gebhart/patrepeval huggingface dataset:
Phase formation and strain relaxation during thermal reaction of Zr and Ti with strained Si1−x−yGexCy epilayers (2000)

Silicides are often used in Si technology for both their ohmic and rectifying properties. In this work, we have compared Zr and Ti germanosilicides as possible metallic contacts on SiGeC alloys in terms of phase formation and stability of the unreacted SiGeC alloy. The germanosilicides are obtained after rapid thermal annealings of Zr or Ti with strained SiGeC layers. The interactions of the metal films with these alloys have been investigated by sheet resistance measurements, x-ray diffraction (XRD), cross-sectional transmission electron microscopy (TEM), and energy dispersive spectroscopy in situ in the TEM. Four crystal x-ray diffraction was performed to measure the residual strain of the unreacted SiGeC epilayer after reaction. The analyses indicate that the final compounds are the C49–Zr(SiGe)2 and C54–Ti(SiGe)2 phases, respectively: In both cases, the compound is formed by monocrystalline grains with various orientations. Nevertheless, neither XRD, nor sheet resistance measurements give any clear information about the C incorporation in the phase, when the reaction occurs with a SiGeC layer. We have observed that the use of Zr completely avoids Ge segregation with an uniform layer formed, while in the case of the reaction with Ti, the grains do not form a continuous layer and Ge-segregation is evidenced: A Ge-rich Si1−z−yGez(Cy) alloy is detected in between the metallic grains. In addition, an early strain relaxation of the unreacted SiGe layer is observed after reaction, and it is much more important after reaction with Ti. During the reaction with nearly compensated SiGeC layers, Zr totally prevents the initial state of strain, while Ti strongly affects the unreacted SiGeC alloy and destroys its initial state. All these results indicate that Zr may be an interesting candidate for realizing germanosilicide contacts on IV–IV alloys, due to its good thermal stability.
A Phase II Study with Danazol in Metastatic Breast Cancer (1987)

Danazol is a synthetic steroid that inhibits the gonadotropin secretion. Its efficacy was tested in 27 patients with metastatic breast cancer at the dose of 200 mg three times daily. Characteristics of patients were as follows. The median age was 57 years (range, 44-85). All patients were postmenopausal, and all had previously received a median of two (range, 1-3) endocrine therapies. Estrogen receptor status was known in 12 (positive in five of 12; negative in seven of 12). Dominant sites of metastases were lung in seven, bone in ten, liver in three, and soft tissue in seven. Six of 27 patients were unevaluable for response (early death, four; lost to follow-up, two). Three of 21 patients showed an objective response, eight of 21 obtained stabilization of disease, and eight progressed. The therapy was well tolerated in the majority: gastric pain was observed in three and nausea in two. Danazol could have a role in the treatment of metastatic breast cancer as an alternative regimen when other treatment has failed.
Noncyclic Scheduling of Cluster Tools With a Branch and Bound Algorithm (2014)

Cluster tools, each of which consists of multiple processing modules, one material handling robot, and loadlocks, are widely used for wafer fabrication processes, such as lithography, etching, and deposition. There have been many approaches and algorithms for cyclic scheduling of cluster tools in which the robot repeats a specified sequence for processing identical wafers. However, the lot order size has recently been decreasing due to the larger wafer size and circuit width reductions. In modern fabs, each wafer lot can have different flow patterns and process times for the same process step, and heterogeneous lots are processed consecutively in a tool. Even some tools in a fab have idle time waiting for wafer lots depending on the work-in-process fluctuations. Such different wafer lots and frequent tool state changes cannot be handled with cyclic scheduling methods, and accordingly noncyclic scheduling methods for such cases are required. Therefore, we develop an efficient branch and bound (B&B) procedure for noncyclic scheduling problems of cluster tools to minimize the makespan. Since a timed Petri net (TPN) is known for its powerful modeling ability and analysis capability, the algorithm is developed based on a TPN. We verify the efficiency of the B&B procedure with various cluster tool scheduling problems. There have been many studies on scheduling cluster tools, but most of them utilize different scheduling approaches or develop problem specialized properties. It is impractical to implement all the different methods to a tool scheduler because the scheduling requirements continuously change depending on wafer types and tool architectures. Hence, it is required to have an efficient solution method to address diverse cluster tool scheduling problems in fabs especially for frequent lot switchings and tool state changes due to larger wafer size and smaller lot order size. Therefore, we develop an efficient branch and bound procedure for noncyclic scheduling of a cluster tool with the makespan measurement. Since TPNs have the powerful modeling ability and analysis capability, the algorithm is developed based on a TPN. From the experimental results, we observe that one lot with 25 wafers can be easily solved in a reasonable time. The proposed method can be used for many different scheduling problems of a cluster tool by generating each corresponding TPN model.
Complete genome sequence and genetic organization of a Taiwan isolate of Zucchini yellow mosaic virus (2001)

The complete nucleotide sequence of the RNA genome of a Taiwan isolate of Zucchini yellow mosaic virus (ZYMV TW-TN3) was determined from five overlapping cDNA clones 9591 nucleotides in length excluding the poly (A) tail. Computer analysis of the sequence revealed a large open reading frame (ORF) that encodes a polyprotein of 3080 amino acids. Comparison of the gene products of TW-TN3 with those of the reported California (CA), Reunion Island (RU), and Singapore (S) isolates of ZYMV revealed that P1 protein is most variable, with amino acid identities of 59.0-93.2%. The 5′untranslated region (UTR) of TW-TN3 shares 61.6-83.3% nucleotide identities, and the 3′UTR shares 90.4-95.7% nucleotide identities, with those of the other isolates. A phylogenetic tree derived from the sequences of P1 proteins of TW-TN3 and the other six reported ZYMV isolates revealed four major genotypes. TW-TN3 was classified in genotype I, and US isolates were in genotype II. The Reunion Island and Singapore isolates were separated into genotypes III and IV, respectively. The distance relationships of P1 protein of genotype I were closer to genotype II, indicating that the Taiwan and US isolates may evolve from the same ancestor. Analyses on the cleavage sites of the C-terminal halves of the polyproteins of TW-TN3, CA, RU, and S isolates revealed that NIa protease cleaves at Q-S, and E-S dipeptide sequences, with a consensus sequence of V-x-x-(Q, E)/(S, A, G). The genetic organization of TW-TN3 was concluded as Vpg/5′ leader/P1 (36kDa)/HC Pro (52kDa)/P3 (40kDa)/6Kl (6kDa)/CIP (71kDa)/6K2 (6kDa)/NIa-Vpg (22kDa)/NIa-Pro (27kDa)/NIb (60kDa)/CP (31kDa)/3′ UTR-poly(A) tract.
Analysis of a Mask-Based Nanowire Decoder (2005)

A key challenge facing nanotechnologies will be controlling nanoarrays, two orthogonal sets of nanowires that form a crossbar, using a moderate number of mesoscale wires. Three methods have been proposed to use mesoscale wires to control individual nanowires. The first is based on nanowire differentiation during manufacture, the second makes random doped connections between nanowires and mesoscale wires, and the third, a mask-based approach, interposes high-K dielectric regions between nanowires and mesoscale wires. All three addressing schemes involve a stochastic step in their implementation. In this paper, we analyze the mask-based approach and show that a large number of mesoscale control wires is necessary for its realization.
Tuning the Chemical Selectivity of SWNT‐FETs for Detection of Heavy‐Metal Ions (2006)

A method to functionalize single-walled carbon nanotubes (SWNTs) in a field-effect transistor (FET) device for the selective detection of heavy-metal ions is presented. In this method, peptide-modified polymers were electrochemically deposited onto SWNTs and the selective detection of metal ions was demonstrated by choosing appropriate peptide sequences. The signal transduction mechanism of the peptide-modified SWNT-FETs has also been studied.
An Approach for Factory-Wide Control Utilizing Virtual Metrology (2007)

In the semiconductor manufacturing industry, market demands and technology trends drive manufacturers towards increases in wafer size and decreases in device size. Application of factory-wide advanced process control (APC) techniques down to the wafer-to-wafer (W2W) level control capability is becoming the only choice to cope with the demanding situation. However, one of the main limitations in undertaking W2W control is the nonavailability of timely metrology data at the wafer level. Recently virtual metrology (VM) techniques have been proposed to provide timely wafer level metrology data; they have the potential to be used in realizing W2W control. In this paper, the VM approach to W2W control on factory level is described. VM for an individual process is realized by utilizing the preprocess metrology and the process data from the underlying tools that is generally collected in real time for fault detection purposes. The VM implementation for factory-wide run-to-run control brings unique opportunities and issues to the forefront such as dealing with expected lower quality of VM data, coordination between VM modules of cascading processes for better prediction quality, flexibility of the factory-wide controller to accommodate lower quality VM data, dynamic adjustments to the target values of individual processes by the factory-wide controller when using VM data, and dealing with metrology delays at the factory level. Near and long-term solutions are presented to address these issues in order to allow VM to be used today and become an integral part of the factory-wide APC solution for W2W control.
Extractors and pseudorandom generators (2001)

We introduce a new approach to constructing extractors. Extractors are algorithms that transform a “weakly random” distribution into an almost uniform distribution. Explicit constructions of extractors have a variety of important applications, and tend to be very difficult to obtain.We demonstrate an unsuspected connection between extractors and pseudorandom generators. In fact, we show that every pseudorandom generator of a certain kind is an extractor.A pseudorandom generator construction due to Impagliazzo and Wigderson, once reinterpreted via our connection, is already an extractor that beats most known constructions and solves an important open question. We also show that, using the simpler Nisan--Wigderson generator and standard error-correcting codes, one can build even better extractors with the additional advantage that both the construction and the analysis are simple and admit a short self-contained description.
Telepresence surgery demonstration system (2002)

Endoscopic surgical methods are replacing open surgery in many procedures, but dexterity and force feedback are not adequate with current tools. To enhance the ability of surgeons to operate endoscopically, we have developed a telepresence system with integrated 3D stereo viewing, a prototype force-reflecting manipulator, and aural feedback. Careful attention was paid to the human factors in the endoscopic surgery setting to make the system natural to use in the hope of eliminating the long training period normally required. The 4-axis (plus gripper) manipulator provides the same degrees of freedom as the laproscopic tools now being used for surgery. The bilateral control system provides for magnified motion and/or force reflection. This approach eliminates the motion reversal, or fulcrum effect, in operating through the abdominal wall. Preliminary dexterity experiments with different force feedback and viewing conditions verify intuitive use and fast learning.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Development of a new mouse model of acute pancreatitis induced by administration of l-arginine (2006)

The pathogenesis of acute pancreatitis is not fully understood. Experimental animal models that mimic human disease are essential to better understand the pathophysiology of the disease and to evaluate potential therapeutic agents. Given that the mouse genome is known completely and that a large number of strains with various genetic deletions are available, it is advantageous to have multiple reliable mouse models of acute pancreatitis. Presently, there is only one predominant model of acute pancreatitis in mice, in which hyperstimulatory doses of cholecystokinin or its analog caerulein are administered. Therefore, the aim of this study was to develop another mouse model of acute pancreatitis. In this study, C57BL/6 mice were injected intraperitoneally with L-arginine in two doses of 4 g/kg each, 1 h apart. Serum amylase, myeloperoxidase, and histopathology were examined at varying time points after injection to assess injury to the pancreas and lung. We found that injection of L-arginine was followed by significant increases in plasma amylase and pancreatic myeloperoxidase accompanied by marked histopathological changes. The injury to the pancreas was slow to develop and peaked at 72 h. Subsequent to peak injury, the damaged areas contained collagen fibers as assessed by increased Sirius red staining. In contrast, D-arginine or other amino acids did not cause injury to the pancreas. In addition, acute inflammation in the pancreas was associated with lung injury. Our results indicate that administration of L-arginine to mice results in severe acute pancreatitis. This model should help in elucidating the pathophysiology of pancreatitis.
Two hepatitis C virus glycoprotein E2 products with different C termini (1994)

Processing of the boundary region between the putative structural and nonstructural regions of the hepatitis C virus precursor polyprotein was analyzed by in vitro translation using reticulocyte lysate in the presence of canine microsomal membranes. At this boundary in the precursor polyprotein, the most carboxy-terminal of the structural proteins, gp70 (E2), is proximal to the amino terminal of the nonstructural protein p21 (NS2). The presence of a novel microsomal membrane-dependent cleavage site was observed at the region upstream of the amino-terminal end of p21 (NS2) in the precursor polyprotein. The cleavage site was assigned to amino acid residues 746/747 in the hepatitis C virus precursor polyprotein. Inefficient cleavage of this site resulted in the production of two forms of E2 products with different sizes of peptide backbones. Translation and cleavage of various C-terminal deletion constructs established the significance of the C-terminal hydrophobic amino acid sequences of E2 products in membrane anchoring.
Characterization and expression analysis of genes encoding α and β carbonic anhydrases in Arabidopsis (2007)

Carbonic anhydrases (CAs) are Zn-containing metalloenzymes that catalyse the reversible hydration of CO(2). We investigated the alphaCA and betaCA families in Arabidopsis, which contain eight alphaCA (At alphaCA1-8) and six betaCA genes (At betaCA1-6). Analyses of expressed sequence tags (ESTs) from The Arabidopsis Information Resource (TAIR) database indicate that all the betaCA encoding sequences, but only three of the At alphaCA, are expressed. Using semi-quantitative PCR experiments, functional CA genes were more strongly expressed in green tissue, but strong expression was also found in roots for betaCA3, betaCA6 and alphaCA2. Two alphaCA genes were shown to respond to the CO(2) environment, while the others were unresponsive. Using the green fluorescent reporter protein gene fused with cDNA sequences coding for betaCAs, we provided evidence that betaCAs were targeted to specific subcellular compartments: betaCA1 and betaCA5 were targeted to the chloroplast, betaCA2 and betaCA3 to the cytosol, betaCA4 to the plasma membrane and betaCA6 to the mitochondria. The targeting and the pattern of gene expression suggest that CA isoforms play specific roles in subcellular compartments, tissues and organs. The data indicate that other CA isoforms than the well-characterized betaCA1 may contribute to the CO(2) transfer in the cell to the catalytic site of ribulose 1.5-bisphosphate carboxylase/oxygenase (Rubisco).
Lysophosphatidic acid‐induced expression of periostin in stromal cells: Prognoistic relevance of periostin expression in epithelial ovarian cancer (2010)

Lysophosphatidic acid (LPA) is a bioactive lipid crucial for the initiation and progression of ovarian cancer. Identification of LPA-induced biomarkers is necessary for predicting prognosis of ovarian cancer patients. Here we report periostin, an extracellular matrix protein, as an LPA-induced protein in stromal cells and as a prognostic marker in patients with epithelial ovarian cancer (EOC). In human EOC tissues, periostin was mainly expressed in cancer-associated stromal fibroblasts, but not in cancer cells. The expression levels of periostin highly correlated with poor survival and tumor recurrence of ovarian cancer patients. Treatment of human adipose tissue-derived stromal cells with LPA or conditioned media from human ovarian adenocarcinoma cell lines, such as SK-OV-3 and OVCAR-3, induced expression of periostin. The periostin expression induced by cancer-conditioned media was abrogated by silencing of the LPA receptor 1 expression using small hairpin RNA lentivirus. Recombinant periostin stimulated adhesion and invasion of SK-OV-3 human ovarian adenocarcinoma cells and induced expression of matrix metalloprotease-2 in the cancer cells. These results suggest that LPA is associated with the expression of periostin in cancer-associated fibroblasts of EOC.
Murine hematopoietic cells with pre-B or pre-B/myeloid characteristics are generated by in vitro transformation with retroviruses containing fes, ras, abl, and src oncogenes. (1986)

In vitro infection of bone marrow or fetal liver cells with retroviruses containing fes, abl, ras, or src oncogenes resulted in the transformation of early B lineage cells. All cell lines tested possessed rearrangements at the Ig heavy chain locus and some had rearrangements at the K chain locus. The majority of the lines corresponded phenotypically to Lyb-2+, Ly-5(B220)+, ThB- large pre-B cells, although some were classified as pro-B cells because of their Lyb-2+, Ly-17+, Ly-5(B220)- phenotype. We identified two cell lines that contained subpopulations of cells that coexpressed the B lineage antigens Lyb-2 and Ly-5(B220) and the myeloid lineage antigen Mac-1. Single-cell FMF cloning of these subpopulations showed that Mac-1+ cells were derived from Mac-1- cells and that these Mac-1+-cloned cells further differentiated into cells with phenotypic and functional characteristics of mature macrophages.
Matrix: a realtime object identification and registration method for augmented reality (2002)

The paper introduces a novel technique for producing augmented reality systems that simultaneously identify real world objects and estimate their coordinate systems. This method utilizes a 2D matrix marker, a square shaped barcode, which can identify a large number of objects. It also acts as a landmark to register information on real world images. As a result, it costs virtually nothing to produce and attach codes to various kinds of real world objects, because the matrix code is printable. We have developed an augmented reality system based on this method, and demonstrated several potential applications.
Integrated circuits for data transmission over twisted-pair channels (1997)

This paper discusses typical architectures and challenges in designing integrated circuits for data transmission over twisted-pair wire channels. To highlight the various architectural approaches, two main applications are discussed-high-bit-rate digital subscriber loop (HDSL) and fast-Ethernet. Although these two applications have orders of magnitude difference in their bit rates, they share many common building blocks including line-drivers, 24 wire hybrids, echo cancellation, digital equalization, and clock recovery. Typical integrated circuit approaches for realizing each of these blocks are presented as well as possible tradeoffs. Finally, future challenges facing integrated circuit designers are presented.
Intratympanic gentamicin for Ménière's disease or syndrome (2011)

Based on the results of the two included studies, intratympanic gentamicin seems to be an effective treatment for vertigo complaints in Ménière's disease, but carries a risk of hearing loss.
How to drill a smooth medium-radius well (1990)

Any operator that has attempted a medium-radius well probably has experienced sticking problems while building hole angle. Such sticking problems could noticeably decrease penetration rate or even cause the loss of the well. Sticking problems are discussed in this article. They may result from sloughing shales, ledging, differential sticking or any routine problems occurring in conventional directional and vertical drilling. In addition, downhole sticking can be caused by using conventional-type stabilizers on medium-radius, nonrotating assemblies. Although conventional stabilizers efficiently centralize and control the drillstem when rotating, they quickly become a liability when sliding. High point contact loads and interference with the wellbore will produce sticking and uneven weight transmission to the bit, which is frequently manifested in reduced penetration rates, even with more conventional steerable assemblies. The author proposes that stabilization should be avoided on medium-radius, nonrotating assemblies.
Crystallization and preliminary X-ray crystallographic studies of dissimilatory nitrite reductase isolated fromHyphomicrobium denitrificansA3151 (2004)

Dissimilatory nitrite reductase isolated from Hyphomicrobium denitrificans A3151 (HdNIR) is a novel copper-containing nitrite reductase (CuNIR) composed of six identical subunits. One plastocyanin-like domain and one green CuNIR-like domain are connected to each other, suggesting that the HdNIR subunit structure resembles a complex of green CuNIR and pseudoazurin (or azurin). Recombinant HdNIR protein was crystallized using the hanging-drop vapour-diffusion method with PEG 4000 as the precipitant at pH 8.9. X-ray diffraction data were collected to 2.35 A resolution. The HdNIR crystal belonged to the tetragonal space group P4(1) (or P4(3)), with unit-cell parameters a = b = 221.9, c = 165.2 A, giving 12 molecules (two hexamers) per asymmetric unit and a solvent content of 64%. A mutant form of HdNIR, C260A, which lacks the type I copper ion in the CuNIR-like domain, was prepared and crystallized under wild-type HdNIR conditions. The C260A mutant crystal belonged to the cubic space group P4(3)32 (or P4(1)32), with unit-cell parameters a = b = c = 153.7 A, giving one molecule per asymmetric unit and a solvent content of 59%. X-ray diffraction data were collected to 3.5 A resolution. To solve the crystal structure of HdNIR, the multiwavelength anomalous dispersion (MAD) method and the molecular-replacement method are currently being used.
The immunogenic part of infliximab is the F(ab')2, but measuring antibodies to the intact infliximab molecule is more clinically useful (2010)

F(ab')(2) is the immunogenic fragment of infliximab. However, ATI level in serum--combined with measurement of trough infliximab level--is better correlated with the clinical response to infliximab or with its loss.