gebhart/patrepeval huggingface dataset:
Ultra-high-quality sequencing assay for comprehensive genetic panel analysis of tumor-derived circulating cell-free DNA in colorectal cancer patients. (2014)

504 Background: Current approaches based on invasive biopsy genetic analysis can fail to capture an accurate picture of the real-time cancer profile due to limited spatial window of biopsy into residual disease throughout the body. Moreover, tumor rebiopsy has significant challenges to be widely used in practice for serial monitoring of disease progression or acquired resistance. Analysis of circulating tumor nucleic acids (ctDNA), on the other hand, presents a new tool for the monitoring and treatment of cancer. However, due to high-quality false positives in current NGS assays, the majority of studies on ctDNA have been limited to hotspot analyses, and typically only involve patients where ctDNA fractions are high (&gt;1-5%). Methods: We have developed a differentiated sequencing assay, Digital Sequencing Technology (DST) that enables detection of rare genomic abnormalities with ultra high-specificity and sensitivity. Our assay is able to eliminate the error and distortion created by sample-prep and sequencing processes in standard NGS workflows and produce near-perfect representations of all rare variants. Results: We have shown that in sequencing a comprehensive cancer panel of 80kbp in 0.1% cancer cell line titration samples, standard Illumina SBS generates many high-quality false positive variant calls in the range of 0.05-5%, while our assay resulted in highly sensitive and completely error-free variant calls across the entire panel. We then profiled ctDNA and matched primary tumor samples in more than 50 plasma samples collected from metastatic colorectal cancer patients. We found mutations in ctDNA with allele frequencies in the range of 0.05-40%. We established the concordance of ctDNA mutations with different clones within primary tumors. We further investigated the potential clinical usefulness of discordant mutants based on the treatment history of each patient. Conclusions: This work indicates the remarkable potential of using our assay in deep analysis of ctDNA, thereby allowing researchers and clinicians to comprehensively and non-invasively monitor the genetic dimension of cancer throughout the body.
Al Gettering for InGaAsN in Metalorganic Chemical Vapor Deposition (2004)

We proposed and demonstrated an Al gettering process for high-quality InGaAsN quantum wells grown by metalorganic chemical vapor deposition. Ammonia flow prior to InGaAsN growth eliminates undesirable Al incorporation in the InGaAsN continuously grown on GaAs/AlGaAs layers. The InGaAsN quantum well without Al contamination showed a smooth surface and strong photoluminescence intensity. An InGaAsN vertical cavity surface-emitting laser structure grown in a single-step process using the Al gettering process showed continuous-wave operations with 2.7 mW of 1279 nm emission at room temperature.
<title>Design review of a high-accuracy UV to near-IR scatterometer</title> (1993)

A unique broadband scatterometer has been designed, built and tested for NASA Goddard. One use of the instrument will be to accurately measure the BRDF of calibration standards used by shuttle astronauts in experiments to measure atmospheric ozone. BRDF accuracy is better than 1% except for angles of incidence and scatter greater than 80 degrees. The source employs a high intensity xenon arc and programmable monochromator that allows measurements to be made anywhere from 0.23 to 0.9 micrometers over adjustable bandwidths as small as four nanometers. The goniometer allows out-of-plane measurements to be made in either transmission or reflection from horizontal samples.
ChemInform Abstract: A Convenient Preparation of 4‐Vinylphenylacetic Acid and Its Methyl Ester. (1995)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
Pd-Mediated C-C Bond Formation with Olefins and Acetylenes on Solid Support: A Scope and Limitations Study (1998)

In this paper we report the scope and limitations of Pd(0)-mediated coupling reactions between aromatic iodides linked to a polystyrene resin and terminal acetylenes and olefins (Heck reactions). Optimized reaction conditions were evaluated with a number of different reagents. The optimized reaction conditions were frequently found to be superior to those previously reported in the literature and resulted in excellent yields of the products upon cleavage from the solid phase.
Gene Therapy Using a Simian Virus 40–Derived Vector Inhibits the Development of In Vivo Human Immunodeficiency Virus Type 1 Infection of Severe Combined Immunodeficiency Mice Implanted with Human Fetal Thymic and Liver Tissue (2002)

To evaluate the in vivo efficacy of gene therapy for treating human immunodeficiency virus type 1 (HIV-1) infection, a novel simian virus (SV) 40-derived vector gene delivery system that efficiently transduces human leukocytes was combined with a model using severe combined immunodeficiency mice infected with HIV-1 and implanted with human fetal thymic and liver tissue (thy/liv-SCID-hu mice). The SV40-derived vector, SV(Aw), which encodes a variable fragment antibody recognizing HIV-1 integrase (IN#33),was injected into the human thymic grafts of thy/liv-SCID-hu mice and induced IN#33 expression in most of the thymocytes in the graft. After in vivo challenge with HIV-1, IN#33 expression inhibited in vivo HIV-1 infection, as evidenced by the markedly lower number of HIV-1-infected thymocytes detected in human thymic grafts injected with the SV(Aw) vector, compared with those injected with a control SV40-derived vector. Thus, these findings demonstrate the utility of this new mouse model system for assessing the in vivo efficacy of HIV-1-specific gene therapy. In addition, these data indicate that SV40-derived vectors may provide a system capable of efficient in vivo gene delivery.
Effect of chimeric antigen receptor (CAR) T cells on clonal expansion of endogenous non-CAR T cells in patients (pts) with advanced solid cancer. (2017)

3011 Background: CAR T cells have produced remarkable responses in heme malignancies, but efficacy in solid cancers is limited. Poor in vivo persistence and heterogeneous expression of the CAR target on tumors are potential barriers to the success of CAR T cell therapy. However, even with transient persistence, CAR T cells may elicit a “vaccine” effect by inducing cancer cell death and subsequent release of tumor antigens that could stimulate tumor-specific T cell activity. Methods: 6 pts with pancreatic ductal adenocarcinoma (PDAC) received repeated 3x per week intravenous (iv) infusions of mRNA-transfected mesothelin-redirected CAR T cells (CARTmeso). Pts with PDAC (n = 5), ovarian carcinoma (n = 5), and mesothelioma (n = 5) received iv infusion of lentiviral-transduced (lenti) CARTmeso with or without cyclophosphamide (Cy) preconditioning. Peripheral blood samples were collected from pts at baseline and defined time points after treatment. Genomic DNA from these samples or from pre-infused CAR T cell product was used for deep sequencing of the TCRbeta chain using the ImmunoSEQ platform. A TCRbeta clone was considered to have expanded from baseline to defined time points after treatment if it showed a two-fold change from baseline and met statistical significance by Fisher’s exact test (p &lt; 0.05). Results: mRNA CARTmeso cells persisted in vivo for &lt; 24 hrs. Unexpectedly, therapy induced clonal T cell expansion detected in the blood by day 14 in all 6 pts. Expanded clones underwent contraction by day 28 in 3 pts. In one pt, peripherally expanded clones were also detected in a tumor biopsy, but without significant intratumoral clonal expansion. Lenti CARTmeso therapy also induced peripheral expansion of T cell clones both present and not present in the infused CAR T cell product. However, with Cy preconditioning, clonal expansion seen after lenti CARTmeso therapy was predominately restricted to clones detected in the CAR T cell product. Conclusions: In pts with advanced solid cancers, CARTmeso stimulates clonal expansion of endogenous T cells, which is lost with Cy conditioning. Findings suggest that CAR T cells may elicit a “vaccine” effect with potential therapeutic implications.
Enhanced extraction of phenol from model oils using ionic liquids elucidated with neutron diffraction (2020)

Aromatic cation ionic liquids (ILs) based on alkylpyridiniums are shown to be good phenol extractants from model oils (hexane/toluene). ILs with hard basic anions are found to have best extraction efficiency consistent with tetraalkylammonium salts ([NR4]X). Key extraction interactions were analysed using small angle neutron diffraction. Trifluoromethanesulphonate ([OTf]- or triflate) anions provide the synergistic effects of reduced cation-phenol centre of mass (COM) distances and increased hydrogen bonding that are linked to the improved extraction efficiency. Increases in cation electron density (methylpyridinium ([Me-Py]+) vs. methylpicolinium ([Me-3-Pic]+)) also reduce cation-phenol COM interaction lengths consistent with small increases in extraction efficiency for the same ionic liquids.
On the universality of the flow properties of soft-particle glasses (2018)

We identify the minimal interparticle interactions necessary for a particle dynamics simulation to predict the structure and flow behaviour of soft particle glasses (SPGs). Generally, two kinds of forces between the particles must be accounted for in simulations of SPGs: viscous or frictional drag forces and elastic contact forces. Far field drag forces are required to dissipate energy in the simulations and capture the effect of the rheology of the suspending fluid. Elastic forces are found to be dominant compared to near-field drag or other forms of friction forces and are the most important component to compute the rheology. The shear stress, the first and second normal stress differences for different interparticle force laws collapse onto universal master curves of the Herschel-Bulkley form by non-dimensionalizing the stress with the yield stress and the shear rate with the viscosity of the suspending fluid divided by the low-frequency shear modulus. The Herschel-Bulkley exponents are close to 0.5 with a slight dependence on the repulsive pairwise elastic forces.
Comparison of Short-term Outcomes After Lumbar Fusion Between an Orthopedic Specialty Hospital and Tertiary Referral Center (2018)

3.
Bio-inspired tunable disorder in a 3D photonic crystal via highly controlled partial wetting and drying (2012)

We use highly controlled partial wetting in chemically encoded 3D photonic crystals to study tunable disorder in structurally colored systems. Our experimental and FDTD analyses also guide our design of a colorimetric indicator for organic liquids.
Standard-compliant detection of fillet weld surface imperfections for MAG-welding using a 3D-line scanner (2021)

Within the paper the use of a 3D-line scanner is evaluated to realize an inline and intime detection of weld imperfections for an automated MAG-welding of fillet welds. The required conditions of the weld are in accordance with the quality level B of the international standard ISO 5817 [1]. The used system is a Wenglor 3D-line scanner with a wavelength of 660 nm and an image recording frequency of at least 200 Hz. This scanner is able to detect, as a stand-alone system, geometry and surface imperfections of the weld. Therefore, algorithms were developed for the reliable recognition of deviations regarding the size, superelevations, undercuts, seam transition angles and the symmetry of the weld with a measurement accuracy of 10 ➭m. With the information, gathered by the line scanner and the corresponding image-data processing algorithms, it is possible to improve the efficiency of automated MAG-welding. The welding process can be interrupted and recalibrated if significant imperfections are detected. This is realized with a short time delay depending on the distance between the welding torch and the camera and the welding speed. The direct feedback could prevent the weldment from getting unusable and saving ressources through minor required efforts for renewing or revising the weld. Additionally, the required visual testing (ISO 17635 [2], ISO 17637 [3]) can be objectified and accelerated by highlighting the parts of the weld which are most probably affected by imperfections. In the future this automated system could possibly replace the manual quality inspection.
Genome archaeology of two laboratory Salmonella enterica enterica sv Typhimurium (2021)

Abstract The Salmonella research community has used strains and bacteriophages over decades, exchanging useful new isolates among laboratories for study of cell surface antigens, metabolic pathways and restriction-modification studies. Here we present the sequences of two laboratory Salmonella strains (STK005, an isolate of LB5000; and its descendant ER3625). In the ancestry of LB5000, segments of ~15 and ~42 kb were introduced from Salmonella enterica sv Abony 103 into Salmonella enterica sv Typhimurium LT2, forming strain SD14; this strain is thus a hybrid of S. enterica isolates. Strains in the SD14 lineage were used to define flagellar antigens from the 1950s to the 1970s, and to define three restriction-modification systems from the 1960s to the 1980s. LB5000 was also used as host in phage typing systems used by epidemiologists. In the age of cheaper and easier sequencing, this resource will provide access to the sequence that underlies the extensive literature.
Visual Cues for Vehicle Control (1993)

Since Gibson's pioneering work in the 1950s, there has been increasing interest in describing the dynamic visual cues operators extract from the “out-the-window” scene to utilize in vehicular control. Despite this interest, we are still a long way from an adequate understanding of what optical information is utilized, and how the information is integrated into an active control strategy. There are a number of reasons for this apparent shortfalling. First, it is difficult to isolate a candidate optical cue; geometry dictates that several candidate cues will co-vary in any natural scene (e.g., edge rate and flow rate). The experimental isolation of an optical cue often results in visual scenes which are quite unnatural, creating the possibility that strategies used in the experimental setting will not generalize to operational settings. Also, much of the laboratory work has focused on demonstrating people's sensitivity to optical variables, utilizing passive verbal judgments rather than active control paradigms. Whereas the demonstration of sensitivity to an optical cue is a logically necessary step, such a demonstration is not sufficient to verify its utility in an active control task. Further, there is the need for an adequate description of the task demands, allowing a proper mapping between what the controller is trying to achieve and the information available to accomplish the task; no single cue (or set of cues) will be appropriate for all vehicular control tasks. Finally, given the robust and opportunistic nature of the human perceptual system, it is possible that the visual cues used for vehicle control will vary from individual to individual, or even within an individual depending on which cues are available and salient in the control environment. The participants in this panel are well versed in the challenges of studying visually based vehicular control. Their presentations will reflect the lessons learned in this field, as well as insights regarding how current and future research can better realize the promise of this domain.
A full lifecycle performance verification methodology for multicore systems-on-chip (2012)

Multicore Systems-on-Chip (MCSoC) are comprised of a rich set of processor cores, specialized hardware accelerators, and I/O interfaces. Functional verification of these complex designs is a critical and demanding task, however, focusing only on functional verification is very risky because the motivation for building such systems in the first place is to achieve high levels of system throughput. Therefore a functionally correct MCSoC that does not exhibit sufficient performance will fail in the market. In addition, limiting performance verification efforts to analyzing individual system components in isolation is insufficient due to: (1) the degree of system-level resource contention that an application domain imposes on the MCSoC, and (2) the degree of configuration flexibility that is typically afforded by an MCSoC. These factors motivate system-level performance verification of MCSoC. This article presents an important industrial case study of MCSoC performance verification involving both pre- and postsilicon analysis, highlighting the methodology used, the lessons learned, and recommendations for improvement.
ChemInform Abstract: Efficient Synthesis of Isoxazoles and Isoxazolines from Aldoximes Using Magtrieve (CrO2). (2009)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 200 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
Remote ischemic preconditioning immediately before percutaneous coronary intervention does not impact myocardial necrosis, inflammatory response, and circulating endothelial progenitor cell counts: A single center randomized sham controlled trial (2012)

Our study indicates that remote IP immediately before PCI does not induce cardioprotection in low to moderate risk patients.
Unsymmetrical Diarylketones from Electron‐Rich Heterocyclic Arenes. (2003)

Abstract For Abstract see ChemInform Abstract in Full Text.
Asparagine and Aspartate Hydroxylation of the Cytoskeletal Ankyrin Family Is Catalyzed by Factor-inhibiting Hypoxia-inducible Factor (2010)

Factor-inhibiting hypoxia-inducible factor (FIH) catalyzes the β-hydroxylation of an asparagine residue in the C-terminal transcriptional activation domain of the hypoxia inducible factor (HIF), a modification that negatively regulates HIF transcriptional activity. FIH also catalyzes the hydroxylation of highly conserved Asn residues within the ubiquitous ankyrin repeat domain (ARD)-containing proteins. Hydroxylation has been shown to stabilize localized regions of the ARD fold in the case of a three-repeat consensus ankyrin protein, but this phenomenon has not been demonstrated for the extensive naturally occurring ARDs. Here we report that the cytoskeletal ankyrin family are substrates for FIH-catalyzed hydroxylations. We show that the ARD of ankyrinR is multiply hydroxylated by FIH both in vitro and in endogenous proteins purified from human and mouse erythrocytes. Hydroxylation of the D34 region of ankyrinR ARD (ankyrin repeats 13-24) increases its conformational stability and leads to a reduction in its interaction with the cytoplasmic domain of band 3 (CDB3), demonstrating the potential for FIH-catalyzed hydroxylation to modulate protein-protein interactions. Unexpectedly we found that aspartate residues in ankyrinR and ankyrinB are hydroxylated and that FIH-catalyzed aspartate hydroxylation also occurs in other naturally occurring AR sequences. The crystal structure of an FIH variant in complex with an Asp-substrate peptide together with NMR analyses of the hydroxylation product identifies the 3S regio- and stereoselectivity of the FIH-catalyzed Asp hydroxylation, revealing a previously unprecedented posttranslational modification.
Discovery and Selection of TMC114, a Next Generation HIV-1 Protease Inhibitor (2004)

The screening of known HIV-1 protease inhibitors against a panel of multi-drug-resistant viruses revealed the potent activity of TMC126 on drug-resistant mutants. In comparison to amprenavir, the improved affinity of TMC126 is largely the result of one extra hydrogen bond to the backbone of the protein in the P2 pocket. Modification of the substitution pattern on the phenylsulfonamide P2' substituent of TMC126 created an interesting SAR, with the close analogue TMC114 being found to have a similar antiviral activity against the mutant and the wild-type viruses. X-ray and thermodynamic studies on both wild-type and mutant enzymes showed an extremely high enthalpy driven affinity of TMC114 for HIV-1 protease. In vitro selection of mutants resistant to TMC114 starting from wild-type virus proved to be extremely difficult; this was not the case for other close analogues. Therefore, the extra H-bond to the backbone in the P2 pocket cannot be the only explanation for the interesting antiviral profile of TMC114. Absorption studies in animals indicated that TMC114 has pharmacokinetic properties comparable to currently approved HIV-1 protease inhibitors.
Use of A U16 snoRNA-containing Ribozyme Library to Identify Ribozyme Targets in HIV-1 (2008)

Hammerhead ribozymes have been shown to silence human immunodeficiency virus-1 (HIV-1) gene expression by site-specific cleavage of viral mRNA. The two major factors that determine whether ribozymes will be effective for post-transcriptional gene silencing are colocalization of the ribozyme and the target RNAs, and the choice of an appropriate target site on the mRNA. An effective screening strategy for potential targets on the viral genome is the use of ribozyme libraries in cell culture. Capitalizing on previous findings that HIV-1 and ribozymes can be colocalized in the nucleolus, we created a novel hammerhead ribozyme library by inserting hammerhead ribozymes with fully randomized stems 1 and 2 into the body of the U16 small nucleolar RNA (snoRNA). Following three rounds of cotransfection with an HIV-1 proviral DNA harboring the herpes simplex virus thymidine kinase (HSV-TK) gene, we selected for gancyclovir-resistant cells and identified a ribozyme sequence that could potentially target both the U5 and gag genes of HIV-1 regions on the HIV-1 genome through partial homologies with these targets. When the ribozymes were converted to full complementarity with the targets, they provided potent inhibition of HIV-1 replication in cell culture. These results provide a novel approach for identifying ribozyme targets in HIV-1.
Numerical and experimental study of a micro gas turbine combustor (2012)

The behavior of the combustor of a Turbec T100P 100 kWe micro gas turbine (MGT) is analyzed at different load conditions by means of computational fluid dynamic modeling (CFD) and experimental investigation. CFD analysis results, comparing various numerical models for a given set of boundary conditions, are discussed in the paper. The k-ε and k-ω SST Reynolds Averaged Navier Stokes models were used to model the turbulence while for the combustion Finite Rate – Eddy Dissipation model was adopted. Westbrook and Dryer's 2-step kinetic mechanism and Zeldovich's mechanism were used to model methane oxidation and NO formation, respectively. The numerical results from the two turbulence models show a similar combustor behavior. The computed concentrations of O2, CO2 and NO are in good agreement with the experimental data, while CO concentration is underestimated of one order of magnitude.