gebhart/patrepeval huggingface dataset:
Rhodopsin kinase: Expression in baculovirus-infected insect cells, and characterization of post-translational modifications (1997)

Structure-function studies of rhodopsin kinase (RK; EC 2.7.1.125) require a variety of mutants. Therefore, there is need for a suitable system for the expression of RK mutant genes. Here we report on a study of expression of the RK gene in baculovirus-infected Sf21 cells and characterization of the enzyme produced as purified to near homogeneity. Particular attention has been paid to the post-translational modifications, autophosphorylation and isoprenylation, found in the native bovine RK. The protein produced has been purified using, successively, heparin-Sepharose, Mono Q, and Mono S FPLC (fast protein liquid chromatography) and was obtained in amounts of about 2 mg from 1 liter of cell culture. The enzyme from the last step of purification was obtained in two main fractions that differ in the level of phosphorylation. The protein peak eluted first carries two phosphate groups per protein, whereas the second protein peak is monophosphorylated. Further, while both peaks are isoprenylated, the isoprenyl groups consist of mixtures of C5, C10, C15, and C20 isoprenyl moieties. From these results, we conclude that the above expression system is suitable for some but not all aspects of structure-function studies.
Influence of Cation Size on the Co‐crystallisation of Benzoic Acid with Different Benzoates (2013)

Abstract In the pharmaceutical industry many new active pharmaceutical ingredients (APIs) are marketed as carboxylic salts because of enhanced solubility and dissolution rates. These salts are, however, often hard to crystallise and/or exhibit a low degree of crystallinity. The reason may be the largely differing sizes of cation and anion. One way out of the resulting “coordination dilemma“ is the formation of co‐crystals of the salt with its neutral acid which delivers additional coordination sites for the cation. In this line, the crystal structure of a new co‐crystal of benzoic acid (HBz) and lithium benzoate (LiBz) with composition 1HBz · 1LiBz was determined and was compared to published ionic co‐crystals of other alkali salts with respect to the structure determining criteria: coordination number of the cation, ratio of HBz:Bz – , mode of coordination of the carboxylic groups (mono‐ or bidentate), and connectivity (edge‐ or corner‐sharing) between neighbouring polyhedra. The new crystal structure is closely related to form A of 2HBz · 1NaBz. Both crystal structures contain dimers with shared edges which are further connected by bridging bidentate ligands to tapes.
Listening to Each Speaker One by One with Recurrent Selective Hearing Networks (2018)

Deep learning-based single-channel source separation algorithms are currently being actively investigated. Among them, Deep Clustering (DC) and Deep Attractor Networks (DANs) have made it possible to separate an arbitrary number of speakers. In particular, they cleverly combine a neural network and a K-means clustering algorithm to obtain source separation masks with the assumption that the correct number of speakers at the test time is known in advance. Unlike DC and DAN, Permutation Invariant Training (PIT) was proposed as a purely neural network-based mask estimator. Essentially, however, PIT can deal with only a fixed number of speakers, given the strong relationship between the dimensions of the output nodes and the assumed number of sources. Considering these limitations and merits of such conventional methods, this paper proposes a purely neural-network based mask estimator that can handle an arbitrary number of sources, and simultaneously estimate the number of sources in the test signal. To accomplish this, while the conventional methods deal with the source separation problem as a one-pass problem, we cast the problem as a recursive multi-pass source extraction problem based on a recurrent neural network (RNN) that can learn and determine how many computational steps/iterations have to be performed depending on the input signals. In this paper, we describe our proposed method in detail, and experimentally show its efficacy in terms of source separation and source counting performance.
Implicit state transition graphs: applications to sequential logic synthesis and test (2002)

Implicit state enumeration is used in developing strategies to solve key problems in sequential logic synthesis and test. It is shown that it is possible to extract implicit state transition graphs (ISTGs) from logic-gate and flip-flop descriptions of sequential circuits that allow equivalent states to be represented by cubes, and edges from different states to be coalesced into one, thereby decreasing significantly the CPU time and memory requirements of the extraction process. Coupled with the enumeration technique, synthesis strategies are proposed for FSMs (finite state machines) described at the logic level. As is illustrated, these synthesis strategies allow the authors to optimize large FSMs. The authors apply an ISTG traversal algorithm for verifying equivalence and detecting redundancies in logic-level sequential circuits. This algorithm is more efficient than previously developed sequential test generation algorithms when used to detect equivalent-state redundancies present in some classes of circuits.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Qmerit-calibrated overlay to improve overlay accuracy and device performance (2015)

In advanced semiconductor industries, the overlay error budget is getting tighter due to shrinkage in technology. To fulfill the tighter overlay requirements, gaining every nanometer of improved overlay is very important in order to accelerate yield in high-volume manufacturing (HVM) fabs. To meet the stringent overlay requirements and to overcome other unforeseen situations, it is becoming critical to eliminate the smallest imperfections in the metrology targets used for overlay metrology. For standard cases, the overlay metrology recipe is selected based on total measurement uncertainty (TMU). However, under certain circumstances, inaccuracy due to target imperfections can become the dominant contributor to the metrology uncertainty and cannot be detected and quantified by the standard TMU. For optical-based overlay (OBO) metrology targets, mark asymmetry is a common issue which can cause measurement inaccuracy, and it is not captured by standard TMU. In this paper, a new calibration method, Archer Self-Calibration (ASC), has been established successfully in HVM fabs to improve overlay accuracy on image-based overlay (IBO) metrology targets. Additionally, a new color selection methodology has been developed for the overlay metrology recipe as part of this calibration method. In this study, Qmerit-calibrated data has been used for run-to-run control loop at multiple devices. This study shows that color filter can be chosen more precisely with the help of Qmerit data. Overlay stability improved by 10~20% with best color selection, without causing any negative impact to the products. Residual error, as well as overlay mean plus 3-sigma, showed an improvement of up to 20% when Qmerit-calibrated data was used. A 30% improvement was seen in certain electrical data associated with tested process layers.
Carbon-Negative Biofuels from Low-Input High-Diversity Grassland Biomass (2006)

Biofuels derived from low-input high-diversity (LIHD) mixtures of native grassland perennials can provide more usable energy, greater greenhouse gas reductions, and less agrichemical pollution per hectare than can corn grain ethanol or soybean biodiesel. High-diversity grasslands had increasingly higher bioenergy yields that were 238% greater than monoculture yields after a decade. LIHD biofuels are carbon negative because net ecosystem carbon dioxide sequestration (4.4 megagram hectare(-1) year(-1) of carbon dioxide in soil and roots) exceeds fossil carbon dioxide release during biofuel production (0.32 megagram hectare(-1) year(-1)). Moreover, LIHD biofuels can be produced on agriculturally degraded lands and thus need to neither displace food production nor cause loss of biodiversity via habitat destruction.
Congenital camptodactyly associated with the 48,XXYY syndrome. (1998)

A male premature infant presented with slow development and congenital camptodactyly of both hands. Chromosome analysis showed a 48,XXYY karyotype. As far as we know, this is the first report describing congenital camptodactyly associated with the 48,XXYY syndrome.
Nature of Transannular Intramolecular Interactions in Group 4 and 6 Metallatranes: A Combined Density Functional Theory and Atoms in Molecules Theory Study (2010)

Density functional calculations coupled with quantum theory of atoms in molecules analysis were carried out on Group 4 and 6 metallatranes with special emphasis on the nature of transannular M···N bonds present in these molecules. Substituents at both the apical and equatorial positions are found to influence the extent of transannular interaction. The degree of pyramidalization around the metal and the bridgehead nitrogen atom play a key role in strengthening or weakening the M···N bond. The stability of these molecules are found to depend to a large extent on the strength of M···N bonds with significant contribution coming in from metal-equatorial and metal-apical bonds. Group 6 metallatranes are found to have stronger transannular bonds and, hence, higher stabilization energies than their Group 4 counterparts. Atoms in molecules theory analysis reveals the presence of a considerable amount of covalent character in the M···N bonds which increase from Group 4 to Group 6.
The effect of wave motion on dry suit insulation and the responses to cold water immersion. (1998)

To simulate open ocean conditions in the laboratory, the standards must take the reduction of suit insulation into account.
Concurrent Inactivation of RB1 and TP53 Pathways in Anaplastic Oligodendrogliomas (2001)

Oligodendrogliomas are characterized by frequent loss of heterozygosity (LOH) on chromosomes 1p and 19q, but additional genetic alterations are likely to be involved. In this study, we screened 28 oligodendrogliomas (WHO grade II) and 20 anaplastic oligodendrogliomas (WHO grade III) for alterations in the RB1/CDK4/p16INK4a/p15INK4b and TP53/p14ARF/MDM2 pathways. In oligodendrogliomas, hypermethylation of RB1 (1 case) and p14ARF (6 cases) were the only detectable genetic changes (7/28, 25%). In anaplastic oligodendrogliomas, the RB1/CDK4/p16INK4a/p15INK4b signaling pathway regulating the G1 -->3 S transition of the cell cycle was altered in 13/20 (65%) cases, by either RBI alteration, CDK4 amplification, or p16IN4a/p15INK4b homozygous deletion or promoter hypermethylation. Further, 50% (10/20) of anaplastic oligodendrogliomas showed alterations in the TP53 pathway through promoter hypermethylation or homozygous deletion of the p14ARF gene and, less frequently, through TP53 mutation or MDM2 amplification. Of 13 anaplastic astrocytomas with an altered RB1 pathway, 9 (69%) also showed a dysregulated TP53 pathway. Thus, simultaneous disruption of the RB1/CDK4/p16INK4a/p15INK4b and the TP53/p14ARF/MDM2 pathways occurs in 45% (9/20) of anaplastic oligodendrogliomas, suggesting that these phenomena contribute to their malignant phenotype.
Mapping of Antigenic Changes in the Haemagglutinin of Hong Kong Influenza (H3N2) Strains using a Large Panel of Monoclonal Antibodies (1982)

A panel of 125 monoclonal antibodies (IgG) was raised against the haemagglutinin of an early representative of the Hong Kong (H3N2) subtype of influenza. They were classified into groups based on their cross-reactions with 16 other virus strains from the same subtype. This classification was performed using methods of numerical taxonomy. Statistical tests supported the validity of the grouping. Ten such groups were identified. Nine antibodies remained unclassified. The locations on the haemagglutinin molecule of amino acid residues influencing the binding of each antibody group were estimated. This was achieved by a study of antibody cross-reactive profiles, coupled with previously published locations of amino acid changes in the primary sequence of different haemagglutinins, and their positions in the tertiary structure of the molecule. The locations of the amino acids affecting antibody binding overlapped between the different antibody groups forming a continuous ring surrounding the probable cell-receptor pocket. The amino acids affecting the binding of each antibody group may or may not represent the actual antibody binding sites. The importance of the different sites of amino acid variation in the haemagglutinin during evolution of the virus is discussed.
A Mechanistic Model for In-Reactor Densification of UO 2 (1985)

Considering vacancy generation and migration in grain and sink at grain boundary, a mechanistic densification model which is dependent on UO temperature and microstructure has been developed. This densification model is a function of time, fission rate, temperature, density, pore size distribution and grain size. The resultant equation derived in this model which is different from Assmann and Stehle's resultant equations for four temperature regions, can be applied directly for all the pellet temperatures. The predictions of the present densification model very well agreed with the experimental data. This model well predicts absolute magnitude and trend in comparison with the empirical algorithm used in KFEDA code.
[Current endemic situation and control strategy of schistosomiasis in lake and marshland regions in China]. (2011)

This paper reviewed the current endemic features and situation of schistosomiasis in lake and marshland regions in China, and discussed the comprehensive control strategy for schistosomiasis with emphasis on infectious sources control, including its theoretical basis, the reality conditions of implementation and technical composition, and also introduced the effectiveness of the pilot trails and their large-scale application as well as several issues in the implementation. The aim of the review is to accelerate the process of schistosomiasis control in lake and marshland regions and promote the achievement of mid- and long-term goals in national schistosomiasis control program.
A Nonneutralizing Human IgM Monoclonal Antibody Inhibiting Hemagglutination of H3N2 Influenza A Strains (1986)

A mouse-human hybridoma has been produced by fusing human splenocytes from a Cooley's anemia patient with the murine myeloma P3-NS1/1-Ag 4-1. The hybridoma is stable after 18 months and secretes human IgM. The antibody reacts with some H3N2 influenza A strains and detects an epitope that is part of the hemagglutinin antigen, but does not affect virus infectivity.
Complete In Vivo Reversal of the Multidrug Resistance Phenotype by Jet-injection of Anti-MDR1 Short Hairpin RNA-encoding Plasmid DNA (2007)

Triggering the RNA interference (RNAi) pathway by inducing the expression of short hairpin RNA (shRNA) molecules has become a promising tool for efficient silencing of a given gene in gene therapy applications. In this study, shRNA encoding DNA was utilized to reverse the classical MDR1/P-glycoprotein (MDR1/P-gp)-mediated multidrug resistance (MDR) phenotype in vivo. For the first time, the nonviral jet-injection technology was applied for delivering naked shRNA-vector constructs for direct intratumoral in vivo transfer. The highly efficient anti-MDR1 shRNA expression vectors were applied twice in the human MDR1/P-gp overexpressing MaTu/ADR cancer xenograft-bearing mice, and twice in the corresponding drug-sensitive parental MaTu tumor xenograft bearing mice as well. Two days after anti-MDR1 shRNA vector injection, the expression level of the MDR1 messenger RNA (mRNA) was decreased by more than 90% and the corresponding MDR1/P-gp protein was no longer detectable in the tumors. Two jet-injections of anti-MDR1 shRNA vectors into the tumors, combined with two intravenous (IV) administrations of doxorubicin, were sufficient to achieve complete reversal of the drug-resistant phenotype. The data show that jet-injection delivery of shRNA-expressing vectors is effective in reversing MDR1/P-gp-mediated MDR in vivo, and is therefore a promising strategy for making tumors with an MDR1/Pgp-dependent MDR phenotype revert to a drug-sensitive state.
Image Retrieval from Vague Description Based on AttnGAN (2018)

Image retrieval plays an important role in the information society. Many studies have been conducted to improve accuracy of the image retrieval. However, there exists a major limitation in their input methods. For example, if users only have a vague description that does not include detailed information such as its name and do not have an appropriate input image, it is difficult to retrieve their desired images. To solve this problem, we propose a novel image retrieval method that enables retrieval of a desired image from a vague description. In the proposed method, we generate a query image from a vague description through an Attentional Generative Adversarial Network. By using the generated query image, the proposed method enables users to retrieve images even if they do not have a clear retrieval description as an input. Experimental results show the effectiveness of our method.
Floating-point signal processing-arithmetic, roundoff-noise, and limit cycles (2003)

The number of representation and the range of floating-point numbers is treated for floating-point signal processing. The addition and multiplication operations which are most important for digital signal processing are explained in detail including the necessary normalization operations. Quantization errors in terms of the probability densities of the relative errors are analyzed in detail for roundoff-quantization, two's-complement-truncation, and magnitude-truncation. The roundoff-noise is determined for a single quantizer and for complex signal processing flowgraphs. The problem of limit cycles is discussed briefly.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Somatostatin receptor imaging of endocrine gastrointestinal tumors. (1992)

111In-octreotide scintigraphy is a simple and sensitive technique for localizing of the primary tumor and its metastases in the majority of patients with carcinoids or endocrine pancreatic tumors.(ABSTRACT TRUNCATED AT 250 WORDS)
Utilization of dried distillers grain from sorghum in baked food systems. (1984)

Five sorghum varieties representing brown, yellow, white, and white waxy types were fermented into alcohol. The residual dried distillers grains (DDG) and commercial samples of DDG obtained from a brewery and a distillery were analyzed chemically and rheologically and were tested for possible applications in baked food systems. Sorghum DDG were higher in protein and lower in starch than the commercial DDG. Replacement of wheat flour with up to 15% DDG dec reased mixing and stability times of the doughs. Bread loaf volume decreased as substitution levels increased. Crumb color was directly related to the color of the DDG and level of substitution. Neutral detergent fiber and crude protein were higher in the sorghum and commercial DDG than wheat or sorghum flour. This resulted in higher neutral detergent fiber and crude protein in bread and cookies as substitution levels increased. With the exception of color, the quality of DDG sugar cookies at substitution levels up to 15% was comparable to that of controls. Molasses cookies containing up to 25% white sorghum DDG were superior to the control
Selective effects of lipiodolized antitumor agents (1984)

Lipiodol Ultra-Fluid (Lipiodol) remains selectively in the tumor for an extended time when applied through arteries feeding the tumor. Although lipophilic antitumor drugs are selective when combined with Lipiodol, wide application of common hydrophilic agents is limited, as these compounds are insoluble in oil. We propose "Lipiodolization" of water-soluble agents using as an intermediate Urografin, a water-soluble contrast medium. Thirteen patients with primary hepatocellular carcinoma were treated with this Lipiodol-Urografin system containing antitumor agents. Marked decrease in serum alpha-fetoprotein (AFP) levels, decrease in tumor size in the hepatic imaging, and histologic studies of the resected specimen revealed this mode of therapy to be effective in 10 of 13 patients (77%) with hepatocellular carcinoma. Lipiodolization of antitumor agents is a new approach to selective cancer chemotherapy.
Data for: Structure-based design of monoamine neurotransmitter reuptake inhibitors (2018)

NMR of synthesized compounds
Rapid Racemization in Thiazolidinediones:  A Quantum Chemical Study (2004)

Ab initio molecular orbital (MO) and density functional studies have been carried out on the keto−enol tautomerization process in thiazolidinediones to understand the mechanism of rapid racemization observed in these systems. MP2(full)/6-31+G* results on model thiazolidinedione 1 indicate that the energy difference between keto and enol tautomers is 24.04 kcal/mol, which is larger than that in acetaldehyde (16.23 kcal/mol). Neither the ring strain in 1 nor the electron delocalization in its tautomers is significant enough to facilitate rapid racemization through this mechanism. Reversible S-oxide formation increases the acidity of the hydrogen at the chiral center as well as provides an alternative path for tautomerization, suggesting that such a mechanism is responsible for the rapid racemization observed under physiological conditions.
Trifluoromethanesulfonic Acid Efficiently Catalyzed the Intramolecular Glycosidation of 1-<i>C</i>-Alkyl-<scp>d</scp>-hexopyranoses to Form the Anhydroketopyranoses Having 6,8-Dioxabicyclo[3.2.1]octane Structures (2005)

The intramolecular glycosidation of the 1-C-alkyl-d-hexopyranose derivatives to form the anhydroketopyranoses having 6,8-dioxabicyclo[3.2.1]octane structures was investigated. We synthesized several 1-C-alkyl-2,3,4-tri-O-benzyl-d-hexopyranoses and found that only 5 mol% trifluoromethanesulfonic acid efficiently promoted the intramolecular glycosidation to afford the desired anhydroketopyranoses in good yields.
SmI<sub>2</sub>-Mediated Intermolecular Coupling of γ-Lactam <i>N</i>-α-Radicals with Activated Alkenes: Asymmetric Synthesis of 11-Hydroxylated Analogues of the Lead Compounds CP-734432 and PF-04475270 (2012)

We report, for the first time, the synthesis of 8-aza-analogues of PGE2. The SmI2-mediated cross coupling reactions of γ-lactam-hemiaminal 9, lactam 2-pyridyl sulfide 17, and lactam 2-pyridyl sulfone 18 with activated alkenes/alkyne were first developed, giving the corresponding γ-lactams in 49-78%, 45-75%, and 75-90%, respectively. The reactions of lactam 2-pyridyl sulfide and 2-pyridyl sulfone proceeded with ≥12:1 trans-diastereoselectivities. This represents the first intermolecular coupling reaction of the γ-lactam N-α-alkyl radicals of types B, B1, and B2 with activated alkenes. Two radical-based mechanisms were suggested. The asymmetric synthesis of the 11-hydroxylated analogue of the highly selective EP4 receptor agonist PF-04475270 (30), the 11-hydroxylated analogue of ocular hypotensive CP-734432 (31), compounds 35 and 36 have been achieved on the basis of this method.