gebhart/patrepeval huggingface dataset:
Quantum Crystallography and Complementary Bonding Analysis of Agostic Interactions in Titanium Amides (2023)

Abstract Agostic interactions involving titanium are textbook examples for C−H bond activation. Therefore, it is surprising that there is no study in the literature in which the hydrogen atom in the C−H⋅⋅⋅Ti interaction has been determined reliably, although nearly all the criteria for assessing the strength and character of the agostic interaction depend on the hydrogen atom and its position. Here, we demonstrate with quantum crystallographic techniques how hydrogen atoms in a series of three titanium amides can indeed be localized accurately and precisely based on routine single‐crystal X‐ray diffraction data. Once the hydrogen positions have been established, theoretical and experimentally fitted bonding analyses reveal that the C−H⋅⋅⋅Ti interaction becomes stronger with increasing inter‐ligand London dispersion stabilization of bulky alkyl groups.
Trace fossils from the Upper Member of the Duolbagáisá Formation (Cambrian Series 2–Miaolingian), northern Norway, with the first diverse Cambrian record of Halimedides¬ (2022)

New information is provided on trace fossils from the Cambrian Series 2 toNew information is provided on trace fossils from the Cambrian Series 2 toMiaolingian in the Upper Member of the Duolbagáisá Formation of northern Norway. This includes the first rich Cambrian material of Halimedides, a tracefossil with more or less regularly spaced swellings of different shapesconnected by a median string. It is known principally from Mesozoic andyounger deep-sea deposits, with a scarce Paleozoic record, making this one ofthe oldest occurrences of this ichnogenus. Other trace fossils occurring with Halimedides include the rare Bergaueria sucta, Palaeophycus imbricatus and Cruziana tenella. Psammichnites gigas and Syringomorpha nilssoni aredocumented photographically for the first time from this unit. The trace fossilassociation shows general similarity with that of the slightly older MickwitziaSandstone Member of southern Sweden and suggests a broad distribution oflate early Cambrian trace-fossil producers across Baltica.
Electrofluidic control of bioactive molecule delivery into soft tissue models based on gelatin methacryloyl hydrogels using threads and surgical sutures (2020)

The delivery of bioactive molecules (drugs) with control over spatial distribution remains a challenge. Herein, we demonstrate for the first time an electrofluidic approach to controlled delivery into soft tissue models based on gelatin methacryloyl (GelMA) hydrogels. This was achieved using a surgical suture, whereby transport of bioactive molecules, including drugs and proteins, was controlled by imposition of an electric field. Commonly employed surgical sutures or acrylic threads were integrated through the hydrogels to facilitate the directed introduction of bioactive species. The platform consisted of two reservoirs into which the ends of the thread were immersed. The anode and cathode were placed separately into each reservoir. The thread was taken from one reservoir to the other through the gel. When current was applied, biomolecules loaded onto the thread were directed into the gel. Under the same conditions, the rate of movement of the biomolecules along GelMA was dependent on the magnitude of the current. Using 5% GelMA and a current of 100 µA, 2 uL of fluorescein travelled through the hydrogel at a constant velocity of 7.17 ± 0.50 um/s and took less than 8 minutes to exit on the thread. Small molecules such as riboflavin migrated faster (5.99 ± 0.40 μm/s) than larger molecules such as dextran (2.26 ± 0.55 μm/s with 4 kDa) or BSA (0.33 ± 0.07 μm/s with 66.5 kDa). A number of commercial surgical sutures were tested and found to accommodate the controlled movement of biomolecules. Polyester, polyglactin 910, glycolide/lactide copolymer and polyglycolic acid braided sutures created adequate fluid connection between the electrodes and the hydrogel. With a view to application in skin inflammatory diseases and wound treatment, wound healing, slow and controlled delivery of dexamethasone 21-phosphate disodium salt (DSP), an anti-inflammatory prodrug, was achieved using medical surgicryl PGA absorbable suture. After 2 hours of electrical stimulation, still 81.1% of the drug loaded was encapsulated within the hydrogel.
Low cost and open source multi-fluorescence imaging system for teaching and research in biology and bioengineering (2017)

Abstract The advent of easy-to-use open source microcontrollers, off-the-shelf electronics and customizable manufacturing technologies has facilitated the development of inexpensive scientific devices and laboratory equipment. In this study, we describe an imaging system that integrates low-cost and open-source hardware, software and genetic resources. The multi-fluorescence imaging system consists of readily available 470 nm LEDs, a Raspberry Pi camera and a set of filters made with low cost acrylics. This device allows imaging in scales ranging from single colonies to entire plates. We developed a set of genetic components (e.g. promoters, coding sequences, terminators) and vectors following the standard framework of Golden Gate, which allowed the fabrication of genetic constructs in a combinatorial, low cost and robust manner. In order to provide simultaneous imaging of multiple wavelength signals, we screened a series of long stokes shift fluorescent proteins that could be combined with cyan/green fluorescent proteins. We found CyOFP1, mBeRFP and sfGFP to be the most compatible set for 3-channel fluorescent imaging. We developed open source Python code to operate the hardware to run time-lapse experiments with automated control of illumination and camera and a Python module to analyze data and extract meaningful biological information. To demonstrate the potential application of this integral system, we tested its performance on a diverse range of imaging assays often used in disciplines such as microbial ecology, microbiology and synthetic biology. We also assessed its potential for STEM teaching in a high school environment, using it to teach biology, hardware design, optics, and programming. Together, these results demonstrate the successful integration of open source hardware, software, genetic resources and customizable manufacturing to obtain a powerful, low cost and robust system for STEM education, scientific research and bioengineering. All the resources developed here are available under open source licenses.
Preferred and maximally acceptable color gamut for reproducing natural image content (2010)

Abstract— With the development of wide‐gamut display technology, the need is clear for understanding the required size and shape of color gamut from the viewers' perspective. To that end, experiments were conducted to explore color‐gamut requirements based on viewers' preferred level of chroma enhancement of standard‐gamut images. Chroma preferences were measured for multiple hues using single‐hue images, and a corresponding hue‐dependent preferred chroma enhancement was successfully applied to natural, multi‐hue images. The multi‐hue images showed overall success, though viewers indicated that reds could be decreased even further in colorfulness, and yellows could be increased, which may argue in favor of multi‐primary displays. Viewer preferences do vary within the population, primarily in overall chroma level, and the differences can be largely accounted for with a single parameter for chroma‐level adjustment that includes the preferred hue dependence. Image content dependencies were also found, but they remain too complex to model. The hue‐dependent chroma preference results can be applied to display design and color‐enhancement algorithms.
Two isozymes of clavaminate synthase central to clavulanic acid formation: cloning and sequencing of both genes from Streptomyces clavuligerus (1992)

Clavaminate synthase (CS) is an alpha-ketoglutarate-dependent oxygenase central to the biosynthesis of clavulanic acid, a potent inhibitor of beta-lactamases. CS catalyzes the oxidative cyclization/desaturation of proclavaminic acid to clavaminic acid in a two-step process involving the intermediacy of dihydroclavaminic acid [Salowe, S. P., Krol, W. J., Iwata-Reuyl, D., & Townsend, C. A. (1991) Biochemistry 30, 2281-2292]. During the purification of CS to homogeneity from Streptomyces clavuligerus [Salowe, S. P., Marsh, E. N., & Townsend, C. A. (1990) Biochemistry 29, 6499-6508], two forms of the enzyme capable of carrying out the complete reaction having very similar molecular weights and kinetic properties were isolated by Mono-Q chromatography. The gene for each has been cloned, sequenced, and found to be significantly homologous (87% identity). The two genes so isolated, cs1 and cs2, have open reading frames of 975 and 978 nucleotides, respectively, encoding proteins of M(r) 35,347 and 35,774. These genes are located in different loci of the genome separated by > 20 kbp. This separation is large for a natural product biosynthetic pathway in bacteria where gene duplication and limited divergence are typically observed to occur within narrower confines of a gene cluster. Sequence comparisons made between cs1/cs2 and other genes encoding iron-dependent proteins involved in penicillin and cephalosporin biosynthesis in the same organism show minimal homology. Further sequence alignments made to other non-heme iron oxygenases reveal unexpected dissimilarity within the alpha-ketoglutarate-dependent class itself. The limited data available suggests evolutionary convergence among these proteins.
Maximum power point tracking method under partial shading conditions (2012)

The occurrence of multiple local maximum due to partial shading conditions poses a challenge to MPPT techniques. Scanning approach is able to search for global MPPs but incurs power loss during the scanning. This paper presents a strategy that reduces the scanning period by skipping parts of the voltage range. The operating principle is based on the simplified analysis of the PV characteristics. In order to account for rapidly changing atmospheric conditions, real-time MPPT technique is employed between the scanning intervals. Boost converter is developed to experimentally verify the proposed MPPT method under various partial shading conditions.
Techniques in Gastrointestinal Endoscopy (2013)

Flexible endoscopy has become an increasingly important skill for gastrointestinal (GI) surgeons, and there is no setting more important than the intraoperative setting for surgeons to employ endoscopic techniques during the course of surgical procedures performed on the GI tract. Endoscopic confirmation of pathology before initiating surgery, intraoperative anastomotic evaluation and margin assessment, and combined laparoscopic-endoscopic approaches to patient care are just a few examples emphasizing the need for surgeons to perform GI endoscopy as a routine adjunct to foregut, bariatric, and colorectal procedures. Intraoperative endoscopy adds value in the operating room and holds the promise of improved surgical outcomes by providing useful clinical information important to point-of-service decision making that allows surgeons to address technical concerns before they manifest as postoperative complications.
Arne Naess and Empirical Semantics (2011)

ABSTRACT This article focuses on Arne Naess's work in the philosophy of language, which he began in the mid-1930s and continued into the 1960s. This aspect of his work is nowadays relatively neglected, but it deserves to be revisited. Firstly, it is intrinsically interesting to the history of analytic philosophy in the twentieth century, because Naess questioned some of the established philosophical methodologies and assumptions of his day. Secondly, it suggests a compelling but unacknowledged intellectual pedigree for some recent developments in linguistics. Naess's philosophy of language developed from his reaction against logical positivism, in particular against what he saw as its unempirical assumptions about language. He went on to establish “empirical semantics”, in which the study of language was based on real-life linguistic data, drawn primarily from questionnaires issued to philosophically naïve subjects. He also experimented with methods for “occurrence analysis”, but concluded that the collection and analysis of sufficiently large bodies of naturally-occurring data was impractical. Empirical semantics was not well received by Naess's philosophical contemporaries. It was also seen as being at odds with contemporary trends in linguistics. However, some present-day branches of linguistics have striking resonances with Naess's work from as much as seventy years ago. In sociolinguistics, questionnaires have become an established means of collecting linguistic data. In corpus linguistics, advances in technology have made Naess's unobtainable ideal of “occurrence analysis” a viable methodology. Some of the principal conclusions reached as a result of this methodology are strikingly similar to Naess's own findings.
Verifying the safety of lane change maneuvers of self-driving vehicles based on formalized traffic rules (2017)

Validating the safety of self-driving vehicles requires an enormous amount of testing. By applying formal verification methods, we can prove the correctness of the vehicles' behavior, which at the same time reduces remaining risks and the need for extensive testing. However, current safety approaches do not consider liabilities of traffic participants if a collision occurs. Utilizing formalized traffic rules to verify motion plans allows this problem to be solved. We present a novel approach for verifying the safety of lane change maneuvers, using formalized traffic rules according to the Vienna Convention on Road Traffic. This allows us to provide additional guarantees that if a collision occurs, the self-driving vehicle is not responsible. Furthermore, we consider misbehavior of other traffic participants during lane changes and propose feasible solutions to avoid or mitigate a potential collision. The approach has been evaluated using real traffic data provided by the NGSIM project as well as simulated lane changes.
High Incidence of Anticytomegalovirus Drug Resistance Among D+R− Kidney Transplant Recipients Receiving Preemptive Therapy (2011)

Anti-cytomegalovirus (CMV) prophylaxis is recommended in D+R- kidney transplant recipients (KTR), but is associated with a theoretical increased risk of developing anti-CMV drug resistance. This hypothesis was retested in this study by comparing 32 D+R- KTR who received 3 months prophylaxis (valganciclovir) with 80 D+R- KTR who received preemptive treatment. The incidence of CMV infections was higher in the preemptive group than in the prophylactic group (60% vs. 34%, respectively; p = 0.02). Treatment failure (i.e. a positive DNAemia 8 weeks after the initiation of anti-CMV treatment) was more frequent in the preemptive group (31% vs. 3% in the prophylactic group; p = 0.001). Similarly, anti-CMV drug resistance (UL97 or UL54 mutations) was also more frequent in the preemptive group (16% vs. 3% in the prophylactic group; p = 0.05). Antiviral treatment failures were associated with anti-CMV drug resistance (p = 0.0001). Patients with a CMV load over 5.25 log(10) copies/mL displayed the highest risk of developing anti-CMV drug resistance (OR = 16.91, p = 0.0008). Finally, the 1-year estimated glomerular filtration rate was reduced in patients with anti-CMV drug resistance (p = 0.02). In summary, preemptive therapy in D+R- KTR with high CMV loads and antiviral treatment failure was associated with a high incidence of anti-CMV drug resistance.
A seed mixture increases dominance of resistance to Bt cotton in Helicoverpa zea (2015)

Widely grown transgenic crops producing insecticidal proteins from Bacillus thuringiensis (Bt) can benefit agriculture, but adaptation by pests threatens their continued success. Refuges of host plants that do not make Bt toxins can promote survival of susceptible insects and delay evolution of resistance, particularly if resistance is inherited as a recessive trait. However, data have been lacking to compare the dominance of resistance when Bt and non-Bt seeds are planted in random mixtures versus separate blocks. Here we report results from greenhouse experiments with transgenic cotton producing Bt toxin Cry1Ac and the bollworm, Helicoverpa zea, showing that the dominance of resistance was significantly higher in a seed mixture relative to a block of Bt cotton. The proportion of larvae on non-Bt cotton plants in the seed mixture was also significantly higher than expected under the null hypothesis of random distribution. In simulations based on observed survival, resistance evolved 2- to 4.5-fold faster in the seed mixture relative to separate blocks of Bt and non-Bt cotton. These findings support previous modelling results indicating that block refuges may be more effective than seed mixtures for delaying resistance in pests with mobile larvae and inherently low susceptibility to the toxins in Bt crops.
Method for mapping Hg0 emissions from gold shops in artisanal and small-scale gold mining communities (2020)

Gold shops in artisanal and small-scale gold mining communities represent major point sources of airborne mercury pollution. Concentrations of elemental mercury (Hg<sup>0</sup>) emitted by these shops can be determined using a portable atomic absorbance spectrometer (AAS) with Zeeman correction. These measured Hg<sup>0</sup> concentrations can then be correlated to position as determined by a hand-held GPS unit, and the resulting data mapped using a Geographic Information System (GIS). A detailed method for obtaining and analyzing data collected near gold shops in Mazuko, Peru is provided. Maps generated using this method were employed to identify point sources of Hg<sup>0</sup> contamination originating from gold shops in ASGM communities and were shared with local city managers to assist in urban planning.•A detailed method is provided to collect and process data, ultimately generating a map that allows for the screening of a community to identify point sources of Hg<sup>0</sup> contamination.•Raw data is provided, as well as a video detailing data processing and mapping using a common spreadsheet program and an open-source GIS.•The generated map can be used for determining areas where people may be exposed to elevated Hg<sup>0</sup> concentrations and/or occupational mercury vapor exposure, targeted enforcement, or outreach to limit Hg<sup>0</sup> pollution.
Electroactive materials for organic electronics: preparation strategies, structural aspects and characterization techniques (2010)

This critical review discusses specific chemical and physicochemical requirements which must be met for organic compounds to be considered as promising materials for applications in organic electronics. Although emphasis is put on molecules and macromolecules suitable for fabrication of field effect transistors (FETs), a large fraction of the discussed compounds can also be applied in other organic or hybrid (organic-inorganic) electronic devices such as photodiodes, light emitting diodes, photovoltaic cells, etc. It should be of interest to chemists, physicists, material scientists and electrical engineers working in the domain of organic electronics (423 references).
On the optimality of multiantenna broadcast scheduling using zero-forcing beamforming (2006)

Although the capacity of multiple-input/multiple-output (MIMO) broadcast channels (BCs) can be achieved by dirty paper coding (DPC), it is difficult to implement in practical systems. This paper investigates if, for a large number of users, simpler schemes can achieve the same performance. Specifically, we show that a zero-forcing beamforming (ZFBF) strategy, while generally suboptimal, can achieve the same asymptotic sum capacity as that of DPC, as the number of users goes to infinity. In proving this asymptotic result, we provide an algorithm for determining which users should be active under ZFBF. These users are semiorthogonal to one another and can be grouped for simultaneous transmission to enhance the throughput of scheduling algorithms. Based on the user grouping, we propose and compare two fair scheduling schemes in round-robin ZFBF and proportional-fair ZFBF. We provide numerical results to confirm the optimality of ZFBF and to compare the performance of ZFBF and proposed fair scheduling schemes with that of various MIMO BC strategies.
Age-Dependent Levels of Select Immunological Mediators in Sera of Healthy Children (1998)

Serum cytokine levels were measured in 275 healthy children of different ages (3 to 17 years). Interleukin-1 receptor antagonist (IL-1RA), soluble IL-2R (sIL-2R) (sCD25), IL-6, IL-8, tumor necrosis factor alpha (TNF-alpha), soluble TNF receptor type II (sTNF-RII) (sCD120b), gamma interferon (IFN-gamma), soluble intercellular adhesion molecule 1 (sICAM-1) (sCD54), soluble E selectin (sE-selectin) (ELAM-1; sCD62E), sCD14, and neopterin were measured with commercial test kits. The mean levels of IL-1RA, sIL-2R, TNF-alpha, sICAM-1, sE-selectin, and sCD14 were higher than in healthy adults. In contrast, IFN-gamma and IL-8 were hardly detectable in children and thereby significantly lower than in adults. In the case of TNF-alpha, sICAM-1, sE selectin, and sCD14, there was a high interindividual variability, apparently unrelated to disease. The profiles of some cytokines, i.e., IL-1RA, IL-6, and TNF-alpha, showed age-related increases that overlapped with known patterns of physical growth. Of note, sIL-2R and sE-selectin instead declined with time. Because of the remarkable age-dependent variability in healthy pediatric subjects, disease-related changes, as well as therapy-dependent alterations, should be considered with caution.
Intraluminal MRI Probe Using Small Size Variable Capacitor (2017)

SUMMARY An intraluminal magnetic resonance imaging (MRI) probe holds promise to achieve a higher resolution image of a small pathological lesion than conventional external probes. Such an intraluminal probe requires precise resonant frequency tuning to 63.865 MHz and impedance matching to 50 Ω, if used for instance in a 1.5‐T scanner. Tuning and matching have to be performed after inserted into the subject body as electric permittivity varies according to the tissue location. Thus, in this study, a novel intraluminal MRI probe, which can be tuned and matched remotely by voltage‐controlled, MOSFET‐type variable capacitors was developed and fabricated. The imaging capability and signal‐to‐noise ratio (SNR) was evaluated in an agar phantom.
Indolequinone Antitumor Agents:  Correlation between Quinone Structure and Rate of Metabolism by Recombinant Human NAD(P)H:Quinone Oxidoreductase. Part 2 (2001)

A series of indolequinones bearing various functional groups has been synthesized, and the effects of substituents on the metabolism of the quinones by recombinant human NAD(P)H:quinone oxidoreductase (NQO1) were studied. Indolequinones were selected for study on the basis of the X-ray crystal structure of the human enzyme, and were designed to probe the effect of substituents particularly at N-1. Metabolism of the quinones by NQO1 revealed that, in general, compounds with electron-withdrawing groups at the indole 3-position were among the best substrates, and that groups larger than methyl at N-1 are clearly tolerated. Compounds with a leaving group at the 3-indolyl methyl position generally inactivated the enzyme. The toxicity toward human colon carcinoma cells with either no detectable activity (BE-WT) or high NQO1 activity (BE-NQ) was also studied in representative quinones. The most toxic compounds were those with a leaving group at the C-3 position; these compounds were 1.1-5.3-fold more toxic to the BE-NQ than the BE-WT cells.