gebhart/patrepeval huggingface dataset:
Tip Surface Interactions in STM and AFM (1987)

The interaction between tip and flat surface in the STM and AFM is reviewed and a new, AC method to determine the absolute value of area of contact and interaction is presented. Evidence that the tip-surface interaction can be purely elastic down to the near single atom scale is obtained, and has been confirmed by TEM on Al2O3. Strengths close to that of an ideal lattice are observed. Applied to the Atomic Force Microscope this AC method will give operation at a controlled, drift free level of interaction. The effects of attractive (surface energy) forces in the STM geometry are discussed, and the equilibrium configurations and extent of inelastic processes for tip and flat are described. A new imaging mechanism in STM is proposed for the cases (e.g., graphite, point contact microscope) where significant tip-surface contact occurs.
Novel Bispecific PSMA/GRPr Targeting Radioligands with Optimized Pharmacokinetics for Improved PET Imaging of Prostate Cancer (2016)

A new series of bispecific radioligands (BRLs) targeting prostate-specific membrane antigen (PSMA) and gastrin releasing peptide receptor (GRPr), both expressed on prostate cancer cells, was developed. Their design was based on the bombesin (BN) analogue, H2N-PEG2-[D-Tyr(6),β-Ala(11),Thi(13),Nle(14)]BN(6-14), which binds to GRPr with high affinity and specificity, and the peptidomimetic urea-based pseudoirreversible inhibitor of PSMA, Glu-ureido-Lys. The two pharmacophores were coupled through copper(I)-catalyzed azide-alkyne cycloaddition to the bis(tetrafluorophenyl) ester of the chelating agent HBED-CC via amino acid linkers made of positively charged His (H) and negatively charged Glu (E): -(HE)n- (n = 0-3). The BRLs were labeled with (68)Ga, and their preliminary pharmacological properties were evaluated in vitro (competitive and time kinetic binding assays) on prostate cancer (PC-3, LNCaP) and rat pancreatic (AR42J) cell lines and in vivo by biodistribution and small animal PET imaging studies in both normal and tumor-bearing mice. The IC50/Ki values determined for all BRLs essentially matched those of the respective monomers. The maximal cellular uptake of the BLRs was observed between 20 and 30 min. The BRLs showed a synergistic ability in vivo by targeting both PSMA (LNCaP) and GRPr (PC-3) positive tumors, whereas the charged -(HE)n- (n = 1-3) linkers significantly reduced the kidney and spleen uptake. The bispecific (PSMA and GRPr) targeting ability and optimized pharmacokinetics of the compounds developed in this study could lead to their future application in clinical practice as more sensitive radiotracers for noninvasive imaging of prostate cancer (PCa) by PET/CT and PET/MRI.
Contigs Built with Fingerprints, Markers, and FPC V4.7 (2000)

Contigs have been assembled, and over 2800 clones selected for sequencing for human chromosomes 9, 10 and 13. Using the FPC (FingerPrinted Contig) software, the contigs are assembled with markers and complete digest fingerprints, and the contigs are ordered and localised by a global framework. Publicly available resources have been used, such as, the 1998 International Gene Map for the framework and the GSC Human BAC fingerprint database for the majority of the fingerprints. Additional markers and fingerprints are generated in-house to supplement this data. To support the scale up of building maps, FPC V4.7 has been extended to use markers with the fingerprints for assembly of contigs, new clones and markers can be automatically added to existing contigs, and poorly assembled contigs are marked accordingly. To test the automatic assembly, a simulated complete digest of 110 Mb of concatenated human sequence was used to create datasets with varying coverage, length of clones, and types of error. When no error was introduced and a tolerance of 7 was used in assembly, the largest contig with no false positive overlaps has 9534 clones with 37 out-of-order clones, that is, the starting coordinates of adjacent clones are in the wrong order. This paper describes the new features in FPC, the scenario for building the maps of chromosomes 9, 10 and 13, and the results from the simulation.
Synthesis and Am/Eu extraction of novel TODGA derivatives (2010)

Various ligands with structural modifications of the N,N,N′,N′-tetraoctyl-3-oxapentanediamide (TODGA) skeleton were synthesised in good yields. These modifications include (1) the increase in chain length from one carbon to two carbons between the central ether oxygen atom and the amide moieties, (2) the addition of substituents on the carbon between the central oxygen atom and the amide moieties on one and both sides of the central oxygen, (3) the replacement of the central oxygen by a (substituted) nitrogen atom and (4) synthesis of a rigidified glycolamide. The effect of the structural modifications on their extraction behaviours toward Am(III) and Eu(III) at various nitric acid concentrations was studied. In most of the cases, the extraction does not exceed that of TODGA in the entire acidity range of 0.001–4 mol/l HNO3. The extraction behaviour of monomethyl–TODGA derivative 10a resembles that of TODGA at high nitric acid concentrations. However, at lower acidities, its D values are much lower, which is beneficial for possible back-extraction steps. The aza-tripodal ligands 18a,b show reverse extraction properties compared to TODGA as far as the pH influence is concerned: at pH 2, the D Am values are 49.9 and 3.1, the D Eu values are 5.9 and 0.2, and the S Am/Eu values are 8 and 11, respectively.
The Stem Cell Factor Receptor/c-Kit as a Drug Target in Cancer (2006)

Tyrosine phosphorylation has a key role in intracellular signaling. Inappropriate proliferation and survival cues in tumor cells often occur as a consequence of unregulated tyrosine kinase activity. Much of the current development of anti-cancer therapies tries to target causative proteins in a specific manner to minimize side-effects. One attractive group of target proteins is the kinases. c-Kit is a receptor tyrosine kinase that normally controls the function of primitive hematopoietic cells, melanocytes and germ cells. It has become clear that uncontrolled activity of c-Kit contributes to formation of an array of human tumors. The unregulated activity of c-Kit may be due to overexpression, autocrine loops or mutational activation. This makes c-Kit an excellent target for cancer therapies in these tumors. In this review we will highlight the current knowledge on the signal transduction molecules and pathways activated by c-Kit under normal conditions and in cancer cells, and the role of aberrant c-Kit signaling in cancer progression. Recent advances in the development of specific inhibitors interfering with these signal transduction pathways will be discussed.
Prediction of the Coding Sequences of Unidentified Human Genes. XVI. The Complete Sequences of 150 New cDNA Clones from Brain Which Code for Large Proteins in vitro (2000)

We have carried out a human cDNA sequencing project to accumulate information regarding the coding sequences of unidentified human genes. As an extension of the preceding reports, we herein present the entire sequences of 150 cDNA clones of unknown human genes, named KIAA1294 to KIAA1443, from two sets of size-fractionated human adult and fetal brain cDNA libraries. The average sizes of the inserts and corresponding open reading frames of cDNA clones analyzed here reached 4.8 kb and 2.7 kb (910 amino acid residues), respectively. From sequence similarities and protein motifs, 73 predicted gene products were functionally annotated and 97% of them were classified into the following four functional categories: cell signaling/communication, nucleic acid management, cell structure/motility and protein management. Additionally, the chromosomal loci of the genes were assigned by using human-rodent hybrid panels for those genes whose mapping data were not available in the public databases. The expression profiles of the genes were also studied in 10 human tissues, 8 brain regions, spinal cord, fetal brain and fetal liver by reverse transcription-coupled polymerase chain reaction, products of which were quantified by enzyme-linked immunosorbent assay.
Advanced network monitoring brings life to the awareness plane (2008)

The latest advances in traffic measurement, analysis, and modeling play an important role in automatically building and maintaining a distributed intelligent monitoring layer that we describe as the awareness plane. The purpose of this article is to describe the components of this awareness plane in the areas of flexible network measurement, application and relationship discovery, and traffic classification, as well as data aggregation and semantically enriched infrastructure models. We present management services and scenarios, and list the research challenges on the path to integrating the components and making them interoperate for future autonomic service and network management approaches.
Reduction of Kidney Uptake in Radiometal Labeled Peptide Linkers Conjugated to Recombinant Antibody Fragments. Site-Specific Conjugation of DOTA-Peptides to a Cys-Diabody (2002)

Arano and co-workers (Arano et al. (1999) Cancer Res. 59, 128-134) have synthesized peptides with an N-terminal radioiodinated hippuric acid and a C-terminal lysine linked to antibody fragments via the epsilon-amino group of lysine that show reduced kidney uptake compared to antibody fragments directly radioiodinated. This approach takes advantage of the lysine specific carboxypeptidase activity of the kidney brush border enzymes that cleave off the radiolabeled peptide linker from the antibody fragment prior to uptake by proximal tubule cells. On the basis of their approach, we have synthesized a tetrapeptide with an N-terminal DOTA (1,4,7,10-tetraazacyclododecane-1,4,7,10-tetraacetic acid) and a C-terminal (N(epsilon)-maleoyl)lysine that was site-specifically conjugated to an anti-CEA diabody (Yazaki et al. (2001) Bioconjugate Chem. 12, 220-228) that was engineered to contain a C-terminal cysteine (Cys-diabody). Biodistributions of the In-111-radiolabeled conjugate in nude mice show significantly reduced kidney uptake (a maximum of 82%ID/g at 6 h) compared to In-111 radiolabeled DOTA-diabody (184%ID/g at 6 h) in which DOTA was conjugated to endogenous lysine residues using DOTA-active ester chemistry. To further reduce kidney uptake, a homologous compound with a C-terminal (N(epsilon)-amino-1,6-hexane-bis-vinyl sulfone)lysine was synthesized and site-specifically conjugated to the Cys-diabody. Biodistributions of this In-111-labeled conjugate reduced kidney uptake to 54%ID/g at 6 h. To explore the effect of the relative positions of the chelate vs the cys-diabody on kidney uptake, we also synthesized a tetrapeptide with an N-terminal bromoacetate for conjugation to Cys-diabody and a C-terminal (N(epsilon)-amidino-propyl-3-thio-vinylsulfonyl-DO3A)lysine. This peptide essentially reverses the positions of the chelate and Cys-diabody attachment points on the peptide, while retaining the linker length on the epsilon-amino group of the lysine. In this case, biodistributions of the In-111-radiolabeled conjugate in nude mice showed high kidney uptake (189%ID/g at 6 h), comparable to that obtained with the In-111-radiolabeled active ester conjugated DOTA-diabody (184%ID/g at 6 h). We conclude that the peptide linker strategy of Arano and co-workers to reduce kidney uptake can be successfully applied to chelate/radiometal complexes and requires that the chelate/radiometal be located at the N-terminus of the peptide and the antibody fragment attachment site on the epsilon-amino group of the lysine. Furthermore, we demonstrated a role for the attachment chemistry to the epsilon-amino group of the lysine on the magnitude of kidney uptake.
Amyotrophic lateral sclerosis: evaluation and treatment of respiratory impairment (2002)

Patients with amyotrophic lateral sclerosis (ALS) invariably develop respiratory muscle weakness and most die from pulmonary complications. There are numerous tests available to evaluate respiratory status in ALS and it is important to understand their various advantages and limitations. Forced vital capacity (FVC) is commonly used but can remain normal despite substantial inspiratory muscle weakness. Maximal pressures measured at the mouth are useful for excluding weakness if they are normal but are difficult to interpret if abnormal. Invasive testing, such as measurement of transdiaphragmatic pressure, provides an accurate measure of inspiratory strength but is not readily available and is not practical for serial measures. There are supportive respiratory techniques that have been shown to benefit patients with ALS. Clinicians should be familiar with these interventions, including mechanically assisted coughing, non-invasive ventilation and tracheostomy with mechanical ventilation. Observational studies have demonstrated improved survival and quality of life with noninvasive ventilation. Tracheostomy with long-term mechanical ventilation is not frequently used but can be an important component of care for ALS. This review describes an approach to respiratory evaluation and care of patients with ALS.
Live Attenuated Malaria Vaccine Designed to Protect Through Hepatic CD8 + T Cell Immunity (2011)

Our goal is to develop a vaccine that sustainably prevents Plasmodium falciparum (Pf) malaria in ≥80% of recipients. Pf sporozoites (PfSPZ) administered by mosquito bites are the only immunogens shown to induce such protection in humans. Such protection is thought to be mediated by CD8(+) T cells in the liver that secrete interferon-γ (IFN-γ). We report that purified irradiated PfSPZ administered to 80 volunteers by needle inoculation in the skin was safe, but suboptimally immunogenic and protective. Animal studies demonstrated that intravenous immunization was critical for inducing a high frequency of PfSPZ-specific CD8(+), IFN-γ-producing T cells in the liver (nonhuman primates, mice) and conferring protection (mice). Our results suggest that intravenous administration of this vaccine will lead to the prevention of infection with Pf malaria.
Toward Quantitative Prediction of Molecular Fluorescence Quantum Efficiency:  Role of Duschinsky Rotation (2007)

It is a highly desirable but difficult task to predict the molecular fluorescence quantum efficiency from first principles. The molecule in the excited state can undergo spontaneous radiation, conversion of electronic energy to nuclear motion, or chemical reaction. For relatively large molecules, it is impossible to obtain the full potential energy surfaces for the ground state and the excited states to study the excited-state dynamics. We show that, under harmonic approximation by considering the Duschinsky rotation effect, the molecular fluorescence properties can be quantitatively calculated from first principles coupled with our correlation function formalism for the internal conversion. In particular, we have explained the peculiar fluorescence behaviors of two isomeric compounds, cis,cis-1,2,3,4-tetraphenyl-1,3-butadiene and 1,1,4,4-tetraphenyl-butadiene, the former being nonemissive in solution and strongly emissive in aggregation or at low temperature, and the latter being strongly emissive in solution. The roles of low-frequency phenyl ring twist motions and their Duschinsky mode mixings are found to be crucial, especially to reveal the temperature dependence. As an independent check, we take a look at the well-established photophysics of 1,4-diphenylbutadiene for its three different conformers. Both the calculated radiative and nonradiative rates are in excellent agreement with the available experimental measurements.
A 21-kDa surface protein of Mycobacterium leprae binds peripheral nerve laminin-2 and mediates Schwann cell invasion (1999)

Nerve damage is the hallmark of Mycobacterium leprae infection, which results from M. leprae invasion of the Schwann cell of the peripheral nervous system. We have recently shown that the laminin-2 isoform, specially the G domain of laminin alpha2 chain, on the Schwann cell-axon unit serves as an initial neural target for M. leprae. However, M. leprae surface molecules that mediate bacterial invasion of peripheral nerves are entirely unknown. By using human alpha2 laminins as a probe, a major 28-kDa protein in the M. leprae cell wall fraction that binds alpha2 laminins was identified. After N-terminal amino acid sequence analysis, PCR-based strategy was used to clone the gene that encodes this protein. Deduced amino acid sequence of this M. leprae laminin-binding protein predicts a 21-kDa molecule (ML-LBP21), which is smaller than the observed molecular size in SDS/PAGE. Immunofluorescence and immunoelectron microscopy on intact M. leprae with mAbs against recombinant (r) ML-LBP21 revealed that the protein is surface exposed. rML-LBP21 avidly bound to alpha2 laminins, the rG domain of the laminin-alpha2 chain, and the native peripheral nerve laminin-2. The role of ML-LBP21 in Schwann cell adhesion and invasion was investigated by using fluorescent polystyrene beads coated with rML-LBP21. Although beads coated with rML-LBP21 alone specifically adhered to and were ingested by primary Schwann cells, these functions were significantly enhanced when beads were preincubated with exogenous alpha2 laminins. Taken together, the present data suggest that ML-LBP21 may function as a critical surface adhesin that facilitates the entry of M. leprae into Schwann cells.
Inhomogeneity correction using an estimated linear field map (1996)

A fast and robust method for correcting magnetic resonance image distortion due to field inhomogeneity is proposed and applied to spiral k-space scanning. The method consists of acquiring a local field map, finding the best fit to a linear map, and using it to deblur the image distortions due to local frequency variations. The linear field map is determined using a maximum likelihood estimator with weights proportional to the pixel intensity. The method requires little additional computation and is robust in low signal regions and near abrupt field changes. Additionally, it can be used in combination with other deblurring methods. The application of this method is illustrated in conjunction with a multislice, T2-weighted, breath-held spiral scan of the liver.
Recent advances in engineering microparticles and their nascent utilization in biomedical delivery and diagnostic applications (2017)

Complex microparticles (MPs) bearing unique characteristics such as well-tailored sizes, various morphologies, and multi-compartments have been attempted to be produced by many researchers in the past decades. However, a conventionally used method of fabricating MPs, emulsion polymerization, has a limitation in achieving the aforementioned characteristics and several approaches such as the microfluidics-assisted (droplet-based microfluidics and flow lithography-based microfluidics), electrohydrodynamics (EHD)-based, centrifugation-based, and template-based methods have been recently suggested to overcome this limitation. The outstanding features of complex MPs engineered through these suggested methods have provided new opportunities for MPs to be applied in a wider range of applications including cell carriers, drug delivery agents, active pigments for display, microsensors, interface stabilizers, and catalyst substrates. Overall, the engineered MPs expose their potential particularly in the field of biomedical engineering as the increased complexity in the engineered MPs fulfills well the requirements of the high-end applications. This review outlines the current trends of newly developed techniques used for engineered MPs fabrication and focuses on the current state of engineered MPs in biomedical applications.
SMASH: A Next-Generation API for Programmable Graphics Accelerators (2000)

The SMASH API is a testbed for real-time, low-level graphics concepts. It is being developed to serve as a concrete target for the development of advanced extensions to OpenGL as well as a driver to test hardware architectures to support these extensions. SMASH is syntactically and conceptually similar to OpenGL but supports (along with other experimental features) a programmable shader sub-API that is compatible with both multi-pass and single-pass implementations of shaders. Arbitrary numbers of shader parameters of various types can be bound to vertices of geometric primitives using a simple immediatemode mechanism. Run-time specification, manipulation, and compilation of shaders is supported. The intermediate-level shading language includes integrated support for per-vertex and perfragment shaders under a common programming model. Implementation of real-time rendering effects using SMASH could be enhanced with metaprogramming toolkits and techniques, up to and including RenderMan-like textual shading languages and C++ toolkits with similar levels of compactness and functionality. We give several examples of how a two-term separable BRDF approximation could be implemented using such higher-level constructs.
Hemilabile N-Xylyl-N′-methylperimidine Carbene Iridium Complexes as Catalysts for C–H Activation and Dehydrogenative Silylation: Dual Role of N-Xylyl Moiety for ortho-C–H Bond Activation and Reductive Bond Cleavage (2013)

Direct dehydrogenative silylation of pyridyl and iminyl substrates with triethylsilane was achieved using (L)Ir(cod)(X) (1) (L = a perimidine-based carbene ligand, X = OAc and OCOPh) complexes as catalysts under toluene refluxing conditions in the presence of norbornene as a hydrogen scavenger, and the silylated products were obtained in good yields. The isolated bis(cyclometalated)iridium complexes, (C(∧)C:)(C(∧)N)IrOAc (2) (C(∧)C: = a cyclometalated perimidine-carbene ligand and C(∧)N = a cyclometalated pyridyl- and iminyl-ligated aromatic substrate), were key intermediates, where cyclometalated five-membered metallacycles of substrates such as phenylpyridine were selectively formed before yielding mono-ortho-silylation products. The bis(cyclometalated)iridium complex ((Xy)C(∧)C:)(C(∧)N)IrOAc (2d) ((Xy)C(∧)C: = a cyclometalated N-xylyl-N'-methylperimidine-carbene ligand and C(∧)N = a 2-pyridylphenyl ligand), reacted with 2 equiv of Et3SiH to give an iridium hydride complex, (L(4))(C(∧)N)Ir(H)(SiEt3) (8d) (L(4) = N-CH3, N-3,5-(CH3)2C6H3 perimidine), via demetalation of a N-3,5-xylyl ring of the carbene ligand of 2d. The formation of 8d was confirmed by isolating the corresponding chloro complex (L(4))(C(∧)N)Ir(Cl)(SiEt3) (8d-Cl) by treatment with CCl4. The N-methyl moiety of the carbene ligand coordinated to 8d was cyclometalated in the presence of norbornene at room temperature to afford ((Me)C(∧)C:)(C(∧)N)Ir(SiEt3) (10d) ((Me)C(∧)C: = a cyclometalated N-xylyl-N'-methylperimidine-carbene), while at high temperature 8d reacted with norbornene and Et3SiH to afford the silylated product, 2-(2-triethylsilyl)phenylpyridine (3a) and norbornane. A deuterium labeling experiment using 2d and Et3SiD (excess) revealed the incorporation of deuterium atoms at two ortho-positions of the N-xylyl group (>90%) and at the 3-position of 2-pyridylphenyl ligand (ca. 40%) within 3 h at room temperature, indicating that the cyclometalation/demetalation of the N-xylylperimidine carbene and 2-phenylpyridine ligands were reversible processes. Isolation of these cyclometalated iridium complexes under controlled conditions and D-labeling experiments thus revealed a dual function of the N-aryl group bound to the perimidine-carbene ligand, which acted as both a neutral carbene ligand and a monoanionic ortho-metalated aryl-carbene ligand through reversible C-H bond activation and Ir-C bond cleavage of the N-aryl group during the catalytic cycle.