gebhart/patrepeval huggingface dataset:
Exposure controlled projection lithography for microlens fabrication (2012)

An Exposure Controlled Projection Lithography (ECPL) process with the ability to fabricate microlenses on transparent substrates is presented. This process (also referred to as maskless lithography) can be used to create polymer microlenses on flat or curved substrates without involving hard tooling. Incident radiation, patterned by a dynamic mask, passes through a transparent substrate to cure photopolymer resin that grows progressively from the substrate surface. A process planning algorithm which incorporates the effects of optical aberrations present in the ECPL system and photopolymer's response to irradiation is presented. An interferometric process monitoring system is also presented which can be used to control the process in real time. Samples of micro optical elements fabricated on flat and non-planar substrates using the ECPL system are also presented, which demonstrate the wide range of fabrication capability of our ECPL process.
Potent and Selective Phosphopeptide Mimetic Prodrugs Targeted to the Src Homology 2 (SH2) Domain of Signal Transducer and Activator of Transcription 3 (2011)

Signal transducer and activator of transcription 3 (Stat3), a target for anticancer drug design, is activated by recruitment to phosphotyrosine residues on growth factor and cytokine receptors via its SH2 domain. We report here structure-activity relationship studies on phosphopeptide mimics targeted to the SH2 domain of Stat3. Inclusion of a methyl group on the β-position of the pTyr mimic 4-phosphocinnamide enhanced affinity 2- to 3-fold. Bis-pivaloyloxymethyl prodrugs containing β-methylcinnamide, dipeptide scaffolds Haic and Nle-cis-3,4-methanoproline, and glutamine surrogates were highly potent, completely inhibiting phosphorylation of Stat3 Tyr705 at 0.5-1 μM in a variety of cancer cell lines. The inhibitors were selective for Stat3 over Stat1, Stat5, Src, and p85 of PI3K, indicating ability to discriminate individual SH2 domains in intact cells. At concentrations that completely inhibited Stat3 phosphorylation, the prodrugs were not cytotoxic to a panel of tumor cells, thereby showing clear distinction between cytotoxicity and effects downstream of activated Stat3.
Sport related proximal femoral fractures: a retrospective review of 31 cases treated in an eight year period (2000)

In an eight year period, 31 patients with proximal femoral fractures resulting from sports accidents were treated by implantation of either a Gamma nail or a dynamic hip screw. Return to work or sports and the time to bone healing did not differ very much between the treatments. Gamma nailing was clearly the best with regard to stability and time to full mobilisation (4.5 days), but required 39 minutes to perform compared with insertion of a dynamic hip screw (27 minutes). The incidence of complications and malalignments did not differ very much between the two, although, when Gamma nailing was first used in the authors' clinic, more intraoperative complications occurred than with the dynamic hip screw. Stable pertrochanteric fractures may be treated with a dynamic hip screw. Unstable pertrochanteric or subtrochanteric fractures are treated with a Gamma nail at the authors' institution.
Characterization and expression of the β-N-acetylhexosaminidase gene family of Tribolium castaneum (2007)

Enzymes belonging to the beta-N-acetylhexosaminidase family cleave chitin oligosaccharides produced by the action of chitinases on chitin into the constituent N-acetylglucosamine monomer. Four genes encoding putative chitooligosaccharidolytic beta-N-acetylhexosaminidases (hereafter referred to as N-acetylglucosaminidases (NAGs)) in the red flour beetle, Tribolium castaneum, namely TcNAG1, TcFDL, TcNAG2, and TcNAG3, and three other related hexosaminidases were identified by searching the recently completed genome [Tribolium Genome Sequencing Consortium, 2007. The first genome sequence of a beetle, Tribolium castaneum, a model for insect development and pest biology. Nature, submitted for publication]. Full-length cDNAs for all four NAGs were cloned and sequenced, and the exon-intron organization of the corresponding genes was determined. Analyses of their developmental expression patterns indicated that, although all four of the NAGs are transcribed during most developmental stages, each gene had a distinct spatial and temporal expression pattern. TcNAG1 transcripts are the most abundant, particularly at the late pupal stage, while TcNAG3 transcripts are the least abundant, even at their peak levels in the late larval stages. The function of each NAG during different developmental stages was assessed by observations of lethal phenotypes after gene-specific double-stranded RNA (dsRNA)-mediated transcript depletion as verified by real-time PCR. TcNAG1 dsRNA was most effective in interrupting all three types of molts: larval-larval, larval-pupal, and pupal-adult. Treated insects died after failing to completely shed their old cuticles. Knockdown of transcripts for the other three NAG genes resulted in phenotypes similar to those of TcNAG1 dsRNA-treated insects, but the effects were somewhat variable and less severe. Sequence comparisons with other enzymatically characterized insect homologs suggested that TcFDL, unlike the other NAGs, may have a role in N-glycan processing in addition to its apparent role in cuticular chitin turnover. These results support the hypothesis that TcNAGs participate in chitin turnover and/or N-glycan processing during insect development and that each NAG fulfills an essential and distinct function.
Evidence for Clonal Evolution among Highly Polymorphic Genes in Methicillin-Resistant Staphylococcus aureus (2005)

The evolution of Staphylococcus aureus has been described as predominantly clonal, based on evidence from seven housekeeping genes. We aimed to test if this was also true for more polymorphic genes. In a collection of 60 isolates including major European epidemic methicillin-resistant S. aureus (MRSA) and sporadic MRSA strains, we compared the partial gene sequences of seven housekeeping genes (arcC, aroE, glpF, gmk, pta, tpi, and yqiL), six core adhesion genes (present in all strains) (clfA, clfB, fnbA, map, sdrC, and spa), and four accessory adhesion genes (not present in all strains) (ebpS, fnbB, sdrD, and sdrE). Nucleotide diversity of adhesion genes was 2- to 10-fold higher than genes used for multilocus sequence typing. All genes showed evidence for purifying selection with a weakly reduced level among accessory adhesion genes. Among these highly variable genes, there was no evidence for a difference in molecular evolution between epidemic and sporadic strains. Gene trees constructed from concatenated sequences of housekeeping, core adhesion, and accessory adhesion genes were highly congruent, indicating clonality, despite some evidence for homologous exchange. Further evidence for clonality was found with an overall positive correlation of allelic and nucleotidic divergence for both seven housekeeping genes and six core adhesion genes. However, for small allelic differences that fit the demarcations of clonal complexes (CCs) there was no such correlation, suggesting that recombination occurred. Therefore, despite an overall clonal population structure, recombination between related isolates within CCs might have contributed to S. aureus evolution.
Effective normalization for copy number variation detection from whole genome sequencing (2012)

Choice of read-count normalization methodology has a substantial effect on CNV calls and the use of genomic mappability or an appropriately chosen control genome can optimize the output of CNV analysis.
A floating gate MOSFET dosimeter requiring no external bias supply (1998)

MOSFET dosimeters incorporating an electrically floating polysilicon gate have been fabricated in a commercial CMOS technology. Charge is placed on the floating gate by tunnelling from a small overlapping injector gate. Subsequent irradiation partially discharges the floating gate, producing a change in threshold voltage which can be used to infer the absorbed dose. No external power source is required during this sensing period. Sensitivities up to 70 mV Gy/sup -1/ (0.7 mV/rad) have been obtained for temperature-compensated matched-pair dosimeters under /sup 60/Co gamma irradiation.
GAMYB-like Genes, Flowering, and Gibberellin Signaling in Arabidopsis (2001)

We have identified three Arabidopsis genes with GAMYB-like activity, AtMYB33, AtMYB65, and AtMYB101, which can substitute for barley (Hordeum vulgare) GAMYB in transactivating the barley alpha-amylase promoter. We have investigated the relationships between gibberellins (GAs), these GAMYB-like genes, and petiole elongation and flowering of Arabidopsis. Within 1 to 2 d of transferring plants from short- to long-day photoperiods, growth rate and erectness of petioles increased, and there were morphological changes at the shoot apex associated with the transition to flowering. These responses were accompanied by accumulation of GAs in the petioles (GA(1) by 11-fold and GA(4) by 3-fold), and an increase in expression of AtMYB33 at the shoot apex. Inhibition of GA biosynthesis using paclobutrazol blocked the petiole elongation induced by long days. Causality was suggested by the finding that, with GA treatment, plants flowered in short days, AtMYB33 expression increased at the shoot apex, and the petioles elongated and grew erect. That AtMYB33 may mediate a GA signaling role in flowering was supported by its ability to bind to a specific 8-bp sequence in the promoter of the floral meristem-identity gene, LEAFY, this same sequence being important in the GA response of the LEAFY promoter. One or more of these AtMYB genes may also play a role in the root tip during germination and, later, in stem tissue. These findings extend our earlier studies of GA signaling in the Gramineae to include a dicot species, Arabidopsis, and indicate that GAMYB-like genes may mediate GA signaling in growth and flowering responses.
Cloning of a Novel Scavenger Receptor Cysteine-Rich Type I Transmembrane Molecule (M160) Expressed by Human Macrophages (2000)

We report the cloning of a novel human type I cell surface Ag mainly expressed by macrophages. The primary structure was established by molecular cloning, which yielded a 4579-bp cDNA sequence encoding a polypeptide chain of 1453 amino acid residues with 16 potential N:-glycosylation sites. We designated this molecule M160. The domain organization features 12 scavenger receptor cysteine-rich domains followed by a transmembrane region and a cytoplasmic domain that occurs in two forms, a predominant form (M160-alpha) of 71 residues and an alternatively spliced form (M160-ss) of 39 residues. M160-alpha contains three possible phosphorylation sites, which are lost in the alternatively spliced form. RT-PCR analyses showed M160 to be expressed by alveolar macrophages and by the monocyte cell lines HL60, U937, and THP1, but not by Jurkat or Raji cells. Stimulation of U937 cells with phorbol ester resulted in an increased expression of M160 from day 5 onward. RT-PCR analysis of 19 different human tissues showed signals for M160-alpha of varying intensity in all tissues, whereas M160-ss was confined to the spleen. We conclude that M160 is a new member of the scavenger receptor cysteine-rich superfamily expressed by the monocyte/macrophage cell lineage.
Clostridium ramosum Osteomyelitis in an Immunocompetent Patient After Traumatic Injury (2014)

Clostridium ramosum is an anaerobic, spore-forming, gram-positive bacterium that is found commonly in the intestinal flora and is very rarely implicated as being pathogenic. It is a member of the genus Clostridium and is generally considered as being less virulent as other members of the Clostridium species such as C perfringens, C difficile, or C tetani. We present the first case reported of osteomyelitis caused by C ramosum in an immunocompetent patient after traumatic injury with failure to respond to antimicrobial treatment.
The Course and Malleability of Aggressive Behavior from Early First Grade into Middle School: Results of a Developmental Epidemiologically‐based Preventive Trial (1994)

The course and malleability of aggressive behavior from beginning elementary school through transition into middle school was investigated. In a developmental epidemiologically defined population of 1000 urban first graders, a two year classroom-based randomized preventive trial was aimed at reducing aggressive behavior, an antecedent of delinquency, violent behavior, and heavy drug use in adolescence and adulthood. Earlier we reported impact in first grade on teacher and peer ratings and on classroom observations. We report here on the course and on sixth grade teacher ratings of aggressive behavior. Improvement was observable during transition times, in first grade and in middle school, among the males in the preventive intervention who were more aggressive in first grade.
Non-standard amino acid incorporation into proteins using Escherichia coli cell-free protein synthesis (2014)

Incorporating non-standard amino acids (NSAAs) into proteins enables new chemical properties, new structures, and new functions. In recent years, improvements in cell-free protein synthesis (CFPS) systems have opened the way to accurate and efficient incorporation of NSAAs into proteins. The driving force behind this development has been three-fold. First, a technical renaissance has enabled high-yielding (>1 g/L) and long-lasting (>10 h in batch operation) CFPS in systems derived from Escherichia coli. Second, the efficiency of orthogonal translation systems (OTSs) has improved. Third, the open nature of the CFPS platform has brought about an unprecedented level of control and freedom of design. Here, we review recent developments in CFPS platforms designed to precisely incorporate NSAAs. In the coming years, we anticipate that CFPS systems will impact efforts to elucidate structure/function relationships of proteins and to make biomaterials and sequence-defined biopolymers for medical and industrial applications.
Binding and Cross-linking Studies Show That Scavenger Receptor BI Interacts with Multiple Sites in Apolipoprotein A-I and Identify the Class A Amphipathic α-Helix as a Recognition Motif (2000)

Scavenger receptor, class B, type I (SR-BI) mediates the selective uptake of high density lipoprotein (HDL) cholesteryl ester without the uptake and degradation of the particle. In transfected cells SR-BI recognizes HDL, low density lipoprotein (LDL) and modified LDL, protein-free lipid vesicles containing anionic phospholipids, and recombinant lipoproteins containing apolipoprotein (apo) A-I, apoA-II, apoE, or apoCIII. The molecular basis for the recognition of such diverse ligands by SR-BI is unknown. We have used direct binding analysis and chemical cross-linking to examine the interaction of murine (m) SR-BI with apoA-I, the major protein of HDL. The results show that apoA-I in apoA-I/palmitoyl-oleoylphosphatidylcholine discs, HDL(3), or in a lipid-free state binds to mSR-BI with high affinity (K(d) congruent with 5-8 microgram/ml). ApoA-I in each of these forms was efficiently cross-linked to cell surface mSR-BI, indicating that direct protein-protein contacts are the predominant feature that drives the interaction between HDL and mSR-BI. When complexed with dimyristoylphosphatidylcholine, the N-terminal and C-terminal CNBr fragments of apoA-I each bound to SR-BI in a saturable, high affinity manner, and each cross-linked efficiently to mSR-BI. Thus, mSR-BI recognizes multiple sites in apoA-I. A model class A amphipathic alpha-helix, 37pA, also showed high affinity binding and cross-linking to mSR-BI. These studies identify the amphipathic alpha-helix as a recognition motif for SR-BI and lead to the hypothesis that mSR-BI interacts with HDL via the amphipathic alpha-helical repeat units of apoA-I. This hypothesis explains the interaction of SR-BI with a wide variety of apolipoproteins via a specific secondary structure, the class A amphipathic alpha-helix, that is a common structural motif in the apolipoproteins of HDL, as well as LDL.
PRECLINICAL STUDIES WITH AN IRX-2 ENHANCED PROSTATE VACCINE (2008)

You have accessJournal of Urology1 Apr 2008PRECLINICAL STUDIES WITH AN IRX-2 ENHANCED PROSTATE VACCINE PH Naylor, HJ Brandwein, CW Naylor, A Nixon, Gabriel P Haas, Ching Y Wang, and JW Hadden PH NaylorPH Naylor More articles by this author , HJ BrandweinHJ Brandwein More articles by this author , CW NaylorCW Naylor More articles by this author , A NixonA Nixon More articles by this author , Gabriel P HaasGabriel P Haas More articles by this author , Ching Y WangChing Y Wang More articles by this author , and JW HaddenJW Hadden More articles by this author View All Author Informationhttps://doi.org/10.1016/S0022-5347(08)60135-4AboutPDF ToolsAdd to favoritesDownload CitationsTrack CitationsPermissionsReprints ShareFacebookLinked InTwitterEmail "PRECLINICAL STUDIES WITH AN IRX-2 ENHANCED PROSTATE VACCINE." The Journal of Urology, 179(4S), p. 45 © 2008 by American Urological AssociationFiguresReferencesRelatedDetails Volume 179Issue 4SApril 2008Page: 45 Advertisement Copyright & Permissions© 2008 by American Urological AssociationMetricsAuthor Information PH Naylor More articles by this author HJ Brandwein More articles by this author CW Naylor More articles by this author A Nixon More articles by this author Gabriel P Haas More articles by this author Ching Y Wang More articles by this author JW Hadden More articles by this author Expand All Advertisement PDF downloadLoading ...
Calin from Hirudo medicinalis, an inhibitor of platelet adhesion to collagen, prevents platelet-rich thrombosis in hamsters (1995)

Interaction between exposed collagen and platelets and/or von Willebrand factor is believed to be one of the initiating events for thrombus formation at sites of damaged endothelium. Interference with this mechanism may provide an anti-thrombotic potential. Calin, a product from the saliva of the leech Hirudo medicinalis, was tested in vitro and for its in vivo activity in a thrombosis model in hamsters. Calin specifically and dose dependently (IC50:6.5 to 13 micrograms/mL) inhibited human platelet aggregation induced by collagen. In addition, specific platelet adhesion onto microtiter wells coated with collagen and detected with a monoclonal antiglycoprotein IIb/IIIa antibody- conjugated with horseradish peroxidase, could be completely prevented with Calin (IC50:22 micrograms/mL). A dose-response curve was constructed in groups of six hamsters in whom a standardized trauma was induced on the femoral vein. Thrombus formation was followed continuously using video recording and processing of the image obtained upon transillumination of the vessel. Intravenous Calin dose- dependently inhibited platelet-rich thrombus formation in this model with an ED50 of 0.07 mg/kg and complete inhibition with 0.2 mg/kg. No effects were seen on coagulation tests or bleeding times, whereas ex vivo aggregation induced by collagen was inhibited dose dependently. Local application of leech saliva, Calin, hirudin, or the combination of the latter two into the bleeding time wound of hamsters resulted in a mild prolongation of the bleeding time (twofold to threefold). A similar experiment in baboons did not cause any prolongation of the bleeding time. This is in sharp contrast with the long-lasting bleeding after a leech bite itself in both species. Calin from the leech Hirudo medicinalis is able, by binding to collagen, to effectively interfere with platelet-collagen interaction, which results in an antithrombotic effect observed in a platelet-rich thrombosis model in hamsters.
Combination Delivery of Antigens and CpG by Lanthanides‐Based Core‐Shell Nanoparticles for Enhanced Immune Response and Dual‐Mode Imaging (2013)

Europium-doped GdPO4 hollow spheres/polymer core-shell nanoparticles are functionalized with ovalbumin (OVA) as a model antigen and an oligonucleotide (CpG) that stimulates the immune response. These functionalized core-shell nanoparticles are used as vaccines, where they enable efficient delivery of an antigen to target sites, tracking of the vaccines using non-invasive clinical imaging technology.
Automatic verification of object code against source code (2002)

An important step when applying formal methods to gain assurance of trusted systems is the verification of object code against source code. One way to mechanically verify that the object code faithfully implements the source code from which it is compiled is to verify the compiler. However, verifying the implementation of an industrial-strength compiler is a very difficult technical problem at the present time. For small fragments of code, it may be easier to verify the equivalence of the source and object code by reasoning about their behavior directly without dealing with the algorithm used for translation. In this paper, we describe a system for automatically verifying MC68020 object code against C source code. The semantics of a small subset of C and MC68020 object code are formalized in the logic of Nqthm (a.k.a. the Boyer-Moore theorem prover). After a large collection of lemmas about C and MC68020 semantics are made available, Nqthm is able to prove the correctness theorems automatically for a small class of programs. For practical use of the system to be possible, we wrote a front-end to Nqthm that generates correctness theorems, given the C source file as input. Using our front-end, we tested our system by verifying the object code produced by the GCC and CC compilers for some small programs.
The Application of Microemulsion Additives in Drilling and Stimulation Results in Enhanced Gas Production (2005)

Abstract A new microemulsion additive has been developed that is effective in remediating damaged wells and is highly effective in fluid recovery and relative permeability enhancement when applied in drilling and stimulation treatments at dilute concentrations.The microemulsion (ME) is an optically clear, thermodynamically stable blend of biodegradable solvent, surfactant, co-solvent and water.The nanometer sized structures have extremely high contact efficiency at low concentrations (0.10-0.5%). Lab data is presented that illustrates how the Microemulsion accelerates the cleanup of injected fluids in tight gas cores. The microemulsion additive results in lower pressures to displace injected fluids from low permeability core samples and proppant packs. The relative perm to gas is increased substantially as the water saturation is decreased. The enhanced relative permeability mechanism is the alteration of the rock-fluid interfacial tension or contact angle.It is demonstrated that this alteration effectively lowers the capillary pressure and capillary end effect associated with fractures in low perm reservoirs by as much as 50%, thus mitigating phase trapping and therefore permitting an increased flow area to the fracture and longer effective frac lengths.Examples of drilling fluids with and without ME are shown in which the relative perm to gas and oil are improved with the application of the microemulsion system. Field examples are shown for fracture treatments of unconventional low permeability coals and shales, where water recovery and productivity are increased by 50% with the application of ME. A production analysis is presented for wells treated in the Barnett Shale that shows longer effective frac lengths and decreased damage surrounding the fracture.