gebhart/patrepeval huggingface dataset:
Molecular serotype identification ofStreptococcus agalactiaeof bovine origin by multiplex PCR-based reverse line blot (mPCR/RLB) hybridization assay (2006)

We used a multiplex PCR-based reverse line blot (mPCR/RLB) hybridization assay and sequencing of a variable region of the cps cluster to identify serotypes of 140 Streptococcus agalactiae (group B Streptococcus; GBS) isolates from cattle. Only 71 (51%) isolates were typeable using antisera, but molecular serotypes (MS) were assigned to 133 (95%) and 139 (99%) isolates by partial cpsE-cpsF-cpsG sequencing and mPCR/RLB, respectively. Ninety-four isolates (67%) belonged to MS III and most belonged to a molecular serosubtype (msst) III-3, which is uncommon among GBS isolates from humans. Our results demonstrate that cps clusters of bovine GBS differ significantly from those of GBS isolates from humans.
Asymmetric Direct Amide Synthesis by Kinetic Amine Resolution: A Chiral Bifunctional Aminoboronic Acid Catalyzed Reaction between a Racemic Amine and an Achiral Carboxylic Acid (2008)

Let's resolve this: A planar chiral benzimidazole ferroceneboronic acid catalyst demonstrates low to moderate asymmetric induction in the kinetic resolution of racemic α-substituted benzylamines by direct amide formation with achiral carboxylic acids (see scheme).
Flight study of induced turbofan inlet acoustic radiation with theoretical comparisons (1985)

This paper presents a study of acoustic tone radiation patterns from a small turbofan engine in flight and compares results with similar static test stand data and a recently developed radiation theory. An interaction tone was induced for test and evaluation purposes by placing a circumferential array of inlet rods just upstream of the fan blades. Overhead and sideline flight directivity patterns showed cut-on of a dominant single-mode tone occurred at the predicted fan speed, and there was an absence of any other significant circumferential or radial modes. In general, good agreement was found between measured flight and static data, with small differences being attributed to inlet geometry and/or forward speed effects. Good agreement was also obtained between flight data and theory for directivity pattern shape, however, the theory consistently predicted higher values for peak radiation angle over a wide range of frequency.
Silencing, Positive Selection and Parallel Evolution: Busy History of Primate Cytochromes c (2011)

Cytochrome c (cyt c) participates in two crucial cellular processes, energy production and apoptosis, and unsurprisingly is a highly conserved protein. However, previous studies have reported for the primate lineage (i) loss of the paralogous testis isoform, (ii) an acceleration and then a deceleration of the amino acid replacement rate of the cyt c somatic isoform, and (iii) atypical biochemical behavior of human cyt c. To gain insight into the cause of these major evolutionary events, we have retraced the history of cyt c loci among primates. For testis cyt c, all primate sequences examined carry the same nonsense mutation, which suggests that silencing occurred before the primates diversified. For somatic cyt c, maximum parsimony, maximum likelihood, and Bayesian phylogenetic analyses yielded the same tree topology. The evolutionary analyses show that a fast accumulation of non-synonymous mutations (suggesting positive selection) occurred specifically on the anthropoid lineage root and then continued in parallel on the early catarrhini and platyrrhini stems. Analysis of evolutionary changes using the 3D structure suggests they are focused on the respiratory chain rather than on apoptosis or other cyt c functions. In agreement with previous biochemical studies, our results suggest that silencing of the cyt c testis isoform could be linked with the decrease of primate reproduction rate. Finally, the evolution of cyt c in the two sister anthropoid groups leads us to propose that somatic cyt c evolution may be related both to COX evolution and to the convergent brain and body mass enlargement in these two anthropoid clades.
Data from Phase I Study of Apitolisib (GDC-0980), Dual Phosphatidylinositol-3-Kinase and Mammalian Target of Rapamycin Kinase Inhibitor, in Patients with Advanced Solid Tumors (2023)

&lt;div&gt;Abstract&lt;p&gt;&lt;b&gt;Purpose:&lt;/b&gt; This first-in-human phase I trial assessed the safety, tolerability, and preliminary antitumor activity of apitolisib (GDC-0980), a dual inhibitor of class I PI3K, and mTOR kinases.&lt;/p&gt;&lt;p&gt;&lt;b&gt;Experimental Design:&lt;/b&gt; Once-daily oral apitolisib was administered to patients with solid tumors for days 1 to 21 or 1 to 28 of 28-day cycles. Pharmacokinetic and pharmacodynamic parameters were assessed.&lt;/p&gt;&lt;p&gt;&lt;b&gt;Results:&lt;/b&gt; Overall, 120 patients were treated at doses between 2 and 70 mg. The commonest ≥G3 toxicities related to apitolisib at the recommended phase 2 dose (RP2D) at 40 mg once daily included hyperglycemia (18%), rash (14%), liver dysfunction (12%), diarrhea (10%), pneumonitis (8%), mucosal inflammation (6%), and fatigue (4%). Dose-limiting toxicities (1 patient each) were G4 fasting hyperglycemia at 40 mg (21/28 schedule) and G3 maculopapular rash and G3 fasting hyperglycemia at 70 mg (21/28 schedule). The pharmacokinetic profile was dose-proportional. Phosphorylated serine-473 AKT levels were suppressed by ≥90% in platelet-rich plasma within 4 hours at the MTD (50 mg). Pharmacodynamic decreases in fluorodeoxyglucose positron emission tomography uptake of &gt;25% occurred in 66% (21/32) of patients dosed at 40 mg once daily. Evidence of single-agent activity included 10 RECIST partial responses (PR; confirmed for peritoneal mesothelioma, &lt;i&gt;PIK3CA&lt;/i&gt; mutant head-and-neck cancer, and three pleural mesotheliomas).&lt;/p&gt;&lt;p&gt;&lt;b&gt;Conclusions:&lt;/b&gt; Apitolisib exhibited dose-proportional pharmacokinetics with target modulation at doses ≥16 mg. The RP2D was 40 mg once-daily 28/28 schedule; severe on-target toxicities were apparent at ≥40 mg, particularly pneumonitis. Apitolisib was reasonably tolerated at 30 mg, the selected dose for pleural mesothelioma patients given limited respiratory reserve. Modest but durable antitumor activity was demonstrated. &lt;i&gt;Clin Cancer Res; 22(12); 2874–84. ©2016 AACR&lt;/i&gt;.&lt;/p&gt;&lt;/div&gt;
Evaluation of the effect of naltrexone coadministration on the pharmacokinetics of oxycodone in a randomized phase 1 clinical trial (2020)

Oral naltrexone does not affect the PK of oral oxycodone under fasted conditions. A naltrexone block can be applied in oxycodone PK trials to minimize adverse opioid effects.
Concentration Effects in Eu Doped SrI$_{2}$ (2010)

This study reports on effects of dopant concentration and crystal size on some of the scintillation properties of SrI <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sub> :Eu <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2+</sup> . For example, the emission shifts to longer wavelengths as the dopant concentration is increased. It also results in scintillation decays getting slower: a 620 ns decay time constant observed for a small 0.5% Eu sample increases to 1650 ns for a 10% Eu sample. Similar changes in the time constant values were also observed when the crystal size was being increased. It also appears that larger samples yielded somewhat less light. These effects are attributed to radiation trapping, in which the scintillation light is multiple time absorbed and consequently emitted by the dopant.
Mixing and Mass Exchange for Cavities in Supersonic Flows (2014)

The ability of wall-mounted cavities to facilitate flameholding is largely dependent on local conditions within the recirculation region, that are, generally, vastly different from the adjacent supersonic flow. The local stoichiometry depends on the mixing within the flameholder and the mass exchange with the core flow. These processes are integrally linked to fuel injection location and its coupling with the recirculation region flow field. In the present study planar laser-induced fluorescence (PLIF) was used to obtain a twodimensional image of the streamwise fuel distribution in a non-reacting, directly-fueled cavity in a Mach 2.2 flow. Fuel was injected from two different locations within the cavity chosen to result in parallel and counterflow mixing with respect to the primary cavity circulation. Injection from both locations resulted in a largely fuel rich recirculation region. Parallel injection from the cavity step was characterized by pooling of fuel within the cavity’s trapped vortices with the majority of mixing occurring in the shear layer and along the cavity walls. Counterflow injection from the cavity floor resulted in a leaner flow field attributed to enhanced mixing with the impinging shear layer, larger quantities of fuel escaping the recirculation region and limited mass exchange between the trapped vortices. The local concentration fields generated by both fueling schemes suggested that under analogous reacting conditions the region around the shear layer would serve as the most probable flame anchoring location.
Opening the gateway to enhanced Eucalyptus (2011)

Eucalyptus is the second most planted tree on earth. Despite this ranking, its mature breeding programs, clonal propagation and deployment and short rotation time make it a leading target for biotechnology improvement. The recently completed eucalyptus genome project provides an enormous opportunity for understanding and developing new traits for eucalyptus forestry. The main obstacle for widespread trait enhancement remains the recalcitrance of commercial eucalyptus clones to transformation and thus the lack of a suitable prototyping system for this species. We believe that the future success of trait development in eucalyptus will be enhanced by close collaboration between academic centers and industrial partners. Some of FuturaGene’s models for academic collaboration will be described in this presentation.

An example of such potential collaborations may involve BRASUZ1, which constituted the germplasm base for the eucalyptus genome project. This key clone was donated by Suzano Pulp and Paper, FuturaGene’s parent, to the genome project. We will present our progress with the transformation protocol for BRASUZ1, which could provide a platform for collaborations. We will also present our perspective on the development of improved transgenic eucalyptus, and an outline for such development programs.
Peptide deformylase inhibitors: a survey of the patent literature (2005)

New antibiotics with new mechanisms of action are desperately needed, as clinically significant bacterial pathogens have not only acquired resistance to nearly all existing antibiotics, but also increasingly exhibit multi-drug resistance. Peptide deformylase (PDF), a highly conserved metalloproteinase, is an essential enzyme in the bacterial life cycle. It catalyses the removal of the terminal formyl group from the N-terminal methionine residue of the nascent bacterial polypeptide chain. Thus, inhibition of PDF, by interfering with the bacterial protein maturation process, is providing a promising new and exciting target for antibiotic therapeutic intervention without interfering with eukaryotic metabolism. Antibiotics based on PDF inhibition have the potential to provide the much needed antibacterial activity against most of the major drug-resistant pathogens and could play a significant role in the treatment of community-acquired upper respiratory tract infections. This review covers all the patenting activity in this field of research up to, and including, March 2005, and will focus on the more significant patents and patent applications.
Learning Nanoscale Motion Patterns of Vesicles in Living Cells (2020)

Detecting and analyzing nanoscale motion patterns of vesicles, smaller than the microscope resolution (~250 nm), inside living biological cells is a challenging problem. State-of-the-art CV approaches based on detection, tracking, optical flow or deep learning perform poorly for this problem. We propose an integrative approach, built upon physics based simulations, nanoscopy algorithms, and shallow residual attention network to make it possible for the first time to analysis sub-resolution motion patterns in vesicles that may also be of sub-resolution diameter. Our results show state-of-the-art performance, 89% validation accuracy on simulated dataset and 82% testing accuracy on an experimental dataset of living heart muscle cells imaged under three different pathological conditions. We demonstrate automated analysis of the motion states and changed in them for over 9000 vesicles. Such analysis will enable large scale biological studies of vesicle transport and interaction in living cells in the future.
IQImbalance Compensation SchemeforMB-OFDMwithTransmit Diversity (2006)

Currently, Multi-band OFDM (MB-OFDM)isconsidered as oneofthemodulation schemes ofUWB andisactively investigated. Itisnecessary toprovide lowcostreceivers forconsumers inorder toreceive widesupport forMB-OFDMsystem. Suchreceivers canbeachieved byutilizing direct conversion architecture. Thedirect conversion architecture hasbeeninvestigated forthepurpose ofcost minimization, miniaturization, and lowpowerconsumption ofwireless receivers. However, thebalancebetween thein-phase component andthequadrature-phase component ofdemodulated signals islost whendirect conversionarchitecture isused. Thisphenomenon iscalled IQimbalance.IQimbalance isoneoftheproblems forthedirect conversion receiver. IQimbalance causes intercarrier interference (ICI) inthedemodulated signals. Inthis paper, anewscheme ofIQimbalance compensation usingtransmit diversity isproposed. Thisscheme enables thesystemtoachieve frequency diversity andcompensate theinfluence ofIQimbalance atthesametime. Itisshownthat theperformanceoftheproposed schemeisbetter thantheconventional IQimbalance compensation scheme. IndexTerms-UWB,MB-OFDM,Direct Conversion, IQImbalance.
Impact of a Combustor-Turbine Interface on Turbine Vane Aerodynamics and Film Cooling (2019)

Abstract Optimizing the aero-thermal performance of the combustor-turbine interface is an important factor in enhancing the efficiency of heavy-duty gas turbines. Also, it is a key requirement to fulfill the lifetime in this hottest area of the gas turbine. Typically transition pieces of can combustors induce a highly non-uniform swirling flow at the turbine inlet. In order to better understand the impact of the non-uniform combustor flow at the first stage vanes, a combined experimental and numerical study was carried out. The experimental facility consisted of a high speed linear cascade with four vane passages, including an upstream transition piece, which was representative of a heavy duty gas turbine can combustor-turbine interface geometry. The experiments were conducted at engine representative Mach numbers and film cooling effectiveness measurements were performed at three different blowing ratios. CFD RANS simulations were undertaken using a commercial flow solver. The numerical model was first validated with the experimental data, using inlet traverse 5-hole probe measurements, pressure taps along the airfoil perimeter and oil flow visualization results. The investigation shows that the position of the vane relative to the combustor transition piece has a significant impact on the vane aerodynamics and also film cooling behavior. This understanding was key to a robust first vane aerothermal design of the GT36.
Supplementary Figure 3 from Diphenyl Difluoroketone: A Curcumin Derivative with Potent <i>In vivo</i> Anticancer Activity (2023)

Supplementary Figure 3 from Diphenyl Difluoroketone: A Curcumin Derivative with Potent &lt;i&gt;In vivo&lt;/i&gt; Anticancer Activity
Functional characterization, localization, and inhibitor sensitivity of the TPR‐FGFR1 fusion in 8p11 myeloproliferative syndrome (2015)

Myeloid and lymphoid neoplasms with fibroblast growth factor receptor 1 (FGFR1) abnormalities, also known as 8p11 myeloproliferative syndrome (EMS), represent rare and aggressive disorders, associated with chromosomal aberrations that lead to the fusion of FGFR1 to different partner genes. We report on a third patient with a fusion of the translocated promoter region (TPR) gene, a component of the nuclear pore complex, to FGFR1 due to a novel ins(1;8)(q25;p11p23). The fact that this fusion is a rare but recurrent event in EMS prompted us to examine the localization and transforming potential of the chimeric protein. TPR-FGFR1 localizes in the cytoplasm, although the nuclear pore localization signal of TPR is retained in the fusion protein. Furthermore, TPR-FGFR1 enables cytokine-independent survival, proliferation, and granulocytic differentiation of the interleukin-3 dependent myeloid progenitor cell line 32Dcl3, reflecting the chronic phase of EMS characterized by myeloid hyperplasia. 32Dcl3 cells transformed with the TPR-FGFR1 fusion and treated with increasing concentrations of the tyrosine kinase inhibitors ponatinib (AP24534) and infigratinib (NVP-BGJ398) displayed reduced survival and proliferation with IC50 values of 49.8 and 7.7 nM, respectively. Ponatinib, a multitargeted tyrosine kinase inhibitor, is already shown to be effective against several FGFR1-fusion kinases. Infigratinib, tested only against FGFR1OP2-FGFR1 to date, is also efficient against TPR-FGFR1. Taking its high specificity for FGFRs into account, infigratinib could be beneficial for EMS patients and should be further investigated for the treatment of myeloproliferative neoplasms with FGFR1 abnormalities.
Identification of critical amino-terminal regions of XylS. The positive regulator encoded by the TOL plasmid (1992)

The XylS protein is the positive regulator of the promoter controlling the meta-cleavage pathway (Pm) for catabolism of certain alkylbenzoates on the TOL plasmid of Pseudomonas. Transcription from Pm is mediated by XylS either in the presence of benzoate effectors or through XylS hyperproduction. Two regions of the NH2 terminus of XylS (residues 37-45) had been predicted to be involved in effector control of XylS transcriptional activation. Different methods were used to induce mutations in this region, including genetic selections (where Pm controlled a tetracycline resistance gene), bisulfite mutagenesis at a unique restriction site, and extensive oligonucleotide mutagenesis at residues 41 and 45. The mutants fell into four classes based on their phenotypes with respect to effector-mediated activation of a Pm-lacZ fusion: (a) effector profiles similar to wild type, (b) no Pm stimulation with benzoates, (c) altered effector specificity, and (d) higher basal Pm activities, in some cases including changes in effector specificity. In some mutants, higher basal Pm activity was apparently due to mutations that increased XylS stability. Substitutions at Arg-41 resulted in all four mutant phenotypes, indicating that this is a critical residue in XylS for effector stimulation of transcription activity.
Abstract 2049: Post transcriptional regulation of RhoB expression (2010)

Abstract Rho GTPases contribute to most steps of cancer initiation and progression, including the acquisition of unlimited proliferation potential, survival, tissue invasion and the establishment of metastases. By contrast to RhoA and RhoC, RhoB has been proposed to act as a tumor suppressor as it is activated in response to various stresses including UV exposure, and since it has been reported to inhibit tumor growth, cell migration and invasion. Unlike RhoA and RhoC, RhoB is often down regulated in human tumour tissues including lung and head and neck cancer and its expression is inversely correlated with tumor aggressiveness. However, the epigenetic regulation of RhoB expression in cancer cells remains to be elucidated. Since several recent works demonstrate that post-transcriptional deregulation of gene expression is involved in carcinogenesis, we have investigated the post-transcriptional regulation of RhoB expression. The RhoB 3’ untranslated region is well conserved between species and has numerous putative binding sites for post-transcriptional regulators such as mRNA binding proteins and microRNAs. By using luciferase assays and polysome analysis, we have found that the translation of the RhoB mRNA is regulated upon UV exposure. One specific miRNA, miR-19b whose expression is regulated by UV, directly targets the RhoB mRNA to control RhoB expression and UV-induced apoptosis. Interestingly, other post-transcriptionnal regulators involved in RhoB expression, such as the mRNA binding proteins HuR and TiaR were also indentified by functional assays using RNA interference strategy. Immunohistochemical analysis on a cohort of human lung tissues ranging from normal to invasive carcinoma are underway to detect a possible correlation between the expression of these proteins and RhoB downregulation in tumor. Note: This abstract was not presented at the AACR 101st Annual Meeting 2010 because the presenter was unable to attend. Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 101st Annual Meeting of the American Association for Cancer Research; 2010 Apr 17-21; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2010;70(8 Suppl):Abstract nr 2049.
Multimode Correlations in Chip-based Frequency Combs (2014)

We demonstrate correlations between non-twin beams of a frequency comb generated from a silicon nitride ring resonator optical parametric oscillator. The normalized correlation coefficient between these two modes is 0.997, corresponding to near-perfect correlations between the two beams.
Capacitance Measurement in Organic Thin-Film Device with Internal Charge Separation Zone (2005)

To verify the concept of electric-field-assisted bipolar charge spouting in organic thin films, model devices with an internal charge separation (ICS) zone were fabricated. A double-insulation-type organic thin-film device, indium–tin–oxide (ITO)/poly-chloro- p -xylylene (PCPX)/tris(8-quinolinolato)aluminum(III) (Alq 3 )/Mg-doped Alq 3 /V 2 O 5 / N , N '-bis(3-methylphenyl)-1,1'-biphenyl-4,4'-diamine (TPD)/PCPX/Al (device with an ICS zone), and four devices with similar structures without the ICS zone were fabricated. The capacitance of the devices under positive and negative applied biases was measured. The device with the ICS zone showed a clear capacitance increase when the bias condition met the electric-field-assisted bipolar charge separation.
Submandibular Gland Invasion by Oral Cavity Cancers: A Systematic Review (2019)

Given this rarity of SMG involvement, preservation of SMG might be feasible in selected patient population. However, additional studies need to examine the functionality of preserved SMGs among patients who receive postoperative adjuvant radiation therapy.
ChemInform Abstract: Effective New Cobalt(II) Dioxygen Carriers Derived from Dimethylglyoxime by the Replacement of the Linking Protons with BF+ 2. (1991)

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.