gebhart/patrepeval huggingface dataset:
Clonal Changes Are Frequent in Relapsed TEL-AML1+ ALL and Predominate in Young Children. (2004)

Abstract The TEL-AML1 fusion gene is present in 25% of childhood B cell precursor ALL and arises generally in utero. Depending on the treatment protocol up to 20% of patients relapse, which represents the highest absolute number of relapses in a genetically well-defined subgroup. As proposed previously, a significant proportion of these relapses seem to derive from a persistent ancestral TEL-AML1+ clone. This notion is based on the observation of different deletions of the non-rearranged TEL allele as well as unrelated clonotypic Ig/TCR rearrangements at diagnosis and relapse. As an extension of these studies, we analyzed the IGH, IGK, TCRD and TCRG gene rearrangements from samples obtained from 41 children with TEL-AML1+ ALL at diagnosis and relapse. Our aim was to determine the development of clonal changes during the course of the diseases and to investigate their potential biological and clinical significance. Based on the immunogenotype at diagnosis and relapse, we divided the patients into two groups. Group I (n=13) consisted of patients with identical Ig/TCR rearrangements, whereas group II (n=28) included those with a change in their immunogenotype. These differences derived either from clonal evolution (32%) or clonal selection (68%) and resulted mainly from losses (0–6, median 5) and/or gains (0–4, median 1) of rearrangements. The number of rearrangements at diagnosis per case also differed (p=0.003) between the two groups (1–5, median 3 in group I; 2–13, median 5 in group II). With regard to individual gene loci, we observed the highest frequency of rearrangements at the IGH (86%) and TCRD (68%) loci in group II at diagnosis, whereas at the corresponding relapses it was only 79% at IGH and 39% at TCRD (p=0.004). The incidence of IGK and TCRG rearrangements was equally high at both occasions (86% and 93%, respectively). The incidence of rearranged loci in group I, on the other hand, concurred with that of the relapse samples of group II. Of special interest is also the fact that the patients of group I were older at diagnosis than those of group II (4.9 versus 3.1 yrs), which is in accordance with our earlier report on age-related variations of Ig/TCR rearrangements. We thus conclude that i) changes in the immunogenotype take place in the majority of children with relapses of a TEL-AML1+ ALL, ii) children with a change in their immunogenotype are younger at initial diagnosis than those with a conserved immunogenotype and iii) there is no association between the immunogenotype patterns and the duration of first remission. We therefore propose that the greater clonal diversity in younger children mirrors the result of a high recombinatorial activity, while the restricted repertoire in older children reflects end-stage patterns due to ongoing recombination/deletion and selection processes during their prolonged latency period. Finally, the likelihood of stability of the various rearrangements (IGK 81%, TCRG 70%, IGH 62% and TCRD 47%) can be used as a hierarchical guideline for MRD studies.
Structure-Reactivity Relationship in Allyl and 2-Propynyl Complexes of Group 10 Metals Relevant to Homogeneous Catalysis (1998)

Abstract Recent developments in the understanding of some fundamental reactions undergone by group 10 metal allyl and propargyl (2-propynyl) complexes are described. Emphasis was placed on the bonding-reactivity relationship of these complexes which are relevant as key intermediate models in transition metal catalyzed transformations of allylic and propargylic substrates as well as related transformations involving unsaturated hydrocarbons. The specific complexes surveyed include group 10 metal complexes of allyl and propargyl ligands bound to the metal both in η1- and η3-fashions. Specific reactions to be discussed include oxidative addition, nucleophilic and electrophilic attack at the allyl or propargyl ligands, and reductive elimination of the allyl ligands.
Amines, Aliphatic (2000)

Abstract The article contains sections titled: 1. Introduction 2. General Chemical Properties 2.1. Salt Formation 2.2. Conversion to Carboxamides 2.3. Conversion to Sulfonamides 2.4. Reaction with Carbonyl Compounds 2.5. Reaction with Carbon Dioxide and Carbon Disulfide 2.6. Reaction with Epoxides 2.7. Alkylation 2.8. Formation of Isocyanates and Ureas 2.9. Reaction with Acrylonitrile 2.10. Formation of Isonitriles 2.11. Oxidation 2.12. Dealkylation 3. General Production Methods 3.1. Production from Alcohols 3.2. Production from Carbonyl Compounds 3.3. Production from Nitriles 3.4. Production from Alkyl Halides 3.5. Production from Nitro Compounds 3.6. Production from Olefins 3.7. Other Processes 4. Lower Alkylamines 4.1. Physical Properties 4.2. Storage and Transportation 4.3. Quality Specifications and Analysis 4.4. Production 4.5. Uses 4.6. Economic Aspects 5. Cycloalkylamines 6. Cyclic Amines 7. Fatty Amines 7.1. Properties 7.2. Production 7.3. Analysis and Quality Control 7.4. Uses 7.5. Economic Aspects 8. Diamines and Polyamines 8.1. Diamines 8.1.1. 1,2‐Diaminoethane (Ethylenediamine) 8.1.2. Diaminopropanes 8.1.3. Higher Diamines 8.2. Oligoamines and Polyamines 8.2.1. Physical Properties 8.2.2. Chemical Properties 8.2.3. Production, Analysis, and Uses 9. Chiral Amines 10. Toxicology and Occupational Health 10.1. General Aspects 10.2. Toxicology of Specific Amines 10.2.1. Alkylamines, Cyclic Amines, and Polyamines 10.2.2. Fatty Amines 11. Acknowledgment
The Direct Organocatalytic Asymmetric Mannich Reaction: Unmodified Aldehydes as Nucleophiles. (2004)

Abstract For Abstract see ChemInform Abstract in Full Text.
A Compact and Ultra-Low-Power Low-Pass Filter Based on Band-to-Band Tunneling Effect (2023)

Continuous-time filters with low-frequency cutoff are crucial building blocks in analog signal processing circuits for speech processing and biomedical applications. The design of an integrated continuous-time filter with a cutoff frequency spanning from sub-Hz to a few kHz is constrained by the ultra-low power and area minimization requirement. In this brief, we have experimentally demonstrated a low pass filter response using only a single partially depleted (PD) silicon on insulator (SOI) transistor. The proposed novel filter is based on band to band tunnelling (BTBT). This low pass filter is on-chip tunable to provide a wide cutoff frequency ranging from 2 Hz to 20 kHz, with a silicon footprint of <inline-formula xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink"> <tex-math notation="LaTeX">$9 \mathbf {\mu m^{2}}$ </tex-math></inline-formula> and the maximum power consumption of 0.6 nW in Global Foundries’ (GF) 45 nm RFSOI technology. The proposed tunneling-based filter is less prone to process variations and mismatches as compared to traditional integrated analog filters. The proposed BTBT-based passive RC filter with spurious free dynamic range (SFDR) of 29 dbc, outperforms previously reported filters in the literature in terms of power consumption and area. The ultra-low power consumption and area efficiency make this proposed low pass filter suitable for the multichannel analog front-end low-frequency filters for noise-tolerant neural network-based applications such as speech recognition and electrophysiological signal recognition.
iQueue: a pervasive data composition framework (2003)

There will soon be a huge number of data sources accessible to applications across the Internet. These include Web services, personal devices such as cellular phones and cars, and sensors measuring physical phenomena. New classes of data-composition applications can exploit this data. However, the data is diverse, voluminous, and often rapidly changing. The sources of data can be mobile, distributed, and failure-prone. Without system support, applications that use this kind of data are difficult to write. The iQueue data composition framework provides system support for data composition, thereby making the task of writing applications easier.
Bounds of mmWave-Based Ranging and Positioning in Multipath Channels (2017)

In this paper, we investigate the accuracy of millimeter-wave (mmWave)-based ranging and positioning in multipath channels. The agent is equipped with massive phased uniform rectangular array (URA) and multiple anchors are considered in localization networks to pursue a higher accuracy. Fundamental limits of both ranging and positioning associated with 3D mmWave transmission and massive URA are derived by Cramer-Rao lower bound (CRLB) in multipath channels. Furthermore, the relationship between the fundamental bound of range estimation and that of position estimation is theoretically clarified. Numerical results show that the proposed scenario achieves a millimeter (mm)-level accuracy for short-distance ranging and positioning in multipath channels.
Pathogenicity and Pyrenocine Production of Curvularia inaequalis Isolated from Zoysia Grass (2000)

Five isolates of Curvularia inaequalis were obtained from blighted leaves of zoysia grass. The optimal growth temperature of the pathogen was 30°C and all isolates caused foliar blighting symptoms on zoysia grass, bent grass, and bermuda grass. Phytotoxic substances were associated with pathogenicity. Two phytotoxins were isolated from liquid cultures of C. inaequalis by ethyl acetate extraction and repeated silica gel column chromatography. On the basis of mass and nuclear magnetic resonance spectral analyses, the compounds were identified as pyrenocines A and B, phytotoxins produced by Pyrenochaeta terrestris. Pyrenocine A caused leaf necrosis in a leaf-wounding bioassay and inhibited growth of all plants tested in a whole plant test. Large crab grass and fall panicum were most susceptible to pyrenocine A. Pyrenocines A and B also caused significant electrolyte leakage from leaf tissues of bermuda grass. Pyrenocine B exhibited much weaker phytotoxic activity than pyrenocine A in all bioassays performed. Both compounds caused leaf tip dieback symptoms in turf grass plants similar to symptoms observed in the field. Thus, pyrenocines A and B are thought to be involved in the development of Curvularia blight disease of turfgrasses caused by C. inaequalis.
31 PRODUCTION EFFICIENCY OF GENE KNOCKOUT PIGS USING GENOME EDITING AND SOMATIC CELL CLONING (2014)

Genome editing technologies have been used as a powerful strategy for the generation of genetically modified pigs. We previously developed genetically modified clone pigs with organogenesis-disabled phenotypes, as well as pigs exhibiting diseases with similar features to those of humans. Here, we report the production efficiency of various gene knockout cloned pigs from somatic cells that were genetically modified using zinc finger nucleases (ZFN) or transcription activator-like effector nucleases (TALEN). The ZFN- or TALEN-encoding mRNAs, which targeted 7 autosomal or X-linked genes, were introduced into porcine fetal fibroblast cells using electroporation. Clonal cell populations carrying induced mutations were selected after limiting dilution. The targeted portion of the genes was amplified using PCR, followed by sequencing and mutation analysis. Among the collected knockout cell colonies, cells showing good proliferation and morphology were selected and used for somatic cell nuclear transfer (SCNT). In vitro-matured oocytes were obtained from porcine cumulus-oocyte complexes cultured in NCSU23-based medium and were used to obtain recipient oocytes for SCNT after enucleation. SCNT was performed as reported previously (Matsunari et al. 2008). The cloned embryos were cultured for 7 days in porcine zygote medium (PZM)-5 to assess their developmental ability. Cloned embryos were transplanted into the oviduct or uterus of oestrus-synchronized recipient gilts to evaluate their competence to develop to fetuses or piglets. Cloned embryos reconstructed with 7 types of knockout cells showed equal development to blastocysts compared with those derived from the wild-type cells (54.5–83.3% v. 60.7%). Our data (Table 1) demonstrated that the reconstructed embryos derived from knockout cells could efficiently give rise to cloned offspring regardless of the type of genome editing methodology (i.e. ZFN or TALEN). Table 1. Production efficiency of gene knockout cloned pigs using genome editing This study was supported by JST, ERATO, the Nakauchi Stem Cell and Organ Regeneration Project, JST, CREST, Meiji University International Institute for Bio-Resource Research (MUIIBR), and JSPS KAKENHI Grant Number 26870630.
Synergistic Antitumor Effects of Combined Epidermal Growth Factor Receptor and Vascular Endothelial Growth Factor Receptor-2 Targeted Therapy (2006)

Results show antitumor synergy for combined EGFR and VEGFR2 targeted therapy, supporting the significant therapeutic potential of this combination strategy.
Synthesis and in Vitro Activity of 17.beta.-(N-Alkyl/arylformamido and N-alkyl/arylalkyl/arylamido)-4-methyl-4-aza-3-oxo-5.alpha.-androstan-3-ones as Inhibitors of Human 5.alpha.-Reductases and Antagonists of the Androgen Receptor (1995)

A number of 17 beta-(N-alkyl/arylformamido)- and 17 beta-[(N-alkyl/aryl)alkyl/arylamido]-3-oxo-4-aza-5 alpha-steroids were prepared from 17 beta-hydroxy-4-azasteroids and evaluated as inhibitors of human 5 alpha-reductase and antagonists of the androgen receptor. Jones' oxidation of 17 beta-hydroxy compounds gave the 17-keto-4-azasteroids, which were treated with amines and NaBH(OAc)3/NaBH3CN to give 17 beta-(N-alkyl/arylamino)-4-azasteroids 10-27. Alternatively, the above-indicated compounds were prepared from amines and 17-keto-4-azasteroids to form imines, which were then reduced with NaBH4. Formylation of amines 10-27 gave 17 beta-(N-alkylformamides) 28-41; however, acylation afforded 17 beta-[(N-alkyl/aryl)alkyl/arylamides] 42-53. In comparison to N,N-diethyl-4-methyl-3-oxo-4-aza-5 alpha-androstane-17 beta-carboxamide (4-MA; IC50 = 4.15 nM), 17 beta-(N-alkylformamido)-4-azasteroids were potent inhibitors of human type I 5 alpha-reductase, IC50 values of compounds 29, 30, 36, and 37 being measured as 3.05, 0.91, 2.19, and 2.35 nM, respectively. The structure-activity relationships suggest that the type I enzyme has preference for N-substituted straight alkyl side chains of four to five carbon atoms. On the other hand, formamides 32 (N-heptyl) and 33 (N-octyl), in addition to inhibiting the type I enzyme (IC50s = 9.57 and 16.9 nM, respectively), showed also strong inhibitory activity (IC50s = 14.0 and 18.4 nM, respectively) for human type II 5 alpha-reductase, in comparison to N-(1',1'-dimethylethyl)-3-oxo-4-aza-5 alpha-androst-1-ene-17 beta-carboxamide (MK-906; IC50 = 4.53 nM). Other compounds in this series showed moderate activities (IC50 > 100 nM) on the type II enzyme. 17 beta-[(N-Alkyl/aryl)alkyl/arylamides] 45, 46, 48, and 51 exhibited highly potent inhibitory activity for human type I 5 alpha-reductase with IC50s of 1.77, 2.42, 2.93, and 5.44 nM, respectively, while moderate to no effect was observed on the type II enzyme (100 < IC50s < 1000 nM), except for compound 48 (IC50 = 3.75 nM). In another substitution pattern, N-aryl/alkylamides were studied; an electron-donating group increased the potency of compound 51, whereas an electron-withdrawing group decreased the potency of compounds 52 and 53 compared to parent compound 50. In addition to their 5 alpha-reductase activities, 17 beta-(N-alkylformamides) were also studied for their inhibitory activities on dihydrotestosterone (DHT)-stimulated proliferation of androgen-sensitive Shionogi mouse mammary carcinoma cells (clone SEM-107).(ABSTRACT TRUNCATED AT 400 WORDS)
Conservation and Covariance in Small Bacterial Phosphoglycosyltransferases Identify the Functional Catalytic Core (2015)

Phosphoglycosyltransferases (PGTs) catalyze the transfer of a C1'-phosphosugar from a soluble sugar nucleotide diphosphate to a polyprenol phosphate. These enzymes act at the membrane interface, forming the first membrane-associated intermediates in the biosynthesis of cell-surface glycans and glycoconjugates, including glycoproteins, glycolipids, and the peptidoglycan in bacteria. PGTs vary greatly in both their membrane topologies and their substrate preferences. PGTs, such as MraY and WecA, are polytopic, while other families of uniquely prokaryotic enzymes have only a single predicted transmembrane helix. PglC, a PGT involved in the biosynthesis of N-linked glycoproteins in the enteropathogen Campylobacter jejuni, is representative of one of the structurally most simple members of the diverse family of small bacterial PGT enzymes. Herein, we apply bioinformatics and covariance-weighted distance constraints in geometry- and homology-based model building, together with mutational analysis, to investigate monotopic PGTs. The pool of 15000 sequences that are analyzed include the PglC-like enzymes, as well as sequences from two other related PGTs that contain a "PglC-like" domain embedded in their larger structures (namely, the bifunctional PglB family, typified by PglB from Neisseria gonorrheae, and WbaP-like enzymes, typified by WbaP from Salmonella enterica). Including these two subfamilies of PGTs in the analysis highlights key residues conserved across all three families of small bacterial PGTs. Mutagenesis analysis of these conserved residues provides further information about the essentiality of many of these residues in catalysis. Construction of a structural model of the cytosolic globular domain utilizing three-dimensional distance constraints, provided by conservation covariance analysis, provides additional insight into the catalytic core of these families of small bacterial PGT enzymes.
Influence of nutraceuticals on cartilage health and integrity (2001)

peer reviewed
Improving the throughput of single-hop networks via multi antenna techniques (2011)

MIMO (Multi-Input Multi-Output) systems, SDMA (Space Division Multiple Access) techniques, and concurrent link communications have been jointly used as a powerful means in improving the throughput performance of single hop MIMO networks. This dissertation aims at presenting two system designs using concurrent link communications for network throughput improvement, and a special focus is put on dealing with realistic system conditions. We start by considering a generic SDMA MAC that is conventionally designed for concurrent link communications. Its throughput performance is investigated by taking into account various practical PHY conditions including: RX MIMO detection methods, channel estimation errors, link adaptation, and TX beamforming. In the sequel, findings derived from our investigation are then integrated as a Net-Eigen MAC, which implements the concurrent link scheme in a distributed way for TX beamforming based MIMO systems. Such Net-Eigen MAC's link throughput value is verified to be no less than single link MAC's counterpart, and its ergodic throughput value is 30% higher than that of single link MAC.
In addition, considering spatial multiplexing based MIMO systems, and inspired by the facts that existing MIMA-MAC strategy cannot always outperform the single link MAC in terms of link throughput, this dissertation will further present an adaptive MAC strategy intelligently switching between the single link scheme and the concurrent link scheme, where the objective is to improve the link throughput by guaranteeing each link's result to be no less than its single link scheme's counterpart. Performance of our proposed MAC is verified via extensive simulations, and its ergodic link throughput is shown to be 20% higher than that of single link MAC.
Mixture of Watson Distributions: A Generative Model for Hyperspherical Embeddings (2007)

Machine learning applications often involve data that can be analyzed as unit vectors on a d-dimensional hypersphere, or equivalently are directional in nature. Spectral clustering techniques generate embeddings that constitute an example of directional data and can result in different shapes on a hypersphere (depending on the original structure). Other examples of directional data include text and some sub-domains of bioinformatics. The Watson distribution for directional data presents a tractable form and has more modeling capability than the simple von Mises-Fisher distribution. In this paper, we present a generative model of mixtures of Watson distributions on a hypersphere and derive numerical approximations of the parameters in an Expectation Maximization (EM) setting. This model also allows us to present an explanation for choosing the right embedding dimension for spectral clustering. We analyze the algorithm on a generated example and demonstrate its superiority over the existing algorithms through results on real datasets.
Low dose cytarabine monotherapy for myelodysplastic syndromes (2011)

This is a protocol for a Cochrane Review (Intervention). The objectives are as follows: The main objective of this systematic review is to evaluate the efficacy and safety of low dose cytarabine for patients with MDS.
Paclitaxel synergizes with exposure time adjusted CD22-targeting immunotoxins against B-cell malignancies (2020)

CD22-targeted recombinant immunotoxins (rIT) are active in hairy cell leukemia or acute lymphoblastic leukemia (ALL), but not in mantle cell lymphoma (MCL) patients. The goal was to enhance rIT efficacy in vivo and to define a strong combination treatment. Activity of Moxetumomab pasudotox (Moxe) and LR combined with paclitaxel was tested against MCL cell lines in vitro and as bolus doses or continuous infusion in xenograft models. In the KOPN-8 ALL xenograft, Moxe or paclitaxel alone was active, but all mice died from leukemia; when combined, 60% of the mice achieved a sustained complete remission. Against MCL cells in vitro, LR was more active than Moxe and the cells had to be exposed to rIT for more than 24 hours for them to die. To maintain high blood levels in vivo, LR was administered continuously by 7-day pumps achieving a well-tolerated steady plasma concentration of 45 ng/ml. In JeKo-1 xenografts, continuously administered LR was 14-fold more active than bolus doses and the combination with paclitaxel additionally improved responses by 135-fold. Maintaining high rIT-plasma levels greatly improves responses in the JeKo-1 model and paclitaxel substantially enhances bolus and continuously infused rIT, supporting a clinical evaluation against B-cell malignancies.
Cyber-physische Systeme im OP-Saal - Ein Machbarkeitsnachweis. (2014)

In einem OP-Saal befinden sich eine grose Anzahl von Medizingeraten und Informationssystemen. Eine herstellerubergreifende Kommunikation bzw. Interoperabilitat ist derzeit kaum bzw. gar nicht moglich. Dieses Problem adressiert die vorliegende Arbeit. Es wird von einer serviceorientierten Kommunikationsarchitektur ausgegangen und gezeigt, wie heutige Medizingerate ohne entsprechende Hardund/oder Software-Schnittstellen integriert werden konnen. Anhand einer prototypischen Umsetzung eines Teils eines endoskopischen Arbeitsplatzes wird die Machbarkeit des vorgestellten Ansatzes gezeigt. Ausgehend von derart vernetzten cyberphysikalischen Systemen (CPS) im OP-Saal ergeben sich erstmals Moglichkeiten der Big-Data-Analysen der anfallenden Daten, da diese nicht mehr lokal auf die Gerate beschrankt sind, sondern global verknupft werden konnen.