gebhart/patrepeval huggingface dataset:
Synthesis of bolaform biosurfactants by an engineered <i>Starmerella bombicola</i> yeast (2016)

Bola-amphiphilic surfactants are molecules with fascinating properties. Their unique configuration consisting of a long hydrophobic spacer connecting two hydrophilic entities renders the molecule more water soluble than the average surfactant, but still allows formation of supramolecular structures. These properties make them extremely suitable for applications in in nanotechnology, electronics, and gene and drug delivery. In general, these compounds are obtained by chemical synthesis. We report here an efficient microbial production process for the fully green synthesis of bolaform surfactants. A sophorolipid-producing Starmerella bombicola yeast strain was disabled in its sophorolipid acetyltransferase and lactone esterase, which should logically result in synthesis of non-acetylated acidic sophorolipids; molecules with the classic amphiphilic structure. Surprisingly, also bolaform glycolipids were obtained, with an additional sophorose linked to the free carboxyl end of the acidic sophorolipids as confirmed by MS and NMR analysis. The obtained titers of 27.7 g/L total product are comparable to wild type values, and the novel molecules account for at least 74% of this. Bola-amphiphile biosynthesis proved to be attributed to the promiscuous activity of both UDP-glucosyltransferases UGTA1 and UGTB1 from the core sophorolipid pathway, displaying activity toward non-acetylated intermediates. The absence of acetyl groups seems to trigger formation of bolaform compounds starting from acidic sophorolipids. Hence, wild type S. bombicola produces these compounds only at marginal amounts in general not reaching detection limits. We created a strain knocked-out in its sophorolipid acetyltransferase and lactone esterase able to produce these novel compounds in economical relevant amounts, opening doors for the application of biological-derived bolaform structures. Biotechnol. Bioeng. 2016;113: 2644-2651. © 2016 Wiley Periodicals, Inc.
Expression pattern and localization of β,β-carotene 15,15′-dioxygenase in different tissues (2001)

Beta,beta-carotene 15,15'-dioxygenase cleaves beta,beta-carotene into two molecules of retinal, and is the key enzyme in the metabolism of beta,beta-carotene to vitamin A. The enzyme has been known for more than 40 years, yet all attempts to purify the protein to homogeneity have failed. Recently, the successful cloning and sequencing of an enzyme with beta,beta-carotene 15,15'-dioxygenase activity from chicken, as well as from Drosophila, has been reported. Here, we describe in detail our attempt to enrich the chicken beta,beta-carotene 15,15'-dioxygenase to such an extent as to allow determination of partial amino acid sequences, which were then used to design degenerate oligonucleotides. Screening of a chicken duodenal expression library yielded a full-length clone containing a coding sequence of 1578 bp. Functional expression in Escherichia coli and in eukaryotic cell lines confirmed that we had cloned the first vertebrate dioxygenase that cleaves beta,beta-carotene at the central 15,15'-double bond. By performing a sequence homology search, the cDNA sequence of the mouse homologue was found as an expressed sequence tag (EST) in the gene bank. At the amino-acid level, the degree of homology between the chicken and mouse sequences is 81%. Thus beta,beta-carotene 15,15'-dioxygenase can be considered as being an enzyme that is evolutionarily rather well conserved. We established the expression pattern of beta,beta-carotene 15,15'-dioxygenase in chicken and mouse tissues with a combination of Northern blots and in situ hybridization. The mRNA for beta,beta-carotene 15,15'-dioxygenase was localized primarily in duodenal villi, as well as in liver and in tubular structures of lung and kidney. These new findings demonstrate that beta,beta-carotene 15,15'-dioxygenase is also expressed in epithelial structures, where it serves to provide the tissue-specific vitamin A supply.
Development and anti‐tumor activities of claudin‐4‐specific monoclonal antibodies (1062.8) (2014)

Claudin (CLDN) is a key component of the epithelial tight junction. Expression of the various CLDNs differs among tissues and is deregulated in malignant tumors. For example, CLDN4 is frequently overexpressed in pancreatic, breast, and ovarian cancers and therefore may be an attractive target for anticancer drugs. However, the low antigenicity of CLDN4 has hampered the development of antibody‐based CLDN4‐targeted cancer therapy. We successfully generated monoclonal antibodies (mAbs) to CLDN4 and evaluated their anti‐tumor activity. Briefly, we immunized rats with plasmids containing the CLDN4 coding sequence. We fused the resulting B cells with myeloma cells and screened 8 hybridoma clones that produced anti‐CLDN4 mAbs. All 8 mAbs bound to CLDN4‐expressing cells but not to those expressing CLDN1, 2, 5, 6, 7or 9. All 8 mAbs showed CLDN4 binding‐dependent activation of the Fcγ receptor. A clone with high affinity to CLDN4 suppressed tumor growth in vitro and in vivo. Interestingly, treatment of cancer cells with the clone of CLDN4‐specific mAb and an anti‐cancer drug (5‐flurouracil or cisplatin) had a synergistic cytotoxic effect. Specifically, mAb treatment increased intracellular drug levels. Our findings indicate that CLDN4 mAbs are promising tools for CLDN4‐targeted cancer therapy. Grant Funding Source : supported by the Ministry of Health, Labor, and Welfare of Japan
Delivery of Exogenous Protein Antigens to Major Histocompatibility Complex Class I Pathway in Cytosol (2002)

A fragment of anthrax lethal factor possesses the interesting function of delivering recombinant protein antigens through the classical major histocompatibility complex (MHC) class I pathway. This region of the lethal factor lacks the domain associated with anthrax cytotoxicity and functions independently of its binary partner, protective antigen. Experiments that used inhibitors at different steps of the MHC class I pathway supported this hypothesis. Application of this discovery to current T cell assays allows for the measurement of cytotoxic T lymphocyte function without resorting to live vectors and provides a useful new tool to design and test T cell–dependent vaccines
The Nicotinic Receptor Genes (1991)

The causative factor(s) of Alzheimer's disease (AD) are presently unknown. However, it has been shown that the number as well as the fraction of high- to low-affinity nicotine binding sites is altered in patients suffering from this disease. This finding, along with the identification of seven genes which code for nicotinic receptors expressed in the mammalian brain, has led to the idea that one nicotinic receptor subtype may be specifically altered in AD. The present article reviews how, through a molecular genetic approach, a family of genes coding for nicotinic acetylcholine receptor subtypes was uncovered. Also discussed is the use of in situ hybridization to determine the distribution of expression of the mRNA encoding for each receptor subtype and the patch clamp technique to characterize their biophysical properties. Determination of the promoters of these genes, as well as the properties of the expressed receptor subtypes, may make it possible to design new specific nicotinic receptor subtype drugs that will treat not only the symptoms of AD but the progression of the disease process as well.
Using BGP as an Auto-Discovery Mechanism for VR-based Layer-3 VPNs (2007)

In any provider-based VPN scheme, the Provider Edge (PE) devices
attached to a common VPN must exchange certain information as a
prerequisite to establish VPN-specific connectivity. The main purpose
of an auto-discovery mechanism is to enable a PE to dynamically
discover the set of remote PEs having VPN members in common. The auto-
discovery mechanism proceeds by having a PE advertises to other PEs,
at a minimum, its own IP address and the list of VPN members
configured on that PE. Once that information is received the remote
PEs will then identify the list of VPN sites members of the same VPN,
and use the information carried within the discovery mechanism to
establish VPN connectivity. This draft defines a BGP based auto-
discovery mechanism for Virtual Router-based layer-3 VPNs. This
mechanism is based on the approach used by BGP/MPLS-IP-VPN for
distributing VPN routing information within the service provider(s).
Expression of drug transporters in the human skin: comparison in different species and models and its implication for drug development (2017)

<p class="ADMETabstracttext">It is clear that many drug transporters (both ABCs and SLCs) are present in the human skin. Different in vitro skin models can be used to investigate the role of drug transporters in the skin despite quantitative differences in expression profile across species. P-gp was shown to have an important influence on transdermal drug absorption in the skin and to function in “absorptive” transport, carrying substrate drugs from the skin surface to the dermis. This observation might be used to modulate drug distribution inside the skin. If drugs can be retained in the epidermis compartment by inhibition of the transporters, such property of the drug would be beneficial for treatment of dermatological diseases. Therefore, it might be feasible to control transdermal delivery of drugs to specific locations in the skin, by modulating the function of the transporters in the skin. We are at the dawn of an exciting period where drug transporters might be novel targets for improvement of drug delivery to the skin and for pharmacological intervention.</p>
p53-induced apoptosis of prostate cancer cells requires XIAP down-regulation (2005)

2263 This study was undertaken to investigate the role of purine analogues in modulating prostate cancer growth and to evaluate the potential X-linked inhibitors of apoptosis (XIAP) as a target for prostate cancer therapy. Purine analogues such as roscovitine and CGP74514A were tested in human prostate cancer models with various p53 status, LnCaP (p53 wt/wt), DU145 (p53mt/mt), and PC3 (p53null). Our results suggest that exposure to roscovitine and CGP74514A induced cell cycle arrest, mitochondria-dependent activation of caspase-9 and caspase-3 and apoptosis of both LnCaP and androgen refractory LnCaP (LnCaP-Rf) cells. The apoptosis in these cells was accompanied by stabilization of p53 and down-regulation of XIAP, but did not require inhibiton of Akt activity. Roscovitine and CGP74514A also induced down-regulation of XIAP in DU145 and PC3 cells, but moderate apoptosis was induced only when the cells were exposed to high dosage of drug, suggesting the requirement for functional p53. Accordingly, over-expression of p53 but not down-regulation of XIAP increased sensitivity of PC3 cells toward roscovitine and CGP74514A. Further, concomitant over-expression of wt p53 and down-regulation of XIAP induced apoptosis of LnCaP, DU145 and PC3 cells even in the absence of roscovitine. Together, these results suggest that lack of functional p53 and increased expression of XIAP contribute toward apoptosis-resistance in androgen-independent prostate cancer cells and should be targeted for inducing apoptosis in these cells.
High-Yield Production of Secreted Active Proteins by the <i>Pseudomonas aeruginosa</i> Type III Secretion System (2008)

The Escherichia coli system is the system of choice for recombinant protein production because it is possible to obtain a high protein yield in inexpensive media. The accumulation of protein in an insoluble form in inclusion bodies remains a major disadvantage. Use of the Pseudomonas aeruginosa type III secretion system can avoid this problem, allowing the production of soluble secreted proteins.
Triggered single photons from a quantum dot (2002)

Summary form only given. A source of single photons, each arriving within a known time interval, would be useful in the new field of quantum cryptography, where security from eavesdropping requires that only one photon be sent at a time. While other recent efforts to generate single photons have relied on saturated absorption in a single quantum emitter such as a molecule our method takes advantage of the emission properties of a single emitter, an InAs dot. When a laser pulse creates multiple electron-hole pairs (excitons), the last pair to recombine creates a photon at a unique wavelength, which can be spectrally separated from the others. This is because Coulomb interactions shift the emission wavelength when multiple excitons are present.
Results With the Neutron Scatter Camera (2009)

We describe the design, calibration, and measurements made with the neutron scatter camera. Neutron scatter camera design allows for the determination of the direction and energy of incident neutrons by measuring the position, recoil energy, and time-of-flight (TOF) between elastic scatters in two liquid scintillator cells. The detector response and sensitive energy range (0.5-10 MeV) has been determined by detailed calibrations using a <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">252</sup> Cf neutron source over its field of view (FOV). We present results from several recent deployments. In a laboratory study we detected a <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">252</sup> Cf neutron source at a stand off distance of 30 m. A hidden neutron source was detected inside a large ocean tanker. We measured the integral flux density, differential energy distribution and angular distribution of cosmic neutron background in the fission energy range 0.5-10 MeV at Alameda, CA (sea level), Livermore, CA (174 m), Albuquerque, NM (1615 m) and Fenton Hill, NM (2630 m). The neutron backgrounds are relatively low, and non-isotropic. The camera has been ruggedized, deployed to various locations and has performed various measurements successfully. Our results show fast neutron imaging could be a useful tool for the detection of special nuclear material (SNM).
A Novel Small Molecule Targets Androgen Receptor and Its Splice Variants in Castration-Resistant Prostate Cancer (2019)

Reactivation of androgen receptor (AR) appears to be the major mechanism driving the resistance of castration-resistant prostate cancer (CRPC) to second-generation antiandrogens and involves AR overexpression, AR mutation, and/or expression of AR splice variants lacking ligand-binding domain. There is a need for novel small molecules targeting AR, particularly those also targeting AR splice variants such as ARv7. A high-throughput/high-content screen was previously reported that led to the discovery of a novel lead compound, 2-(((3,5-dimethylisoxazol-4-yl)methyl)thio)-1-(4-(2,3-dimethylphenyl)piperazin-1-yl)ethan-1-one (IMTPPE), capable of inhibiting nuclear AR level and activity in CRPC cells, including those resistant to enzalutamide. A novel analogue of IMTPPE, JJ-450, has been investigated with evidence for its direct and specific inhibition of AR transcriptional activity via a pulldown assay and RNA-sequencing analysis, PSA-based luciferase, qPCR, and chromatin immunoprecipitation assays, and xenograft tumor model 22Rv1. JJ-450 blocks AR recruitment to androgen-responsive elements and suppresses AR target gene expression. JJ-450 also inhibits ARv7 transcriptional activity and its target gene expression. Importantly, JJ-450 suppresses the growth of CRPC tumor xenografts, including ARv7-expressing 22Rv1. Collectively, these findings suggest JJ-450 represents a new class of AR antagonists with therapeutic potential for CRPC, including those resistant to enzalutamide.
Synthetic Biomimetic Carbonate-Hydroxyapatite Nanocrystals for Enamel Remineralization (2008)

New biomimetic carbonate-hydroxyapatite nanocrystals (CHA) have been designed and synthesized in order to obtain a remineralization of the altered enamel surfaces. Synthesized CHA mimic for composition, structure, nano dimension and morphology bone apatite crystals and their chemical-physical properties resemble closely those exhibited by enamel natural apatite. CHA can chemically bound themselves on the surface of natural enamel apatite thanks to their tailored biomimetic characteristics. The remineralization effect induced by CHA represents a real new deposition of carbonate-hydroxyapatite into the eroded enamel surface scratches forming a persistent biomimetic mineral coating, which covers and safeguards the enamel structure. The experimental results point out the possibility to use materials alternative to fluoride compounds which is commonly utilized to contrast the mechanical abrasions and acid attacks. The apatitic synthetic coating is less crystalline than enamel natural apatite, but consists of a new biomimetic apatitic mineral deposition which progressively fills the surface scratches. Therefore the application of biomimetic CHA may be considered an innovative approach to contrast the acid and bacteria attacks.
Elimination of lithographic hotspots which have been waived by means of pattern matching (2011)

A persistent problem in verification flows is to eliminate waivers defined as patterns that are known to be safe on silicon even though they are flagged by the verification recipes. The difficulty of the problem stems from the complexity of these patterns, and thus, using a standard verification language to describe them becomes very tedious and can deliver unexpected results. In addition, these patterns have a dynamic nature, hence, updating all production verification recipes to waive these non critical patterns becomes more time consuming. In this work, we are presenting a new method to eliminate waivers directly after verification recipes have been executed, where a new rule file will be generated automatically based on the type of errors under investigation. The core of the method is based on pattern matching to compare generated errors from verifications runs with a library of pattern waivers. This flow will eliminate the need to edit any production recipe, and complicated coding will not be required. Finally, this flow is compatible with most of the technology nodes.
Application of Nonlinear Lamb Wave Mixing Method for Residual Stress Measurement in Metal Plate (2023)

Abstract Harmonic nonlinear ultrasound can offer high sensitivity for residual stress measurements; however, it cannot be used for local stress measurements at a point in space and exhibits nonlinear distortions in the experimental system. This paper presents a feasibility study on the measurement of residual stress in a metal plate using a nonlinear Lamb wave-mixing technique. The resonant conditions for two Lamb waves to generate a mixing frequency wave are obtained via theoretical analysis. Finite element simulations are performed to investigate the nonlinear interactions between the two Lamb waves. Results show that two incident A0 waves interact in regions of material nonlinearity and generate a rightward S0 wave at the sum frequency. Residual stress measurement experiments are conducted on steel plate specimens using the collinear Lamb wave-mixing technique. By setting different delays for two transmitters, the generated sum-frequency component at different spatial locations is measured. Experimental results show that the spatial distribution of the amplitude of the sum-frequency component agrees well with the spatial distribution of the residual stress measured using X-rays. The proposed collinear Lamb wave-mixing method is effective for measuring the distribution of residual stress in metal plates.
Lithographically Patterned Nanowire Electrodeposition: A Method for Patterning Electrically Continuous Metal Nanowires on Dielectrics (2008)

Lithographically patterned nanowire electrodeposition (LPNE) is a new method for fabricating polycrystalline metal nanowires using electrodeposition. In LPNE, a sacrificial metal (M(1)=silver or nickel) layer, 5-100 nm in thickness, is first vapor deposited onto a glass, oxidized silicon, or Kapton polymer film. A (+) photoresist (PR) layer is then deposited, photopatterned, and the exposed Ag or Ni is removed by wet etching. The etching duration is adjusted to produce an undercut approximately 300 nm in width at the edges of the exposed PR. This undercut produces a horizontal trench with a precisely defined height equal to the thickness of the M(1) layer. Within this trench, a nanowire of metal M(2) is electrodeposited (M(2)=gold, platinum, palladium, or bismuth). Finally the PR layer and M(1) layer are removed. The nanowire height and width can be independently controlled down to minimum dimensions of 5 nm (h) and 11 nm (w), for example, in the case of platinum. These nanowires can be 1 cm in total length. We measure the temperature-dependent resistance of 100 microm sections of Au and Pd wires in order to estimate an electrical grain size for comparison with measurements by X-ray diffraction and transmission electron microscopy. Nanowire arrays can be postpatterned to produce two-dimensional arrays of nanorods. Nanowire patterns can also be overlaid one on top of another by repeating the LPNE process twice in succession to produce, for example, arrays of low-impedance, nanowire-nanowire junctions.
Automatic mutual exclusion (2007)

We propose a new concurrent programming model, Automatic Mutual Exclusion (AME). In contrast to lock-based programming, and to other programming models built over software transactional memory (STM), we arrange that all shared state is implicitly protected unless the programmer explicitly specifies otherwise. An AME program is composed from serializable atomic fragments. We include features allowing the programmer to delimit and manage the fragments to achieve appropriate program structure and performance. We explain how I/O activity and legacy code can be incorporated within an AME program. Finally, we outline ways in which future work might expand on these ideas. The resulting programming model makes it easier to write correct code than incorrect code. It favors correctness over performance for simple programs, while allowing advanced programmers the expressivity they need.
Spatial-domain low-coherence quantitative phase microscopy for cancer diagnosis (2010)

A microscopy technique, spatial-domain low-coherence quantitative phase microscopy (SL-QPM) is proposed for speckle-free, quantitative phase imaging of subcellular structures with subnanometer sensitivity. We quantified, for the first time to our knowledge, the refractive index of the cell nuclei on original unmodified histology specimens. We demonstrate that the refractive index of cell nucleus is highly sensitive in detecting cancer, especially in histologically normal-appearing cells from cancer patients. Because this technique is sensitive and does not require special sample processing, it can be disseminated to all clinical settings.
CO2 extraction from seawater using bipolar membrane electrodialysis (2012)

An efficient method for extracting the dissolved CO2 in the oceans would effectively enable the separation of CO2 from the atmosphere without the need to process large volumes of air, and could provide a key step in the synthesis of renewable, carbon-neutral liquid fuels. While the extraction of CO2 from seawater has been previously demonstrated, many challenges remain, including slow extraction rates and poor CO2 selectivity, among others. Here we describe a novel solution to these challenges – efficient CO2 extraction from seawater using bipolar membrane electrodialysis (BPMED). We characterize the performance of a custom designed and built CO2-from-seawater prototype, demonstrating the ability to extract 59% of the total dissolved inorganic carbon from seawater as CO2 gas with an electrochemical energy consumption of 242 kJ mol−1(CO2).
New Antibacterial Agent (U-24,544) Isolated from <i>Streptomyces griseus</i> (1967)

Antibiotic U-24,544 is a new agent isolated from the culture broth of a streptomycete strain. The antibiotic inhibits a variety of gram-positive and gram-negative bacteria in vitro, but is ineffective in treatment of experimental bacterial infections in mice. It is fairly cytotoxic in mammalian cell cultures and remarkably nontoxic in mice.