gebhart/patrepeval huggingface dataset:
ChemInform Abstract: Intramolecular, Metal‐Promoted (6π+2π) Triene/Alkyne Cycloaddition Reactions. (1997)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
ST102 Structural Basis for Broad and Potent HIV-1 neutralization by CD4-mimetic miniproteins (2013)

The HIV-1 envelope gp120 glycoprotein is made up of three autonomously folding domains that adopt different conformations in response to ligand binding. During HIV entry, the CD4 receptor engages a ∼14 Å deep cavity that penetrates the hydrophobic core of gp120 at the intersection of these three domains. Mutagenesis studies have demonstrated the importance of residues lining this cavity for virus entry. Here we use a set of CD4-mimetic miniproteins with different inserts into the Phe 43 cavity, to probe the structure of the cavity and decipher its role in ligand binding and neutralization. Through virological, biochemical and structural analyses we show that optimal filling of the Phe 43 cavity with a flexible ligand can lead to high affinity binding and broad and potent neutralization. CD4-mimetic miniprotein M48-U1, with a cyclohexylmethoxyphenyl insertion into the Phe 43 cavity showed best neutralization properties. M48-U1 bound YU2 gp120 with 25 pM affinity and neutralized all circulating HIV-1 isolates, except clade A/E viruses. The crystal structure of M48-U1 bound toYU2 gp120 was solved at 1.49 Å resolution. This was compared to the 2.1 Å resolution structure of a novel CD4-mimetic miniprotein, M48-U7 that inserts a flexible 5-phenoxypentan-1-ol moiety into the Phe 43 cavity. Structural analyses reveal residual ligand flexibility in the bound state. The M48-U1/U7-bound Phe 43 cavity resembled the cavity conformation in unliganded gp120 coree. These results provide an understanding of the structure-function relationship of Phe 43 cavity filling and define a mechanism for the broad and potent neutralization by the CD4-mimetic miniprotein M48-U1.
Low operating current and high temperature operation of 650 nm AlGaInP high power laser diodes with real refractive index guided self-aligned structure (1998)

Low operating current and high temperature operation has been achieved in 650 nm AlGaInP high power double quantum well laser diodes with a real refractive index guided self-aligned (RISA) structure. The attained operating current for 50 mW CW at 70/spl deg/C is as low as 98 mA, which is almost a half of the lowest value ever reported.
Frontispiz: DNA‐Based Synthetic Growth Factor Surrogates with Fine‐Tuned Agonism (2021)

Aptamere Eine neue Strategie für die Entwicklung synthetischer Wachstumsfaktor-Agonisten, die eine gewünschte Signalaktivität hervorrufen, wird von Ryosuke Ueki, Shinsuke Sando et al. im Forschungsartikel auf S. 22927 vorgestellt.
Interactions between Bifidobacterium and Bacteroides and human milk oligosaccharides and their associations with infant cognition (2023)

While ample research on independent associations between infant cognition and gut microbiota composition and human milk (HM) oligosaccharides (HMOs) has been reported, studies on how the interactions between gut microbiota and HMOs may yield associations with cognitive development in infancy are lacking. We aimed to determine how HMOs and species of Bacteroides and Bifidobacterium genera interact with each other and their associations with cognitive development in typically developing infants. A total of 105 mother-infant dyads were included in this study. The enrolled infants [2.9–12 months old (8.09 ± 2.48)] were at least predominantly breastfed at 4 months old. A total of 170 HM samples from the mothers and fecal samples of the children were collected longitudinally. Using the Mullen Scales of Early Learning to assess cognition and the scores as the outcomes, linear mixed effects models including both the levels of eight HMOs and relative abundance of Bacteroides and Bifidobacterium species as main associations and their interactions were employed with adjusting covariates; infant sex, delivery mode, maternal education, site, and batch effects of HMOs. Additionally, regression models stratifying infants based on the A-tetrasaccharide (A-tetra) status of the HM they received were also employed to determine if the associations depend on the A-tetra status. With Bacteroides species, we observed significant associations with motor functions, while Bif. catenulatum showed a negative association with visual reception in the detectable A-tetra group both as main effect (value of p = 0.012) and in interaction with LNFP-I (value of p = 0.007). Additionally, 3-FL showed a positive association with gross motor (p = 0.027) and visual reception (p = 0.041). Furthermore, significant associations were observed with the interaction terms mainly in the undetectable A-tetra group. Specifically, we observed negative associations for Bifidobacterium species and LNT [breve (p = 0.011) and longum (p = 0.022)], and positive associations for expressive language with 3′-SL and Bif. bifidum (p = 0.01), 6′-SL and B. fragilis (p = 0.019), and LNFP-I and Bif. kashiwanohense (p = 0.048), respectively. Our findings suggest that gut microbiota and HMOs are both independently and interactively associated with early cognitive development. In particular, the diverse interactions between HMOs and Bacteroides and Bifidobacterium species reveal different candidate pathways through which HMOs, Bifidobacterium and Bacteroides species potentially interact to impact cognitive development in infancy.
Common Interactions between S100A4 and S100A9 Defined by a Novel Chemical Probe (2013)

S100A4 and S100A9 proteins have been described as playing roles in the control of tumor growth and metastasis. We show here that a chemical probe, oxyclozanide (OX), selected for inhibiting the interaction between S100A9 and the receptor for advanced glycation end-products (RAGE) interacts with both S100A9 and S100A4. Furthermore, we show that S100A9 and S100A4 interact with RAGE and TLR4; interactions that can be inhibited by OX. Hence, S100A4 and S100A9 display similar functional elements despite their primary sequence diversity. This was further confirmed by showing that S100A4 and S100A9 dimerize both in vitro and in vivo. All of these interactions required levels of Zn++ that are found in the extracellular space but not intracellularly. Interestingly, S100A4 and S100A9 are expressed by distinct CD11b+ subpopulations both in healthy animals and in animals with either inflammatory disease or tumor burden. The functions of S100A9 and S100A4 described in this paper, including heterodimerization, may therefore reflect S100A9 and S100A4 that are released into the extra-cellular milieu.
Use of Phosphonylated Nitroxides and Alkoxyamines in Controlled/"Living" Radical Polymerization (2000)

A new series of stable β-phosphonylated nitroxides bearing a β-hydrogen and different corresponding alkoxyamines were prepared in good yields using commercially available chemicals. The N-tert-butyl-N-(1-diethylphosphono-2,2-dimethylpropyl) nitroxide 3 (SG1), and the N-tert-butyl-N-(1-diethylphosphono-2,2-dimethylpropyl)-N-(1-phenylethoxy) amine 10, were used in controlled / "living" polymerization of styrene. The use of either the bicomponent system (SG1 / AIBN) or the monocomponent system (10) resulted in reasonably fast and well controlled polymerizations. The equilibrium constant K for the reversible homolysis of 10 was shown to be much larger (450 times) than for its TEMPO analog 16. This difference accounts for the fast kinetic and the negligible kinetic contribution of the thermal self initiation during the polymerization of styrene in the presence of 10. The X-ray structures of 10 and 16 were determined and compared.
Boosting textual compression in optimal linear time (2005)

We provide a general boosting technique for Textual Data Compression. Qualitatively, it takes a good compression algorithm and turns it into an algorithm with a better compression performance guarantee. It displays the following remarkable properties: (a) it can turn any memoryless compressor into a compression algorithm that uses the “best possible” contexts; (b) it is very simple and optimal in terms of time; and (c) it admits a decompression algorithm again optimal in time. To the best of our knowledge, this is the first boosting technique displaying these properties.Technically, our boosting technique builds upon three main ingredients: the Burrows--Wheeler Transform, the Suffix Tree data structure, and a greedy algorithm to process them. Specifically, we show that there exists a proper partition of the Burrows--Wheeler Transform of a string s that shows a deep combinatorial relation with the k th order entropy of s . That partition can be identified via a greedy processing of the suffix tree of s with the aim of minimizing a proper objective function over its nodes. The final compressed string is then obtained by compressing individually each substring of the partition by means of the base compressor we wish to boost.Our boosting technique is inherently combinatorial because it does not need to assume any prior probabilistic model about the source emitting s , and it does not deploy any training, parameter estimation and learning. Various corollaries are derived from this main achievement. Among the others, we show analytically that using our booster, we get better compression algorithms than some of the best existing ones, that is, LZ77, LZ78, PPMC and the ones derived from the Burrows--Wheeler Transform. Further, we settle analytically some long-standing open problems about the algorithmic structure and the performance of BWT-based compressors. Namely, we provide the first family of BWT algorithms that do not use Move-To-Front or Symbol Ranking as a part of the compression process.
Reversion and non-reversion mechanisms of resistance to PARP inhibitor or platinum chemotherapy in BRCA1/2 -mutant metastatic breast cancer (2019)

Abstract Background Little is known about mechanisms of resistance to PARP inhibitors and platinum chemotherapy in patients with metastatic breast cancer and BRCA1 /2 mutations. Further investigation of resistance in clinical cohorts may point to strategies to prevent or overcome treatment failure. Patients and Methods We obtained tumor biopsies from metastatic breast cancer patients with BRCA1/2 deficiency before and after acquired resistance to PARP inhibitor or platinum chemotherapy. Whole exome sequencing was performed on each tumor, germline DNA, and circulating tumor DNA. Tumors underwent RNA sequencing, and immunohistochemical staining for RAD51 foci on tumor sections was performed for functional assessment of intact homologous recombination. Results Pre- and post-resistance tumor samples were sequenced from 8 patients (4 with BRCA1 and 4 with BRCA2 mutation; 4 treated with PARP inhibitor and 4 with platinum). Following disease progression on DNA-damaging therapy, four patients (50%) acquired at least one somatic reversion alteration likely to result in functional BRCA1/2 protein detected by tumor or circulating tumor DNA sequencing. Two patients with germline BRCA1 deficiency acquired genomic alterations anticipated to restore homologous recombination through increased DNA end resection: loss of TP53BP1 in one patient and amplification of MRE11A in another. RAD51 foci were acquired post-resistance in all patients with genomic reversion, consistent with reconstitution of homologous recombination. All patients whose tumors demonstrated RAD51 foci post-resistance were intrinsically resistant to subsequent lines of DNA-damaging therapy. Conclusions Genomic reversion in BRCA1/2 was the most commonly observed mechanism of resistance, occurring in 4 of 8 patients. Novel sequence alterations leading to increased DNA end resection were seen in two patients, and may be targetable for therapeutic benefit. The presence of RAD51 foci by immunohistochemistry was consistent with BRCA1/2 protein functional status from genomic data and predicted response to later DNA-damaging therapy, supporting RAD51 focus formation as a clinically useful biomarker.
272 Clinical significance of anti-dna/nr2 antibodies in de novo npsle and post-steroid npsle (2017)

<h3>Background and aims</h3> Anti-DNA/NR2 antibodies are a subset of anti DNA autoantibodies that cross-react with the extracellular domain of the GluN2A/GluN2B subunits of the N-methyl-d-aspartate receptor 2 (NR2), which induce apoptosis of hippocampus neurons and psychiatric disorder in mice and humans. Neuropsychiatric SLE (NPSLE) can develop after initiation of steroid (post-steroid neuropsychiatric manifestation: PSNP) or before treatment (<i>de novo</i> NPSLE). The objective of this study was to clarify the prevalence of anti-DNA/NR2 antibodies in PSNP-SLE and <i>de novo</i> NPSLE <h3>Methods</h3> This study involved a cohort of patients with NPSLE who were admitted to Hokkaido University Hospital. NPSLE patients were classified into two groups, <i>de novo</i> NPSLE and PSNP-SLE. Serum anti-DNA antibodies and anti-DNA/NR2 antibodies were measured using in-house ELISAs. <h3>Results</h3> Serum samples were obtained from 29 patients with <i>de novo</i> NPSLE, 26 with PSNP-SLE and 83 healthy controls (HC). The levels of anti-DNA antibodies in patients with <i>de novo</i> NPSLE and PSNP-SLE were significantly higher than those in healthy controls (<i>de novo</i> NPSLE, PSNP-SLE, HC: 1.34±0.09, 1.40±0.14, 0.33±0.03, p&lt;0.0001). The levels of anti-DNA/NR2 antibodies were highest in <i>de novo</i> NPSLE and in PSNP-SLE and HC (<i>de novo</i> NPSLE, PSNP-SLE, HC: 0.75±0.10, 0.60±0.07, 0.49±0.03). In PSNP-SLE, the frequency of mood disorders was higher than that in <i>de novo</i> NPSLE (58% vs 31% p&lt;0.05). <h3>Conclusions</h3> The levels of anti-DNA/NR2 in PSNP-SLE are lower than in <i>de novo</i> NPSLE, indicating the differences in the pathogenesis of these two conditions.
An atlas of epithelial cell states and plasticity in lung adenocarcinoma (2022)

Abstract Understanding cellular processes underlying early lung adenocarcinoma (LUAD) development is needed to devise intervention strategies 1 . Here, we studied 246,102 single epithelial cells from 16 early-stage LUADs and 47 matched normal lung samples. Epithelial cells comprised diverse normal alveolar and airway lineages as well as cancer cell populations. Diversity among cancer cells was strongly linked to LUAD patient-specific oncogenic drivers. KRAS -mutant cancer cells were unique in their transcriptional features, strikingly reduced differentiation, low levels of DNA copy number changes, and increased variability amongst the cells themselves. The local niche of LUADs, relative to that of normal lungs, was enriched with intermediary cells in lung alveolar differentiation with potential to transition to KRAS -mutant cancer cells. A subset of alveolar intermediate cells with elevated KRT8 expression ( KRT8 + alveolar cells; KACs) showed increased plasticity, and their gene expression profiles were enriched in lung precancer and LUAD and signified poor survival. Murine KACs were evident in lungs of tobacco carcinogen-exposed mice that develop KRAS -mutant LUADs but not in the saline-treated control group. While murine KACs emerged prior to tumor onset, they persisted for months after carcinogen cessation, acquired driver Kras mutations and, like their human counterparts, were poorly differentiated and harbored KRAS- specific transcriptional programs. This study provides new insights into early LUAD development and identifies potential targets for treatment.
Fuel economy of engine oils based on polyalkylene glycols (2011)

The driver for automotive OEMs to work on alternative engine oils is the need for fuel economy and no adverse effect of the engine oil on the durability of particulate filters and catalysts. The alternative engine oils should for mid-term also comply with a positive environmental Profile.
Effects of serum vitamin D level on ventricular repolarization in children and adolescents (2021)

Decline in vitamin D levels causes ventricular repolarization anomaly. As the decrease in vitamin D levels deepens, repolarization times become longer. These results could indicate that decrease in vitamin D levels can increase sensitivity to ventricular arrhythmias (Tab. 3, Ref. 45). Text in PDF www.elis.sk Keywords: adolescent, arrhythmia, child, vitamin D, ventricular repolarization.
Novel modulation schemes for conventional and sparse matrix converters facilitating reactive power transfer independent of active power flow (2004)

Two novel modulation schemes are proposed which facilitate the transfer of reactive power from the load side to the mains side of a three-phase AC-AC sparse matrix converter (SMC) or a conventional matrix converter. The derivation of the modulation schemes, which rely on a decoupling of the output voltage and the input current formation, is described in detail. Furthermore, the operating limits concerning modulation index and reactive current magnitude are determined. Finally, digital simulations and measurements on a 7.5 kW prototype of a very sparse matrix converter verify all theoretical considerations.
The Influence of Ozone: Superstoichiometric Oxygen in Atomic Layer Deposition of Fe 2 O 3 Using tert ‐Butylferrocene and O 3 (2020)

Abstract Understanding the chemical mechanisms at play in atomic layer deposition (ALD) is critical for effective process development and expansion of ALD into more complex classes of materials. In this work, a mechanistic study of iron oxide deposited by ALD using tert ‐butylferrocene and ozone as reactants is performed. Iron oxide ALD using ozone is a useful model system for mechanistic studies due to the prevalence of ozone‐based ALD processes and the uses of iron oxide in ternary and quaternary metal oxides. Results show that saturation conditions require significantly greater exposures of both reactants than is typically reported in the literature, and growths per cycle of greater than one monolayer of Fe 2 O 3 per cycle are observed and explained. A growth mechanism is proposed whereby increased ozone exposure results in uptake of superstoichiometric oxygen into the film. X‐ray characterizations reveal the presence of excess oxygen stored near the surface of films deposited with larger ozone exposures and show that increased ozone exposures cause crystalline domain rearrangement and conversion of the film from the γ‐maghemite phase to the α‐hematite phase. The mechanism described here has implications for the wider class of ozone‐based ALD processes, and potential applications of this growth phenomenon are discussed.
Stabilizing the amplitude and phase of few-cycle light: optical waveform synthesis (2000)

Full electronic control of the carrier-envelope phase in a train of sub-6-fs laser pulses has been achieved with simultaneous reduction of the pulse energy noise to unprecedented levels. Few-cycle femtosecond optical waveforms can now be synthesized with precisely reproducible electric and magnetic Fields.
Simulating biological reactions: A modular approach (2000)

We develop a general framework for simulating a sequence of bio- logical reactions using small simulation modules. We demonstrate the useful- ness of such a framework by implementing a simulator called the cybercycler. The cybercycler contains DNA hybridization, polymerization, ligation, and melting modules linked together to simulate a thermocycling process. This simulator enables us to interpret the behavior of our own programmed mu- tagenic unary counter in the laboratory. We describe the modules we imple- mented and then present a comparison of output from the cybercycler with the results of laboratory experiments to evaluate the eectiv eness of the cy- bercycler simulator. We dene a concrete specication for transformation modules and for populations of molecules passed between modules. This speci- cation enables the construction of tools for simulating an arbitrarily complex sequence of biological reactions. We provide Java interfaces and classes for building such tools. Biological reactions implementing any non-trivial form of DNA-based compu- tation are likely to be extremely complex: computations intended to solve large problems will require large populations of molecules, and the biological reactions used to carry out the computations will transform these populations in compli- cated ways. The prospect of reasoning about all the products being formed in these reactions is quite daunting. In our laboratory, we have constructed a simple unary counter to experimentally demonstrate the feasibility of DNA-based computation using programmed muta- genesis (12, 14). While the counter has been engineered to operate cleanly (13), the repeated thermocycling that increments the counter causes a wealth of product species to be formed after just a few cycles. This reaction complexity makes it dif- cult to predict or even interpret the results of frequent thermocycling; even when the results are predictable and interpretable, simply keeping track of the myriad interactions taking place during the reaction remains a signican t challenge.
DNA Molecules in Microfluidic Oscillatory Flow (2005)

The conformation and dynamics of a single DNA molecule undergoing oscillatory pressure-driven flow in microfluidic channels is studied using Brownian dynamics simulations, accounting for hydrodynamic interactions between segments in the bulk and between the chain and the walls. Oscillatory flow provides a scenario under which the polymers may remain in the channel for an indefinite amount of time as they are stretched and migrate away from the channel walls. We show that by controlling the chain length, flow rate and oscillatory flow frequency, we are able to manipulate the chain extension and the chain migration from the channel walls. The chain stretch and the chain depletion layer thickness near the wall are found to increase as the Weissenberg number increases and as the oscillatory frequency decreases.
The effect of anodal/cathodal biphasic electrical stimulation on insulin release (2019)

We studied the effects of electrical stimulation on insulin release from rat insulinoma (INS-1) cells. The anodal/cathodal biphasic stimulation (ACBPS) electrical waveform resulted in a voltage- and stimulation duration-dependent increase in insulin release. ACBPS elicited insulin release both in the presence and absence of glucose. Basal and ACBPS-induced insulin secretion could be inhibited by mitochondrial poisons and calcium channel blockers, indicating that insulin release was dependent on adenosine triphosphate (ATP) and the influx of calcium. ACBPS parameters that released insulin caused no detectable plasma membrane damage or cytotoxicity, although temporary morphological changes could be observed immediately after ACBPS. ACBPS did not alter the plasma membrane transmembrane potential but did cause pronounced uptake of MitoTracker Red into the mitochondrial membrane, indicating an increased mitochondrial membrane potential. While the ATP:ADP ratio after ACBPS did not change, the guanosine triphosphate (GTP) levels increased and increased GTP levels have previously been associated with insulin release in INS-1 cells. These results provide evidence that ACBPS can have significant biological effects on cells. In the case of INS-1 cells, ACBPS promotes insulin release without causing cytotoxicity.