDE2 clone as a probe led to the isolation of two more groups of clones (rat-PDE3 and ratPDE4). Unlike ratPDE1 and ratPDE2, these clones hybridized to transcripts present predominantly in the Sertoli cell. In the middle of the coding region, all four groups of clones were homologous to each other. The deduced amino acid sequences of part of this region were also homologous to the D. melanogaster dunce PDE and to PDEs from bovine and yeast. These data indicate that a family of genes homologous to the D. melanogaster dunce-encoded PDE is present in the rat and that these genes are differentially expressed in somatic and germ cells of the seminiferous tubule. These findings provide a molecular basis for the observed heterogeneity of cAMP PDEs.