gebhart/patrepeval huggingface dataset:
An Analyzer for Message Sequence Charts. (1996)

Message sequence charts (MSCs) are used in the design phase of a distributed system to record intended system behaviors. They serve as informal documentation of design requirements that are referred to throughout the design process and even in the final system integration and acceptance testing. We show that message sequence charts are open to a variety of semantic interpretations. The meaning of an MSC can depend on, for instance, whether one allows or denies the possibility of message loss or message overtaking, and on the particulars of the message queuing policy to be adopted. We describe
Dynamic Opacity Optimization for Scatter Plots (2015)

Scatterplots are an effective and commonly used technique to show the relationship between two variables. However, as the number of data points increases, the chart suffers from "over-plotting" which obscures data points and makes the underlying distribution of the data difficult to discern. Reducing the opacity of the data points is an effective way to address over-plotting, however, setting the individual point opacity is a manual task performed by the chart designer. We present a user-driven model of opacity scaling for scatter plots built from crowd-sourced responses to opacity scaling tasks using several synthetic data distributions, and then test our model on a collection of real-world data sets.
ChemInform Abstract: Reactivity of Dianionic Hexacoordinated Silicon Complexes Toward Nucleophiles: A New Route to Organosilanes from Silica. (1988)

Abstract The hexacoordinated Si complex (III) is prepared from catechol (I) and silica (II).
Analytical Validation of a Novel Multi-Gene Assay for Patients With Eosinophilic Esophagitis (2014)

Introduction: A previously developed multi-gene RT-PCR expression assay of 77 human genes (ENGAUGE™-GI-Eosinophilic Esophagitis) was analytically validated for the identification of a positive Eosinophilic Esophagitis (EoE) diagnosis as well as differentiation from GERD and ability to predict a relapse of EoE. We validated the performance of this assay with respect to RT-PCR amplification efficiency and ability to correctly diagnose EoE in a clinical reference laboratory environment. We designed this study to determine the assay’s reproducibility and robustness in sections taken from formalin-fixed paraffin-embedded (FFPE) tissue blocks, taking the histology result as the gold standard. Methods: Tissue material from 22 patients was studied. Extracted RNA was reverse transcribed and assayed for 50 up-regulated and 27 down-regulated EoE related genes using GAPDH as the reference gene. A custom designed TaqMan Low Density Array (TLDA) card on an ABI ViiA™ 7 Real-Time PCR System was used along with previously described experimental conditions. Raw CT values were compared between 2 laboratories for proportionality for each sample being analyzed; as was the ability to conform to a EoE score that indicated a positive diagnosis of EoE. Results: Acceptable performance ranges were observed for each gene across the samples tested. Amplification efficiencies for the assay genes averaged 96.5% (range, 92.3-104.1%). In 21 of the 22 cases, samples were classified correctly, demonstrating high reproducibility in the classification for tests performed at 2 separate laboratories on the same sample. Of the one false negative sample, insufficient RNA amount was obtained, therefore the sample did not pass quality control. Of the remaining twenty-one samples, ENGAUGE™-GI-Eosinophilic Esophagitis accurately diagnosed EoE with a sensitivity and specificity of 100% and 100%, respectively. Conclusion: A site performance study was conducted to evaluate the reliability and reproducibility of a gene test panel (ENGAUGE™-GI-Eosinophilic Esophagitis) for EoE samples. Results indicate that this test produces clinically robust and reproducible results under typical experimental and CLIA laboratory conditions.
Short Communication (1995)

In the present work we elucidate that the identification of active sequences for a given target is one of the principle hurdles of antisense oligonucleotide therapeutics. A number of 100 oligonucleotides directed against different target genes of HSV-1 and different locations within those genes were screened for antiviral activity. To facilitate comparison, the same length and the same chemical modification were used for all oligonucleotides: 20mers with two phosphorothioate linkages at both the 5'- and the 3'-end. No sequence-independent effects were observed with this type of modification. Surprisingly, only six oligonucleotides did show significant antiviral activity, the most active one (#6) being directed against the translation initiation site of IE 110.
Scalable Protection for MPEG-4 (2005)

The newly adopted MPEG-4 fine granularity scala- bility (FGS) video coding standard offers easy and flexible adap- tation to varying network bandwidths and different application needs. Encryption for FGS should preserve such adaptation capa- bilities and enable intermediate stages to process encrypted data directly without decryption. In this paper, we propose two novel encryption algorithms for MPEG-4 FGS that meet these require- ments. The first algorithm encrypts an FGS stream (containing both the base and the enhancement layers) into a single access layer and preserves the original fine granularity scalability and error resilience performance in an encrypted stream. The second algo- rithm encrypts an FGS stream into multiple quality layers divided according to either peak signal-to-noise ratio (PSNR) or bit rates, with lower quality layers being accessible and reusable by a higher quality layer of the same type, but not vice versa. Both PSNR and bit-rate layers are supported simultaneously so a layer of either type can be selected on the fly without decryption. The base layer for the second algorithm may be unencrypted to allow free view of the content at low-quality or content-based search of a video data- base without decryption. Both algorithms are fast, error-resilient, and have negligible compression overhead. The same approach can be applied to other scalable multimedia formats. Index Terms—Digital rights management, FGS, fine granularity scalability (FGS), layered access control, MPEG-4, multimedia protection, scalable protection, scalable video encryption, selective encryption, video encryption.
Purification of a Phosphorous-Containing Scheelite Ore Concentrate: A “Design-of-Experiment” Study (1999)

Abstract A “design-of-experiment” (DOE) approach was used to study the purification of a scheelite ore concentrate in HCI. The ore concentrate contained about 65% CaWO4, 18% CaCC3, 14% Ca10(PO4)6(OH)2, and 3% SiO2. In addition to these major phases, the ore concentrate also contained trace amounts of toxic elements such as arsenic, lead, and uranium. These elements were associated with the apatitic part of the ore. The results of DOE experiments indicated that calcite can be selectively removed with a low HCI concentration, and the resulting calcium-containing solution may be used for other applications. Apatite can then be removed with a high concentration of HCI. This solution contains toxic elements such as arsenic, lead, and uranium because of the association of these elements with apatite. High temperature seemed to enhance the dissolution of unwanted tungsten (scheelite part of the ore concentrate), perhaps due to the formation of P- and As-containing heteropoly anions of W, such as PW12O40 3- and AsW12O40 3- (formation of heteropoly anions may be favored at high temperature).
Studies on the optimal conditions for synthesizing poly(butylene succinate‐co‐terephthalate) copolyesters with targeted properties (2011)

ABSTRACT The aliphatic‐aromatic copolyesters are becoming more important due to their desirable mechanical properties and biodegradability. In this study, a series of Poly(butylene succinate‐co‐terephthalate) (PBST) of various monomer compositions were synthesized from succinic acid (SA), dimethyl terephthalate (DMT), and 1,4‐butanediol (BDO) in the presence of tetrabutyl titanate (Ti(Obu) 4 ). The experiment was divided into three parts. The first part is a 2 3 factorial design with permutations of three factors, namely, temperature, molar ratio of BDO/DMT, and molar ratio of SA/DMT in polycondensation. Our statistical analysis showed that the temperature has a more significant effect on the intrinsic viscosity ([η]) of PBST than the other two factors. The number‐average molecular weight (M n ) of the PBST was determined from the intrinsic viscosity by using the Berkowitz model of M n = 1.521 × 10 5 [η] 1.5 . The second part of the experiment is a time course investigation of polycondensation under various temperatures, molar ratios of BDO/(DMT + SA), and concentrations of Ti(Obu) 4 . Our results showed the best polycondensation occurred at 1.5 hr with [η] reaching 0.49 dL/g when the temperature was held at 250 °C, BDO/(SA + DMT) = 1.2 mol/mol with SA/(SA + DMT) = 50 mol%, and 0.97 mmol of Ti(Obu) 4 per mol of SA + DMT. The third part of the experiment involves searching for the best molar ratio of SA/(SA + DMT) in obtaining desirable polymer properties and biodegradability. The results showed that the highest melting point of PBST can be as high as 177 °C at SA/(SA + DMT) = 30 mol%. The maximum tensile strength of 25.6 MPa is obtained at SA/(SA + DMT) = 30 mol%. The maximum elongation at break of 269.3% and the maximum Young's modulus of 754.8 MPa are reached at SA/(SA + DMT) = 60 mol% and at SA/(SA + DMT) = 30 mol%, respectively. The fastest lipase‐decomposition rate of PBST reached 100 % at day six for samples with molar ratio SA/(SA + DMT) = 80 mol%. © 2011 Curtin University of Technology and John Wiley & Sons, Ltd.
Two Cross-Protective Antigen Sites on Foot-and-Mouth Disease Virus Serotype O Structurally Revealed by Broadly Neutralizing Antibodies from Cattle (2021)

Foot-and-mouth disease virus (FMDV) is a highly contagious virus that infects cloven-hoofed animals. Neutralizing antibodies play critical roles in antiviral infection. Although five known antigen sites that induce neutralizing antibodies have been defined, studies on cross-protective antigen sites are still scarce. We mapped two cross-protective antigen sites using 13 bovine-derived broadly neutralizing monoclonal antibodies (bnAbs) capable of neutralizing 4 lineages within 3 topotypes of FMDV serotype O. One antigen site was formed by a novel cluster of VP3-focused epitopes recognized by bnAb C4 and C4-like antibodies. The cryo-electron microscopy (cryo-EM) structure of the FMDV-OTi (O/Tibet/99)-C4 complex showed close contact with VP3 and a novel interprotomer antigen epitope around the icosahedral 3-fold axis of the FMDV particle, which is far beyond the known antigen site 4. The key determinants of the neutralizing function of C4 and C4-like antibodies on the capsid were βB (T65), the B-C loop (T68), the E-F loop (E131 and K134), and the H-I loop (G196), revealing a novel antigen site on VP3. The other antigen site comprised two group epitopes on VP2 recognized by 9 bnAbs (B57, B73, B77, B82, F28, F145, F150, E46, and E54), which belong to the known antigen site 2 of FMDV serotype O. Notably, bnAb C4 potently promoted FMDV RNA release in response to damage to viral particles, suggesting that the targeted epitope contains a trigger mechanism for particle disassembly. This study revealed two cross-protective antigen sites that can elicit cross-reactive neutralizing antibodies in cattle and provided new structural information for the design of a broad-spectrum molecular vaccine against FMDV serotype O. <b>IMPORTANCE</b> FMDV is the causative agent of foot-and-mouth disease (FMD), which is one of the most contagious and economically devastating diseases of domestic animals. The antigenic structure of FMDV serotype O is rather complicated, especially for those sites that can elicit a cross-protective neutralizing antibody response. Monoclonal neutralization antibodies provide both crucial defense components against FMDV infection and valuable tools for fine analysis of the antigenic structure. In this study, we found a cluster of novel VP3-focused epitopes using 13 bnAbs against FMDV serotype O from natural host cattle, which revealed two cross-protective antigen sites on VP2 and VP3. Antibody C4 targeting this novel epitope potently promoted viral particle disassembly and RNA release before infection, which may indicate a vulnerable region of FMDV. This study reveals new structural information about cross-protective antigen sites of FMDV serotype O, providing valuable and strong support for future research on broad-spectrum vaccines against FMD.
Hollow cathode plasma assisted chemical vapor deposition of diamond (1988)

A method which combines thermal and plasma dissociation of a methane/hydrogen gas mixture for low-pressure chemical vapor deposition of diamond is described. A hot, thin-walled, refractory metal cathode is used to generate a high-current, low-voltage discharge. The substrates are located on the anode and immersed in the plasma emanating from the cathode tip. No auxiliary substrate heating is employed. Polycrystalline diamond particles and films are obtained on silicon (100) and molybdenum substrates at growth rates of 1–3 μm/h.
Limitation of Discharge Capacity and Mechanisms of Air‐Electrode Deactivation in Silicon–Air Batteries (2012)

The electrocatalytical process at the air cathode in novel silicon-air batteries using the room-temperature ionic liquid hydrophilic 1-ethyl-3-methylimidazolium oligofluorohydrogenate [EMI⋅2.3 HF⋅F] as electrolyte and highly doped silicon wafers as anodes is investigated by electrochemical means, X-ray photoelectron spectroscopy (XPS), and electron paramagnetic resonance (EPR) spectroscopy. The results obtained by XPS and EPR provide a model to describe the limited discharge capacity by means of a mechanism of air-electrode deactivation. In that respect, upon discharge the silicon-air battery's cathode is not only blocked by silicon oxide reduction products, but also experiences a major modification in the MnO₂ catalyst nature. The proposed modification of the MnO₂ catalyst by means of a MnF₂ surface layer greatly impacts the Si-air performance and describes a mechanism relevant for other metal-air batteries, such as the lithium-air. Moreover, the ability for this deactivation layer to form is greatly impacted by water in the electrolyte.
15-Deoxyspergualin in Patients with Refractory ANCA-Associated Systemic Vasculitis (2003)

The combination of cyclophosphamide (CYC) and oral corticosteroids is effective in the majority of patients with antineutrophil cytoplasmic antibody-associated vasculitis (AASV), but it carries substantial risk of drug-related morbidity and mortality. New regimens are desired, especially in refractory cases. The immunosuppressant 15-deoxyspergualin (DSG) is effective in experimental autoimmune disease and transplantation as well as in acute kidney transplant rejection in humans. To assess the efficacy and safety of DSG, an open label multicenter trial was conducted in patients with AASV who were either unresponsive or had contraindications for standard immunosuppressants. Included were 19 cases of Wegener granulomatosis and one case of microscopic polyangiitis. Nine of them had received CYC shortly before study entry without apparent therapeutic success. DSG (0.5 mg/kg per d) was given for 2 to 3 wk until the WBC count dropped to 3000/ micro l followed by a rest until at least a WBC of 4000/ micro l was reached again. This was repeated up to six cycles. During the study, no other immunosuppressants besides steroids were allowed. Disease improvement during treatment with DSG was achieved in 70% of cases (six cases of complete remission; eight cases of partial remission). Leucopenia occurred in each patient in a regular pattern during the cycles and was transient without exception. No mortality or septicemia was observed. Mild to moderate infections mainly in the respiratory tract were observed but resolved under adequate treatment without sequel. It is concluded that treatment with DSG is successful in patients with refractory Wegener granulomatosis under careful monitoring of WBC count.
Phage Biodiversity in Artisanal Cheese Wheys Reflects the Complexity of the Fermentation Process (2017)

Dairy fermentations constitute a perfect "breeding ground" for bacteriophages infecting starter cultures, particularly strains of <i>Lactococcus lactis.</i> In modern fermentations, these phages typically belong to one of three groups, i.e., the 936, P335, and c2 phage groups. Traditional production methods present fewer chemical and physical barriers to phage proliferation compared to modern production systems, while the starter cultures used are typically complex, variable, and undefined. In the current study, a variety of cheese whey, animal-derived rennet, and vat swab samples from artisanal cheeses produced in Sicily were analysed for the presence of lactococcal phages to assess phage diversity in such environments. The complete genomes of 18 representative phage isolates were sequenced, allowing the identification of 10 lactococcal 949 group phages, six P087 group phages, and two members of the 936 group phages. The genetic diversity of these isolates was examined using phylogenetic analysis as well as a focused analysis of the receptor binding proteins, which dictate specific interactions with the host-encoded receptor. Thermal treatments at 63 °C and 83 °C indicate that the 949 phages are particularly sensitive to thermal treatments, followed by the P087 and 936 isolates, which were shown to be much less sensitive to such treatments. This difference may explain the relatively low frequency of isolation of the so-called "rare" 949 and P087 group phages in modern fermentations.
Computing confidence scores for all sub parse trees (2008)

Computing confidence scores for applications, such as dialogue system, information retrieving and extraction, is an active research area. However, its focus has been primarily on computing word-, concept-, or utterance-level confidences. Motivated by the need from sophisticated dialogue systems for more effective dialogs, we generalize the confidence annotation to all the subtrees, the first effort in this line of research. The other contribution of this work is that we incorporated novel long distance features to address challenges in computing multi-level confidence scores. Using Conditional Maximum Entropy (CME) classifier with all the selected features, we reached an annotation error rate of 26.0% in the SWBD corpus, compared with a subtree error rate of 41.91%, a closely related benchmark with the Charniak parser from (Kahn et al., 2005).
Controlled Temperature Gradient Improves Freezing Alloy (1991)

Controlled gradient of temperature in advancing zone of solidification increases fatigue life of directionally solidified nickel-base superalloy. Improved solidification process eliminates, reduces, or controls microstructure of deleterious brittle phases, including carbides and gamma/gamma prime eutectic. Also reduces microsegregation and makes discrete carbides (if present) become fine and blocky. Expected to improve properties of other alloys, of both directionally-solidified polycrystalline and single-crystal forms.
A Continuous-Time 0–3 MASH ADC Achieving 88 dB DR With 53 MHz BW in 28 nm CMOS (2014)

We present design and measurement details for a 0-3 multi-stage noise-shaping (MASH) ADC that achieves a dynamic range of 88 dB over 53 MHz signal bandwidth. The ADC utilizes a zeroth-order front-end, i.e., a 17-level flash ADC, to perform a coarse quantization and a third-order 7-level continuous-time ΔΣ back-end to digitize the residue error of the front-end. The ADC achieves the high thermal noise power efficiency of a continuous-time feedforward ΔΣ modulator and the flat signal transfer function of a flash ADC. The test chip, implemented in a 28 nm CMOS process, clocks at 3.2 GHz. The average noise spectral density with small input signals is -167 dBFS/Hz and the dynamic range is 88 dB. The test chip ADC consumes a total power of 235 mW from triple power supplies of 0.9/1.8/-1.0 V. The thermal-noise figure-of-merit, defined as FOM = DR + 10log 10 (BW/P) is 171.6 dB.
MPLS Extension Header Architecture (2019)

Extension Headers (EH) carry information on in-network services and
functions in an MPLS network. This document describes an architecture
for EHs and what actions an EH capable Label Switching Router (LSR)
takes when finding or not finding an EH in the packet. Multiprotocol
Label Switching (MPLS) is a widely deployed forwarding technology. It
uses label stack entries that are pre-pended to either the EH or the
ACH which in turn is pre-pended to the payload. The label stack
entries are used to identify the forwarding actions by each LSR.
Actions may include pushing, swapping or popping the labels, and using
the labels to determine the next hop for forwarding the packet. Labels
may also be used to establish the context under which the packet is
forwarded. The extension headers are carried after the MPLS Label
Stack, and the presence of EHs are indicated in the label stack by an
Extension Header Indicator (EHI).
3D DfT architecture for pre-bond and post-bond testing (2010)

Process technology developments enable the creation of three-dimensional stacked ICs (3D-SICs) interconnected by means of Through-Silicon Vias (TSVs). This paper presents a 3D Design-for-Test (DfT) architecture for such 3D-SICs that allows pre-bond die testing as well as post-bond stack testing of both partial and complete stacks. The architecture enables on a modular test approach, in which the various dies, their embedded IP cores, the inter-die TSV-based interconnects, and the external I/Os can be tested as separate units to allow flexible optimization of the 3D-SIC test flow. The architecture builds on and reuses existing DfT hardware at the core, die, and product level. Its main new component is a die-level wrapper, which can be based on either IEEE Std 1500 or IEEE Std 1149.1. The paper presents a conceptual overview of the architecture, as well as implementation aspects. Experimental results show that the implementation costs are negligible for medium to large dies.
Electrochemical determination of ultralow levels (<10<sup>−12</sup> M) of mercury by anodic stripping voltammetry using a chemically modified electrode (1994)

Abstract A glassy carbon electrode (GCE) coated with 4,7,13,16,21,24‐hexaoxa‐1,10‐diazabicyclo[8.8.8]hexacosane, Kryptofix‐222, has been used for the very sensitive and selective analysis of very low levels of mercury. A detection limit lower than 10 −12 M (<0.2 ppt) was obtained applying anodic stripping voltammetry (ASV). The parameters that governed the sensitivity and possible interferences by other ions have been examined in detail. The electrode has been successfully applied for determining mercury in seawater, wastewater, and also in human saliva and amniotic fluid. The modified electrode exhibited high stability and, therefore, could be used repeatedly without mechanical regeneration.
Learning to Represent Edits. (2018)

We introduce the problem of learning distributed representations of edits. By combining a “neural editor” with an “edit encoder”, our models learn to represent the salient information of an edit and can be used to apply edits to new inputs. We experiment on natural language and source code edit data. Our evaluation yields promising results that suggest that our neural network models learn to capture the structure and semantics of edits. We hope that this interesting task and data source will inspire other researchers to work further on this problem.