gebhart/patrepeval huggingface dataset:
Diagnosis of Multiple Hold-Time and Setup-Time Faults in Scan Chains (2005)

This paper presents a diagnosis technique to locate hold-time (HT) faults and setup-time (ST) faults in scan chains. This technique achieves deterministic diagnosis results by applying thermometer scan input (TSI) patterns, which have only one rising or one falling transition. With TSI patterns, the diagnosis patterns can be easily generated by existing single stuck-at fault test pattern generators with few modifications. In addition to the first fault, this technique diagnoses remaining faults by applying thermometer scan input with padding (TSIP) patterns. For the benchmark circuits (up to 6.6 K scan cells), experiments show that the diagnosis resolutions are no worse than 15, even in the presence of multiple faults in a scan chain.
Prevention of endotoxemia-induced acute respiratory distress syndrome-like lung injury in rabbits by a monoclonal antibody to IL-8. (1997)

We have herein established an endotoxemia-induced acute respiratory distress syndrome (ARDS)-like lung injury administered a sublethal dose of lipopolysaccharide (LPS) intravenously 36 hours after the intratracheal instillation of heat-killed Streptococcus pyogenes (OK-432). At 36 hours after OK-432 priming, a mild infiltration into the lungs, consisting of a small number of neutrophils and macrophages, was observed without destruction of pulmonary architecture. A subsequent challenge with a sublethal dose of LPS induced pathologic changes characteristic of ARDS--such as extensive edema in alveolar lumina, marked infiltration composed of a large number of neutrophils and a few macrophages, fibrin deposit in alveolar space, and destruction of pulmonary architecture--resulting in severe hypoxemia. Concomitantly, LPS challenge after priming with OK-432 induced a marked elevation of IL-8 levels in serum and bronchoalveolar lavage fluid with local IL-8 production in lungs, as revealed by immunohistochemical analysis. An anti-IL-8 antibody treatment almost completely prevented pulmonary edema, destruction of pulmonary architecture, and impairment in gas exchange as well as neutrophil infiltration in lungs; there was also a significant reduction in the rate of acute lethality. These results provide evidence that IL-8 has a pivotal role in the induction of ARDS associated with endotoxemia, probably by recruiting and activating neutrophils locally.
Signal transduction through homologs of the Ste20p and Ste7p protein kinases can trigger hyphal formation in the pathogenic fungus Candida albicans (1996)

The CST20 gene of Candida albicans was cloned by functional complementation of a deletion of the STE20 gene in Saccharomyces cerevisiae. CST20 encodes a homolog of the Ste20p/p65PAK family of protein kinases. Colonies of C. albicans cells deleted for CST20 revealed defects in the lateral formation of mycelia on synthetic solid "Spider" media. However, hyphal development was not impaired in some other media. A similar phenotype was caused by deletion of HST7, encoding a functional homolog of the S. cerevisiae Ste7p protein kinase. Overexpression of HST7 partially complemented the deletion of CST20. Cells deleted for CST20 were less virulent in a mouse model for systemic candidiasis. Our results suggest that more than one signaling pathway can trigger hyphal development in C. albicans, one of which has a protein kinase cascade that is analogous to the mating response pathway in S. cerevisiae and might have become adapted to the control of mycelial formation in asexual C. albicans.
The burden of malaria mortality among African children in the year 2000 (2006)

These estimates, based on the best available data and methods, clearly demonstrate malaria's enormous mortality burden. We emphasize that these estimates are an approximation with many limitations and that the estimates do not account for malaria's large indirect burden. We describe information needs that, if filled, might improve the validity of future estimates.
Identification of the G Protein-activating Domain of the Natriuretic Peptide Clearance Receptor (NPR-C) (1999)

We have shown recently that the 37-amino acid intracellular domain of the single-transmembrane, natriuretic peptide clearance receptor, NPR-C, which is devoid of kinase and guanylyl cyclase activities, activates selectively Gi1 and Gi2 in gastric and tenia coli smooth muscle. In this study, we have used synthetic peptide fragments of the N-terminal, C-terminal, and middle regions of the cytoplasmic domain of NPR-C to identify the G protein-activating sequence. A 17-amino acid peptide of the middle region (Arg469-Arg485), denoted Peptide 4, which possesses two N-terminal arginine residues and a C-terminal B-B-X-X-B motif (where B and X are basic and non-basic residues, respectively) bound selectively to Gi1 and Gi2, activated phospholipase C-beta3 via the betagamma subunits, inhibited adenylyl cyclase, and induced smooth muscle contraction, in similar fashion to the selective NPR-C ligand, cANP4-23. A similar sequence (Peptide 3), but with a partial C-terminal motif, had minimal activity. Sequences which possessed either the N-terminal basic residues (Peptide 1) or the C-terminal B-B-X-X-B motif (Peptide 2) were inactive. Peptide 2, however, inhibited G protein activation and cellular responses mediated by the stimulatory Peptide 4 and by cANP4-23, suggesting that the B-B-X-X-B motif mediated binding but not activation of G protein, thus causing Peptide 2 to act as a competitive inhibitor of G protein activation.
Carajas and Maraba Viruses, Two New Vesiculoviruses Isolated from Phlebotomine Sand Flies in Brazil (1984)

Two new rhabdoviruses, designated Carajas and Maraba, are described. Both were isolated from phlebotomine sand flies (Lutzomyia spp.) collected in the Amazon basin of Brazil. One recovery of Carajas virus was made from male sand flies. By complement-fixation and neutralization tests both agents were shown to be members of the vesicular stomatitis virus (VSV) serogroup (genus Vesiculovirus). The pathogenicity of the two viruses in mice and Vero cells is similar to that of VSV-Indiana and VSV-New Jersey. Both Carajas and Maraba viruses replicated in Lutzomyia longipalpis following intrathoracic inoculation, and both agents were transovarially transmitted in this sand fly species.
Critical contribution of VH–VL interaction to reshaping of an antibody: The case of humanization of anti‐lysozyme antibody, HyHEL‐10 (2008)

To clarify the effects of humanizing a murine antibody on its specificity and affinity for its target, we examined the interaction between hen egg white lysozyme (HEL) and its antibody, HyHEL-10 variable domain fragment (Fv). We selected a human antibody framework sequence with high homology, grafted sequences of six complementarity-determining regions of murine HyHEL-10 onto the framework, and investigated the interactions between the mutant Fvs and HEL. Isothermal titration calorimetry indicated that the humanization led to 10-fold reduced affinity of the antibody for its target, due to an unfavorable entropy change. Two mutations together into the interface of the variable domains, however, led to complete recovery of antibody affinity and specificity for the target, due to reduction of the unfavorable entropy change. X-ray crystallography of the complex of humanized antibodies, including two mutants, with HEL demonstrated that the complexes had almost identical structures and also paratope and epitope residues were almost conserved, except for complementary association of variable domains. We conclude that adjustment of the interfacial structures of variable domains can contribute to the reversal of losses of affinity or specificity caused by humanization of murine antibodies, suggesting that appropriate association of variable domains is critical for humanization of murine antibodies without loss of function.
In pursuit of antisense. (1996)

The first generation of antisense oligodeoxynucleotides (ODNs) are now undergoing clinical trials, but their effects may reflect biological activities unrelated to their ability to bind RNA. Nevertheless, preclinical animal studies now suggest that phosphorothioate ODNs may be more permeable in certain animal tissues than in cell culture, raising hopes that antisense mechanisms can be exploited pharmacologically.
Models of attention in computing and communication (2003)

Creating computing and communication systems that sense and reason about human attention by fusing together information from multiple streams.
Modeling the storage architectures of commercial database systems (1985)

Modeling the storage structures of a DBMS is a prerequisite to understanding and optimizing database performance. Previously, such modeling was very difficult because the fundamental role of conceptual-to-internal mappings in DBMS implementations went unrecognized. In this paper we present a model of physical databases, called the transformation model, that makes conceptual-to-internal mappings explicit. By exposing such mappings, we show that it is possible to model the storage architectures (i.e., the storage structures and mappings) of many commercial DBMSs in a precise, systematic, and comprehendible way. Models of the INQUIRE, ADABAS, and SYSTEM 2000 storage architectures are presented as examples of the model's utility. We believe the transformation model helps bridge the gap between physical database theory and practice. It also reveals the possibility of a technology to automate the development of physical database software.
Use of Near Infrared Spectroscopy to Estimate Cerebral Blood Flow in Conscious and Anaesthetized Adult Subjects (1996)

OWEN-REECE, H.; ELWELL, C. E.; HARKNESS, W.; GOLDSTONE, J.; DELPY, D. T.; WYATT, J. S.; SMITH, M.; Matjasko, M. Jane M.D. Sheryl Nagle, M.D. Author Information
ChemInform Abstract: ENAMIDINES. PART 3. SYNTHESIS OF 4‐AMINOPYRIMIDINE DERIVATIVES FROM N1‐ALKENYL‐N2‐(ALKYLCARBAMOYL)BENZAMIDINES (1983)

Abstract Unter den gegebenen Reaktionsbedingungen erfolgt Cyclisierung der Benzamidine (I) zu den Pyrimidinen (II).
Specificity, magnitude, and kinetics of MOG‐specific CD8+ T cell responses during experimental autoimmune encephalomyelitis (2004)

Experimental autoimmune encephalomyelitis (EAE) has traditionally been thought to be almost exclusively mediated by CD4(+) effector T cells. Here, we provide evidence for the existence of mouse CD8(+) T cells that are specific for an epitope of the myelin oligodendrocyte glycoprotein (MOG). Using a panel of truncated MOG peptides, we have identified the minimal epitope recognized by these T cells as MOG 37-46. This peptide, while possessing relatively low affinity for H-2D(b), efficiently stimulates IFN-gamma production from MOG-specific CD8(+) T cell lines in vitro and induces EAE in vivo. To further characterize the magnitude and kinetics of expansion of the MOG-specific CD8(+) T cell population in vivo, we used MOG 37-50/H-2D(b) MHC tetramers to visualize MOG-specific CD8(+) effectors in the peripheral lymphoid organs and central nervous system during the course of EAE induction and progression. Our results identify MOG-specific CD8(+) T cells in the central nervous system prior to and after the onset of disease, suggesting that CD8(+) T cells are a possible target for therapeutic intervention during EAE.
Expression and Stereochemical and Isotope Effect Studies of Active 4-Oxalocrotonate Decarboxylase (2000)

4-Oxalocrotonate decarboxylase (4-OD) and vinylpyruvate hydratase (VPH) from Pseudomonas putida mt-2 form a complex that converts 2-oxo-3-hexenedioate to 2-oxo-4-hydroxypentanoate in the catechol meta fission pathway. To facilitate mechanistic and structural studies of the complex, the two enzymes have been coexpressed and the complex has been purified to homogeneity. In addition, Glu-106, a potential catalytic residue in VPH, has been changed to glutamine, and the resulting E106QVPH mutant has been coexpressed with 4-OD and purified to homogeneity. The 4-OD/E106QVPH complex retains full decarboxylase activity, with comparable kinetic parameters to those observed for 4-OD in the wild-type complex, but is devoid of any detectable hydratase activity. Decarboxylation of (5S)-2-oxo-3-[5-D]hexenedioate by either the 4-OD/VPH complex or the mutant complex generates 2-hydroxy-2,4E-[5-D]pentadienoate in D(2)O. Ketonization of 2-hydroxy-2,4-pentadienoate by the wild-type complex is highly stereoselective and results in the formation of 2-oxo-(3S)-[3-D]-4-pentenoate, while the mutant complex generates a racemic mixture. These results indicate that 2-hydroxy-2, 4-pentadienoate is the product of 4-OD and that 2-oxo-4-pentenoate results from a VPH-catalyzed process. On this basis, the previously proposed hypothesis for the conversion of 2-oxo-3-hexenedioate to 2-oxo-4-hydroxypentanoate has been revised [Lian, H., and Whitman, C. P. (1994) J. Am. Chem. Soc. 116, 10403-10411]. Finally, the observed (13)C kinetic isotope effect on the decarboxylation of 2-oxo-3-hexenedioate by the 4-OD/VPH complex suggests that the decarboxylation step is nearly rate-limiting. Because the value is not sensitive to either magnesium or manganese, it is likely that the transition state for carbon-carbon bond cleavage is late and that the metal positions the substrate and polarizes the carbonyl group, analogous to its role in oxalacetate decarboxylase.
Development of Optimized AAV Serotype Vectors for High-Efficiency Transduction at Further Reduced Doses (2016)

We have described the development of capsid-modified next-generation AAV vectors for both AAV2 and AAV3 serotypes, in which specific surface-exposed tyrosine (Y), serine (S), threonine (T), and lysine (K) residues on viral capsids were modified to achieve high-efficiency transduction at lower doses. We have also described the development of genome-modified AAV vectors, in which the transcriptionally inactive, single-stranded AAV genome was modified to achieve improved transgene expression. Here, we describe that combination of capsid modifications and genome modifications leads to the generation of optimized AAV serotype vectors, which transduce cells and tissues more efficiently, both in vitro and in vivo, at ∼20-30-fold reduced doses. These studies have significant implications in the potential use of the optimized AAV serotype vectors in human gene therapy.
Soluble Domain 1 of Platelet–Endothelial Cell Adhesion Molecule (PECAM) Is Sufficient to Block Transendothelial Migration In Vitro and In Vivo (1997)

The inflammatory response involves sequential adhesive interactions between cell adhesion molecules of leukocytes and the endothelium. Unlike the several adhesive steps that precede it, transendothelial migration (diapedesis), the step in which leukocytes migrate between apposed endothelial cells, appears to involve primarily one adhesion molecule, platelet-endothelial cell adhesion molecule (PECAM, CD31). Therefore, we have focused on PECAM as a target for antiinflammatory therapy. We demonstrate that soluble chimeras made of the entire extracellular portion of PECAM, or of only the first immunoglobulin domain of PECAM, fused to the Fc portion of IgG, block diapedesis in vitro and in vivo. Furthermore, the truncated form of the PECAM-IgG chimera does not bind stably to its cellular ligand. This raises the possibility of selective anti-PECAM therapies that would not have the untoward opsonic or cell-activating properties of antibodies directed against PECAM.
Protocol to identify a topological superconducting phase in a three-terminal device (2021)

We develop a protocol to determine the presence and extent of a topological phase with Majorana zero modes in a hybrid superconductor-semiconductor device. The protocol is based on conductance measurements in a three-terminal device with two normal leads and one superconducting lead. A radio-frequency technique acts as a proxy for the measurement of local conductance, allowing a rapid, systematic scan of the large experimental phase space of the device. Majorana zero modes cause zero bias conductance peaks at each end of the wire, so we identify promising regions of the phase space by filtering for this condition. To validate the presence of a topological phase, a subsequent measurement of the non-local conductance in these regions is used to detect a topological transition via the closing and reopening of the bulk energy gap. We define data analysis routines that allow for an automated and unbiased execution of the protocol. Our protocol is designed to screen out false positives, especially trivial Andreev bound states that mimic Majorana zero modes in local conductance. We apply the protocol to several examples of simulated data illustrating the detection of topological phases and the screening of false positives.
Long‐Term Persistence of Mumps Antibody after Receipt of 2 Measles‐Mumps‐Rubella (MMR) Vaccinations and Antibody Response after a Third MMR Vaccination among a University Population (2008)

Lower levels of NA observed among persons who received MMR2 > or =15 years ago demonstrates antibody decay over time. MMR3 vaccination of most seronegative persons marked the capacity to mount an anamnestic response.
An Aggressive Bone Marrow Evaluation Including Immunocytology With GD2 for Advanced Retinoblastoma (2006)

There is general agreement that bone marrow (BM) examination for staging in patients with retinoblastoma should be limited to cases with advanced disease. However, there are limited data about the yield of sampling multiple sites with aspirations and biopsies and immunocytology. Our policy for BM examination included: 2 aspirates and 2 biopsies at the posterior iliac crest scheduled only for cases with postlaminar optic nerve extension (n=56), scleral invasion (n=10) or orbital (n=5) or metastatic disease at diagnosis (n=7) or at extraocular relapse (n=18). Immunocytology with the antibodies 3A7 or 3F8 for the ganglioside GD2 was performed. From 1/1994 to 3/2005, 277 newly diagnosed patients and 5 at extraocular relapse were included. BM invasion was not found in any of the 66 patients enucleated with disease confined to the globe, but was found in 11/27 of those with overt extraocular disease. There were 2/11 cases with at least 1 negative aspirate with positive biopsy and/or immunocytology for GD2. GD2 positivity was found in 9/9 cases. A more aggressive BM evaluation has a low yield in enucleated patients with high-risk features but disease limited to the globe. However, in cases with overt extraocular dissemination, the use of BM biopsy and immunocytology for GD2 allowed for the detection of cases that would have been missed by aspirations alone. GD2 was intensively expressed and it may also be used to monitor disease response and the presence of minimal residual disease.
Achievable Rates for Probabilistic Shaping (2017)

For a layered probabilistic shaping (PS) scheme with a general decoding metric, an achievable rate is derived using Gallager's error exponent approach and the concept of achievable code rates is introduced. Several instances for specific decoding metrics are discussed, including bit-metric decoding, interleaved coded modulation, and hard-decision decoding. It is shown that important previously known achievable rates can also be achieved by layered PS. A practical instance of layered PS is the recently proposed probabilistic amplitude shaping (PAS).
Design and Fabrication of Metasurface on Conventional Optical Fiber Facet for Linearly Polarized Mode (LP11) Generation at Visible Light Wavelength (2016)

We design and fabricate metasurface on the facet of conventional G.652 single mode fiber (SMF). We also experimentally investigate the linearly polarized mode (LP11) generation in SMF using the fabricated metasurface at the wavelength of 632.8 nm.
Extension of the International Conference on Harmonization Tripartite Guideline for Stability Testing of New Drug Substances and Products to Countries of Climatic Zones III and IV (1998)

The International Conference on Harmonization (ICH) Tripartite Guideline "Stability Testing of New Drug Substances and Products" sets out the stability testing requirements for a registration application within the three areas of the European Union, Japan, and the United States. These areas are assigned to climatic zone II with the storage condition of 25 degrees C/60% RH. This paper describes the adjustments that are necessary to extend the guideline to countries of climatic zones III and IV. At first storage conditions were derived with 30 degrees C/35% RH for climatic zone III and 30 degrees C/70% RH for climatic zone IV. Both conditions contain a margin of safety compared to calculated and measured data in warehouses. Furthermore, they cover the extreme temperatures above 30 and 40 degrees C which may arise in these climatic zones. Six months at 40 degrees C/75% RH was fixed as storage condition for accelerated testing to assess organoleptic and physicochemical test criteria and to make predictions for chemical stability. The predictive factor is 3.3 for 30 degrees C (6 months at 40 degrees C corresponds to 20 months at 30 degrees C). Extreme temperatures which may arise during shipment are covered by the results of stress investigations (e.g., 3 months at 50 degrees C). The next adjustment is necessary for the selection of the packaging containers. They must reflect the requirements for solid, semisolid, and liquid dosage forms caused by the two storage conditions. In the evaluation the temperature difference of 10 degrees C (40-30 degrees C) instead of 15 degrees C has to be considered, which limits the preliminary shelf lives in critical cases to 18 months instead of 24 months. Finally, statement/labeling must reflect the storage conditions. All of the other basic principles for the drug substances and drug products, such as selection and number of batches, test criteria, test procedures, specifications, testing frequency, and storage period can be applied without any change.
Aetiology and treatInent of stuttering (2004)

The Two-Pole Centre Theory can explain the aetiology and treatment of stuttering. Phonation for speech is controlled by the two-pole centre, which consists of the cerebral cortex and the cerebral subcortex. There are three different levels: the cerebral cortex level, the thalanzic brain level and the medullary level. The cerebral cortex controls any forms of phonation (e.g. singing, reading, vocal imitation) except habitual phonation. Human emotion is under thalamic control. It is the interaction of the cortex, the subcortex and the thalamic brain that produces the psychological problem for stutterers, the development of stuttering, and the auxiliary actions of stutterers when they are speaking. Our clinic data (over 1000 cases) shows that in the overwhelming majority of cases (87.5%) stuttering originates from imitating other stutterers. This paper suggests that speech adaptation should proceed by establishing the conditional reflex controlled under the cerebral subcortex. The cortex controls only the content of thought, without controlling the phonation itself Habitual phonation is a kind of reflex action that is not controlled by the cerebral cortex. Most of the time it is possible for stutterers to maintain the beneficial effects of treatment by themselves. Many treatments for stuttering are equally successful. The phonatory method we use varies from individual to individual.