gebhart/patrepeval huggingface dataset:
Effects of random link removal on the photonic band gaps of honeycomb networks (2010)

We explore the effects of random link removal on the photonic band gaps of honeycomb networks. Missing or incomplete links are expected to be common in practical realizations of this class of connected network structures due to unavoidable flaws in the fabrication process. We focus on the collapse of the photonic band gap due to the defects induced by the link removal. We show that the photonic band gap is quite robust against this type of random decimation and survives even when almost 58% of the network links are removed.
DISTRIBUTED PROCESSING USING LOCAL OPERATING NETWORKS (1992)

LON networks constitute a class of technology that allows intelligent devices such as actuators and sensors to communicate with one another using a standard protocol. In this way, a LON network is similar to a local area network (LAN) that allows office computers to communicate with each other. LON technology supports distributed, peer‐to‐peer communications. Individual network devices can communicate directly with one another, and a central control system is not required.
Transfer of Autologous Gene-modified T Cells in HIV-infected Patients with Advanced Immunodeficiency and Drug-resistant Virus (2007)

Drug toxicity and viral resistance limit the long-term efficacy of antiviral drug treatment for human immunodeficiency virus (HIV) infection. Thus, alternative therapies need to be explored. We tested the infusion of T lymphocytes transduced with a retroviral vector (M87o) that expresses an HIV entry-inhibitory peptide (maC46). Gene-modified autologous T cells were infused into ten HIV-infected patients with advanced disease and multidrug-resistant virus during anti-retroviral combination therapy. T-cell infusions were tolerated well, with no severe side effects. A significant increase of CD4 counts was observed after infusion. At the end of the 1-year follow-up, the CD4 counts of all patients were still around or above baseline. Gene-modified cells could be detected in peripheral blood, lymph nodes, and bone marrow throughout the 1-year follow-up, and marking levels correlated with the cell dose. No significant changes of viral load were observed during the first 4 months. Four of the seven patients who changed their antiviral drug regimen thereafter responded with a significant decline in plasma viral load. In conclusion, the transfer of gene-modified cells was safe, led to sustained levels of gene marking, and may improve immune competence in HIV-infected patients with advanced disease and multidrug-resistant virus.
Sequence, Purification, and Cloning of an Intracellular Serine Protease, Quiescent Cell Proline Dipeptidase (1999)

We recently observed that specific inhibitors of post-proline cleaving aminodipeptidases cause apoptosis in quiescent lymphocytes in a process independent of CD26/dipeptidyl peptidase IV. These results led to the isolation and cloning of a new protease that we have termed quiescent cell proline dipeptidase (QPP). QPP activity was purified from CD26(-) Jurkat T cells. The protein was identified by labeling with [(3)H]diisopropylfluorophosphate and subjected to tryptic digestion and partial amino acid sequencing. The peptide sequences were used to identify expressed sequence tag clones. The cDNA of QPP contains an open reading frame of 1476 base pairs, coding for a protein of 492 amino acids. The amino acid sequence of QPP reveals similarity with prolylcarboxypeptidase. The putative active site residues serine, aspartic acid, and histidine of QPP show an ordering of the catalytic triad similar to that seen in the post-proline cleaving exopeptidases prolylcarboxypeptidase and CD26/dipeptidyl peptidase IV. The post-proline cleaving activity of QPP has an unusually broad pH range in that it is able to cleave substrate molecules at acidic pH as well as at neutral pH. QPP has also been detected in nonlymphocytic cell lines, indicating that this enzyme activity may play an important role in other tissues as well.
Two-dimensional Fourier transform electronic spectroscopy (2001)

Two-dimensional Fourier transform electronic spectra of the cyanine dye IR144 in methanol are used to explore new aspects of optical 2D spectroscopy on a femtosecond timescale. The experiments reported here are pulse sequence and coherence pathway analogs of the two-dimensional magnetic resonance techniques known as COSY (correlated spectroscopy) and NOESY (nuclear Overhauser effect spectroscopy). Noncollinear three pulse scattering allows selection of electronic coherence pathways by choice of phase matching geometry, temporal pulse order, and Fourier transform variables. Signal fields and delays between excitation pulses are measured by spectral interferometry. Separate real (absorptive) and imaginary (dispersive) 2D spectra are generated by measuring the signal field at the sample exit, performing a 2D scan that equally weights rephasing and nonrephasing coherence pathways, and phasing the 2D spectra against spectrally resolved pump–probe signals. A 3D signal propagation function is used to correct the 2D spectra for excitation pulse propagation and signal pulse generation inside the sample. At relaxation times greater than all solvent and vibrational relaxation timescales, the experimental 2D electronic spectra can be predicted from linear spectroscopic measurements without any adjustable parameters. The 2D correlation spectra verify recent computational predictions of a negative region above the diagonal, a displacement of the 2D peak off the diagonal, and a narrowing of the 2D cross-width below the vibrational linewidth. The negative region arises from 4-level four-wave mixing processes with negative transition dipole products, the displacement off the diagonal arises from a dynamic Stokes shift during signal radiation, and the narrow 2D cross-width indicates femtosecond freezing of vibrational motion.
Breast cancer research: where we are and where we should go (2000)

Every new year, a common ritual is to reflect on the past year and resolve to improve, in increments, one's life for the next. With the new millennium upon us, the introspection and the projections take on a grander scale. Certainly, the span of a thousand years dwarfs the lifetime of any individual. Therefore, the thoughts and the hopes are for a community, and not the individual. Furthermore, the millennial resolutions we make are about achieving dreams beyond the boundaries of current reality. In breast cancer research, given the progress in the field, it is an appropriate time for us to take stock of our past accomplishments, and to make projections on where we would like to be. Then, with these plans in hand, we may plan the first steps on a journey that will encompass the next 30 generations.
Silver nylon cloth: in vitro and in vivo evaluation of antimicrobial activity. (1987)

The topical agents used in burn care today, although beneficial, do have limitations, the most important of which is the failure to prevent or treat burn wound infections in patients with extensive injuries. Therefore, we evaluated the antimicrobial activity of two silver nylon fabrics (SN and HRS) on the growth of S. aureus, P. aeruginosa, and C. albicans. The theoretical advantages of these nylon fabrics over presently available silver compounds is their ability to continuously release silver ions into the burn wound as long as the material is in contact with the wound. Additionally, the release of silver from these fabrics can be augmented electrolytically. The results of these experiments indicated that both materials were microbicidal in vitro for all three test organisms. Furthermore, the antimicrobial activity could be significantly augmented by passing a weak DC current through the material, which increased the rate of release of silver ions from the fabrics. In vivo, HRS was as effective as silver sulfadiazine in preventing colonization of the burn wound. The use of silver nylon fabrics thus appears to be a promising way of delivering large quantities of silver ions into the burn wound without the potential side effects of a carrier molecule or cream.
Surface plasmon resonance for high‐throughput ligand screening of membrane‐bound proteins (2009)

Technologies based on surface plasmon resonance (SPR) have allowed rapid, label-free characterization of protein-protein and protein-small molecule interactions. SPR has become the gold standard in industrial and academic settings, in which the interaction between a pair of soluble binding partners is characterized in detail or a library of molecules is screened for binding against a single soluble protein. In spite of these successes, SPR is only beginning to be adapted to the needs of membrane-bound proteins which are difficult to study in situ but represent promising targets for drug and biomarker development. Existing technologies, such as BIAcoreTM, have been adapted for membrane protein analysis by building supported lipid layers or capturing lipid vesicles on existing chips. Newer technologies, still in development, will allow membrane proteins to be presented in native or near-native formats. These include SPR nanopore arrays, in which lipid bilayers containing membrane proteins stably span small pores that are addressable from both sides of the bilayer. Here, we discuss current SPR instrumentation and the potential for SPR nanopore arrays to enable quantitative, high-throughput screening of G protein coupled receptor ligands and applications in basic cellular biology.
Progressive engineering of a homing endonuclease genome editing reagent for the murine X-linked immunodeficiency locus (2014)

LAGLIDADG homing endonucleases (LHEs) are compact endonucleases with 20-22 bp recognition sites, and thus are ideal scaffolds for engineering site-specific DNA cleavage enzymes for genome editing applications. Here, we describe a general approach to LHE engineering that combines rational design with directed evolution, using a yeast surface display high-throughput cleavage selection. This approach was employed to alter the binding and cleavage specificity of the I-Anil LHE to recognize a mutation in the mouse Bruton tyrosine kinase (Btk) gene causative for mouse X-linked immunodeficiency (XID)-a model of human X-linked agammaglobulinemia (XLA). The required re-targeting of I-AniI involved progressive resculpting of the DNA contact interface to accommodate nine base differences from the native cleavage sequence. The enzyme emerging from the progressive engineering process was specific for the XID mutant allele versus the wild-type (WT) allele, and exhibited activity equivalent to WT I-AniI in vitro and in cellulo reporter assays. Fusion of the enzyme to a site-specific DNA binding domain of transcription activator-like effector (TALE) resulted in a further enhancement of gene editing efficiency. These results illustrate the potential of LHE enzymes as specific and efficient tools for therapeutic genome engineering.
Chemical Vapor Deposition Growth of Graphene using Other Hydrocarbon Sources (2011)

Graphene has attracted a lot of research interests due to its exotic properties and a wide spectrum of potential applications. Chemical vapor deposition (CVD) from gaseous hydrocarbon sources has shown great promises for large-scale graphene growth. However, high growth temperature, typically 1000°C, is required for such growth. Here we demonstrate a revised CVD route to grow graphene on Cu foils at low temperature, adopting solid and liquid hydrocarbon feedstocks. For solid PMMA and polystyrene precursors, centimeter-scale monolayer graphene films are synthesized at a growth temperature down to 400°C. When benzene is used as the hydrocarbon source, monolayer graphene flakes with excellent quality are achieved at a growth temperature as low as 300°C. The successful low-temperature growth can be qualitatively understood from the first principles calculations. Our work might pave a way to undemanding route for economical and convenient graphene growth.
Efficient broadband silicon-on-insulator grating coupler with low backreflection (2011)

We design and fabricate an efficient broadband grating coupler on a 400 nm thick silicon-on-insulator wafer. The measured coupling loss is 3 dB when coupling to a single-mode fiber at 1310 nm wavelength with TE polarization. The spectral FWHM and backreflection are determined to be 58 nm and -27 dB, respectively.
Vibrational coherence transfer characterized with Fourier-transform 2D IR spectroscopy (2004)

Two-dimensional infrared (2D IR) spectroscopy of the symmetric and asymmetric C[Triple Bond]O stretching vibrations of Rh(CO)(2)acac in hexane has been used to investigate vibrational coherence transfer, dephasing, and population relaxation in a multilevel vibrational system. The transfer of coherence between close-lying vibrational frequencies results in extra relaxation-induced peaks in the 2D IR spectrum, whose amplitude depends on the coherence transfer rate. Coherence transfer arises from the mutual interaction of the bright CO stretches with dark states, which in this case reflects the mutual d-pi(*) back bonding of the Rh center to both the terminal carbonyls and the acetylacenonate ligand. For 2D IR relaxation experiments with variable waiting times, coherent dynamics lead to the modulation of peak amplitudes, while incoherent population relaxation and exchange results in the growth of the relaxation-induced peaks. We have modeled the data by propagating the density matrix with the Redfield equation, incorporating all vibrational relaxation processes during all three experimental time periods and including excitation reorientation effects arising from relaxation. Coherence and population transfer time scales from the symmetric to the asymmetric stretch were found to be 350 fs and 3 ps, respectively. We also discuss a diagrammatic approach to incorporating all vibrational relaxation processes into the nonlinear response function, and show how coherence transfer influences the analysis of structural variables from 2D IR spectroscopy.
Growth inhibition of human prostate cells in vitro by novel inhibitors of androgen synthesis. (1996)

The long-standing strategy for the treatment of metastatic prostate cancer has been to reduce androgenic stimulation of tumor growth by removal of the testes, the primary site of testosterone synthesis. However, a low level of androgenic stimulation may continue, even after castration, by the conversion of adrenal androgens to 5alpha-dihydrotestosterone (DHT) in the prostate tumor cells. Two important enzymes of the androgen biosynthetic pathway are 17alpha-hydroxylase/C17,20-lyase, which regulates an early step in the synthesis of testosterone and other androgens in both the testes and adrenal glands, and 5alpha-reductase, which converts testosterone to the more potent androgen, DHT, in the prostate. We have identified new inhibitors of these enzymes that may be of use in achieving a more complete ablation of androgens in the treatment of metastatic prostate cancer. Three derivatives of androstene were shown to inhibit 17alpha-hydroxylase/C17,20-lyase with potencies 2-20-fold greater than that of ketoconazole, a previously established inhibitor of this enzyme. Derivatives of pregnane and pregnene displayed activities against 5alpha-reductase that were comparable to that of N-(1,1-dimethyl-ethyl)-3-oxo-4-aza-5alpha-androst-1-ene-17beta-car boxamide. All of the 5alpha-reductase inhibitors were able to at least partially inhibit the mitogenic effect of testosterone in either histocultures of human benign prostatic hypertrophic tissue or in cultures of the LNCaP human prostatic tumor cell line. For these compounds, it appears that this inhibition can be attributed to a reduction of DHT synthesis in these cultures, because no inhibitory effect was observed in DHT-treated cultures, and none of the compounds had a cytotoxic effect. Surprisingly, one of the inhibitors of 17alpha-hydroxylase/C17,20-lyase, 17beta-(4-imidazolyl)-5-pregnen-3beta-ol, was also able to inhibit the mitogenic effect of testosterone in both the histoculture and cell culture assays and had an effect against DHT as well. In transcriptional activation assays, it was found that this compound is an antagonist of both the wild-type androgen receptor and the mutant androgen receptor, which is present in LNCaP cells. In conclusion, the abilities of these compounds to inhibit androgen synthesis and, in some cases, to exert antiandrogen activity, did in fact translate to an inhibitory effect on the growth of human prostatic tissue in vitro, suggesting their potential utility in the treatment of prostatic cancer.
Photodynamic Therapy-induced Apoptosis in Epidermoid Carcinoma Cells (2001)

Photodynamic therapy (PDT), a novel and promising cancer treatment that employs a combination of a photosensitizing chemical and visible light, induces apoptosis in human epidermoid carcinoma A431 cells. However, the precise mechanism of PDT-induced apoptosis is not well characterized. To dissect the pathways of PDT-induced apoptosis, we investigated the involvement of mitochondrial damage by examining a second generation photosensitizer, the silicon phthalocyanine 4 (Pc 4). By using laser-scanning confocal microscopy, we found that Pc 4 localized to cytosolic membranes primarily, but not exclusively, in mitochondria. Formation of mitochondrial reactive oxygen species (ROS) was detected within minutes when cells were exposed to Pc 4 and 670-675 nm light. This was followed by mitochondrial inner membrane permeabilization, depolarization and swelling, cytochrome c release, and apoptotic death. Desferrioxamine prevented mitochondrial ROS production and the events thereafter. Cyclosporin A plus trifluoperazine, blockers of the mitochondrial permeability transition, inhibited mitochondrial inner membrane permeabilization and depolarization without affecting mitochondrial ROS generation. These data indicate that the mitochondrial ROS are critical in initiating mitochondrial inner membrane permeabilization, which leads to mitochondrial swelling, cytochrome c release to the cytosol, and apoptotic death during PDT with Pc 4.
Public Health Implications of Antiretroviral Therapy and HIV Drug Resistance (1998)

Widespread use of antiretroviral agents and increasing occurrence of human immunodeficiency virus (HIV) strains resistant to these drugs have given rise to a number of important issues. Some of these concerns are distinct from the obvious question of the relationship between drug resistance and treatment failure and have potentially widespread public health implications. The relevant issues include but are not limited to the following: (1) frequency with which drug-resistant virus may be transmitted via sexual, intravenous, or mother-to-child routes; (2) ability of drug-resistant variants to be transmitted, a question that relates, in part, to the relative fitness of such strains; (3) effectiveness of antiviral therapy in diminishing viral burden in both blood and genital secretions, and whether this may be compromised in persons harboring resistant virus; and (4) importance of patient adherence to antiviral therapy and its relationship to sustained reduction in viral load to minimize the appearance in and transmission of drug-resistant virus from both blood and genital secretions. Thus, prevention of both development of HIV drug resistance as well as transmission of drug-resistant variants is a central issue of public health importance. Unless this topic is appropriately addressed, the likelihood is that drug-resistant variants of HIV, if able to successfully replicate, will sustain the epidemic and limit the effectiveness of antiviral therapy.
Distinct Mechanisms of STAT Phosphorylation via the Interferon-α/β Receptor (2000)

Interferon-alpha (IFNalpha) can activate several members of the signal transducers and activator of transcription (STAT) transcription factor family, a process that requires the tyrosine kinases Jak1 and Tyk2. Here we provide evidence that IFNalpha-mediated activation of various STAT proteins is regulated by distinct mechanisms. Piceatannol, previously reported as a Syk/ZAP70-specific kinase inhibitor, selectively inhibits the tyrosine phosphorylation of STAT3 and STAT5, but not of STAT1 and STAT2. This inhibition is paralleled by the loss of Jak1 and IFNAR1 tyrosine phosphorylation in response to IFNalpha, whereas Tyk2 and IFNAR2 tyrosine phosphorylation is unaffected. Last, the IFNalpha-induced serine phosphorylation of STAT1 and STAT3 is not inhibited by piceatannol but is sensitive to the Src kinase-specific inhibitor PP2. Thus, our results not only demonstrate that the IFNalpha/beta receptor utilizes distinct mechanisms to trigger the tyrosine phosphorylation of specific STAT proteins, but they also indicate a diverging pathway that leads to the serine phosphorylation of STAT1 and STAT3.
Identification of two active site residues in human angiotensin I-converting enzyme. (1994)

Angiotensin I-converting enzyme (ACE) contains two zinc-dependent catalytic domains (N and C domains) each bearing the motif HEXXH where the two histidines form two of the three amino acid zinc ligands. Sequence alignment of each ACE domain with other zinc metalloproteases, indicates a glutamate residues which putatively constitutes the third zinc ligand and an aspartate residue which may form an indirect zinc interaction. We investigated the functional roles of the glutamate and aspartate residues in the ACE C domain (Glu987 and Asp991) using a cDNA encoding an inactive N domain. We mutated Glu987 to aspartate (E987D) or valine (E987V) and Asp991 to glutamate (D991E) or alanine (D991A). Catalytically active mutants (E987D, D991E and D991A) exhibited similar Km values for hippuryl-His-Leu compared to non-mutated C domain. E987D displayed a 300-fold decrease in kcat and a 25-fold reduction in sensitivity to the ACE inhibitor trandolaprilat, whose binding is zinc-dependent. E987V was catalytically inactive and did not bind [3H]trandolaprilat. D991E and D991A exhibited a 3.8- and 22-fold decrease in kcat, respectively, and the Ki' values for trandolaprilat were increased 8- and 29-fold. These results provide strong evidence that Glu987 constitutes the third zinc ligand in the ACE C domain and suggest a role for Asp991 in positioning the C domain active site zinc ion.