gebhart/patrepeval huggingface dataset:
Isolating, imaging, and electrically characterizing individual organic molecules on the Si(100) surface with the scanning tunneling microscope (2000)

Molecular electronics shows great potential as an approach for fabricating nanoelectronic devices and circuits. Despite this potential, many fundamental problems remain unsolved. This article outlines a three pronged approach that addresses key molecular electronic issues for molecules supported on ultrahigh vacuum scanning tunneling microscopy (UHVSTM) patterned hydrogen passivated Si(100) surfaces. First, feedback controlled lithography (FCL) has been developed as a reliable technique for making templates of individual dangling bonds on the Si(100)–2×1:H surface. FCL detects individual H desorption events while patterning, thereby compensating for variations in tip structure. When the surface is then exposed to a flux of molecules, they bind individually to the prepatterned sites. With this technique, norbornadiene and copper phthalocyanine (CuPc) molecules have been intentionally isolated into predefined patterns. STM images reveal intramolecular detail and suggest mechanical behavior such as molecular rotation. Second, using STM spectroscopy, molecules’ electronic properties have been revealed. Filled state tunneling conductance maps of CuPc molecules exhibit an enhanced density of electronic states. However, in empty states, a ring of reduced local density of states surrounds each CuPc molecule. Finally, an all-UHV scheme for isolating and, ultimately, electrically contacting STM-patterned nanostructures has been developed that utilizes a predefined p–n junction on a Si(100) substrate. With STM potentiometry, the junction is easily located, allowing for efficient registration of nanostructures after intermediate processing steps. In addition, by STM patterning across the depletion region, the electrical properties of selectively deposited nanostructures can be directly evaluated when the p–n junction is reverse biased.
Electrochemical Deposition of Silver Nanocrystallites on the Atomically Smooth Graphite Basal Plane (1996)

A potentiostatic pulse method has been employed to electrochemically deposit silver nanocrystallites on the atomically smooth graphite basal plane surface. Voltage pulses having amplitudes of 100, 250, and 500 mV vs Ag0 and durations of 10 or 50 ms were applied to graphite surfaces immersed in dilute (≈1.0 mM) aqueous silver nitrate. During the deposition pulse, the current increased in approximate proportion to (time)1/2 as expected for an instantaneous nucleation and three-dimensional growth mode of deposition. Consistent with this growth mode, noncontact atomic force microscopy (NC-AFM) examination of graphite surfaces following silver deposition revealed the existence of silver particles at a coverage of near 1010 cm-2 which were well-separated from one another on atomically smooth regions of the graphite basal plane surface. These particles were disk-shaped having a height of 15−50 Å and an apparent diameter which varied from 200 to 600 Å; particle dimensions increased smoothly with the coulometric loading, QAg, over the interval from 0.31 to 36 μC cm-2 and in approximate proportion to QAg1/3. Significantly, silver nanocrystallites present on the atomically smooth regions of a graphite surface could not be observed by using either the scanning tunneling microscope (STM) or a conventional repulsive mode atomic force microscope (AFM). In addition to NC-AFM, the characterization of these silver nanocrystallites by transmission electron microscopy lattice imaging and Auger electron spectroscopy is reported.
Environmental Genotoxicity in an Estonian Oil Shale Industrial Area (1996)

The genotoxicity of environmental samples (ambient air, drinking and river waters, purified waste water and oil shale ash) from an oil shale mining and processing area was studied by using the Ames Salmonella/microsome assay. Salmonella typhimurium strains TA98 and YG1021 were used, with and without metabolic activation with rat liver homogenate S9. The water samples were treated with amberlite adsorbent XAD-2 for concentrating non-polar compounds. The air samples were collected on glass fibre filters by using a high volume air sampler, and extracted with dichloromethane by using a Soxhlet apparatus. The air samples were mutagenic in both strains, both with and without S9-mix. The air mutagenicity data were compared with data from similar tests on cigarette smoke condensate as a positive control. Based on the fact that the average 8-hour respiratory volume at occupational activities is between 10m 3 and 20m 3 , the load of airborne mutagenicity at the cokery plant during one week was estimated to be equal to the mutagenicity produced by the mainstream smoke of one cigarette. The drinking and river water samples were tested with both strains, but no dose-related increases in water counts per plate were noted. The oil shale ash sample showed no mutagenic activity, but showed cytotoxicity at the higher doses tested.
Polymer−Drug Interactions in Tyrosine-Derived Triblock Copolymer Nanospheres: A Computational Modeling Approach (2009)

A combination of molecular dynamics (MD) simulations and docking calculations was employed to model and predict polymer-drug interactions in self-assembled nanoparticles consisting of ABA-type triblock copolymers, where A-blocks are poly(ethylene glycol) units and B-blocks are low molecular weight tyrosine-derived polyarylates. This new computational approach was tested on three representative model compounds: nutraceutical curcumin, anticancer drug paclitaxel and prehormone vitamin D3. Based on this methodology, the calculated binding energies of polymer-drug complexes can be correlated with maximum drug loading determined experimentally. Furthermore, the modeling results provide an enhanced understanding of polymer-drug interactions, revealing subtle structural features that can significantly affect the effectiveness of drug loading (as demonstrated for a fourth tested compound, anticancer drug camptothecin). The present study suggests that computational calculations of polymer-drug pairs hold the potential of becoming a powerful prescreening tool in the process of discovery, development and optimization of new drug delivery systems, reducing both the time and the cost of the process.
Coffee consumption, type 2 diabetes and impaired glucose tolerance in Swedish men and women (2004)

The results of this study indicated that high consumers of coffee have a reduced risk of type 2 diabetes and impaired glucose tolerance. The beneficial effects may involve both improved insulin sensitivity and enhanced insulin response.
Array-based gene expression, CGH and tissue data defines a 12q24 gain in neuroblastic tumors with prognostic implication (2010)

The presented systematic and rapid framework, which integrates aCGH, gene expression and tissue data to obtain novel targets and biomarkers for cancer, identified a low-level gain of the 12q24.31 as a potential new biomarker for neuroblastoma progression. Furthermore, results of in silico data mining suggest a new neuroblastoma target gene, DIABLO, within this region, whose functional and therapeutic role remains to be elucidated in follow-up studies.
Human Ribosomal G-Quadruplexes Regulate Heme Bioavailability (2020)

ABSTRACT The in vitro formation of stable G-quadruplexes (G4s) in human ribosomal RNA (rRNA) was recently reported. However, their formation in cells and their cellular roles have not been resolved. Here, by taking a chemical biology approach that integrates results from immunofluorescence, G4 ligands, heme affinity reagents, and a genetically encoded fluorescent heme sensor, we report that human ribosomes can form G4s in vivo that regulate heme bioavailability. Immunofluorescence experiments indicate that the vast majority of extra-nuclear G4s are associated with rRNA. Moreover, titrating human cells with a G4 ligand alters the ability of ribosomes to bind heme and disrupts cellular heme bioavailability as measured by a genetically encoded fluorescent heme sensor. Overall, these results suggest ribosomes are central hubs of heme metabolism.
Immunogenomic landscape of neuroendocrine small cell prostate cancer. (2019)

217 Background: Neuroendocrine small cell prostate cancer (NEPC) is a lethal variant of prostate cancer (PCa) unresponsive to hormone therapy and associated with poor prognosis. Cisplatin induces short-lived responses and therefore alternative novel therapeutic options are urgently needed. Methods: Prostate specimens from radical prostatectomy or transurethral resection (benign prostate specimens n = 4, primary untreated or neoadjuvant hormone-treated adenocarcinoma n = 30, castrate-resistant prostate cancer-CRPC n = 38 and NEPC n = 16) were evaluated for PD-L1 (SpringBio, M4420), AR, chromogranin A, synaptophysin, NSE and CD56 expression by immunohistochemistry (IHC). Archival tissue from liver, lymph nodes and prostate from 30 additional patients with de novo and treatment emergent NEPC were analyzed for PD-L1 expression by IHC. The intensity was assessed as percentage of positive cells / mm2 of tissue. Targeted and whole exome sequencing of the high-density tumor areas were performed and correlated to the PD-L1 status (PD-L1+ve: &gt; 1% of positive cells). OS was calculated from the date of diagnosis of NEPC to death. We set out to define PD-L1 expression and immunogenomic characteristics of NEPC. Results: PD-L1 was expressed in 0%, 5%, 10% and 41% of benign, adenocarcinoma, CRPC and NEPC specimens, respectively. The PD-L1 expression intensity was significantly higher in patients with NEPC (mean: 40%, range: 5-100%) compared to benign, adenocarcinoma and CRPC samples (mean: 0%, 2% and 8%, respectively, P &lt; 0.0001). There was a higher prevalence of biallelic DNA Repair Defects (DRD) in the PD-L1+ve vs PD-L1-ve patients (65% vs 0%, P = 0.005). The median OS of the NEPC patients was 8.5 months vs 10.5 months in PD-L1+ve vs PD-L1-ve tumors (HR 1.24, 95% CI: 0.59-2.75, p = 0.55). Conclusions: NEPC have greater PD-L1 expression than adenoCa and CRPC. Biallelic DRD was exclusively observed in PD-L1+ve patients. Since PD-L1 expression and DRD have been associated to response to PARP and PD1/PD-L1 inhibitors in prostate and other cancers, further studies evaluating the activity of those agents in NEPC patients are warranted.
Solidification of Polymers (2012)

No AccessMaterials Science of Polymers for EngineersSep 2012Solidification of PolymersTim A. Osswald, Georg MengesTim A. OsswaldSearch for more papers by this author, Georg MengesSearch for more papers by this authorhttps://doi.org/10.3139/9781569905241.008SectionsAboutPDF ToolsAdd to FavoritesDownload CitationTrack CitationsCopy LTI LinkPDF key 'share (en)' returned an object instead of string.FacebookTwitterEmailLinkedIn previous chapternext chapter FiguresReferencesRelatedDetails 2012Pages: 295-337Print ISBN: 978-1-56990-514-2eISBN: 978-1-56990-524-1 Copyright & Permissions© 2012 Carl Hanser Verlag GmbH & Co. KGPDF downloadLoading ...
Laser-Ablated Vortex Fluidic-Mediated Synthesis of Superparamagnetic Magnetite Nanoparticles in Water Under Flow (2018)

Selective formation of only one iron oxide phase is a major challenge in conventional laser ablation process, as is scaling up the process. Herein, superparamagnetic single-phase magnetite nanoparticles of hexagonal and spheroidal-shape, with an average size of ca. 15 nm, are generated by laser ablation of bulk iron metal at 1064 nm in a vortex fluidic device (VFD). This is a one-step continuous flow process, in air at ambient pressure, with in situ uptake of the nanoparticles in the dynamic thin film of water in the VFD. The process minimizes the generation of waste by avoiding the need for any chemicals or surfactants and avoids time-consuming purification steps in reducing any negative impact of the processing on the environment.
The Impact of Obesity on Outcomes Following Resection for Gastric Cancer (2016)

Obesity may complicate resection for gastric cancer increasing the duration of surgical procedure, hospital stay and postoperative morbidity and mortality. However, BMI did not predict OS in our patients. Consequently, BMI may be too simple as a parameter to evaluate sophisticated interactions between different body fat compartments and inflammatory and immune responses and thus to predict long-term oncologic outcomes.
Influence of Single-Walled Carbon Nanotubes on the Performance of Poly(Azomethine-Ether) Composite Materials (2017)

The present work is aimed to fabricate a new set of composite materials containing conducting poly(azomethine-ether) reinforced with single-walled carbon nanotubes in the form of single-walled carbon nanotube/poly(azomethine-ether)1–5 for excellent enhanced thermal as well as conducting behavior of poly(azomethine-ether). Single-walled carbon nanotubes of variable loading have been embedded into conducting poly(azomethine-ether) using in situ polymerization technique. Before attempting the polymerization, 1,3-thiazole established poly(azomethine-ether) and its conformable monomers have been prepared and their chemical structures have been correlated by spectral analyses. Furthermore, ηinh and Mw values for poly(azomethine-ether) were found 0.89 dL g−1 and 39723.6, respectively. The fabricated single-walled carbon nanotube/poly(azomethine-ether)1–5 composites were specified and characterized by wide-angle X-ray diffraction patterns, Fourier transform infrared spectroscopy, thermal behavior, scanning electron microscopy, and transmission electron microscopy characterization techniques. A perfect indicative response for this composite material was estimated by Fourier transform infrared spectra and X-ray diffraction as well. Both techniques displayed all intensive characteristic peaks regarding single-walled carbon nanotubes and poly(azomethine-ether) in the spectra or diffraction pattern for single-walled carbon nanotube/poly(azomethine-ether)1–5. The role of single-walled carbon nanotubes on the performance of poly(azomethine-ether) was considerably examined. Single-walled carbon nanotube/poly(azomethine-ether)1–5 showed relatively higher thermal stability. Single-walled carbon nanotube/poly(azomethine-ether)1 displayed the lowest final composite degradation temperature value (552°C), whereas single-walled carbon nanotube/poly(azomethine-ether)5 displayed the highest value (621°C). T10 and T25 values showed a gradual temperature increased while single-walled carbon nanotubes increased. Single-walled carbon nanotube/poly(azomethine-ether)1 showed the lowest thermal stability and single-walled carbon nanotube/poly(azomethine-ether)5 showed the highest thermal stability between all fabricated products. Furthermore, transmission electron microscopy images showed a prominent increase in single-walled carbon nanotubes diameters (40–60 nm). The conductivity values were significantly increased while single-walled carbon nanotubes content was increased and reached to the semiconductors. ε′ values were also increased in both single-walled carbon nanotube/poly(azomethine-ether)4,5 which have higher single-walled carbon nanotubes content.
4-(Piperidin-1-yl)-4H-benzo[b]tetrazolo[1,5-d][1,4]diazepin-5(6H)-one (2010)

There are two crystallographically unique mol-ecules present in the asymmetric unit of the title compound, C(14)H(16)N(6)O; in both mol-ecules, the seven-membered diazepinone ring adopts a boat-like conformation and the chair conformation piperidine ring is an axial substituent on the diazepinone ring. In the crystal, each mol-ecule forms hydrogen bonds with its respective symmetry equivalents. Hydrogen bonding between mol-ecule A and symmetry equivalents forms two ring motifs, the first formed by inversion-related N-H⋯O inter-actions and the second formed by C-H⋯O and C-H⋯N inter-actions. The combination of both ring motifs results in the formation of an infinite double tape, which propagates in the a-axis direction. Hydrogen bonding between mol-ecule B and symmetry equivalents forms one ring motif by inversion-related N-H⋯O inter-actions and a second ring motif by C-H⋯O inter-actions, which propagate as a single tape parallel with the c axis.
Food volume calculation in different imaging scenarios (2011)

In order to understand the etiology of obesity related to people's diet, we have developed a method to calculate food volume (portion size) from a single digital image in which a dining plate was used as a reference. In order to evaluate the error of this method, we observe the relationship between the relative error under different food imaging scenarios, such as angles of camera rotation and distances between food and camera. Based on our result, an error reduction scheme is proposed to improve the accuracy in image-based food volume estimation.
A Chitosan‐Based Sinus Sealant for Reduction of Adhesion Formation in Rabbit and Sheep Models (2012)

This chitosan-based sealant demonstrates promise for reducing adhesion formation in sinus surgery.
Physiological role of olfactory receptors in alveolar macrophages (2020)

New therapeutic approaches are required to decelerate the progression of COPD and severe asthma with non-type2 inflammation. Alveolar macrophages (AM) might be suitable targets because of their key role in the pathophysiologies. Pre-clinical studies and clinical trials currently investigate the potential of ectopic olfactory receptors (OR), the largest subgroup of G-protein coupled receptors, as therapeutic targets in several non-respiratory diseases. Pre-clinical data about their potential in obstructive lung diseases are lacking. <b>Method:</b> OR2AT4 and OR1A1/OR1A2 are suitable candidates and their synthetic agonists Sandalore or (‑)Citronellal, respectively, might repair dysregulated molecular processes in COPD or asthma like calcium signaling and phagocytosis of alveolar macrophages. AM were isolated from the bronchoalveolar lavage (BAL) of patients with (suspected) COPD or asthma. Both, OR2AT4 and OR1A2 proteins were detected by western blot and in the membrane of the AM by immunocytochemical staining. Their mRNAs were not detected by well controlled RT-PCR. Sandalore and Citronellal, both induced a concentration-dependent and transient increase of intracellular calcium. For Sandalore this was blocked by Oxyphenylon (OR2AT4 blocker), MDL12330A (adenylate cyclase blocker) and withdrawal of extracellular calcium with EGTA suggesting the involvement of the cAMP-dependent pathway. The phagocytotic activity was reduced by both agonists. AM functionally express OR2AT4 and OR1A2 but do not perform de-novo synthesis. Both ORs interfere with the calcium balance of the cells and inhibit phagocytosis. This is first indication for OR2AT4 and OR1A2 as therapeutic targets in obstructive lung diseases.
Sürekli miknatisli senkron motorlarda epoksi malzemesinin motor termal performansina etkisi (2016)

This paper focuses on the influence of epoxy material on permanent magnet (PM) synchronous motor performance. A design specifications for an industrial application is defined, magnetic design and detailed finite element analyses (FEA) are carried out. Properties of epoxy materials used in PM motors are summarized, thermal performances are obtained and compared. For the final design, a prototype is built and both electrical and thermal tests are completed. Thermal tests with and without epoxy material are carried out and the influence of the chosen material on the machine performance is investigated in detail.
Stereochemical Assignment of the C21–C38 Portion of the Desertomycin/Oasomycin Class of Natural Products by Using Universal NMR Databases: Prediction (2000)

Stereochemistry can be predicted: The stereoselective synthesis of the C21-C38 degradation product derived from oasomycins A and B has confirmed the stereochemistry predicted from a comparitive study of the NMR chemical shifts of the C21-C38 portion of the natural products with those obtained for its diastereomers.
Power to Detect Risk Alleles Using Genome-Wide Tag SNP Panels (2007)

Advances in high-throughput genotyping and the International HapMap Project have enabled association studies at the whole-genome level. We have constructed whole-genome genotyping panels of over 550,000 (HumanHap550) and 650,000 (HumanHap650Y) SNP loci by choosing tag SNPs from all populations genotyped by the International HapMap Project. These panels also contain additional SNP content in regions that have historically been overrepresented in diseases, such as nonsynonymous sites, the MHC region, copy number variant regions and mitochondrial DNA. We estimate that the tag SNP loci in these panels cover the majority of all common variation in the genome as measured by coverage of both all common HapMap SNPs and an independent set of SNPs derived from complete resequencing of genes obtained from SeattleSNPs. We also estimate that, given a sample size of 1,000 cases and 1,000 controls, these panels have the power to detect single disease loci of moderate risk (lambda approximately 1.8-2.0). Relative risks as low as lambda approximately 1.1-1.3 can be detected using 10,000 cases and 10,000 controls depending on the sample population and disease model. If multiple loci are involved, the power increases significantly to detect at least one locus such that relative risks 20%-35% lower can be detected with 80% power if between two and four independent loci are involved. Although our SNP selection was based on HapMap data, which is a subset of all common SNPs, these panels effectively capture the majority of all common variation and provide high power to detect risk alleles that are not represented in the HapMap data.
Behavior of the Meat-Borne Bacterium Lactobacillus sakei during Its Transit through the Gastrointestinal Tracts of Axenic and Conventional Mice (2009)

A Lactobacillus sakei strain named FLEC01 was isolated from human feces and characterized genotypically. Comparison of the genetic features of this strain with those of both the meat-borne L. sakei strain 23K and another human isolate, LTH5590, showed that they belong to different but closely related clusters. The three L. sakei strains did not persist and only transited through the gastrointestinal tracts (GITs) of conventional C3H/HeN mice. In contrast, they all colonized the GITs of axenic mice and rapidly reached a population of 10(9) CFU/g of feces, which remained stable until day 51. Five days after mice were fed, a first subpopulation, characterized by small colonies, appeared and reached 50% of the total L. sakei population in mice. Fifteen to 21 days after feeding, a second subpopulation, characterized by rough colonies, appeared. It coexisted with the two other populations until day 51, and its cell shapes were also affected, suggesting a dysfunction of the cell division or cell wall. No clear difference between the behaviors of the meat-borne strain and the two human isolates in both conventional and axenic mice was observed, suggesting that L. sakei is a food-borne bacterium rather than a commensal one and that its presence in human feces originates from diet. Previous observations of Escherichia coli strains suggest that the mouse GIT environment could induce mutations to increase their survival and colonization capacities. Here, we observed similar mutations concerning a food-grade gram-positive bacterium for the first time.