gebhart/patrepeval huggingface dataset:
Estimation of prenatal aorta intima-media thickness in ultrasound examination (2012)

Prenatal events such as intrauterine growth restriction have been shown to be associated with an increased thickness of abdominal aorta in the fetus. Therefore the measurement of abdominal aortic intima-media thickness (aIMT) has been recently considered a sensitive marker of artherosclerosis risk. To date measure of aortic diameter and of aIMT has been performed manually on US fetal images, thus being susceptible to intra- and inter- operator variability. This work introduces an automatic algorithm that identifies abdominal aorta and estimates its diameter and aIMT from videos recorded during routine third trimester ultrasonographic fetal biometry. Firstly, in each frame, the algorithm locates and segments the region corresponding to aorta by means of an active contour driven by two different external forces: a static vector field convolution force and a dynamic pressure force. Then, in each frame, the mean diameter of the vessel is computed, to reconstruct the cardiac cycle: in fact, we expect the diameter to have a sinusoidal trend, according to the heart rate. From the obtained sinusoid, we identify the frames corresponding to the end diastole and to the end systole. Finally, in these frames we assess the aIMT. According to its definition, we consider as aIMT the distance between the leading edge of the blood-intima interface, and the leading edge of the media-adventitia interface on the far wall of the vessel. The correlation between end-diastole and end-systole aIMT automatic and manual measures is 0.90 and 0.84 respectively.
Bench-To-Clinic Development of Imageable Drug-Eluting Embolization Beads: Finding the Balance (2018)

This review describes the historical development of an imageable spherical embolic agent and focuses on work performed in collaboration between Biocompatibles UK Ltd (a BTG International group company) and the NIH to demonstrate radiopaque bead utility and bring a commercial offering to market that meets a clinical need. Various chemistries have been investigated and multiple prototypes evaluated in search of an optimized product with the right balance of handling and imaging properties. Herein, we describe the steps taken in the development of DC Bead LUMI™, the first commercially available radiopaque drug-eluting bead, ultimately leading to the first human experience of this novel embolic agent in the treatment of liver tumors.
APPLICATION OF A DC SQUID TO RF AMPLIFICATION: NQR (1986)

Superconducting QUantum Interference Devices (SQUIDs) have been used for more than•a decade for the detection of magnetic resonance.l-lOUntil recently, these devices had mostly been confined
Computer-Driven Keratometer (1991)

Simple optical system measures corneal deformations. Shuttered laser briefly illuminates subject's eye through reticle, projecting concentric rings of light on eye. Reflected by beam splitter and mirror into solid-state video camera, ring pattern compared with reference pattern by computer. Keratometer assists in rapid diagnosis of eye ailments and preparation of cornea for surgery. Unit does not require critical alignment with eye; results more reliable, and easier to use.
Peptide identification via constrained multi-objective optimization: Pareto-based genetic algorithms: Research Articles (2005)

Automatic peptide identification from collision-induced dissociation tandem mass spectrometry data using optimization techniques is made difficult by large plateaus in the fitness landscapes of scoring functions, by the fuzzy nature of constraints from noisy data and by the existence of diverse but equally justifiable probabilistic models of peak matching. Here, two different scoring functions are combined into a parallel multi-objective optimization framework. It is shown how multi-objective optimization can be used to empirically test for independence between distinct scoring functions. The loss of selection pressure during the evolution of a population of putative peptide sequences by a Pareto-driven genetic algorithm is addressed by alternating between two definitions of fitness according to a numerical threshold. Copyright © 2005 John Wiley & Sons, Ltd.
β-Cell Differentiation from a Human Pancreatic Cell Line in Vitro and in Vivo (2001)

Cell transplantation therapy for diabetes is limited by an inadequate supply of cells exhibiting glucose-responsive insulin secretion. To generate an unlimited supply of human beta-cells, inducibly transformed pancreatic beta-cell lines have been created by expression of dominant oncogenes. The cell lines grow indefinitely but lose differentiated function. Induction of beta-cell differentiation was achieved by stimulating the signaling pathways downstream of the transcription factor PDX-1, cell-cell contact, and the glucagon-like peptide (GLP-1) receptor. Synergistic activation of those pathways resulted in differentiation into functional beta-cells exhibiting glucose-responsive insulin secretion in vitro. Both oncogene-expressing and oncogene-deleted cells were transplanted into nude mice and found to exhibit glucose-responsive insulin secretion in vivo. The ability to grow unlimited quantities of human beta-cells is a major step toward developing a cell transplantation therapy for diabetes.
Continuous wave operation of long wavelength(λ ≃ 11 µm) inter-miniband lasers (2000)

A long wavelength (λ ≃ 11 µm) quantum cascade laser based on inter-miniband transitions in semiconductor superlattices is reported. The device operates continuous wave up to a temperature of 85 K, with a maximum output power of 75 mW at 25 K, both record values for unipolar lasers of comparable wavelength.
Assessing the SEU resistance of CMOS latches using alpha-particle sensitive test circuits (1990)

The importance of Cosmic Rays on the performance of integrated circuits (IC's) in a space environment is evident in the upset rate of the Tracking and Data Relay Satellite (TDRS) launched in Apr. 1983. This satellite experiences a single-event-upset (SEU) per day which must be corrected from the ground. Such experience caused a redesign of the Galileo spacecraft with SEU resistant IC's. The solution to the SEU problem continues to be important as the complexity of spacecraft grows, the feature size of IC's decreases, and as space systems are designed with circuits fabricated at non-radiation hardened foundries. This paper describes an approach for verifying the susceptibility of CMOS latches to heavy-ion induced state changes. The approach utilizes alpha particles to induce the upsets in test circuits. These test circuits are standard cells that have offset voltages which sensitize the circuits to upsets. These results are then used to calculate the upsetability at operating voltages. In this study results are presented for the alpha particle upset of a six-transistor static random access memory (SRAM) cell. Then a methodology is described for the analysis of a standard-cell inverter latch.
Direct super-resolution and registration using raw CFA images (2004)

Super-resolution has been applied mainly to grayscale images, but producing a high-resolution color image using a single CCD sensor has not been investigated in detail until recently. This work aims at producing a high-resolution color image directly from raw "color mosaic" images obtained by a single CCD equipped with a color filter array. This method is based on a generalized formulation of super-resolution that simultaneously performs both resolution enhancement and demosaicing. The other key factor of our topic is a precise sub-pixel registration of multiple raw images. We examined direct registration of raw images based on an imaging model, which shows precise estimation of motion among severely aliased raw images. The proposed method is verified through experiments using synthetic and real images.
A hybrid-level multi-phase charge-recycler with reduced number of external capacitors for low-power LCD column drivers (2002)

This paper presents hybrid-level charge recycling scheme which can be helpful in implementing low power LCD column drivers. The proposed scheme eliminates the necessity of polarity reversing circuit of the conventional method, simplifying the control. Another technique which merges two external capacitors into one is also described. This makes the multi-level recycling operation in column driving IC more practical.
ERCC-1 gene expression levels and outcome to FOLFOX chemotherapy in patients enrolled in CONFIRM1 and CONFIRM2 (2008)

4131 Background: ERCC-1 is a nucleotide excision repair gene associated with DNA repair of DNA adducts induced by platinum based chemotherapy. ERCC-1 mRNA levels have been shown to predict outcome in patients with NSCLC, gastric, bladder and ovarian cancer when treated with platinum based chemotherapy. We tested whether ERCC-1 gene expression is associated with outcome in patients with metastatic colon cancer treated with FOLFOX in first and second line treatment with or without PTK/ZK Methods: 191 formalin fixed paraffin embedded (FFPE) tumor samples from patients enrolled in CONFIRM 1 and CONFIRM2 were analyzed. 85 patients from CONFIRM1 (42 pts treated with FOLFOX, 43 pts with FOLFOX/PTK/ZK) and 106 from CONFIRM2 (54 pts treated with FOLFOX, 52 with FOLFOX/PTK/ZK). FFPE tissues were dissected using laser-captured microdissection and analyzed for ERCC-1 mRNA expression using a quantitative real-time RT-PCR method. Gene expression values (relative mRNA levels) are expressed as ratios between the target gene and internal reference gene (beta-actin). Results: Low ERCC-1 gene expression was associated with better response to FOLFOX chemotherapy in first and second line chemotherapy (p=0.047, p=0.054). ERCC-1 gene expression was associated with overall survival in first and second line FOLFOX chemotherapy (p=0.014, p=0.14). pts with high ERCC-1 did not have any benefit from FOLFOX chemotherapy, but had benefit from treatment of FOLFOX+PTK/ZK, this drug and ERCC1 expression interaction was statistically significant (p=0.015). Conclusions: These results suggest that ERCC-1 gene expression levels predict response and overall survival in patients with metastatic colorectal cancer enrolled in CONFIRM1 and 2. ERCC-1 gene expression levels may allow the selection of patients who benefit likely from FOLFOX chemotherapy. We could show for the first time that VEGFR TKI efficacy may depend on ERCC-1 status. Further studies are warranted to study this unexpected interaction. Author Disclosure Employment or Leadership Consultant or Advisory Role Stock Ownership Honoraria Research Expert Testimony Other Remuneration Bayer, Novartis, Response Genetics, Inc Bristol-Myers Squibb, Genentech, ImClone, Merck, Pfizer, Response Genetics, Inc Novartis, Response Genetics, Inc Genentech, Merck, Pfizer, Roche, sanofi-aventis Dhont Family Foundation, NCI, NIH, Novartis
SarA level is a determinant of <i>agr</i> activation in <i>Staphylococcus aureus</i> (1998)

The control of virulence determinant expression in Staphylococcus aureus is a complex process involving global regulatory loci such as sar and agr. The sar locus consists of a 372 bp sarA open reading frame (ORF) preceded by a triple promoter region interspersed with two putative smaller ORFs (ORF3 and ORF4). The triple promoter system yields three overlapping sar transcripts (sarA, sarC and sarB of 0.56, 0.8 and 1.2 kb respectively). We have recently shown that the SarA protein binds to the agr promoter region to stimulate the transcription of RNAII and RNAIII, two major transcripts encoded within the agr locus. To assess the role of the region upstream of sarA in agr expression, we evaluated the contribution of ORF3 and ORF4 to SarA protein expression and to agr activation by introducing nonsense mutations into the respective ORFs. Northern analysis of sar mutant clones containing these mutations carried on a shuttle plasmid revealed that all three sar-related transcripts are present. Using anti-SarA monoclonal antibodies with defined epitopes in a competitive ELISA to determine the SarA protein level, we found that the introduction of a stop codon in ORF3 on a shuttle plasmid carrying the intact sar locus in a sar mutant led to a significant decrease in SarA protein level compared with the non-mutated control. The effect of a nonsense mutation in ORF4 on SarA levels is much less. Likewise, an analogous sar mutant clone with a deletion in ORF3 also displayed a lower SarA level than its intact counterpart. The reduction in SarA expression correlated with a lower level of agr activation in the corresponding sar mutant clone. These data suggest that ORF3, and to a lesser degree ORF4, may affect agr expression by modulating SarA protein expression.
A monoclonal antibody against N-terminus of alpha-atrial natriuretic polypeptide (alpha-ANP): a useful tool for preferential detection of naturally circulating ANP. (1988)

A monoclonal antibody directed against the N-terminus of alpha-atrial natriuretic polypeptide (alpha-ANP), named KY-ANP-II, was produced by fusion of a non-producing mouse myeloma cell line, X63-Ag8.653, with spleen cells from a BALB/c mouse immunized with synthetic alpha-human ANP (alpha-hANP) conjugated to bovine thyroglobulin. The obtained antibody showed a high affinity for alpha-hANP with a Ka of 6.6 X 10(10) M-1. With this monoclonal antibody, a specific radioimmunoassay for alpha-hANP was established. The minimal detectable level of alpha-hANP in this radioimmunoassay was 0.8 fmol (2.5 pg)/tube, and IC50 was 8 fmol (25 pg)/tube. The radioimmunoassay recognized alpha-rat ANP on an equimolar basis, whereas there was no detectable cross-reactivity with alpha-ANP [4-28] or alpha-ANP [5-28]. Thus, the monoclonal antibody can detect a hormonal form of ANP, alpha-ANP, but not neuropeptide forms of ANP, alpha-ANP [4-28] and alpha-ANP [5-28]. These results indicate that KY-ANP-II becomes a useful tool for preferential detection of a circulating form of ANP and for investigation of the physiological and pathophysiological significance of ANP as a hormone.
Pulses in the two-cycle regime from a SESAM-assisted KLM Ti:sapphire laser and sub 10-fs pulse characterization (2003)

Summary form only given. Proper measurement of sub-10-fs pulses is still controversial and challenging. The duration of world record ultrashort optical pulses has previously been estimated from interferometric autocorrelation (IAC) traces. Other techniques, such as spectral phase interferometry for direct electric-field reconstruction (SPIDER) and frequency-resolved optical gating (FROG) have been developed that retrieve both amplitude and phase of the pulse. We discuss the limitations of SPIDER, FROG, and IAC for ultrashort pulses. Pulse durations can be significantly underestimated by fitting parameters of an ideal sech/sup 2/-soliton to the IAC.
Analysis of T3SS-independent Autonomous Internalization of the Bacterial Effector Protein SspH1 from Salmonella typhimurium (2014)

Previous studies identified the effector protein YopM of Yersinia enterocolitica as a novel bacterial cell-penetrating protein. YopM’s ability to translocate across the host cell plasma membrane independently of Yersinia’s type III secretion system (T3SS) is mediated by its two N-terminal α-helices. The SspH1 effector protein of Salmonella typhimurium shares significant homology in sequence and structure with YopM, which prompted us to investigate potential cell-penetrating abilities of this effector protein. For this, we recombinantly expressed SspH1 in Escherichia coli and analyzed a potential T3SS-independent translocation of the protein by cell fractionation of HeLa cells, immunofluorescence microscopy and FACS analyses. The functionality of the recombinant protein as an E3 ubiquitin- ligase was determined using in vitro -ubiquitination assays. Additionally, an effect of the recombinant protein on the expression of pro-inflammatory cytokines was analyzed by quantitative real time PCR. In this study, we could show that the SspH1 effector protein of Salmonella typhimurium is able to translocate autonomously into eukaryotic cells without requiring additional factors. Furthermore, we could show that recombinant SspH1 is a functional E3 ubiquitin ligase that is able to undergo auto-ubiquitination following T3SS-independent translocation and to reduce the expression of Interleukin-8 in IL-1β stimulated cells.
Discovery and characterization of a series of Axl kinase inhibitors using the CLIMBTM process. (2007)

2380 Axl is a receptor tyrosine kinase, which was first discovered as a transforming oncogene in CML. Axl signaling, through binding its ligand, Gas6, has been demonstrated to play a role in cell growth and protection from apoptosis in normal and cancer cells, especially through counteraction of the pro-apoptotic activities of E1A, and is emerging as an important target for a number of human malignancies, both solid and hematological. This protection is believed to operate through the action of Src and PI3K (via the Akt pathway), which are known proto-oncogenes themselves. Gas6/Axl mediated survival of endothelial cells has shown the involvement of ‘classical’ survival pathways including Akt phosphorylation, NF-kB activation, Bcl-2 stimulation and ultimately caspase 3 inhibition. Expression of Axl and Gas6 has been implicated in defense against apoptosis in a variety of tumor subtypes. Axl signaling has also been shown to control diverse processes in endothelial cells, including growth, survival, migration and morphologic differentiation- mechanisms central to tumor growth and formation. Axl has been shown to be a key regulator of several angiogenic processes. Aberrant angiogenesis in the case of cancer feeds tumor growth and facilitates metastasis. All of these findings indicate the importance of Axl in regulating processes that increase cell survival and that are vital for neovascularization. Blocking processes regulated by Axl will be important in fully inhibiting angiogenesis and cell proliferation, thereby complementing existing cancer therapies. Therefore it is clear that there is an important need for small molecule inhibitors of Axl kinase in the clinic, and we have set out to create such an entity. We have developed a proprietary drug discovery process, called CLIMBTM, which we utilized for the identification of novel Axl modulating compounds with therapeutic potential. Over a million compounds were initially screened virtually but less than 100 compounds were physically tested, yielding hits with IC50s less than 10 uM. From these initial hits structural modifications have been made to improve biochemical and cell-based potency and have yielded a collection of leads which have effects in cells consistent with Axl inhibition, including sensitization to apoptosis and down regulation of Axl-dependent signaling pathways. We present here the process of selection and optimization of a series of lead Axl inhibitors for use in anticancer therapeutic regimens.
Design and Implementation of an Integrated Magnetic Spectrometer for Multiplexed Biosensing (2013)

Magnetic spectroscopy allows for characterization of the magnetic susceptibility of magnetic beads across a broad frequency range. This enables differentiation and quantification of multiple beads of varying types concurrently present in the active volume of a sensor's surface. A magnetic spectrometer can be used for multi-probe tagging and identification akin to multi-color fluorescent bio-sensing. We propose a new sensing methodology to perform magnetic spectroscopy and analyze various important design parameters such as SNR and gain uniformity. We present a proof-of-concept design of a fully integrated CMOS magnetic spectrometer that can detect, quantify, and characterize magnetic materials in the 1.1 GHz to 3.3 GHz frequency range, where we demonstrate magnetic multiplexing capability using a mixture of two different kinds of magnetic beads. The sensor consumes less than 2 mW of DC power within the whole frequency range, requires no external biasing magnetic fields, is implemented in a standard CMOS process, and can be powered and operated completely from a USB interface. The magnetic spectrometer not only increases the throughput and multiplexing of biosensing experiments for a given sensor area, but also can enable additional applications, such as magnetic flow cytometry and signal-collocation assays of multiple probes.
High-Reliability Plastic Package for Integrated Circuits (1973)

Two orders of magnitude improvement in the reliability of plastic packages has been achieved as the result of a systematic study of basic failure mechanisms and the development of improved materials, handling procedures and process controls. This improved integrated-circuit packaging system has resulted in plastic-encapsulated product capable of matching the reliability of hermetic packages under severe environmental stress.
Processor Generates and Extracts Silicon (1983)

Processor under development continuously generates pure silicon and separates it from reaction by-products. Silicon separator/collector intercepts impinging jet of reaction products and selectively funnels silicon into larger collector. Salt byproduct is removed by tubular condenser held at 1,000 degrees C, and then flows into collector, where it solidifies. Vacuum locks permit periodic salt removal without disturbing continuous operation.
Rewiring the Glucose Transportation and Central Metabolic Pathways for Overproduction of <i>N</i>‐Acetylglucosamine in <i>Bacillus subtilis</i> (2017)

N-acetylglucosamine (GlcNAc) is an important amino sugar extensively used in the healthcare field. In a previous study, the recombinant Bacillus subtilis strain BSGN6-P<sub>xylA</sub> -glmS-pP43NMK-GNA1 (BN0-GNA1) had been constructed for microbial production of GlcNAc by pathway design and modular optimization. Here, the production of GlcNAc is further improved by rewiring both the glucose transportation and central metabolic pathways. First, the phosphotransferase system (PTS) is blocked by deletion of three genes, yyzE (encoding the PTS system transporter subunit IIA YyzE), ypqE (encoding the PTS system transporter subunit IIA YpqE), and ptsG (encoding the PTS system glucose-specific EIICBA component), resulting in 47.6% increase in the GlcNAc titer (from 6.5 ± 0.25 to 9.6 ± 0.16 g L<sup>-1</sup> ) in shake flasks. Then, reinforcement of the expression of the glcP and glcK genes and optimization of glucose facilitator proteins are performed to promote glucose import and phosphorylation. Next, the competitive pathways for GlcNAc synthesis, namely glycolysis, peptidoglycan synthesis pathway, pentose phosphate pathway, and tricarboxylic acid cycle, are repressed by initiation codon-optimization strategies, and the GlcNAc titer in shake flasks is improved from 10.8 ± 0.25 to 13.2 ± 0.31 g L<sup>-1</sup> . Finally, the GlcNAc titer is further increased to 42.1 ± 1.1 g L<sup>-1</sup> in a 3-L fed-batch bioreactor, which is 1.72-fold that of the original strain, BN0-GNA1. This study shows considerably enhanced GlcNAc production, and the metabolic engineering strategy described here will be useful for engineering other prokaryotic microorganisms for the production of GlcNAc and related molecules.