gebhart/patrepeval huggingface dataset:
Ultrasonic beamforming system for interrogating multiple implantable sensors (2015)

In this paper, we present an ultrasonic beamforming system capable of interrogating individual implantable sensors via backscatter in a distributed, ultrasound-based recording platform known as Neural Dust [1]. A custom ASIC drives a 7 × 2 PZT transducer array with 3 cycles of 32V square wave with a specific programmable time delay to focus the beam at the 800mm neural dust mote placed 50mm away. The measured acoustic-to-electrical conversion efficiency of the receive mote in water is 0.12% and the overall system delivers 26.3% of the power from the 1.8V power supply to the transducer drive output, consumes 0.75μJ in each transmit phase, and has a 0.5% change in the backscatter per volt applied to the input of the backscatter circuit. Further miniaturization of both the transmit array and the receive mote can pave the way for a wearable, chronic sensing and neuromodulation system.
Coronary Endothelial Dysfunction After Heart Transplantation Predicts Allograft Vasculopathy and Cardiac Death (2001)

Endothelial dysfunction, as detected by abnormal responses to acetylcholine, preceded the development of clinical end points. These data implicate endothelial dysfunction in the development of clinically significant vasculopathy and suggest that serial studies of endothelial function have clinical utility.
Immunotoxins made with a recombinant form of Pseudomonas exotoxin A that do not require proteolysis for activity. (1993)

We used recombinant DNA technology to construct a mutant form of Pseudomonas exotoxin A (PE) called cysPE35 that contains amino acids 280-364 and 381-613 of PE. cysPE35 begins at the native PE proteolytic cleavage site and contains a single cysteine residue at position 287 that can be used to conjugate the toxin to monoclonal antibodies (MAbs). Unlike immunotoxins containing larger mutant forms of PE, such as PE40 or PE38, immunotoxins containing cysPE35 linked through a disulfide bond do not require proteolysis to generate a toxin fragment able to translocate to the cytosol. cysPE35 was conjugated to several MAbs and their activities were studied in vitro and in vivo. The concentration of toxin that inhibited protein synthesis as measured by a decrease in [3H]leucine incorporation of 50% of cysPE35 conjugated through a disulfide bond to the MAb HB21, which targets the human transferrin receptor, was 1 ng/ml on A431 cells. The MAb HB21 conjugated through a thioether bond to cysPE35 was much less active (concentration of toxin that inhibited protein synthesis as measured by a decrease in [3H]leucine incorporation of 50%, 200 ng/ml). An immunotoxin containing PE38 conjugated through either a disulfide or thioether bond to the MAb HB21 had a concentration of toxin that inhibited protein synthesis as measured by a decrease in [3H]leucine incorporation of 50% of 5 ng/ml, indicating that proteolysis of PE38 may be rate limiting in the action of these immunotoxins. Two other MAbs, LL2 and B3, were also conjugated through a disulfide bond to cysPE35. Both immunotoxins were also more active against cultured cells than conjugates using PE38 or PE40, and caused complete regression of human tumor xenografts growing in nude mice. In conclusion, we have constructed a mutant form of PE which must be coupled to MAbs through a disulfide bond to produce fully active immunotoxins that do not require proteolysis to generate a toxin fragment able to reach the cell cytosol.
THz and mm-Wave Sensing of Corneal Tissue Water Content: Electromagnetic Modeling and Analysis (2015)

Terahertz (THz) spectral properties of human cornea are explored as a function of central corneal thickness (CCT) and corneal water content, and the clinical utility of THz-based corneal water content sensing is discussed. Three candidate corneal tissue water content (CTWC) perturbations, based on corneal physiology, are investigated that affect the axial water distribution and total thickness. The THz frequency reflectivity properties of the three CTWC perturbations were simulated and explored with varying system center frequency and bandwidths (Q-factors). The modeling showed that at effective optical path lengths on the order of a wavelength the cornea presents a lossy etalon bordered by air at the anterior and the aqueous humor at the posterior. The simulated standing wave peak-to-valley ratio is pronounced at lower frequencies and its effect on acquired data can be modulated by adjusting the bandwidth of the sensing system. These observations are supported with experimental spectroscopic data. The results suggest that <i>a priori</i> knowledge of corneal thickness can be utilized for accurate assessments of corneal tissue water content. The physiologic variation of corneal thickness with respect to the wavelengths spanned by the THz band is extremely limited compared to all other structures in the body making CTWC sensing unique amongst all proposed applications of THz medical imaging.
PATRICIA—Practical Algorithm To Retrieve Information Coded in Alphanumeric (1968)

PATRICIA is an algorithm which provides a flexible means of storing, indexing, and retrieving information in a large file, which is economical of index space and of reindexing time. It does not require rearrangement of text or index as new material is added. It requires a minimum restriction of format of text and of keys; it is extremely flexible in the variety of keys it will respond to. It retrieves information in response to keys furnished by the user with a quantity of computation which has a bound which depends linearly on the length of keys and the number of their proper occurrences and is otherwise independent of the size of the library. It has been implemented in several variations as FORTRAN programs for the CDC-3600, utilizing disk file storage of text. It has been applied to several large information-retrieval problems and will be applied to others.
Mass Spectrometric Identification of Mtb81, a Novel Serological Marker for Tuberculosis (2000)

We have used serological proteome analysis in conjunction with tandem mass spectrometry to identify and sequence a novel protein, Mtb81, which may be useful for the diagnosis of tuberculosis (TB), especially for patients coinfected with human immunodeficiency virus (HIV). Recombinant Mtb81 was tested by an enzyme-linked immunosorbent assay to detect antibodies in 25 of 27 TB patients (92%) seropositive for HIV as well as in 38 of 67 individuals (57%) who were TB positive alone. No reactivity was observed in 11 of 11 individuals (100%) who were HIV seropositive alone. In addition, neither sera from purified protein derivative (PPD)-negative (0 of 29) nor sera from healthy (0 of 45) blood donors tested positive with Mtb81. Only 2 of 57 of PPD-positive individuals tested positive with Mtb81. Sera from individuals with smear-positive TB and seropositive for HIV but who had tested negative for TB in the 38-kDa antigen immunodiagnostic assay were also tested for reactivity against Mtb81, as were sera from individuals with lung cancer and pneumonia. Mtb81 reacted with 26 of 37 HIV(+) TB(+) sera (70%) in this group, compared to 2 of 37 (5%) that reacted with the 38-kDa antigen. Together, these results demonstrate that Mtb81 may be a promising complementary antigen for the serodiagnosis of TB.
Gene cloning of chitinase A1 from Bacillus circulans WL-12 revealed its evolutionary relationship to Serratia chitinase and to the type III homology units of fibronectin. (1990)

A chitinase gene of Bacillus circulans WL-12 was cloned into Escherichia coli by transforming HB101 cells with a recombinant plasmid composed of chromosomal DNA fragments prepared from B. circulans WL-12 and the plasmid vector pKK223-3. DNA sequencing analysis revealed that the region necessary for the normal expression of chitinase activity contained one open reading frame of 2097 base pairs which codes for the precursor of chitinase A1. The precursor of chitinase A1 contained a long signal sequence of 41 amino acids with an extremely long N-terminal hydrophilic segment of 15 amino acids. Cloned chitinase produced in E. coli had at its N terminus an additional 8 amino acids that were not found in B. circulans mature chitinase A1. The N-terminal two-thirds of the deduced amino acid sequence of chitinase A1 showed a 33% amino acid match to chitinase A of Serratia marcescens. This region of chitinase A1 is immediately followed by tandemly repeating 95-amino acid segments that are 70% homologous to each other. Statistical analysis revealed that these repeating segments are homologous to the type III homology units of fibronectin, a multifunctional extracellular matrix and plasma protein of higher eukaryotes. This observation indicates that type III homology units originated prior to the emergence of eukaryotes and may be distributed in a wide range of organisms.
The nucleotide sequence of the glycoprotein gB gene of infectious laryngotracheitis virus: analysis and evolutionary relationship to the homologous gene from other herpesviruses (1991)

A 3698 bp region of the genome of infectious laryngotracheitis virus (ILTV) was sequenced and found to contain the entire glycoprotein gB gene and the C-terminal region of a gene homologous to the ICP 18.5 protein gene of herpes simplex virus type 1. The ILTV gB gene encoded a protein with an Mr of 100K possessing all the characteristics of a transmembrane glycoprotein. Alignment of the ILTV gB sequence with homologous sequences from six other herpesviruses revealed that 10 cysteine residues on the surface of the molecule were completely conserved and that the positions of several N-linked glycosylation sites were largely conserved. Evolutionary trees based on the gB amino acid sequences from a total of 13 herpesviruses were constructed and the relationships among these herpesviruses were examined.
Purification and reconstitution of the sodium- and potassium-coupled glutamate transport glycoprotein from rat brain (1990)

The sodium- and potassium-coupled L-glutamate transporter from rat brain has been purified to near homogeneity by reconstitution of transport as an assay, assuming that inactivated and active transporters cochromatograph. The purification steps involve lectin chromatography of the membrane proteins solubilized with 3-[(3-chloramidopropyl)dimethylammonio]-1-propanesulfonate (CHAPS), fractionation on hydroxylapatite, and ion-exchange chromatography. The specific activity is increased 30-fold. The actual purification is higher since 3-5-fold inactivation occurs during the purification. The efficiency of reconstitution was about 20%. The properties of the pure transporter are fully preserved. They include ion dependence, electrogenicity, affinity, substrate specificity, and stereospecificity. Sodium dodecyl sulfate-polyacrylamide electrophoresis revealed one main band with an apparent molecular mass of around 80 kDa and a few minor bands. Comparison of polypeptide composition with L-glutamate transport activity throughout the fractionation procedure reveals that only the 80-kDa band can be correlated with activity. The GABA transporter, which has the same apparent molecular mass (Radian et al., 1986), is separated from it during the last two purification steps. Immunoblot experiments reveal that the antibodies against the GABA transporter only reacted with fractions exhibiting GABA transport activity and not with those containing the glutamate transporter. We conclude that the 80-kDa band represents the functional sodium- and potassium-coupled L-glutamate transporter.
Synthese des Dihydro‐zizyphins G (1981)

Die Herstellung 14gliedriger Peptidalkaloide wurde zunächst an Modell‐Edukten wie dem Pentafluorphenylester (1) , Z = Benzyloxycarbonyl, untersucht. Auf dem dabei gefundenen Weg gelang es schließlich, Dihydro‐zizyphin G (2) , A–A = CH 2 –CH 2 , als erste Verbindung dieses Typs zu synthetisieren.
Repeatability of Barkhausen transitions in thin films (1994)

Barkhausen transition fields for anisotropic Permalloy films, measured by the resonance enhancement technique, were found to be a function of the maximum field to which a sample was subjected before the occurrence of these transitions. In these experiments, the Barkhausen transitions were monitored after repeated cycling of the field applied along the easy axis between given maximum positive and negative values to obtain a nearly repeatable initial state. For a film with an H/sub c/ of 1.4 oe, the Barkhausen transition fields for repeated passes through Hc differed from each other by no more than 4.2% if the field was cycled between /spl plusmn/48 oe. For a cycling field between /spl plusmn/22.5 oe, the corresponding deviation increased to 9.9%.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Estimation of effective and total erythropoiesis in myelodysplasia using serum transferrin receptor and erythropoietin concentrations, with automated reticulocyte parameters. (1994)

The erythroid abnormality in patients with myelodysplasia (MDS) is multifactorial, with ineffective erythropoiesis and poor in vitro progenitor response to erythropoietin (EPO). Serum EPO concentration is variable among patients for a given haemoglobin concentration. We studied 19 non-transfusion-dependent patients with MDS, and 13 healthy elderly control subjects in an attempt to define the factors governing variability in serum EPO and to further characterise the anaemia of MDS. Serum EPO concentration was appropriate for the degree of anaemia in 15/19 MDS patients, and was positively related to mean cell volume (MCV), mean cell haemoglobin (MCH), and percentage highly fluorescent reticulocytes (% HFR), but not to absolute or percentage reticulocyte count. Although the observed/predicted ratio for serum transferrin receptor (TfR) concentration was low in 12 of 19 MDS subjects, no relationship to haemoglobin concentration, reticulocytes or serum EPO was seen. Serum TfR was positively correlated with WBC and platelet counts. Serum TfR was higher in patients with sideroblastic anaemia than refractory anaemia. Standardized in vivo p50 was positively correlated to red cell 2,3 diphosphoglycerate concentration, although this was not the only factor influencing the oxygen dissociation curve. We conclude that effective erythroid output responsive to endogenous EPO drive in MDS is positively related to MCV, MCH and % HFR. Serum TfR may not represent effective output as precisely as % HFR, but may be proportional to total marrow erythropoietic activity.
Precision, Damage-Free Etching by Electron-Enhanced Reactions: Results and Simulations (2013)

Ion-enhanced dry etch methods inflict "etch process damage" through surface ion bombardment. These inherent limitations in conventional dry etch methods create potential roadblocks to achieving device properties necessary for scaling below 32 nm. We describe an alternative dry etch method in which electrons with energies below about 100 eV stimulate precision etching of features as small as 20 nm without damage. This Low Energy Electron Enhanced Etching (LE4) method also gives atomically smooth etched surfaces, very high selectivity between materials, and maintains stoichiometry of compound materials. LE4 etches low K dielectric materials with no loss of carbon, and gives Line Width Roughness (LWR) values dramatically smaller than achieved by ion-enhanced etching. We have developed the Electron Force Field (eFF) method to describe electron dynamics in highly excited electronic states, and use it to show preferential bond breaking and product desorption after electronic excitation of the sample surface.
Amorphous In–Ga–Zn–O coplanar homojunction thin-film transistor (2009)

A fabrication process of coplanar homojunction thin-film transistors (TFTs) is proposed for amorphous In–Ga–Zn–O (a-IGZO), which employs highly doped contact regions naturally formed by deposition of upper protection layers made of hydrogenated silicon nitride (SiNX:H). The direct deposition of SiNX:H reduced the resistivity of the semiconductive a-IGZO layer down to 6.2×10−3 Ω cm and formed a nearly ideal Ohmic contact with a low parasitic source-to-drain resistance of 34 Ω cm. Simple evaluation of field-effect mobilities (μsat) overestimated their values especially for short-channel TFTs, while the channel resistance method proved that μsat was almost constant at 9.5 cm2 V−1 s−1.
Orientational sampling and rigid‐body minimization in molecular docking (1993)

The biological activities of proteins depend on specific molecular recognition and binding. Computational methods for predicting binding modes can facilitate the discovery and design of ligands and yield information on the factors governing complementarity. The DOCK suite of programs has been applied to several systems; here, the degree of orientational sampling required to reproduce and identify known binding modes, with and without rigid-body energy minimization, is investigated for four complexes. There is a tradeoff between sampling and minimization. The known binding modes can be identified with intensive sampling alone (10,000 to 20,000 orientations generated per system) or with moderate sampling combined with minimization. Optimization improves energies significantly, particularly when steric clashes are present, and brings many orientations closer to the experimentally observed position. Whether or not minimization is performed, however, sampling must be sufficient to find at least one structure in the vicinity of the presumed true binding mode. Hybrid approaches combining docking and minimization are promising and will become more viable with the use of faster algorithms and the judicious selection of fewer orientations for minimization.
RNA interference: an exciting new approach for target validation, gene expression analysis and therapeutics (2003)

Recent discoveries suggest that nature employs a novel approach for the regulation of gene expression by the silencing of endogenous genes. This phenomenon referred to as RNA interference (RNAi) is a posttranscriptional gene-silencing strategy that involves the intermediacy of double-stranded RNA (dsRNA) that complex with and destroy a target messenger RNA (mRNA) (1-4). The targeting and destruction of mRNA has been demonstrated to be highly specific and more selective compared to the antisense approach. Furthermore, it has also been shown that exogenously administered 21- to 23-mer dsRNA, referred to as small interfering RNA (siRNA), is equally efficient as a gene-silencing tool compared to the much longer dsRNA. These discoveries have led to the exciting possibility of using RNAi not only as a potential tool for elucidating the function of genes and analyzing gene expression, but also as a novel therapeutic modality. This review will highlight various aspects of this rapidly advancing field.
The Wire Grid as a Near-Infrared Polarizer (1960)

Wire grids have been fabricated with microscopic elements and periodicity. These wire grids behave as linear polarizers over large portions of the infrared spectrum, confirming predictions from electromagnetic theory. The method of fabrication of grids with periods as small as 463 mμ is described. Limits on the performance of a wire-grid polarizer are set by fineness of period, optical constants of the metal, spectral transmission of the supporting substrate, and by skin-depth effects. Within these limits, excellent polarizer performance may be obtained over a very wide band of wavelengths, and these new wire-grid polarizers do, in fact, cover the range 2–15 μ and beyond. Appreciable polarization is observed at near-infrared and visible wavelengths. Wire grids may be used in convergent beams of radiation or in restricted geometrical arrangements, unlike many pile-of-plate or prism polarizers. These wire-grid polarizers have proved useful in measuring the imperfections of other types of infrared polarizers.
Technical Considerations of Revision Anterior Cruciate Ligament Surgery (1996)

Revision anterior cruciate ligament surgery will become more common as the number of primary anterior cruciate ligament reconstructions increases. Also contributing to this increase are those patients who had anterior cruciate ligament reconstruction using synthetic ligaments and other nonanatomic techniques that are no longer used. Preoperative planning is imperative to a successful outcome. This begins with determining the primary, and often times secondary, mechanism of failure for each patient. The determination of the etiology of failure is the first step in a carefully constructed preoperative plan, including the type of revision, skin incision, graft removal, hardware removal, tunnel placement, graft selection, graft fixation, and rehabilitation. The precise preoperative plan should have enough flexibility to accommodate unanticipated findings in the operating room. Rehabilitation protocols must be designed specifically for the revision surgery patient and be flexible enough to accommodate changes based on surgical findings and techniques. Finally, the importance of counseling the patient preoperatively regarding the potential results which, in general, are somewhat less satisfactory than with most primary reconstructions, must be emphasized. However, with proper planning, attention to detail, and adherence to basic principles of anterior cruciate ligament reconstruction, revision anterior cruciate ligament surgery can provide a satisfying solution to difficult knee instability cases.
Hafnium diboride thin films by chemical vapor deposition from a single source precursor (2005)

High quality, stoichiometric thin films of hafnium diboride are deposited by chemical vapor deposition from the precursor Hf[BH4]4 at deposition temperatures as low as 200°C. An activation energy of 0.43eV(41kJ∕mol) is obtained for the overall process as monitored by temperature programmed reaction studies. Films deposited at low temperatures (&amp;lt;500°C) are structurally amorphous to x-ray diffraction; a 12nm thick film is sufficient to prevent copper diffusion into silicon during a 600°C anneal for 30min. Films deposited above 500°C are crystalline, but have a columnar microstructure with low density. All the films are metallic, but the low temperature amorphous films have the lowest resistivity ∼440μΩcm. The process is also highly conformal, e.g., a 65nm wide trench with a 19:1 depth-width aspect ratio was coated uniformly.
Selective gate-length biasing for cost-effective runtime leakage control (2004)

With process scaling, leakage power reduction has become one of the most important design concerns. Multi-threshold techniques have been used to reduce runtime leakage power without sacrificing performance. In this paper, we propose small biases of transistor gate-length to further minimize power in a manufacturable manner. Unlike multi-V th techniques, gate-length biasing requires no additional masks and may be performed at any stage in the design process.Our results show that gate-length biasing effectively reduces leakage power by up to 25% with less than 4% delay penalty. We show the feasibility of the technique in terms of manufacturability and pin-compatibility for post-layout power optimization. We also show up to 54% reduction in leakage uncertainty due to inter-die process variation in circuits when biased gate-lengths, versus only unbiased one, are used. Circuits selectively biased show much less sensitivity to both intra and inter die variations.
Digital holographic microscopy: a new 3D imaging technique (2006)

Keywords: [MVD] Reference LOA-CONF-2006-013 Record created on 2009-07-20, modified on 2017-05-10
Activating K-Ras mutations outwith ‘hotspot’ codons in sporadic colorectal tumours – implications for personalised cancer medicine (2010)

The identification of mutations outwith previously described hotspot codons increases the K-Ras mutation burden in colorectal tumours by one-third. Future mutation screening to facilitate optimal patient selection for treatment with EGFR-targeted therapies should therefore be extended to codon 146, and in addition should consider the unique molecular signatures associated with individual K-Ras mutations.