gebhart/patrepeval huggingface dataset:
HDR syndrome with a novel mutation in GATA3 mimicking a congenital X-linked stapes gusher: a case report (2017)

To our knowledge, this is the first case of HDR syndrome with a novel de novo variant mimicking a congenital X-linked stapes gusher syndrome. Novel mutations and the diversity of clinical manifestations expand the genotypic and phenotypic spectrum of HDR syndrome. Diagnosis of HDR syndrome is still challenging, but clinicians should consider it in their differential diagnosis for children with a wide range of clinical manifestations including hypocalcemia induced seizures and deafness. We hope that this case will contribute to further understanding and studies of HDR-associated GATA3 mutations.
Miniature Optics For Optical Recording (1988)

This paper provides an overview of the optical subsystems used in optical recording, their present status, and future trends. Using reflectivity-sensing and polarization-sensing optical heads as examples, the many requirements that must be integrated into one assembly are described along with the individual technology alternatives. The state-of-the-art of conventional free-space optical, holographic, and hybrid elements is also described along with an integrated head assembly using waveguide optics. Future directions and requirements for these technologies are indicated.
Space-time TCM with improved performance on fast fading channels (2001)

New space-time trellis-coded modulation (STTC) which best satisfies the design criteria proposed by Tarokh, et al. (see IEEE Trans. Inform. Theory, vol.44, p.746-65, 1998) over fast fading channels are presented. STTC with a feedforward structure have been constructed by a systematic and exhaustive search. Simulation results and parameter comparison show that these codes offer a better performance on fast fading channels than other known codes while maintaining a comparable performance on slow fading channels.
<title>Wire-bond inspection in IC assembly</title> (1996)

Wire-bonding in IC assembly process involves making a physical connection between the IC 'die' and the 'lead' by bonding wires between the two. Inspection of wire-bond quality is a' highly labor-intensive process and currently efforts are being made to automate it. This paper presents the results of a research conducted into developing a comprehensive automated wire- bond visual inspection system that is capable of performing final accept/reject inspection, providing on-line process feedback, and assisting in process validation. The proposed inspection system consists of the inspection of the bond on a bond pad, the bond on a lead and the inter-connecting wire between a bond pad and its corresponding lead. The algorithms are based on simple and easily extractable features that ensure achieving the desired accuracy and speed. A novel but simple illumination system is proposed to obtain the images of the inter- connecting wires. The proposed system is validated using several state-of-the-art IC samples. This work is sponsored by the Ministry of Science Technology and Environment, Malaysia and Intel Technology Pvt. Ltd., Malaysia.
Lipid Modification of Secreted Signaling Proteins (2006)

Proteins of the Hedgehog, Wnt and Epidermal Growth Factor Receptor (EGFR) ligand families are secreted signals that induce concentration-dependent responses in surrounding cells. Although these proteins must diffuse through the aqueous extracellular environment, recent work has shown that hydrophobic lipid modifications are essential for their functions. All three classes of ligands are palmitoylated in the secretory pathway by related enzymes, and Hedgehog also carries a C-terminal cholesterol modification as a result of its autocatalytic cleavage. Palmitoylation is required for Wingless secretion and contributes to the signaling activity of Hedgehog and Wnt3a, but is not required for secretion or receptor activation by the EGFR ligand Spitz. While lipid modifications enhance the long-range activity of Sonic hedgehog, they restrict the range and increase the local concentration of Spitz. We discuss the diverse functions and the possible extent of palmitoylation of secreted ligands.
<title>Dry release process of anhydrous HF gas-phase etching for the fabrication of a vibrating microgyroscope</title> (1999)

A micro gyroscope, which vibrates in two orthogonal axes on the substrate plane, is designed and fabricated. Fabrication processes of the micro gyroscope are composed of anisotropic silicon etching by RIE, dry release by newly developed anhydrous HF gas-phase etching (GPE) of the buried sacrificial oxide layer, stress relief by multi-step annealing, metal electrode formation. The GPE process was verified as a very effective method for the release of compliant microstructures of micro gyroscope. The developed GPE system with anhydrous HF gas and CH<SUB>3</SUB>OH vapor was characterized and its etching properties were discussed. We successfully fabricated micro gyroscope with no virtually process-induced stiction and no residual products after GPE of TEOS, LTO, and thermal oxide on silicon substrates.
Nanopore sensing of individual transcription factors bound to DNA (2015)

Transcription factor (TF)-DNA interactions are the primary control point in regulation of gene expression. Characterization of these interactions is essential for understanding genetic regulation of biological systems and developing novel therapies to treat cellular malfunctions. Solid-state nanopores are a highly versatile class of single-molecule sensors that can provide rich information about local properties of long charged biopolymers using the current blockage patterns generated during analyte translocation, and provide a novel platform for characterization of TF-DNA interactions. The DNA-binding domain of the TF Early Growth Response Protein 1 (EGR1), a prototypical zinc finger protein known as zif268, is used as a model system for this study. zif268 adopts two distinct bound conformations corresponding to specific and nonspecific binding, according to the local DNA sequence. Here we implement a solid-state nanopore platform for direct, label- and tether-free single-molecule detection of zif268 bound to DNA. We demonstrate detection of single zif268 TFs bound to DNA according to current blockage sublevels and duration of translocation through the nanopore. We further show that the nanopore can detect and discriminate both specific and nonspecific binding conformations of zif268 on DNA via the distinct current blockage patterns corresponding to each of these two known binding modes.
IC performance prediction from electrical test measurements (2003)

A model for integrated circuit (IC) binning has been built using measurements collected on a high-volume manufacturing line. This model uses electrical measurements collected before packaging in order to predict the high-speed performance of manufactured parts before final test. A small set of measurable parameters responsible for the variation in fabricated parts was identified. The statistically significant, linear performance prediction model was built using data from a 1-Mbit CMOS EPROM production line. The applications of the model include aiding the packaging decision, production planning and scheduling, process characterization, and control and design for manufacturability.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Effect of high power ultrasound on aqueous solution of DNA (2009)

The effect of (20 kHz continuous wave) ultrasound (power from 17 to 77 W) on the damage of nitrogen bases, the loss of double-helical structure, strand breaks and fragmentation of Calf spleen DNA were studied in vitro. The relative ultrasound sensitivity of the hydrogen bonded base pairs A-T and G-C were also studied. The techniques used in this investigation were ultraviolet absorption spectroscopy and constant-field gel electrophoresis (CFGE). The results showed that ultrasound decreased the hydrogen-bonded nucleotides. The ultrasound sensitivity was greater for the A-T base pairs than for the G-C base pairs. It was also shown that high power ultrasound damaged the nitrogen bases. The loss of the double helical structure by the ultrasound was mainly due to the separation of certain sections of the DNA by single strand breaks (SSB) and also to a small extent due to base damage. The size of the DNA fragments decreased as the ultrasound power increased and finally a plateau effect was seen at the highest powers.         

	 

	Key words: DNA damage, ultrasound, spectroscopy.
Evidence for the rapid expansion of microRNA-mediated regulation in early land plant evolution (2007)

Our data provide evidence for a surprisingly diverse and complex miRNA population in Physcomitrella. Thus, the number and function of miRNAs must have significantly expanded during the evolution of early land plants. As we have described here within, the coupled maturation of two miRNAs from a shared precursor has not been previously identified in plants.
Isolation and characterization of <i>Cupriavidus basilensis</i> HMF14 for biological removal of inhibitors from lignocellulosic hydrolysate (2009)

The formation of toxic fermentation inhibitors such as furfural and 5-hydroxy-2-methylfurfural (HMF) during acid (pre-)treatment of lignocellulose, calls for the efficient removal of these compounds. Lignocellulosic hydrolysates can be efficiently detoxified biologically with microorganisms that specifically metabolize the fermentation inhibitors while preserving the sugars for subsequent use by the fermentation host. The bacterium Cupriavidus basilensis HMF14 was isolated from enrichment cultures with HMF as the sole carbon source and was found to metabolize many of the toxic constituents of lignocellulosic hydrolysate including furfural, HMF, acetate, formate and a host of aromatic compounds. Remarkably, this microorganism does not grow on the most abundant sugars in lignocellulosic hydrolysates: glucose, xylose and arabinose. In addition, C. basilensis HMF14 can produce polyhydroxyalkanoates. Cultivation of C. basilensis HMF14 on wheat straw hydrolysate resulted in the complete removal of furfural, HMF, acetate and formate, leaving the sugar fraction intact. This unique substrate profile makes C. basilensis HMF14 extremely well suited for biological removal of inhibitors from lignocellulosic hydrolysates prior to their use as fermentation feedstock.
MEDUSA: an ultra-lightweight multi-spectral camera for a HALE UAV (2007)

The ESA-PRODEX funded MEDUSA project aims to develop a light weight high resolution multi-spectral earth observation instrument, which will be embarked on a solar-powered high altitude long endurance (HALE) UAV, operated at stratospheric altitudes (15 to 18km). The MEDUSA instrument is designed to fill the gap between traditional airborne and spaceborne instruments regarding resolution and coverage. It targets applications such as crisis management and cartography, requiring high resolution images with regional coverage, flexible flight patterns, high update rates and long mission lengths (weeks to months). The MEDUSA camera is designed to operate at a ground resolution of 30 cm at 18 km altitude in the visible spectrum (400-650 nm), and a swath of 3000m. The central part of the payload is a focal plane assembly consisting of two frame sensors (PAN and RGB). The wide swath is realized with a custom designed highly sensitive CMOS sensor of 10000x1200 pixels. A GPS receiver and Inertial Measurement Unit (IMU) provide accurate position and attitude information. A direct downlink allows near-real time data delivery to the user. The on-board data processing consists mainly of basic image corrections and data compression (JPEG2000). The challenge lies mainly in fulfilling the requirements within the extreme environmental and physical constraints of the HALE UAV. Compared to traditional airborne and spaceborne systems, the MEDUSA camera system is ultra light weight (about 2 kg) and is operated in a low pressure and low temperature environment. System modeling and simulation is used to make careful trade-offs between requirements and subsystem performances. On 27th November 2006 the phase C/D for the design, production and test of the camera has started at VITO with the support of 9 industrial partners. The MEDUSA camera is expected to transmit its first images the end of 2008.
The herpes simplex virus type-1 origin binding protein. DNA helicase activity. (1993)

The herpes simplex virus type 1 (HSV-1) origin binding protein, the product of the UL9 gene, catalyzes the unwinding of DNA in the 3'-5' direction. Helicase activity is coupled to the hydrolysis of ATP or dATP and to a lesser extent to CTP, dCTP, or UTP. It requires a divalent cation (Mg2+ > Mn2+ > Ca2+) with an optimum at 2.5 mM MgCl2. Activity is optimal at high pH (8.5-9.5) and high temperature (45 degrees C) and is inhibited at ionic strengths > 50 mM NaCl. The helicase activity is specifically stimulated by the HSV-1-encoded single-stranded DNA-binding protein, ICP8, which increases both the rate and extent of helicase activity. Helicase action appears to be stoichiometric, requiring a DNA-dependent assembly of a multimeric UL9 protein complex. Under optimal conditions, the rate of DNA unwinding is approximately 75 base pairs/min.
The Application of Robotics to the Drilling Process (1988)

Abstract Robotics, a recently popularized phrase, has captured the interest of the general public as well as the drilling industry. This paper reviews the history of robotic applications in drilling and their outcome for the purpose of determining future trends. An analysis of the obstacles and limitations common to all industries is used to adjust the trend projection, and a survey of current efforts and programs is presented to complete the presentation. Applications analyzed include the automatic drilling rig, various pipe-racking systems, and recent offerings in pipe-handling machines.
Guided Uncertainty Reduction in Automatically Generated Business Simulations (2009)

Model-Driven Performance Engineering enables the automatic generation of simulation models based on business process models and monitored process instance data. When we applied an initial version of our tooling to a number of real world processes, we experienced that we need to support the mapping of monitored process instance data into simulation models under consideration of cases where confidence in these data is low, for instance due to a high variance in monitored resource demands, or a low number of executed process instances. The current paper proposes an architecture which utilizes a decision tree for the intelligent mapping of monitored process instance data into simulation models and, as a by-product, which ranks uncertainties within the imported data.
Fluorinated Isocyanates and Their Derivatives as Intermediates for Biologically Active Compounds (1977)

Abstract Fluorinated aromatic isocyanates are valuable intermediates for the production of herbicides and insecticides. Unexpected rearrangements during the synthesis of 2‐(trifluoromethyl)phenyl isocyanates provide an entry to N ‐trifluoromethylaminobenzoyl fluorides, a novel class of compounds having fungicidal properties. Carbamoyl fluorides, the products of HF addition to isocyanates, undergo ready sulfenylation. Use of these intermediates for the synthesis of N ‐sulfenylcarbamate insecticides led to the discovery of the new principle of detoxification of carbamates by sulfenylation.
Parylene Surface-Micromachined Membranes for Sensor Applications (2004)

This paper reports the design, fabrication process, and testing results of Parylene surface-micromachined membranes with integrated strain gauges or thermal resistors made of thin film metals. The membrane is suspended above the substrate. This paper demonstrates the feasibility of sensor applications with a force (tactile) sensor and a fluid shear stress sensor.
Group-Transfer Polymerization of <i>tert</i>-Butyl Methacrylate and [3-(Methacryloxy)propyl]pentamethyldisiloxane:  Synthesis and Characterization of Homopolymers and Random and Block Copolymers (1996)

A synthetic approach for preparing block copolymers consisting of both a [3-(methacryloxy)propyl]pentamethyldisiloxane (SiMA) block and tert-butyl methacrylate (t-BMA) block using group-transfer polymerization (GTP) was developed. The SiMA polymerizes slowly with oxyanion catalysis but at reasonable rates using bifluoride catalysis. A model reaction eliminated a possible explanation for the slow rate of polymerization of SiMA with oxyanion catalyzed GTP. For high conversion of t-BMA to be achieved, additional bifluoride catalyst had to be added to the reactor after the t-BMA addition. Often, especially at −44 °C, after the polymerization stalled, additional conversion of the t-BMA did not occur until a critical concentration of bifluoride catalyst was established. After this level was reached, the polymerization of t-BMA occurred quickly and to high conversion.
The Glucagon-like Peptide-2 Receptor Mediates Direct Inhibition of Cellular Apoptosis via a cAMP-dependent Protein Kinase-independent Pathway (2000)

Glucagon and the glucagon-like peptides regulate metabolic functions via signaling through a glucagon receptor subfamily of G protein-coupled receptors. Activation of glucagon-like peptide-2 receptor (GLP-2R) signaling maintains the integrity of the intestinal epithelial mucosa via regulation of crypt cell proliferation. Because GLP-2 decreases mortality and reduces intestinal apoptosis in rodents after experimental injury, we examined whether GLP-2R signaling directly modifies the cellular response to external injury. We show here that activation of GLP-2R signaling inhibits cycloheximide-induced apoptosis in baby hamster kidney fibroblasts expressing a transfected GLP-2 receptor. GLP-2 reduced DNA fragmentation and improved cell survival, in association with reduced activation of caspase-3 and decreased poly(ADP-ribose) polymerase cleavage and reduced caspase-8 and caspase-9-like activities. Both GLP-2 and forskolin reduced mitochondrial cytochrome c release and decreased the cycloheximide-induced cleavage of caspase-3 in the presence or absence of the PKA inhibitor H-89. Similarly, GLP-2 increased cell survival following cycloheximide in the presence of the kinase inhibitors PD98054 and LY294002. These findings provide evidence that signaling through G protein-coupled receptors of the glucagon superfamily is directly linked to regulation of apoptosis and suggest the existence of a cAMP-dependent protein kinase-, phosphatidylinositol 3-kinase-, and mitogen-activated protein kinase-independent pathway coupling GLP-2R signaling to caspase inhibition and cell survival.
Design Method for Distributed Raman Amplification Systems Based on Statistical Properties in Optical Fibers (2005)

To avoid over-engineered and expensive systems, it is important that the design takes account of variations in optical fiber characteristics due to the presence of many fiber pieces and splices in optical fiber networks. We present a design method for optical fiber networks that employ distributed Raman amplification (DRA), that considers variations in both optical losses at signal and pump wavelengths, Raman gain characteristics and splice losses. Our method can be applied to the design of both newly developed systems and installed systems. We show design examples based on our method and reveal the practicability of our method.
Transmission Characteristic Measurement of Two-Mode Optical Fiber with a Nearly Optimum Index-Profile (1980)

Two-mode optical fibers are studied experimentally and theoretically. A fiber with a nearly optimum index profile, designed for the material dispersion-free spectral region of 1.3 mu m has been fabricated. The fiber core diameter is 20 mu m with a 0.26 percent of relative-index difference between the core and cladding. Group delay time differences Delta tau between LP/sub 01/ and LP/sub 11/ modes are measured in the spectral region 1.06-1.44 mu m by using a fiber Raman laser. As a result, the zero-modal dispersion characteristic is confirmed to occur near 1.4 mu m. It is shown that a gently sloping Delta tau characteristic against V-value is obtained when the central index dip in core index profile is eliminated. In the present test fiber, Delta tau = 230 ps/km, caused by a V-value deviation of 5 percent from the optimum V/sub 0/ at which Delta tau = 0. The theory predicts 200 ps/km with an optimum index profile.
Phage display-derived inhibitor of the essential cell wall biosynthesis enzyme MurF (2008)

To develop antibacterial agents having novel modes of action against bacterial cell wall biosynthesis, we targeted the essential MurF enzyme of the antibiotic resistant pathogen Pseudomonas aeruginosa. MurF catalyzes the formation of a peptide bond between D-Alanyl-D-Alanine (D-Ala-D-Ala) and the cell wall precursor uridine 5'-diphosphoryl N-acetylmuramoyl-L-alanyl-D-glutamyl-meso-diaminopimelic acid (UDP-MurNAc-Ala-Glu-meso-A2pm) with the concomitant hydrolysis of ATP to ADP and inorganic phosphate, yielding UDP-N-acetylmuramyl-pentapeptide. As MurF acts on a dipeptide, we exploited a phage display approach to identify peptide ligands having high binding affinities for the enzyme. Screening of a phage display 12-mer library using purified P. aeruginosa MurF yielded to the identification of the MurFp1 peptide. The MurF substrate UDP-MurNAc-Ala-Glumeso-A2pm was synthesized and used to develop a sensitive spectrophotometric assay to quantify MurF kinetics and inhibition. MurFp1 acted as a weak, time-dependent inhibitor of MurF activity but was a potent inhibitor when MurF was pre-incubated with UDP-MurNAc-Ala-Glu-meso-A2pm or ATP. In contrast, adding the substrate D-Ala-D-Ala during the pre-incubation nullified the inhibition. The IC50 value of MurFp1 was evaluated at 250 μM, and the Ki was established at 420 μM with respect to the mixed type of inhibition against D-Ala-D-Ala. MurFp1 exerts its inhibitory action by interfering with the utilization of D-Ala-D-Ala by the MurF amide ligase enzyme. We propose that MurFp1 exploits UDP-MurNAc-Ala-Glu-meso-A2pm-induced structural changes for better interaction with the enzyme. We present the first peptide inhibitor of MurF, an enzyme that should be exploited as a target for antimicrobial drug development.
Design of diffractive phase elements that produce focal annuli: a new method (1995)

A new optimization method based on the general theory of amplitude-phase retrieval is proposed for designing the diffractive phase elements (DPE's) that produce focal annular patterns. A set of equations for determining the phase distribution of the DPE is given. The profile of a surface-relief DPE can be designed with an iterative algorithm. Numerical calculations are carried out for several examples. A comparison of the performance of the DPE's designed with the Gerchberg-Saxton algorithm and the new algorithm is presented. The effect of quantization of the phase distribution of the DPE's on the results is also investigated. The results show that the new algorithm can successfully achieve the design of the DPE's that convert the uniform incident beam into the focal annular patterns.
Spindle Assembly Checkpoint Protein Dynamics Reveal Conserved and Unsuspected Roles in Plant Cell Division (2009)

We conclude that plant BUBR1, BUB3.1 and MAD2 proteins may have the SAC protein functions conserved from yeast to humans. The association of BUB3.1 with both unattached kinetochore and phragmoplast suggests that in plant, BUB3.1 may have other roles beyond the spindle assembly checkpoint itself. Finally, this study of the SAC dynamics pinpoints uncharacterised roles of this surveillance mechanism in plant cell division.