gebhart/patrepeval huggingface dataset:
Generation of Large Chromosomal Deletions in Koji Molds Aspergillus oryzae and Aspergillus sojae via a Loop-Out Recombination (2008)

We established a technique for efficiently generating large chromosomal deletions in the koji molds Aspergillus oryzae and A. sojae by using a ku70-deficient strain and a bidirectional marker. The approach allowed deletion of 200-kb and 100-kb sections of A. oryzae and A. sojae, respectively. The deleted regions contained putative aflatoxin biosynthetic gene clusters. The large genomic deletions generated by a loop-out deletion method (resolution-type recombination) enabled us to construct multiple deletions in the koji molds by marker recycling. No additional sequence remained in the resultant deletion strains, a feature of considerable value for breeding of food-grade microorganisms. Frequencies of chromosomal deletions tended to decrease in proportion to the length of the deletion range. Deletion efficiency was also affected by the location of the deleted region. Further, comparative genome hybridization analysis showed that no unintended deletion or chromosomal rearrangement occurred in the deletion strain. Strains with large deletions that were previously extremely laborious to construct in the wild-type ku70(+) strain due to the low frequency of homologous recombination were efficiently obtained from Delta ku70 strains in this study. The technique described here may be broadly applicable for the genomic engineering and molecular breeding of filamentous fungi.
Table S1 from A Novel Engineered Anti-CD20 Tracer Enables Early Time PET Imaging in a Humanized Transgenic Mouse Model of B-cell Non-Hodgkins Lymphoma (2023)

&lt;p&gt;PDF file 56K, Organs uptake presented in the table were mean {plus-minus} SD {percent}ID/g measured by either ROI (Fig. S1) or by ex vivo weighing (Bio) sacrificed after 24h p.i and counting the tissues in gamma counter. L= Liver, K= Kidney, BP = blood pool, and arrow = tumor. ND: not detected. T: O = tumor to organ ratio liver, kidney and spleen&lt;/p&gt;
Class II HMG-CoA Reductase Inhibitors targeting Methicillin-Resistant Staphylococcus pseudintermedius (2017)

Staphylococcus pseudintermedius is a component of the normal flora of companion animals that contributes to opportunistic infections in dogs. Clinical isolates of S. pseudintermedius (chiefly methicillin-resistant S. pseudintermedius (MRSP)) have been identified that exhibit resistance to nearly all antibiotic classes. There is a need for new antibiotics that target novel pathways within resistant pathogens such as MRSP. A possible novel antibacterial target in Gram-positive cocci is class II HMG-CoA reductase (HMGR), a key enzyme present in the mevalonate pathway that is essential for bacterial survival. In this study we examined novel synthetic compounds that are potent inhibitors of bacterial HMGRs. The compounds inhibited growth, in low micromolar concentration, of clinical isolates of methicillin-sensitive S. pseudintermedius (MSSP) and MRSP via the broth microdilution assay. The MTS assay confirmed the most potent compound (6) wasnot toxic to different mammalian cell lines (up to 128 µM). A time-kill assay revealed this compound rapidly eradicates a high inoculum of MRSP within two hours. This study provides evidence that compound 6 is a promising agent that warrants further investigation as a novel treatment option for MRSP infections.
Narrow Line-width 1.31-μm Wavelength Tunable Quantum Dot Laser using Sandwiched Sub-Nano Separator Growth Technique (2011)

By using sandwiched sub-nano separator, we successfully fabricated a 210-kHz linewidth ultra-broadband 1.31-μm wavelength tunable external cavity quantum dot laser, which can be useful for coherent transmission systems in O-band.
Supercavity Modes in Dielectric Resonators Excited by Two Current Sources (2021)

Detailed mechanisms are studied for achieving high quality factors (Q-factor) of high index resonators that exhibit strong confinement of electromagnetic fields and low loss. Exciting supercavity modes is a promising technique to increase the Q-factor in these resonators. Conventional techniques achieve supercavity modes by optimizing material properties and dimensions of such resonators. On the other hand, this work demonstrates that exciting resonators with more complex nearfield current sources instead of a single loop or patch, leads to strong supercavity modes for smaller resonators. Simulation results indicate that Q-factors achieved with the proposed method can be at least 3 times higher than with a conventional single one.
[10]-Gingerdiols as the Major Metabolites of [10]-Gingerol in Zebrafish Embryos and in Humans and Their Hematopoietic Effects in Zebrafish Embryos (2013)

Gingerols are a series of major constituents in fresh ginger with the most abundant being [6]-, [8]-, and [10]-gingerols (6G, 8G, and 10G). We previously found that ginger extract and its purified components, especially 10G, potentially stimulate both the primitive and definitive waves of hematopoiesis (blood cell formation) in zebrafish embryos. However, it is still unclear if the metabolites of 10G retain the efficacy of the parent compound toward pathological anemia treatment. In the present study, we first investigated the metabolism of 10G in zebrafish embryos and then explored the biotransformation of 10G in humans. Our results show that 10G was extensively metabolized in both zebrafish embryos and humans, in which two major metabolites, (3S,5S)-[10]-gingerdiol and (3R,5S)-[10]-gingerdiol, were identified by analysis of the MS(n) spectra and comparison to authentic standards that we synthesized. After 24 h of treatment of zebrafish embryos, 10G was mostly converted to its metabolites. Our results clearly indicate that the reductive pathway is a major metabolic route for 10G in both zebrafish embryos and humans. Furthermore, we investigated the hematopoietic effect of 10G and its two metabolites, which show similar hematopoietic effects as 10G in zebrafish embryos.
Elevated Levels of the Complement Activation Product C4d in Bronchial Fluids for the Diagnosis of Lung Cancer (2015)

Molecular markers in bronchial fluids may contribute to the diagnosis of lung cancer. We previously observed a significant increase of C4d-containing complement degradation fragments in bronchoalveolar lavage (BAL) supernatants from lung cancer patients in a cohort of 50 cases and 22 controls (CUN cohort). The present study was designed to determine the diagnostic performance of these complement fragments (hereinafter jointly referred as C4d) in bronchial fluids. C4d levels were determined in BAL supernatants from two independent cohorts: the CU cohort (25 cases and 26 controls) and the HUVR cohort (60 cases and 98 controls). A series of spontaneous sputum samples from 68 patients with lung cancer and 10 controls was also used (LCCCIO cohort). Total protein content, complement C4, complement C5a, and CYFRA 21-1 were also measured in all cohorts. C4d levels were significantly increased in BAL samples from lung cancer patients. The area under the ROC curve was 0.82 (95%CI = 0.71-0.94) and 0.67 (95%CI = 0.58-0.76) for the CU and HUVR cohorts, respectively. In addition, unlike the other markers, C4d levels in BAL samples were highly consistent across the CUN, CU and HUVR cohorts. Interestingly, C4d test markedly increased the sensitivity of bronchoscopy in the two cohorts in which cytological data were available (CUN and HUVR cohorts). Finally, in the LCCCIO cohort, C4d levels were higher in sputum supernatants from patients with lung cancer (area under the ROC curve: 0.7; 95%CI = 0.56-0.83). In conclusion, C4d is consistently elevated in bronchial fluids from lung cancer patients and may be used to improve the diagnosis of the disease.
Correction: Aptamer-functionalized neural recording electrodes for the direct measurement of cocaine in vivo (2017)

Correction for 'Aptamer-functionalized neural recording electrodes for the direct measurement of cocaine in vivo' by I. Mitch Taylor et al., J. Mater. Chem. B, 2017, 5, 2445-2458.
Prognostic value of protein tyrosine kinase 6 (PTK6) for long-term survival of breast cancer patients (2008)

The cytoplasmic tyrosine kinase PTK6 (BRK) shows elevated expression in approximately two-thirds of primary breast tumours, and is implicated in EGF receptor-dependent signalling and epithelial tumorigenesis. Using immunohistochemistry, we performed a retrospective study on 426 archival breast cancer samples from patients with long-term follow-up and compared the protein expression levels of PTK6, the HER receptors, Sam68 (a substrate of PTK6), and signalling proteins including MAP kinase (MAPK), phosphorylated MAPK (P-MAPK), and PTEN. We show that PTK6 expression is of significant prognostic value in the outcome of breast carcinomas. In multivariate analysis, the disease-free survival of patients of >or=240 months was directly associated with the protein expression level of PTK6 (P<or=0.001), but was also inversely associated with nodal status (P<or=0.001) and tumour size (P<or=0.01). PTK6 expression in tumour tissue significantly correlated (P<or=0.05) with the expression of PTEN, MAPK, P-MAPK, and Sam68. To investigate whether these correlations may be due to molecular interactions between PTK6 and these proteins, we used protein extracts from the T47D cell line for immunoprecipitation and western blot analysis. By this, interactions could be demonstrated between PTK6 and MAPK, P-MAPK, HER2/neu, HER3, HER4, PTEN, and Sam68. On the basis of these results, we suggest that PTK6 may serve as a future target for the development of novel treatments in breast cancer.
Capturing tumor complexity in vitro: Comparative analysis of 2D and 3D tumor models for drug discovery (2016)

Two-dimensional (2D) cell cultures growing on plastic do not recapitulate the three dimensional (3D) architecture and complexity of human tumors. More representative models are required for drug discovery and validation. Here, 2D culture and 3D mono- and stromal co-culture models of increasing complexity have been established and cross-comparisons made using three standard cell carcinoma lines: MCF7, LNCaP, NCI-H1437. Fluorescence-based growth curves, 3D image analysis, immunohistochemistry and treatment responses showed that end points differed according to cell type, stromal co-culture and culture format. The adaptable methodologies described here should guide the choice of appropriate simple and complex in vitro models.
Efforts Towards the Development of New Antitubercular Agents: Potential for Thiolactomycin Based Compounds (2008)

Development of new chemotherapeutic drugs is the need of the hour to improve tuberculosis control, particularly in the developing world. In the last fourty years no new compound has been brought to the market for the treatment of tuberculosis. However, in recent years there is an enhanced activity in the research and development of new drugs for TB. Some compounds are presently in clinical development, while others are being investigated pre-clinically in an attempt to explore new molecules for the target based treatment of TB. Simultaneously some new targets are being identified and validated for their practical usefulness. Structures based on thiolactomycin could have considerable potential in the development of target based anti-TB agents. The present review provides an overview of the drugs that are being clinically used and the compounds that are in advanced stages of clinical as well as preclinical studies. We have also attempted to highlight the efforts that are being made in the development of new molecules based on thiolactomycin as lead compound, including studies from this laboratory.
Intestinal deletion of fatty acid transport protein 4 in mice increases blood chylomicrons (2020)

Polymorphisms of fatty acid transport protein 4 (FATP4) are associated with blood lipoproteins and insulin resistance. As FATP4 is localized in intracellular organelles and highly expressed in mouse small intestine, Fatp4 role in fat absorption in mice is still controversial. As our recent studies have suggested Fatp4 role in triglyceride (TAG) metabolism, we here investigated intestinal fat absorption and blood TAG-chylomicrons (CM) in villin-Cre specific inactivation of the Fatp4 gene with exon 3 deletion (entFatp4KO mice).
Gold-Hyperdoped Germanium with Room-Temperature Sub-Band-Gap Optoelectronic Response (2020)

Short-wavelength-infrared (SWIR; 1.4--3.0 \textmu{}m) photodetection is important for various applications. Inducing a low-cost silicon-compatible material, such as germanium, to detect SWIR light would be advantageous for SWIR applications compared with using conventional (III-V or II-VI) SWIR materials. Here, we present a scalable nonequilibrium method for hyperdoping germanium with gold for dopant-mediated SWIR photodetection. Using ion implantation followed by nanosecond pulsed laser melting, we obtain a single-crystal material with a peak gold concentration of 3 \ifmmode\times\else\texttimes\fi{} ${10}^{19}\phantom{\rule{0.1em}{0ex}}{\mathrm{cm}}^{\ensuremath{-}3}$ $({10}^{3}$ times the solubility limit). This hyperdoped germanium has fundamentally different optoelectronic properties from those of intrinsic and conventionally doped germanium. This material exhibits sub-band-gap absorption of light up to wavelengths of at least 3 \textmu{}m, with a sub-band-gap optical absorption coefficient comparable to that of commercial SWIR photodetection materials. We show that germanium hyperdoped with gold exhibits sub-band-gap SWIR photodetection at room temperature, in contrast with previous doped-germanium photodetector studies, which only show a low-temperature response. This material is a potential pathway to low-cost room-temperature silicon-compatible SWIR photodetection.
Power and thermal constraints of modern system-on-a-chip computer (2013)

Power and thermal are major constraints for delivering compute performance in high-end CPU and are expected to be so in the future. For high end processors, junction temperature has been considered the toughest physical constraint that needs to be tightly managed. Recent trends in form-factors and the increased focus on thin and light systems such as Ultra Book, tablet computers and smartphones, shift the challenge away from junction temperature. Ergonomic thermal considerations and power delivery are becoming the limiters for delivering high computational performance density and need to be managed and controlled. In this paper we describe the major physical constraints, design considerations and modern power and thermal management techniques and demonstrate them on an Intel Core(tm) i7 system.
04 Immunization of melanoma patients with peptide-pulsed dendritic cells (DC) (1999)

Punt, C. J. A.1; de Vries, I. J. M.2; Eggert, A. A. O.2; Scharenborg, N. H.2; Verstraten, H. G. G.2; Ruiter, D. J.3; Adema, G. J.2; Figdor, C. G.2 Author Information
Design and Analysis of an Adaptive Real-Time Advisory System for Improving Real World Fuel Economy in a Hybrid Electric Vehicle (2010)

&lt;div class="section abstract"&gt;&lt;div class="htmlview paragraph"&gt;Environmental awareness and fuel economy legislation has resulted in greater emphasis on developing more fuel efficient vehicles. As such, achieving fuel economy improvements has become a top priority in the automotive field. Companies are constantly investigating and developing new advanced technologies, such as hybrid electric vehicles, plug-in hybrid electric vehicles, improved turbo-charged gasoline direct injection engines, new efficient powershift transmissions, and lighter weight vehicles. In addition, significant research and development is being performed on energy management control systems that can improve fuel economy of vehicles.&lt;/div&gt; &lt;div class="htmlview paragraph"&gt;Another area of research for improving fuel economy and environmental awareness is based on improving the customer's driving behavior and style without significantly impacting the driver's expectations and requirements. Ford Motor Company developed an adaptive real-time advisory system for fuel economy improvement in a hybrid electric vehicle that automatically identifies the driver's style, intentions and preferences and provides guidance through haptic and visual mechanisms to the driver for selecting the optimal driving strategy that results in maximum fuel economy. The adaptive real-time advisory system was validated on an experimental Ford Escape Hybrid vehicle using haptic and visual feedback mechanisms in an extensive test study to quantify the fuel economy improvements. In this study, fuel economy data from various types of drives on a pre-determined route was collected without and with the adaptive real-time advisory system to compute the mean fuel economy improvement. In addition, the real world fuel economy improvement using the haptic and visual feedback mechanisms was statistically quantified. The study results demonstrated that the adaptive real-time advisory system achieved a 6% and 3% mean real world fuel economy improvement using haptic and visual feedback mechanisms respectively without significantly compromising the driver's expectations and vehicle performance.&lt;/div&gt;&lt;/div&gt;
Floating Interlayer and Surface Electrons in 2D Materials: Graphite, Electrides, and Electrenes (2021)

Over the last half century, layered materials have been at the forefront of materials science, spearheading the discovery of new phenomena and functionalities. Certain layered materials are known to possess electronic states unassociated with any of the constituent atoms, having a large proportion of their probability amplitude in the space between the layers. Usually, such a nucleus-free interlayer state has energy above the Fermi level and is unoccupied. However, the energy decreases when cations are intercalated and may cross the Fermi level, as in the case of C<sub>6</sub>Ca, a superconductor with a <i>T</i> <sub>c</sub> of 11.5 K. A major thrust to the research of interlayer electrons comes with the discovery of layered electrides, which are alternating stacks of positively charged ionic layers and negatively charged sheets of electrons in the interlayer space. When intercalation compounds and layered electrides are thinned down to the atomic scale, the interlayer states survive as surface states floating over the surface. This review provides a unified overview of the two classes of materials hosting interlayer floating electrons near the Fermi level, intercalation compounds and layered electrides, and their properties, including high electron mobility, low work function, ultralow interlayer friction, superconductivity, and plasmonic properties.
Wireless multicast performance improvement strategies based on autonomous handover (2006)

In this letter, we propose three strategies for the improvement of multicast performance that can increase cell throughput of unidirectional multicast service by utilizing the concept of autonomous handover to improve the performance of cell-boundary users. We show that these proposed schemes can improve cell throughput by about 10%-25%, over the conventional scheme not utilizing autonomous handover.
A Mathematical Analysis of a Free-Flooded Finite-Length Radiating Magnetostrictive Shell (1974)

A mathematical analysis with accompanying computer program of the electroacoustic performance of a single finite-length magnetostrictive circular cylinder submerged in an unbounded medium and radiating sound is presented. The cylinder is a thin hyperelastic orthotropic shell constructed of metal laminations and has unrestricted radius to length ratios. Wound toroidally with current carrying coils, it is magnetostrictively excited in axisymmetric modes over selected frequency ranges. In the analysis the vibration of the shell is developed in modes by means of dynamic equations with boundary conditions [Warburton, J. Mech. Eng. Sci. 7, 399 (1965)] and the magnetostriction transduction is described by a set of linearized constitutive relations, also modified to account for hysteresis and eddy currents. New definitions are constructed of modal electromechanical coupling coefficients and modal mass. For an input set of dimensions, electric drive, and selected frequency range, the computer program delivers in vacuo modal frequencies, modal shapes, surface velocities, and electrical and mechanical motional impedances. Typical examples of computer output are given together with a discussion of certain important “barrel modes.” Comparison is made with selected experimental results.
New developments in the field of mastocytosis and mast cell activation syndromes: a summary of the Annual Meeting of the European Competence Network on Mastocytosis (ECNM) 2019 (2019)

Mastocytosis are a group of hematologic neoplasms characterized by an accumulation of atypical mast cells in one or several organs/tissues, often accompanied by mast cell activation. Whereas in children the disease manifestations are mostly limited to the skin, in adults the disease is usually systemic (systemic mastocytosis; SM) and involves the bone marrow and/or other internal organs. Several variants of SM have been defined. Whereas most patients have indolent SM, some patients have advanced SM, which underlines the complexity of SM. In 2002, a European consortium of clinicians and scientists initiated a multidisciplinary, multi-national cooperative network, termed the 'European Competence Network on Mastocytosis' (ECNM), with the aim to improve diagnosis and therapy of patients with mastocytosis and other mast cell activation disorders. Since then, members of the ECNM have organized Annual Meetings in several European countries. The present article provides a summary of advances in the field presented during the 17th Annual ECNM meeting held in Salzburg in October 2019.
Design of Shape-Adaptive Deployable Slat-Cove Filler for Airframe Noise Reduction (2021)

Mechanical instabilities and elastic nonlinearities are emerging means for designing deployable and shape adaptive structures. Dynamic snap-through buckling is investigated here as a means to tailor the deployment and retraction of a slat-cove filler (SCF), a morphing component used to reduce airframe noise. Upon deployment, leading-edge slats create a cove between themselves and the main wing, producing unsteady flow features that are a significant source of airframe noise. A SCF is designed here to autonomously snap out as the slat deploys, providing a smoother aerodynamic profile that reduces flow unsteadiness. The nonlinear structural behavior of the SCF is studied, and then tailored, to achieve a desirable snapping response. Three SCF configurations are considered: 1) a constant thickness (monolithic) superelastic shape-memory alloy (SMA) SCF, 2) a variable-thickness SMA SCF, and 3) a set of stiffness-tailored fiberglass composite SCFs. Results indicate that, although monolithic SMA SCFs provide a simple solution, thickness variations in both the SMA and stiffness-tailored composite SCF designs allow a decrease of the energy required for self-deployment and a reduction of the severity of the impact between the SCF and the slat during stowage. The enhanced nonlinear behavior from stiffness tailoring reduces peak material strains in comparison to previous SMA SCF designs that leveraged material superelasticity for shape adaptation. The stiffness tailoring is readily achieved through the use of layered composites, facilitating considerable weight savings compared to the dense SMA designs. The aeroelastic response of different SCFs is calculated using fluid/structure interaction analyses, and it is shown that both SMA and composite SCF designs can deploy and retract in full flow conditions.
ChemInform Abstract: HOST‐GUEST COMPLEXATION. 2. STRUCTURAL UNITS THAT CONTROL ASSOCIATION CONSTANTS BETWEEN POLYETHERS AND TERT‐BUTYLAMMONIUM SALTS (1977)

Abstract Aus dem Diol (I) und dem dem Ditosylat (II) entsteht der Polyäther (III).Die entsprechende Reaktion des cis‐ 2,5‐Dihydroxymethyl‐tetrahydrofurans mit dem Ditosylat des Triäthylenglykols liefert in Gegenwart von K‐tert.‐butanolat den Kronenäther (IV) (Ausbeute 23%) und das Dimere (V) (8%), das möglicherweise als ein syn‐cis‐cis/anti‐cis‐cis‐Gemisch vorliegt.