gebhart/patrepeval huggingface dataset:
Parathyroid Hormone-Related Protein Is an Essential Growth Factor for Human Clear Cell Renal Carcinoma and a Target for the von Hippel-Lindau Tumor Suppressor Gene (2004)

Clear cell renal carcinoma (CCRC) is responsible for 2% of cancer-related deaths worldwide and is resistant to virtually all therapies, indicating the importance of a search for new therapeutic targets. Parathyroid hormone-related protein (PTHrP) is a polyprotein derived from normal and malignant cells that regulates cell growth. In the current study, we show that blocking PTHrP with antibodies or antagonizing the common parathyroid hormone (PTH)/PTHrP receptor, the PTH1 receptor, dramatically blunts the expansion of human CCRC in vitro by promoting cell death. Importantly, in nude mice, anti-PTHrP antibodies induced complete regression of 70% of the implanted tumors by inducing cell death. In addition, we demonstrate that the von Hippel-Lindau tumor suppressor protein, which functions as a gatekeeper for CCRC, negatively regulates PTHrP expression at the post-transcriptional level. These studies indicate that PTHrP is an essential growth factor for CCRC and is a novel target for the von Hippel-Lindau tumor suppressor protein. Taken together, these results strongly suggest that targeting the PTHrP/PTH1 receptor system may provide a new avenue for the treatment of this aggressive cancer in humans.
Embracing change with extreme programming (1999)

Traditional software engineering means have been characterized by a rather predictable process in the past. Users tell once and for all exactly what they want. Programmers design the system that will deliver those features. They code it; test it, and all is well. But all was not always well. The users did not tell once and for all exactly what they wanted. They changed their minds, and the users were not the only problem. Programmers could misjudge their progress. The academic software engineering community took the high cost of changing software as a challenge, creating technologies like relational databases, modular programming, and information hiding. This is where extreme programming comes in. Rather than planning, analyzing, and designing for the far-flung future, XP exploits the reduction in the cost of changing software to do all of these activities a little at a time, throughout software development. The paper discusses the major practices of XP.
Offloading in Mobile Edge Computing: Task Allocation and Computational Frequency Scaling (2017)

In this paper, we propose an optimization framework of offloading from a single mobile device (MD) to multiple edge devices. We aim to minimize both total tasks' execution latency and the MD's energy consumption by jointly optimizing the task allocation decision and the MD's central process unit (CPU) frequency. This paper considers two cases for the MD, i.e., fixed CPU frequency and elastic CPU frequency. Since these problems are NP-hard, we propose a linear relaxation-based approach and a semidefinite relaxation (SDR)-based approach for the fixed CPU frequency case, and an exhaustive search-based approach and an SDR-based approach for the elastic CPU frequency case. Our simulation results show that the SDR-based algorithms achieve near optimal performance. Performance improvement can be obtained with the proposed scheme in terms of energy consumption and tasks' execution latency when multiple edge devices and elastic CPU frequency are considered. Finally, we show that the MD's flexible CPU range can have an impact on the task allocation.
Enrichment of Bovine X and Y Spermatozoa by Free‐Flow Electrophoresis (1994)

Conditions of separation of bovine spermatozoa according to their differences in electrophoretic mobility were studied using free-flow electrophoresis. Distribution of spermatozoa in the electric field depends on composition of buffer system, field intensities and temperature. Conditions are described for reproducible separation of anodically migrating spermatozoa into two distinct peaks both for cold-immobilized (10-13 degrees C) and for motile cells (25 degrees C). Electrophoresis with the buffer used at 25 degrees C and field intensities of 70-100 V/cm provided high percentages of motile spermatozoa (50-90%) in all fractions. However, the sperm distribution across the fractions was the result of superimposed passive electrophoretic motion towards the anode and the active galvanotactic migration towards the cathode. Separation of X- and Y-spermatozoa was verified by quantification of Y-spermatozoa by means of both in situ hybridization, using Y-specific DNA fragments, and the Y-specific fluorescence staining (f-body test). Y-spermatozoa could be enriched in anodic fractions (112 and 144% relative to control). X-spermatozoa were enriched in cathodic fractions (80 and 68% Y-spermatozoa, as compared to control).
A Multiple-Gate CCD-Photodiode Sensor Element for Imaging Arrays (1978)

The addition of barrier and storage gates between the photodiodes and transfer gates of a CCD imaging array provides improved and versatile operating characteristics compared with present silicon scanners. An experimental scanner, made with multiple-gate photoelements, has new functional capabilities which result from the on-chip structure. These include exposure control in real-time which can compensate for temporal illumination variations during the integration cycle, linearization of the output signal with respect to light intensity, and adaptive level setting to normalize the output based on the whitest portion of the image. Complete charge transfer into the shift register is achieved at reduced shift-register voltages. The use of photodiodes and the absence of polysilicon in the photosensitive region improve spectral response and overall sensitivity. A sixteen element 4-phase, 2-level polysilicon CCD imager was designed, fabricated, and used to test the improved photoelement structure.
Evaluation of ZK110841 and AH6809, an agonist and an antagonist of prostaglandin DP‐receptors on human platelets, with a PGD<sub>2</sub>‐responsive cell line from bovine embryonic trachea (1990)

ZK110841 and AH6809, an agonist and an antagonist of prostaglandin DP-receptors on human platelets, were evaluated with a fibroblastic cell line from bovine embryonic trachea (EBTr) which specifically responds to prostaglandin D2 (PGD2). ZK110841, equipotent to PGD2, elevated the adenosine 3':5'-cyclic monophosphate (cyclic AMP) level in EBTr cells dose-dependently, being more than 100 fold over the basal level at 1 microM. The half-maximally effective concentration of PGD2 or ZK110841 was 10-30 nM. Increasing concentrations (10(-7)-10(-4) M) of AH6809 (which possesses negligible intrinsic agonist activity) produced parallel shifts to the right of dose-response curves to PGD2 and ZK110841. Schild plots of these data were linear (correlation close to unity) and pA2 values against PGD2 and ZK110841 were calculated to be 6.36 and 6.57, respectively, indicating that AH6809 is a simple and competitive antagonist. These results demonstrate that ZK110841, AH6809 and EBTr cells will be useful for characterization of DP-receptors.
Routing and interface assignment in multi-channel multi-interface wireless networks (2005)

Multiple channels are available for use in IEEE 802.11. Multiple channels can increase the available network capacity, but require new protocols to exploit the available capacity. This paper studies the problem of improving the capacity of multi-channel wireless networks by using multiple interfaces. We consider the scenario when multiple interfaces are available, but the number of available interfaces is lesser than the number of available channels. We provide a classification of interface assignment strategies, and propose a new strategy that does not require modifications to IEEE 802.11. We also identify routing heuristics that are suitable for use with the proposed interface assignment strategy.
Keyword search in text cube: Finding top-k relevant cells (2010)

Abstract. We study the problem of keyword search in a data cube with text-rich dimension(s) (so-called text cube). The text cube is built on a multidimensional text database, where each row is associated with some text data (e.g., a document) and other structural dimensions (attributes). A cell in the text cube aggregates a set of documents with matching attribute values in a subset of dimensions. A cell document is the concatenation of all documents in a cell. Given a keyword query, our goal is to find the top-k most relevant cells (ranked according to the relevance scores of cell documents w.r.t. the given query) in the text cube. We define a keyword-based query language and apply IR-style relevance model for scoring and ranking cell documents in the text cube. We propose two efficient approaches to find the top-k answers. The proposed approaches support a general class of IR-style relevance scoring formulas that satisfy certain basic and common properties. One of them uses more time for pre-processing and less time for answering online queries; and the other one is more efficient in pre-processing and consumes more time for online queries. Experimental studies on the ASRS dataset are conducted to verify the efficiency and effectiveness of the proposed approaches. 1.
Blimp-1-Dependent Repression of <i>Pax-5</i> Is Required for Differentiation of B Cells to Immunoglobulin M-Secreting Plasma Cells (2002)

B-cell lineage-specific activator protein (BSAP), encoded by the Pax-5 gene, is critical for B-cell lineage commitment and B-cell development but is not expressed in terminally differentiated B cells. We demonstrate a direct connection between BSAP and B-lymphocyte-induced maturation protein 1 (Blimp-1), a transcriptional repressor that is sufficient to drive plasmacytic differentiation. Blimp-1 binds a site on the Pax-5 promoter in vitro and in vivo and represses the Pax-5 promoter in a binding-site-dependent manner. By ectopically expressing Blimp-1 or a competitive inhibitor of Blimp-1, we show that Blimp-1 is both necessary and sufficient to repress Pax-5 during plasmacytic differentiation of primary splenic B cells. Blimp-1-dependent repression of Pax-5 is sufficient to regulate BSAP targets CD19 and J chain and is necessary but not sufficient to induce XBP-1. We further show that repression of Pax-5 is required for Blimp-1 to drive differentiation of splenocytes to immunoglobulin M-secreting cells. Thus, repression of Pax-5 plays a critical role in the Blimp-1-dependent program of plasmacytic differentiation.
Performance evaluation of random access in wireless networks with multiple destinations (2005)

Most studies of wireless random-access systems have addressed single-destination networks (e.g., an isolated base station in a cellular network). Here, we consider networks with multiple destinations, where transmissions intended for one destination can interfere with those intended for others. In our earlier work on stabilized slotted Aloha in a symmetrical two-destination system, we derived analytically an invariance result that states that the maximum overall throughput is obtained when the channel traffic is equal to one packet per slot at each of the two destinations. The value of throughput that is achieved at this optimal point depends on the degree of overlap between the two regions, i.e., on the level of interference at each destination that is caused by packets that were intended for the other destination. In this paper, we generalize our results by presenting a complete analysis for two-destination systems that are characterized by an interference model in which interference range exceeds communication range.
Anti–VLA4/VCAM-1—Induced Mobilization Requires Cooperative Signaling Through the kit/mkit Ligand Pathway (1998)

Although a large body of data on mobilization have yielded valuable clues, the mechanism(s) dictating egress of stem/progenitor cells during baseline hematopoiesis and after their mobilization are poorly understood. We have previously provided functional in vivo evidence that cytoadhesion molecules, specifically the beta1 integrins, are involved in mobilization; however, the mechanism by which this was achieved was unclear. To provide further insights into the anti-very late antigen 4 (VLA4)/anti-vascular cell adhesion molecule 1 (VCAM-1)-induced mobilization, we used these antibodies to treat mutant mice with compromised growth factor receptor function. We found that mobilization by anti-VLA4 does not depend on a functional granulocyte colony-stimulating factor, interleukin-7 (IL-7), or IL-3alpha receptor. By contrast, the functional kit receptor is required, because W/Wv mice responded minimally, whereas Steel-Dickie (Sl/Sld) responded normally. Both Wv and Sl/Sld mice did not respond to anti-VCAM-1 treatment, in contrast to their +/+ littermates and despite normal levels of VCAM-1 expression in bone marrow cells. The defective response to anti-VCAM-1 in W/Wv mice was corrected after their transplantation with +/+ cells. mev/mev mice showed increased numbers of circulating progenitors before treatment and a heightened response after anti-VLA4 or anti-VCAM-1 treatment. Downmodulation of kit expression was detected in normal bone marrow cells after anti-VLA4 treatment. On the strength of the above findings we conclude that (1) anti-VLA4/VCAM-1-induced mobilization likely requires signaling for stimulation of cell migration; (2) this cooperative signaling involves the kit/kit ligand pathway, and provides a novel example of integrin/cytokine crosstalk; and (3) migration mediated through the kit/kit ligand pathway may be a common contributor to different mobilization stimuli. Dissection of the exact molecular pathways that lead to mobilization remains a future challenge.
BMP4 promotes chondrocyte proliferation and hypertrophy in the endochondral cranial base (2003)

Defects in the growth and development of the endochondral bones that comprise the cranial base contribute to several craniofacial dysmorphic syndromes. Since Bone Morphogenetic Protein (BMP) signaling regulates chondrocyte differentiation and endochondral ossification in developing long bones, we have tested the hypothesis that BMP signaling also participates in regulating development of the cranial base. During in vivo developmental progression of the cranial base in mice, a burst of skeletal growth and chondrocyte maturation was identified in the perinatal period. Using a novel serum-free organ culture system, cranial base structures were cultured as explants in the presence of BMP4 or noggin, and analyzed for morphological and molecular changes. Growth of perinatal cranial base explants was inhibited by treatment with noggin, a BMP inhibitor. Exogenous BMP4 promoted cartilage growth, matrix deposition and chondrocyte proliferation in a dose dependent manner. Correspondingly, expression level of the cartilage markers Sox9 and collagen type II were also increased. Alkaline phosphatase and collagen type X expression were up-regulated and expressed in ectopic hypertrophic chondrocytes after treatment of the cultures with 100 ng/ml BMP4 for seven days. This increase in chondrocyte hypertrophy was accompanied by increased indian hedgehog (Ihh) and parathyroid hormone/parathyroid hormone related peptide (PTH/PTHrP) receptor (PPR) expression, but not increased PTHrP expression. We conclude that endogenous BMPs are required to maintain cartilage growth, and exogenous BMP4 can enhance cartilage maturation and induce ectopic chondrocyte hypertrophy in the cranial base. Therefore, appropriate levels of BMP signaling are important for normal cranial base development.
<title>Synthetic aperture radar imagery scene segmentation using fractal processing</title> (1992)

This paper demonstrates the application of fractal random process models and their related scaling parameters as features in the analysis and segmentation of clutter in high-resolution polarimetric synthetic aperture radar (SAR) imagery. Specifically, the fractal dimension of natural clutter sources, such as grass and trees, is computed and used as a texture feature for a Bayesian classifier. The SAR shadows are segmented in a separate manner using the original backscatter power as a discriminant. The proposed segmentation process yields a three-class segmentation map for the scenes considered in this study (with three clutter types: shadows, trees and grass). The difficulty of computing texture metrics in high-speckle SAR imagery is also addressed. In particular, a two-step preprocessing approach consisting of polarimetric minimum speckle filtering followed by non-coherent spatial averaging is used. The relevance of the resulting segmentation maps to constant-false-alarm-rate (CFAR) target detection techniques is also discussed.
Ongoing diversification of the rearranged immunoglobulin light-chain gene in a bursal lymphoma cell line. (1990)

The chicken immunoglobulin light-chain gene (IgL) encodes only a single variable gene segment capable of recombination. To generate an immune repertoire, chickens diversify this unique rearranged VL gene segment during B-cell development in the bursa of Fabricius. Sequence analysis of IgL cDNAs suggests that both gene conversion events derived from VL segment pseudogene templates (psi VL) and non-template-derived single-base-pair substitutions contribute to this diversity. To facilitate the study of postrecombinational mechanisms of immunoglobulin gene diversification, avian B-cell lines were examined for the ability to diversify their rearranged IgL gene during in vitro passage. One line that retains this ability, the avian leukosis virus-induced bursal lymphoma cell line DT40, has been identified. After passage for 1 year in culture, 39 of 51 randomly sequenced rearranged V-J segments from a DT40 population defined novel subclones of the parental tumor. All cloned V-J segments displayed the same V-J joint, confirming that the observed diversity arose after V-J rearrangement. Most sequence variations that we observed (203 of 220 base pairs) appeared to result from psi VL-derived gene conversion events; 16 of the 17 novel single nucleotide substitutions were transitions. Based on these data, it appears that immunoglobulin diversification during in vitro passage of DT40 cells is representative of the diversification that occurs during normal B-cell development in the bursa of Fabricius.
Gastric antisecretory and antiulcer/cytoprotective effects of 2-cyano-3-(ethylthio-3-methylthio)-2-propenoic acid methyl ester. (1989)

AY-28,200 (2-cyano-3-(ethylthio-3-methylthio)-2-propenoic acid methyl ester), a new gastric antisecretory/antiulcer agent, inhibited basal and pentagastrin-stimulated gastric acid secretion in the conscious rat (ED50 = 7.6 and 1.9 mg/kg i.g., respectively). For inhibition of basal secretion, peak activity was attained in 5 to 6 h after dosing and was maintained for more than 10 h, with no gastric antisecretory activity occurring at 24 h. The K+ stimulated H+-K+ ATPase activity from rabbit gastric microsomes was inhibited by AY-28,200 (IC50 = 22 mumol/l). AY-28,200 inhibited ethanol-induced gastric lesions, at 3 mg/kg p.o. AY-28,200's cytoprotective effects against ethanol lasted for more than 4 h. AY-28,200 blocked acetylsalicylic acid and stress-induced gastric ulcers but was inactive against indomethacin-induced gastric ulcers. These results suggest that AY-28,200 is a parietal cell proton pump inhibitor with cytoprotective properties, and may produce its cytoprotective effect by stimulating the formation of endogenous prostaglandins.
Randomized Discontinuation Design: Application to Cytostatic Antineoplastic Agents (2002)

The randomized discontinuation design is a feasible alternative phase II study design for determining activity of possibly cytostatic anticancer agents.
PERFORMANCE OF DIFFERENT ROLLER DESIGNS IN TERMINATING RYE COVER CROP AND REDUCING VIBRATION (2006)

Rollers may provide a viable alternative to herbicides for terminating cover crops; however, excessive vibrationgenerated by rollers and transferred to tractors hinders the adoption of this technology in the United States. To avoid excessivevibration, producers must limit their operational speed, which increases time and cost of rolling. The effect of speed on covercrop termination rate and vibration level was tested on several roller designs. Two field experiments were conducted withdifferent roller designs to terminate a cover crop of rye (Secale cereale L.). In the first experiment, three single-section rollerdesigns (long straight bars, curved blunt bars, and a smooth roller with an oscillating crimping bar) were tested at 1.6, 4.8,and 8 km/h operating speeds. In the second experiment, two triple-section commercial width rollers, one with long straightbars and the other, a smooth roller with an oscillating crimping bar, were tested at speeds 3.2 and 6.4 km/h. Data from thefirst experiment showed that all three roller designs terminated at levels greater than 90% with the highest termination rateproduced by the smooth roller with crimping bar (93.4%). Three weeks after rolling, termination rates varied from 88.3% to94.0% for all designs and speed ranges, all of which were sufficient mortality rates for rye before planting a cash crop withoutneed to use herbicide. Reduced vibration levels measured on the tractors frame were generated by the smooth roller withoscillating crimping bar with the highest vibration levels being generated by the roller with the straight bars. In the secondexperiment, three weeks after rolling significantly higher rye termination rates resulted from the roller with long straight bars(96%) in comparison with the smooth roller (94%). Despite these differences, both rollers effectively terminated rye priorto planting without use of herbicides. The smooth roller with crimping bar transferred significantly lower vibration levels tothe tractors frame than long straight bar roller at both speeds but vibration levels exceeded acceptable health and comfortlevels.
Optimization of Azoles as Anti-Human Immunodeficiency Virus Agents Guided by Free-Energy Calculations (2008)

Efficient optimization of an inactive 2-anilinyl-5-benzyloxadiazole core has been guided by free energy perturbation (FEP) calculations to provide potent non-nucleoside inhibitors of human immunodeficiency virus (HIV) reverse transcriptase (NNRTIs). An FEP "chlorine scan" was performed to identify the most promising sites for substitution of aryl hydrogens. This yielded NNRTIs 8 and 10 with activities (EC50) of 820 and 310 nM for protection of human T-cells from infection by wild-type HIV-1. FEP calculations for additional substituent modifications and change of the core heterocycle readily led to oxazoles 28 and 29, which were confirmed as highly potent anti-HIV agents with activities in the 10-20 nM range. The designed compounds were also monitored for possession of desirable pharmacological properties by use of additional computational tools. Overall, the trends predicted by the FEP calculations were well borne out by the assay results. FEP-guided lead optimization is confirmed as a valuable tool for molecular design including drug discovery; chlorine scans are particularly attractive since they are both straightforward to perform and highly informative.