gebhart/patrepeval huggingface dataset:
STRATEGIC PLANNING, IMPACT ASSESSMENT, AND TECHNICAL AID: THE SOUSS-MASSA INTEGRATED WATER MANAGEMENT PROJECT (2004)

Government agencies, like individuals, can "lose sight" of the impacts of their policies on natural and social systems. Environmental impact analysis (EIA), strategic environmental analysis (SEA), and strategic planning are all aspects of analyzing and projecting the impacts of various management decisions on the public and on natural systems. Integrated river-basin management is another aspect of this type of planning. Integrated management requires several basic conditions. Among these are clear communications among all the actors involved in managing the basin's water resources, one or more sets of data which are shared by all decision-makers, and tools by which the decision-makers can evaluate policies (impact assessment). In the Souss Massa River Basin in Morocco, the result of un-coordinated policies for economic development has led to declining water tables as well as potentially damaging surface and groundwater pollution. The Government of Morocco (GOM), recognizing the need for coordinated and integrated water management, passed a law creating new River Basin Agencies. Aiding those agencies and their partners in developing integrated management is the objective of the USAID-sponsored Souss-Massa Integrated Water Management (SIWM) project. The project activities have been designed to develop and support communications, data sharing and model building within the institutions in the Souss-Massa Basin as a demonstration for all Moroccan river basins but space and time constraints require a more pointed discussion. The focus of this paper is on capacity building for strategic planning and integrated management being undertaken and, to the extent possible, some of the lessons learned.
The production of human parvovirus capsid proteins in Escherichia coli and their potential as diagnostic antigens (1990)

We have expressed a number of polypeptides derived from the capsid proteins of the human parvovirus B19 in Escherichia coli. These include native VP1 (84K) and VP2 (58K) proteins and also fusions to beta-galactosidase containing differing amounts of the amino terminus of the VP1/2 polypeptide. Although each of these was expressed at high levels and the majority were produced as full-length proteins, only one was soluble. This soluble polypeptide, p132, is a beta-galactosidase fusion protein that includes 145 amino acids from B19 which are entirely derived from the region unique to VP1. Despite containing such a small portion of VP1, which itself constitutes only 4% of total capsid protein, p132 reacted with all our known anti-B19 IgM-positive human serum samples. We conclude that this region contains epitopes which must be prominently exposed on the intact virus. We have demonstrated the use of this recombinant antigen in a simple diagnostic assay for B19-specific antibodies which can be used for initial screening of human serum samples. In a survey of 103 serum specimens, our ELISA positively identified all samples (19/19) which were positive by IgM antibody capture radioimmunoassay. The recombinant p132 antigen is efficiently produced and readily purified from E. coli, and its use as a diagnostic antigen should increase the availability of routine clinical testing for human parvovirus infection.
VERIFICATION PLANNING TO FUNCTIONAL CLOSURE OF PROCESSOR-BASED SoCs (2006)

Functional verification consumes more than 70 % of the labor invested in today’s SoC designs. Yet, even with such a large investment in verification, there’s more risk of functional failure at tapeout than ever before. The primary reason is that the design team does not know where they are, in terms of functional correctness, relative to the tapeout goal. They lack a functional verification map for reference that employs coverage as its primary element. Coverage, in the broadest sense, is responsible for measuring verification progress across a plethora of metrics and for helping engineers assess their location relative to design completion.[1] The map to be referenced must be created by the design team upfront, so they know not only where they are starting from-specification but no implementationbut also where they are going: fully functional first silicon. The metrics of the map must be chosen for their utility: RTL written, software written, features, properties, assertion count, simulation count, failure rate, and coverage closure rate. The map is the verification plan, an executable natural language document [2],[3] that defines the scope of the verification problem and its solution. The scope of the problem is defined by implicit and explicit coverage models.[1] The solution to the verification problem is described by the methodology employed to achieve full coverage: dynamic and static verification. Simulation (dynamic) contributes to coverage closure through RTL execution. Formal analysis (static) contributes to coverage closure through proven properties. By annotating the verification plan with these (and other) progress metrics, it becomes a live, executable document that directs the design team to their goal. Most verification planning today lacks the rigor required to recognize the full scope of the verification problem faced by the design team. The reason for this is that substantial effort is required to write a thorough verification plan. If that plan is obsolete as soon as it is written, the effort is not justified. However, by transforming the verification plan into an active specification that controls the verification process, the planning effort is more than justified. This article illustrates the application of an executable verification plan to a processor-based SoC.
The VideoToolbox software for visual psychophysics: transforming numbers into movies (1997)

The VideoToolbox is a free collection of two hundred C subroutines for Macintosh computers that calibrates and controls the computer-display interface to create accurately specified visual stimuli. High-level platform-independent languages like MATLAB are best for creating the numbers that describe the desired images. Low-level, computer-specific VideoToolbox routines control the hardware that transforms those numbers into a movie. Transcending the particular computer and language, we discuss the nature of the computer-display interface, and how to calibrate and control it.
A Framework for Local Anonymity in the Internet (1997)

We describe and evaluate options for providing anonymous IP service, argue for the further investigation of local anonymity, and sketch a framework for the implementation of locally anonymous networks. 1 Introduction Anonymity is not the same as confidentiality. Existing systems such as IPSEC can ably protect the contents of IP-based communication [Atk95, Pos81b], making it impractical for network eavesdroppers to deduce the purpose of observed traffic. However, the fact of the traffic itself is not hidden; the sender and receiver of each packet is clearly visible in the packet headers even when the packet is end-to-end encrypted. Such information should sometimes be protected as well. Suppose that Alice, the CEO of Apricot, decides to buy out the publicly-traded firm Banananon. When other Apricot officers learn of the plans, the subsequent flurry of connections from the executive suite to the Banananon&amp;apos;s web site could betray Alice&amp;apos;s intent. If Alice&amp;apos;s network administrator Eve react...
Unidirectional fluxes of rhodamine 123 in multidrug-resistant cells: evidence against direct drug extrusion from the plasma membrane. (1994)

P-glycoprotein (Pgp), a plasma membrane protein overexpressed in multidrug-resistant tumor cells, is an ATPase thought to actively export cytotoxic drugs. It has been proposed that Pgp transports drugs directly from the lipid bilayer to the external medium ("vacuum cleaner" hypothesis). A possible mechanism for this model is that the Pgp is a flippase--i.e., it catalyzes the translocation of hydrophobic substrates from the inner to the outer leaflet of the cell membrane. Two immediate predictions of the vacuum cleaner and flippase hypotheses are that the apparent unidirectional influx of substrate should be less in Pgp-expressing than in Pgp-lacking cells and that this difference should be abolished by inhibition of the Pgp. We used Chinese hamster fibroblasts with different levels of Pgp expression to measure true unidirectional fluxes of rhodamine 123 (R123), a Pgp-transported fluorescent dye that accumulates in mitochondria (hence, its cytosolic concentration remains low at short times after external addition). The unidirectional efflux of R123 was proportional to the level of Pgp expression and was reduced by Pgp inhibitors. The unidirectional influx of R123 was the same in sensitive and resistant cells--i.e., independent of the level of Pgp expression and insensitive to inhibitors of R123 efflux. From these results, we rule out the vacuum cleaner and flippase hypotheses and conclude that Pgp extracts the actively transported substrates from the cytosol and not from the plasma membrane.
Pseudo-Cyclization through Intramolecular Hydrogen Bond Enables Discovery of Pyridine Substituted Pyrimidines as New Mer Kinase Inhibitors (2013)

Abnormal activation or overexpression of Mer receptor tyrosine kinase has been implicated in survival signaling and chemoresistance in many human cancers. Consequently, Mer is a promising novel cancer therapeutic target. A structure-based drug design approach using a pseudo-ring replacement strategy was developed and validated to discover a new family of pyridinepyrimidine analogues as potent Mer inhibitors. Through SAR studies, 10 (UNC2250) was identified as the lead compound for further investigation based on high selectivity against other kinases and good pharmacokinetic properties. When applied to live cells, 10 inhibited steady-state phosphorylation of endogenous Mer with an IC50 of 9.8 nM and blocked ligand-stimulated activation of a chimeric EGFR-Mer protein. Treatment with 10 also resulted in decreased colony-forming potential in rhabdoid and NSCLC tumor cells, thereby demonstrating functional antitumor activity. The results provide a rationale for further investigation of this compound for therapeutic application in patients with cancer.
Downregulation of c-myc expression by antisense oligonucleotides inhibits proliferation of human smooth muscle cells. (1993)

c-myc antisense oligomers reduced c-myc expression and produced a significant growth inhibition of human SMCs, indicating an important role of c-myc gene activation in the process of SMC proliferation. Furthermore, extracellular stability and rapid cellular uptake provide the basis for future studies assessing the therapeutic role of the c-myc antisense approach in reducing SMC proliferation in the process of vascular restenosis.
Settlement in the Absence of Anticipated Adjudication (2017)

This Article begins with an account of the lawyer’s role in settlement in what we might call the traditional litigation scenario—that is, litigation in which settlement negotiations are conducted in the shadow of anticipated adjudication. This Article then considers four scenarios in which the anticipation of adjudication is altered—resource inadequacy, judicial settlement pressure, lengthy calendar, and class actions not certified for litigation—and asks what effect we should expect each scenario to have on the interests of lawyers and clients regarding settlement. The final part asks what light this analysis sheds on the phenomenon of vanishing trials and concludes with a comment on the importance of anticipated adjudication to achieving justice in litigation settlements.
Erythropoietin bioassays using fetal mouse liver cells: validations and technical improvements. (1983)

Studies are described which were designed to compare an erythropoietin (Ep) bioassay using the uptake of 125I-deoxyuridine (125-I-UdR) into whole cells cultured in micro-titer plates with an established method where the cells were cultured in 1 ml volumes using the incorporation of 59Fe into heme as the endpoint. The results demonstrate the validity of the substitution of 125I-UdR uptake into whole cells as a replacement for 59Fe incorporation into heme as an assay endpoint and the adaptation of the method to a semi-micro scale with automated cell harvesting. A culture time significantly shorter than 24 h is demonstrated not to be of practical benefit. Two methods are proposed to saturate the growth promoting effects of iron-containing transferrin. The performance of semi-micro, serum-containing bioassay employing untreated serum as the test material is shown to be superior to previous systems for the biological measurement of Ep.
The SWISS-PROT protein sequence data bank, recent developments (1993)

Journal Article The SWISS-PROT protein sequence data bank, recent developments Get access Amos Bairoch, Amos Bairoch Search for other works by this author on: Oxford Academic PubMed Google Scholar Brigitte Boeckmann Brigitte Boeckmann 1European Molecular Biology LaboratoryHeidelberg, Germany Search for other works by this author on: Oxford Academic PubMed Google Scholar Nucleic Acids Research, Volume 21, Issue 13, 1 July 1993, Pages 3093–3096, https://doi.org/10.1093/nar/21.13.3093 Published: 01 July 1993
Induction of lung and exocrine pancreas tumors in F344 rats by tobacco-specific and Areca-derived N-nitrosamines. (1988)

The tobacco-specific N-nitrosamines 4-(methylnitrosamino)-1-(3-pyridyl)-1-butanone (NNK) and 4-(methylnitrosamino)-1-(3-pyridyl)-1-butanol (NNAL), as well as the Areca-derived N-nitrosoguvacoline (NG) were assayed for carcinogenicity in male F344 rats by lifetime administration in the drinking water. Groups of 30 to 80 rats were treated with 0.5 ppm, 1.0 ppm, or 5.0 ppm of NNK; 5.0 ppm of NNAL, 20 ppm of NG, a mixture of 20 ppm of NG and 1 ppm of NNK, and water only in the control group. The approximate total doses of the nitrosamines (mmol/kg of body weight) in these groups were: NNK, 0.073, 0.17, and 0.68; NNAL, 0.69; NG, 4.1; NG and NNK, 4.1 and 0.17. As in previous assays in which NNK was tested by s.c. injection, the lung was its principle target organ. Lung tumor incidences in the 0.5-, 1.0-, and 5.0-ppm groups were nine of 80, 20 of 80, and 27 of 30 compared to six of 80 in the control rats. This trend was significant, P less than 0.005. Significant incidences of nasal cavity and liver tumors were observed only in the rats treated with 5.0 ppm of NNK. In contrast to the results of the s.c. bioassays of NNK, tumors of the exocrine pancreas were observed in five of 80 and nine of 80 rats treated with 0.5 and 1.0 ppm. This trend was significant, P less than 0.025. This is the first example of pancreatic tumor induction by a constituent of tobacco smoke. It is also the first finding of duct-like carcinomas in the rat pancreas, including one tumor containing epidermoid, keratin-generating tissue. NNAL, the major metabolite of NNK, induced lung tumors in 26 of 30 rats and pancreatic tumors in eight of 30 rats. It appears to be the proximate pancreatic carcinogen of NNK. NG induced pancreatic tumors in four of 30 rats, P less than 0.05. This finding requires confirmation. The mixture of NG and NNK induced lung tumors in eleven of 30 rats. There were no apparent synergistic interactions of NG and NNK. The observation of benign and malignant tumors of the lung and pancreas of rats treated with the tobacco-specific nitrosamines NNK and NNAL is discussed in respect to the causal association between cigarette smoking and cancer of the lung and pancreas.
Influenza A(H7N9) virus gains neuraminidase inhibitor resistance without loss of in vivo virulence or transmissibility (2013)

Without baseline human immunity to the emergent avian influenza A(H7N9) virus, neuraminidase inhibitors are vital for controlling viral replication in severe infections. An amino acid change in the viral neuraminidase associated with drug resistance, NA-R292K (N2 numbering), has been found in some H7N9 clinical isolates. Here we assess the impact of the NA-R292K substitution on antiviral sensitivity and viral replication, pathogenicity and transmissibility of H7N9 viruses. Our data indicate that an H7N9 isolate encoding the NA-R292K substitution is highly resistant to oseltamivir and peramivir and partially resistant to zanamivir. Furthermore, H7N9 reassortants with and without the resistance mutation demonstrate comparable viral replication in primary human respiratory cells, virulence in mice and transmissibility in guinea pigs. Thus, in stark contrast to oseltamivir-resistant seasonal influenza A(H3N2) viruses, H7N9 virus replication and pathogenicity in these models are not substantially altered by the acquisition of high-level oseltamivir resistance due to the NA-R292K mutation.
Nucleic Acid Vaccine-Induced Immune Responses Require CD28 Costimulation and Are Regulated by CTLA4 (1998)

Immunization with plasmids expressing specific genes (DNA or nucleic acid vaccination (NAV)) elicits robust humoral and cell-mediated immune responses. The mechanisms involved in T cell activation by NAV are incompletely characterized. We have examined the costimulatory requirements of NAV. CD28-deficient mice did not mount Ab or CTL responses following i.m. immunization with eukaryotic expression plasmids encoding the bacterial gene beta-galactosidase (beta gal). Because these mice retained their ability to up-regulate the CTLA4 receptor (a negative regulator of T cell activation), we examined CTLA4's role in the response of wild-type BALB/c mice to NAV. Intact anti-CTLA4 mAb but not Fab fragments suppressed the primary humoral response to pCIA/beta gal without affecting recall responses, indicating CTLA4 activation inhibited Ab production but not T cell priming. Blockade of the ligands for CD28 and CTLA4, CD80 (B7-1) and CD86 (B7-2), revealed distinct and nonoverlapping function. Blockade of CD80 at initial immunization completely abrogated primary and secondary Ab responses, whereas blockade of CD86 suppressed primary but not secondary responses. Simultaneous blockade of CD80 + CD86 was less effective at suppressing Ab responses than either alone. Enhancement of costimulation via coinjection of B7-expressing plasmids augmented CTL responses but not Ab responses, and without evidence of Th1 to Th2 skewing. These findings suggest complex and distinct roles for CD28, CTLA4, CD80, and CD86 in T cell costimulation following nucleic acid vaccination.
Evolution and characterization of a benzylguanine-binding RNA aptamer (2015)

Repurposing the "protein-labeling toolkit" for RNA research could be a pragmatic approach for developing new RNA-labeling methods. We have evolved an RNA aptamer that tightly binds benzylguanine (bG), the key ligand for the protein SNAP-tag. The aptamer tightly binds bG fluorophores and can be purified from cellular RNA with bG agarose under native conditions.
Fluvoxamine alleviates ER stress via induction of Sigma-1 receptor (2014)

We recently demonstrated that endoplasmic reticulum (ER) stress induces sigma-1 receptor (Sig-1R) expression through the PERK pathway, which is one of the cell's responses to ER stress. In addition, it has been demonstrated that induction of Sig-1R can repress cell death signaling. Fluvoxamine (Flv) is a selective serotonin reuptake inhibitor (SSRI) with a high affinity for Sig-1R. In the present study, we show that treatment of neuroblastoma cells with Flv induces Sig-1R expression by increasing ATF4 translation directly, through its own activation, without involvement of the PERK pathway. The Flv-mediated induction of Sig-1R prevents neuronal cell death resulting from ER stress. Moreover, Flv-induced ER stress resistance reduces the infarct area in mice after focal cerebral ischemia. Thus, Flv, which is used frequently in clinical practice, can alleviate ER stress. This suggests that Flv could be a feasible therapy for cerebral diseases caused by ER stress.
Isolated allogeneic bone marrow-derived mesenchymal cells engraft and stimulate growth in children with osteogenesis imperfecta: Implications for cell therapy of bone (2002)

Treatment with isolated allogeneic mesenchymal cells has the potential to enhance the therapeutic effects of conventional bone marrow transplantation in patients with genetic disorders affecting mesenchymal tissues, including bone, cartilage, and muscle. To demonstrate the feasibility of mesenchymal cell therapy and to gain insight into the transplant biology of these cells, we used gene-marked, donor marrow-derived mesenchymal cells to treat six children who had undergone standard bone marrow transplantation for severe osteogenesis imperfecta. Each child received two infusions of the allogeneic cells. Five of six patients showed engraftment in one or more sites, including bone, skin, and marrow stroma, and had an acceleration of growth velocity during the first 6 mo postinfusion. This improvement ranged from 60% to 94% (median, 70%) of the predicted median values for age- and sex-matched unaffected children, compared with 0% to 40% (median, 20%) over the 6 mo immediately preceding the infusions. There was no clinically significant toxicity except for an urticarial rash in one patient just after the second infusion. Failure to detect engraftment of cells expressing the neomycin phosphotransferase marker gene suggested the potential for immune attack against therapeutic cells expressing a foreign protein. Thus, allogeneic mesenchymal cells offer feasible posttransplantation therapy for osteogenesis imperfecta and likely other disorders originating in mesenchymal precursors.
Purification and Properties of Fatty Acyl Thioesterase I from Escherichia coli (1972)

247, No. 10 Fisher Chemical Co.supplied phenol reagent and glycolic acid
Early termination schemes for fast intra mode decision in High Efficiency Video Coding (2013)

The emerging High-Efficiency Video Coding video coding standard has shown the significant coding performance improvement compared to the H.264/AVC with the cost of huge complexity increase. Hence, HEVC fast encoding algorithms are highly demanded for real-time applications. In this paper, we propose several early termination schemes for fast intra prediction in HEVC. More specifically, variation of coding mode costs are used to terminate current coding unit (CU) mode decision as well as TU size selection, where the CU costs are derived at the rough mode decision phase using Hadamard transform. Neighboring modes' costs are also used to skip full rate-distortion optimized quantization (RDOQ). For all available test sequences provided by the JCT-VC, it demonstrates about 32% encoding time reduction for All Intra configuration with BD-RATE increase about 1.1%. Our proposal is complementary to some of other fast intra prediction methods such as fast rough mode decision. We expect more encoder speedup by integrating our method with other published works.
Generation of transplantable, functional satellite‐like cells from mouse embryonic stem cells (2009)

Satellite cells are myogenic stem cells responsible for the postnatal regeneration of skeletal muscle. Here we report the successful in vitro induction of Pax7-positive satellite-like cells from mouse embryonic stem (mES) cells. Embryoid bodies were generated from mES cells and cultured on Matrigel-coated dishes with Dulbecco's modified Eagle medium containing fetal bovine serum and horse serum. Pax7-positive satellite-like cells were enriched by fluorescence-activated cell sorting using a novel anti-satellite cell antibody, SM/C-2.6. SM/C-2.6-positive cells efficiently differentiate into skeletal muscle fibers both in vitro and in vivo. Furthermore, the cells demonstrate satellite cell characteristics such as extensive self-renewal capacity in subsequent muscle injury model, long-term engraftment up to 24 wk, and the ability to be secondarily transplanted with remarkably high engraftment efficiency compared to myoblast transplantation. This is the first report of transplantable, functional satellite-like cells derived from mES cells and will provide a foundation for new therapies for degenerative muscle disorders.