gebhart/patrepeval huggingface dataset:
Cache conscious star-join in MapReduce environments (2013)

With the popularity of big data and cloud computing, data parallel framework MapReduce based data warehouse systems are used widely. Column store is a default data placement in these systems. Traditionally star join is a core operation in the data warehouse. However, little related work study star join in column store and MapReduce environments. This paper proposes two new cache conscious algorithms Multi-Fragment-Replication Join (MFRJ) and MapReduce-Invisible Join (MRIJ) in MapReduce environments. All these algorithms avoid fact table data movement and are cache conscious in each MapReduce node. In addition, fact table is partitioned into several column groups for cache optimization in MFRJ; One group contains all of foreign key columns and each measure column is a group. In MRIJ, each column is separately processed one by one which has higher cache utilization and avoids frequently cache miss from one column to the other column. MRIJ is composed of several map operation on dimension tables and one MapReduce job. We also apply MRIJ on RCFile in Hive. All operations are processed in mapping phase and avoid high cost of shuffle and reduce operation. If the dimension tables are big enough and cannot cache in local memory, MRIJ is divided into two phases, firstly each dimension table join with corresponding foreign key column in fact table as commonly map reduce join concurrently or serially; secondly all internal results joined for final results based on position index. This strategy also can be applied to other multi-table join. In order to reduce network I/O, dimension table and the fact table foreign key column are co-location storage. Our experimental results in cluster environments show that our algorithms outperform existing approaches in Hive system.
Transcriptional Regulation of Human CYP27 Integrates Retinoid, Peroxisome Proliferator-Activated Receptor, and Liver X Receptor Signaling in Macrophages (2004)

Cholesterol uptake and efflux are key metabolic processes associated with macrophage physiology and atherosclerosis. Peroxisome proliferator-activated receptor gamma (PPARgamma) and liver X receptor alpha (LXRalpha) have been linked to the regulation of these processes. It remains to be identified how activation of these receptors is connected and regulated by endogenous lipid molecules. We identified CYP27, a p450 enzyme, as a link between retinoid, PPARgamma, and LXR signaling. We show that the human CYP27 gene is under coupled regulation by retinoids and ligands of PPARs via a PPAR-retinoic acid receptor response element in its promoter. Induction of the enzyme's expression results in an increased level of 27-hydroxycholesterol and upregulation of LXR-mediated processes. Upregulated CYP27 activity also leads to LXR-independent elimination of CYP27 metabolites as an alternative means of cholesterol efflux. Moreover, human macrophage-rich atherosclerotic lesions have an increased level of retinoid-, PPARgamma-, and LXR-regulated gene expression and also enhanced CYP27 levels. Our findings suggest that nuclear receptor-regulated CYP27 expression is likely to be a key integrator of retinoic acid receptor-PPARgamma-LXR signaling, relying on natural ligands and contributing to lipid metabolism in macrophages.
5 alpha-reductase expression by prostate cancer cell lines and benign prostatic hyperplasia in vitro. (1996)

5 alpha-reductase (5 alpha R) activity in two human prostate cancer cell lines was compared to that in benign prostatic hyperplasia (BPH) tissue and COS cells transfected with and expressing the human genes for 5 alpha-reductase type 1 (5 alpha R1) and type 2 (5 alpha R2). Comparisons were based on pH profiles and sensitivities to selective inhibitors of 5 alpha-reductase In the cancer lines, activity was greatest over the pH range 7-8, compared to a sharp peak of activity between pH 5-5.5 in BPH tissue and COS cells expressing 5 alpha R2. Finasteride and SKF105,657 were potent inhibitors of 5 alpha-reductase activity in BPH tissue and COS cells expressing 5 alpha R2, but weak inhibitors in the cancer lines and in COS cells expressing 5 alpha R1. In contrast, UK117,026 was a more potent inhibitor of 5 alpha-reductase activity in the prostate cancer cell lines and in COS cells expressing 5 alpha R1. These data indicate that human prostate cancer cell lines express 5 alpha-reductase activity similar to that in COS cells transfected with 5 alpha R1, but different from that in BPH tissue. This may be a consequence of in vitro culture. Alternatively, it may reflect a change occurring as a result of neoplastic transformation in which case it will be important to select appropriate inhibitors in the clinic.
MALE CONTRACEPTION: CURRENT STATUS AND FUTURE PROSPECTS (1988)

Modern research in male contraception is focusing on 4 areas: 1) hormonal control of spermatogenesis, the complex processes of spermiogenesis in the testis where the spermatogonia stem cells mitotically divide into spermatocytes, which meiotically divide into nondividing spermatids, which become the spermatozoa; 2) direct (nonhormonal) inhibition of spermatogenesis; 3) the suppression of sperm maturation in the epididymis; and 4) the immunological suppression of fertility through the identification of an antisperm antibody. Hormonal suppression of spermatogenesis requires depression of testosterone levels in the testis, either by direct inhibition of the Leydig cells or by inhibition of the hypothalamic production of luteinizing hormone-releasing hormone, which induces the pituitary secretion of luteinizing hormone, which induces the secretion of testosterone. Testosterone suppression in the testis must be accompanied by exogenous androgen supplements or there will be loss of libido and potency. Preparations under investigation in the hormonal suppression of spermatogenesis include monthly injections of 200 mg depot medroxyprogesterone acetate with 200 mg testosterone enanthate; danazol with testosterone enanthate; anabolic steroids, such as 19-NT-hydroxyphenylpropionate; cyproterone acetate, an antiandrogen with progestational effects; and luteinizing hormone-releasing hormone agonists, which down-regulate pituitary receptors, or luteinizing hormone-releasing hormone antagonists, which competitively block receptor activation. None of these preparations have yet struck a balance where they can completely but reversibly block spermatogenesis at doses which do not have toxic or feminizing effects. 3 nonhormonal agents which suppress sperm production are gossypol, extract of Trypterigium wilfordii, and tolnidamine. Gossypol, an extract of cottonseed oil, has been widely studied in China and has been found 99% effective in producing azoospermia or severe oligospermia. However, it is extremely toxic, damages cells in the seminiferous epithelium, and causes hypokalemia. Over time, its effects become irreversible, and its mutagenicity and teratogenicity are not known. Agents which suppress sperm maturation in the epididymis act after cell division is complete and hence are not mutagenic, but they are extremely toxic. Alpha-chlorohydrin and 6-chloro-6 deoxysugars act by inhibiting the glycolytic enzyme glyceraldehyde-3-phosphate dehydrogenase with the result that sperm cannot metabolize sugar. The sulfonamide compound, sulfasalazine, disrupts sperm motility by a mechanism not yet known. The development of a contraceptive vaccine relies on the identification of the antigenic determinants on sperm surface. Even if such a vaccine could be developed, there remains the problem of reversibility. None of the methods now being studied have demonstrated that they can reliably prevent unwanted pregnancy, and none have been around long enough for their longterm side effects to be known.
Interactions of oligonucleotide analogs containing methylphosphonate internucleotide linkages and 2′-O-methylribonucleosides (1994)

The interactions of oligonucleotide analogs, 12-mers, which contain deoxyribo- or 2'-O-methylribose sugars and methylphosphonate internucleotide linkages with complementary 12-mer DNA and RNA targets and the effect of chirality of the methylphosphonate linkage on oligomer-target interactions was studied. Oligomers containing a single Rp or Sp methylphosphonate linkage (type 1) or oligomers containing a single phosphodiester linkage at the 5'-end followed by 10 contiguous methylphosphonate linkages of random chirality (type 2) were prepared. The deoxyribo- and 2'-O-methylribo- type 1 12-mers formed stable duplexes with both the RNA and DNA as determined by UV melting experiments. The melting temperatures, Tms, of the 2'-O-methylribo-12-mer/RNA duplexes (49-53 degrees C) were higher than those of the deoxyribo-12mer/RNA duplexes (31-36 degrees C). The Tms of the duplexes formed by the Rp isomers of these oligomers were approximately 3-5 degrees C higher than those formed by the corresponding Sp isomers. The deoxyribo type 2 12-mer formed a stable duplex, Tm 34 degrees C, with the DNA target and a much less stable duplex with the RNA target, Tm < 5 degrees C. In contrast, the 2'-O-methylribo type 2 12-mer formed a stable duplex with the RNA target, Tm 20 degrees C, and a duplex of lower stability with the DNA target, Tm < 5 degrees C. These results show that the previously observed greater stability of oligo-2'-O-methylribonucleotide/RNA duplexes versus oligodeoxyribonucleotide/RNA duplexes extends to oligomers containing methylphosphonate linkages and that the configuration of the methylphosphonate linkage strongly influences the stability of the duplexes.
Zymomonas Mobilis—Science and Industrial Application (1993)

Zymomonas mobilis is undoubtedly one of the most unique bacterium within the microbial world. Known since 1912 under the names Termobacterium mobilis, Pseudomonas linderi, and Zymomonas mobilis, reviews on its uniqueness have been published in 1977 and 1988. The bacterium Zymomonas mobilis not only exhibits an extraordinarily uniqueness in its biochemistry, but also in its growth behavior, energy production, and response to culture conditions, as well as cultivation techniques used. This uniqueness caused great interest in the scientific, biotechnological, and industrial worlds. Its ability to couple and uncouple energy production in favor of product formation, to respond to physical and chemical environment manipulation, as well as its restricted product formation, makes it an ideal microorganism for microbial process development. This review explores the advances made since 1987, together with new developments in the pure scientific and applied commercial areas.
Adenovirus E1A targets key regulators of cell proliferation. (1992)

Studies of E1A support the notion that small DNA tumour viruses target cellular pathways at key points that are amenable to regulation. In the case of E1A, these targets appear to be points of control of cellular proliferation and, in particular, proteins that regulate the progression of cells from G0 and G1 phases of the cell cycle into the S phase. In several cases, recent studies have identified complexes between the viral targets and other cellular proteins. These interactions may provide insight not only into the mechanism of E1A mediated transformation but also into the control of proliferation in normal cells.
Differential gene expression associated with postnatal equine articular cartilage maturation (2008)

Differential expression of genes encoding matrix proteins and matrix-modifying enzymes between neonates and adults reflect a cellular maturation process in articular chondrocytes. Up-regulated transcripts in neonatal cartilage are consistent with growth and expansion of the articular surface. Expression patterns in mature articular cartilage indicate a transition from growth to homeostasis, and tissue function related to withstanding shear and weight-bearing stresses.
Optimizing GH Therapy in Adults and Children (2001)

Until the advent of modern neuroradiological imaging techniques in 1989, a diagnosis of GH deficiency in adults carried little significance other than as a marker of hypothalamo-pituitary disease. The relatively recent recognition of a characteristic clinical syndrome associated with failure of spontaneous GH secretion and the potential reversal of many of its features with recombinant human GH has prompted a closer examination of the physiological role of GH after linear growth is complete. The safe clinical practice of GH replacement demands a method of judging overall GH status, but there is no biological marker in adults that is the equivalent of linear growth in a child by which to judge the efficacy of GH replacement. Assessment of optimal GH replacement is made difficult by the apparent diverse actions of GH in health, concern about the avoidance of iatrogenic acromegaly, and the growing realization that an individual's risk of developing certain cancers may, at least in part, be influenced by cumulative exposure to the chief mediator of GH action, IGF-I. As in all areas of clinical practice, strategies and protocols vary between centers, but most physicians experienced in the management of pituitary disease agree that GH is most appropriately begun at low doses, building up slowly to the final maintenance dose. This, in turn, is best determined by a combination of clinical response and measurement of serum IGF-I, avoiding supraphysiological levels of this GH-dependent peptide. Numerous studies have helped define the optimum management of GH replacement during childhood. The recent requirement to measure and monitor GH status in adult life has called into question the appropriateness of simplistic weight- and surface area-based dosing regimens for the management of GH deficiency in childhood, with reliance on linear growth as the sole marker of GH action. It is clear that the monitoring of parameters other than linear growth to help refine GH therapy should now be incorporated into childhood GH treatment protocols. Further research will be required to define the optimal management of the transition from pediatric to adult GH replacement; this transition will only be possible once the benefits of GH in mature adults are defined and accepted by pediatric and adult endocrinologists alike.
TheStaphylococcus qacHgene product: a new member of the SMR family encoding multidrug resistance (1998)

The prevalence of disinfectant-resistant food-related microorganisms is of concern to the food industry. The Staphylococcus saprophyticus strain ST2H6 isolated from a poultry processing plant contained a 2.4-kb plasmid (p2H6) harbouring qacH, which encodes resistance to disinfectants based on quaternary ammonium compounds. The complete p2H6 nucleotide sequence revealed an open reading frame encoding a putative protein of 107 amino acid residues with strong similarity to members of the small multidrug resistance protein family. QacH also conferred high-level ethidium bromide resistance and low-level proflavine resistance and thus differed phenotypically from the similar proteins Smr and QacG. Fluorimetry indicated that the high-level ethidium bromide resistance was due to improved efflux energised by the proton motive force. Site-directed mutagenesis substituting the Asp-24 residue with Glu-24 had no effect on resistance characteristics. An additional open reading frame on p2H6 encoded a putative protein with similarity to rolling circle replication proteins.
A vehicle-to-vehicle communication protocol for cooperative collision warning (2004)

This paper proposes a vehicle-to-vehicle communication protocol for cooperative collision warning. Emerging wireless technologies for vehicle-to-vehicle (V2V) and vehicle-to-roadside (V2R) communications such as DSRC are promising to dramatically reduce the number of fatal roadway accidents by providing early warnings. One major technical challenge addressed in this paper is to achieve low-latency in delivering emergency warnings in various road situations. Based on a careful analysis of application requirements, we design an effective protocol, comprising congestion control policies, service differentiation mechanisms and methods for emergency warning dissemination. Simulation results demonstrate that the proposed protocol achieves low latency in delivering emergency warnings and efficient bandwidth usage in stressful road scenarios.
A cautionary tale (1991)

Recently we have been investigating various methods for improving the retrieval of documents. One frequently used context for such studies is to work with a known database and set of queries, where sufficient work has previously been done to establish an "official" set of relevant documents for each query. Working within such a context, we have discovered at least one instance wherein the combination of the document descriptions in the database, the query, and the set of documents deemed relevant foredooms our attempts at retrieval improvement to failure. This note is to caution other researchers against such possibilities, and to recommend that the database in question, that of the National Physical Laboratory (NPL), as represented on Virginia Disk 1, be retired from use.
A model for thyroid hormone-receptor interactions (1979)

Theoretical electronic structure calculations on the thyroid hormones and analogues, as well as model hormone--receptor interactions, have been carried out. These studies (a) support the concept that the 4'-OH group is a H-bond donor to the in vivo nuclear receptor and suggest that at the receptor this OH group is trans to the 3' (distal) substituent; (b) indicate that there is an important intramolecular interaction between 3' and 4' substituents, and those 3' substituents that most favor both 4' OH orientation trans to the 3' group and a more acidic OH group substantially increase binding and biological activity; and (c) support the concept that there is a direct correlation between the conformational free energy of the aromatic rings and biological activity.
Incorporating a Secure Coprocessor in the Database-as-a-Service Model (2006)

In this paper, we suggest an extension to the database-as-a-service (DAS) model that introduces a secure coprocessor (SC) at an untrusted database service provider in order to overcome drawbacks in the plain DAS model. The processor serves as a neutral party between the clients and service providers with the goal of increasing security of outsourced data. Additionally, it supports a much broader range of queries performed and reduces both bandwidth and computational burdens on the client. We expect these improvements to make the DAS model more viable and attractive from a client's perspective.
Velocity inversion using a stratified reference (1985)

Abstract We present an inversion algorithm for backscattered ('stacked') seismic data which will reconstruct the velocity profile in realistic earth conditions. The basic approach follows that of the original (constant reference speed) Cohen and Bleistein paper (1979a) in that high-frequency asymptotics and perturbation methods are used. However, we use a reference speed which may vary with depth, and this greatly enhances the validity of the perturbation assumption and hence the inversion results. The new algorithm enjoys the same economies and stability properties of the original algorithm, making it very competitive with current migration schemes.Four major assumptions are made: (1) the acoustic wave equation is an adequate model; (2) stacked data have amplitude information worth preserving fairly accurately; (3) the actual reflectivity coefficients can be adequately modeled as perturbations from a continuous reference velocity which depends only on the depth variable; and (4) the subsurface can be adequately modeled as a series of layers with jump discontinuities in the velocity (or impedance) at the interfaces.While the algorithm is particularly suited for data generated by a number of reflecting surfaces, its validity for a single reflector is demonstrated by applying the algorithm to Kirchhoff data for a quite general surface.A key feature of the approach used is the repeated application of high-frequency asymptotic methods. A noteworthy point is that the underlying integral equation is in the form of a generalized Fourier integral equation; the method for its (approximate) inversion may prove to be applicable to a wide range of such problems.
Conserved patterns of protein interaction in multiple species (2005)

To elucidate cellular machinery on a global scale, we performed a multiple comparison of the recently available protein-protein interaction networks of Caenorhabditis elegans, Drosophila melanogaster, and Saccharomyces cerevisiae. This comparison integrated protein interaction and sequence information to reveal 71 network regions that were conserved across all three species and many exclusive to the metazoans. We used this conservation, and found statistically significant support for 4,645 previously undescribed protein functions and 2,609 previously undescribed protein interactions. We tested 60 interaction predictions for yeast by two-hybrid analysis, confirming approximately half of these. Significantly, many of the predicted functions and interactions would not have been identified from sequence similarity alone, demonstrating that network comparisons provide essential biological information beyond what is gleaned from the genome.
Adaptive beamforming for photoacoustic imaging using linear array transducer (2008)

Photoacoustic signals, detected by a transducer array, need to be beamformed for subsequent use in a limited view angle tomography such as B-scan imaging. In the presence of the light scattering or phase aberration, the spatial resolution and contrast in the photoacoustic images are degraded. Phase aberration due to tissues with inhomogeneous acoustic speeds is a major source for image degradation. However, a constant speed of sound (e.g., 1540 m/s) is typically assumed in photoacoustic imaging. Such an assumption can affect the quality of photoacoustic image since changes in sound velocity cause significant phase errors in beamforming. An adaptive weighting method such as coherence factor (CF) technique can improve the ultrasound and photoacoustic image quality significantly. In addition, photoacoustic images can be further improved by applying adaptive beamforming techniques developed for ultrasound imaging. In this study, an adaptive photoacoustic image reconstruction technique that combines an adaptive weighting factor (CF) and an adaptive apodization called minimum variance method (MV) is introduced. Although MV method calculates the optimal apodization weighting factors which minimize the variance of the beamformed signal, it can lead to unexpected weighting factors since it is data dependant. In this case, CF weighting can help to avoid this problem by weighting the output from the MV method based on signal coherence. Simulations were performed to analyze the spatial resolution using a point targets and to demonstrate improvement in phase aberration correction. Numerical studies demonstrated the superior performance of MV adaptive method combined with CF weighting.
Second Generation of Hydroxyethylamine BACE-1 Inhibitors: Optimizing Potency and Oral Bioavailability (2008)

BACE-1 inhibition has the potential to provide a disease-modifying therapy for the treatment of Alzheimer's disease. Optimization of a first generation of BACE-1 inhibitors led to the discovery of novel hydroxyethylamines (HEAs) bearing a tricyclic nonprime side. These derivatives have nanomolar cell potency and are orally bioavailable.