gebhart/patrepeval huggingface dataset:
Electronic structure differences between H2-, Fe-, Co-, and Cu-phthalocyanine highly oriented thin films observed using NEXAFS spectroscopy (2013)

Phthalocyanines, a class of macrocyclic, square planar molecules, are extensively studied as semiconductor materials for chemical sensors, dye-sensitized solar cells, and other applications. In this study, we use angular dependent near-edge x-ray absorption fine structure (NEXAFS) spectroscopy as a quantitative probe of the orientation and electronic structure of H2-, Fe-, Co-, and Cu-phthalocyanine molecular thin films. NEXAFS measurements at both the carbon and nitrogen K-edges reveal that phthalocyanine films deposited on sapphire have upright molecular orientations, while films up to 50 nm thick deposited on gold substrates contain prostrate molecules. Although great similarity is observed in the carbon and nitrogen K-edge NEXAFS spectra recorded for the films composed of prostrate molecules, the H2-phthalocyanine exhibits the cleanest angular dependence due to its purely out-of-plane π* resonances at the absorption onset. In contrast, organometallic-phthalocyanine nitrogen K-edges have a small in-plane resonance superimposed on this π* region that is due to a transition into molecular orbitals interacting with the 3dx(2)-y(2) empty state. NEXAFS spectra recorded at the metal L-edges for the prostrate films reveal dramatic variations in the angular dependence of specific resonances for the Cu-phthalocyanines compared with the Fe-, and Co-phthalocyanines. The Cu L3,2 edge exhibits a strong in-plane resonance, attributed to its b1g empty state with dx(2)-y(2) character at the Cu center. Conversely, the Fe- and Co- phthalocyanine L3,2 edges have strong out-of-plane resonances; these are attributed to transitions into not only b1g (dz(2)) but also eg states with dxz and dyz character at the metal center.
High-resolution and energy-filtered TEM of the interface between hematite and ilmenite exsolution lamellae: Relevance to the origin of lamellar magnetism (2003)

The interfaces between fine-scale exsolution lamellae of hematite and ilmenite from an igneous rock in Rogaland, Norway have been studied by conventional transmission electron microscopy (TEM), high-resolution TEM, and energy-filtered TEM (EFTEM), to investigate the lamellar magnetism hypothesis for the origin of the unusual magnetic properties of this rock. Very fine hematite and ilmenite lamellae, less than 50 nm in length and parallel to (001) of their host, were abundant throughout the hemo-ilmenite sample. Dark-field and EFTEM observations indicated the hematite and ilmenite have very sharp structural and compositional interfaces with their hosts. The interfaces between the coarse hematite and ilmenite lamellae (length >1 μm) and their hosts have some interface dislocations to relieve elastic coherency strain. On the other hand, very fine lamellae (length <50 nm) have no interface dislocations and are perfectly coherent. The interface dislocations for lamellae on the order of 100 nm in length are distributed heterogeneously, and more than 80% of the length of the interfaces seen by TEM is dislocation free. Thus, most of the interfaces in the sample are coherent. These results are in accord with the predictions of Monte Carlo simulations of the exsolution process (Harrison and Becker 2001) and with the hypothesis that coherent and sharp structural and compositional interfaces are the origin of lamellar magnetism (Robinson et al. 2002).
VLSI implementation of discrete wavelet transform (1996)

This paper presents a VLSI implementation of discrete wavelet transform (DWT). The architecture is simple, modular, and cascadable for computation of one or multidimensional DWT. It comprises of four basic units: input delay, filter, register bank, and control unit. The proposed architecture is systolic in nature and performs both high- and low-pass coefficient calculations with only one set of multipliers. In addition, it requires a small on-chip interface circuitry for interconnection to a standard communication bus. A detailed analysis of the effect of finite precision of data and wavelet filter coefficients on the accuracy of the DWT coefficients is presented. The architecture has been simulated in VLSI and has a hardware utilization efficiency of 87.5%. Being systolic in nature, the architecture can compute DWT at a data rate of N/spl times/10/sup 6/ samples/s corresponding to a clock speed of N MHz.
CONTROL CHARACTERISTICS OF SINGLE-SWITCH, THREE-PHASE BUCK RECTIFIERS (1998)

A pulse frequency modulation control method for single-switch three-phase buck rectifiers is comprehensively studied in this paper The proposed pulse frequency control method leads the three-phase buck rectifier to a high performance system that can draw the nearly sinusoidal input-line currents The simulated and experimental results demonstrate that the system provides low total harmonic distortion of the input-line currents, high-power factor, and good output voltage regulation.
Abstract 5097: Co-targeting of convergent, switchable nucleotide biosynthetic pathways induces synthetic lethality in leukemia (2014)

Abstract Pharmacological targeting of metabolic processes in cancer must overcome redundancy in biosynthetic pathways. Deoxycytidine triphosphate (dCTP) can be produced by the de novo pathway (DNP) via ribonucleotide reductase, and/or by the nucleoside salvage pathway (NSP) via deoxycytidine kinase (dCK). The NSP's role in supporting tumor DNA replication is unknown. Here we show that survival of acute lymphoblastic leukemia cells upon inhibition of DNP-dependent dCTP production requires a functional NSP. Thus, DNP inhibition triggers a compensatory switch to NSP-mediated dCTP production. This metabolic switch can be imaged by positron emission tomography, thereby providing a non-invasive method for monitoring pharmacological targeting of the DNP. Blocking both DNP dCTP production using thymidine and the switch to NSP using a new dCK inhibitor induces replication stress overload and synthetic lethality in leukemia cells, without significant host toxicity. This co-targeting therapy may be broadly applicable against other malignancies characterized by high levels of replication stress. Citation Format: Caius G. Radu, David A. Nathanson, Johannes Czernin. Co-targeting of convergent, switchable nucleotide biosynthetic pathways induces synthetic lethality in leukemia. [abstract]. In: Proceedings of the 105th Annual Meeting of the American Association for Cancer Research; 2014 Apr 5-9; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2014;74(19 Suppl):Abstract nr 5097. doi:10.1158/1538-7445.AM2014-5097
Asymmetric Methanolysis of Cyclic meso-Anhydrides with Tripodal 2,6-trans-1,2,6-Trisubstituted Piperidine as Chiral Amine Catalyst (2007)

An optically active tripodal amine, (2S,6S)-2,6-bis(o-hydroxyphenyl)-1-(2-pyridylmethyl)piperidine, was proven to be a potent chiral catalyst (1-5 mol%) for methanolytic asymmetric desymmetrization of cyclic meso-anhydrides to hemiesters. A good level of enantioselectivities (up to 81% ee) was achieved for various substrates, some of which were reported to be poor substrates for methanolysis using known chiral amines as catalysts.
Explainable automated pain recognition in cats (2023)

Manual tools for pain assessment from facial expressions have been suggested and validated for several animal species. However, facial expression analysis performed by humans is prone to subjectivity and bias, and in many cases also requires special expertise and training. This has led to an increasing body of work on automated pain recognition, which has been addressed for several species, including cats. Even for experts, cats are a notoriously challenging species for pain assessment. A previous study compared two approaches to automated 'pain'/'no pain' classification from cat facial images: a deep learning approach, and an approach based on manually annotated geometric landmarks, reaching comparable accuracy results. However, the study included a very homogeneous dataset of cats and thus further research to study generalizability of pain recognition to more realistic settings is required. This study addresses the question of whether AI models can classify 'pain'/'no pain' in cats in a more realistic (multi-breed, multi-sex) setting using a more heterogeneous and thus potentially 'noisy' dataset of 84 client-owned cats. Cats were a convenience sample presented to the Department of Small Animal Medicine and Surgery of the University of Veterinary Medicine Hannover and included individuals of different breeds, ages, sex, and with varying medical conditions/medical histories. Cats were scored by veterinary experts using the Glasgow composite measure pain scale in combination with the well-documented and comprehensive clinical history of those patients; the scoring was then used for training AI models using two different approaches. We show that in this context the landmark-based approach performs better, reaching accuracy above 77% in pain detection as opposed to only above 65% reached by the deep learning approach. Furthermore, we investigated the explainability of such machine recognition in terms of identifying facial features that are important for the machine, revealing that the region of nose and mouth seems more important for machine pain classification, while the region of ears is less important, with these findings being consistent across the models and techniques studied here.
AUTOMATIC PERFORMANCE ANALYSIS AND DYNAMIC TUNING OF DISTRIBUTED APPLICATIONS (2003)

The classical way of tuning parallel/distributed applications is based on the analysis of the monitoring information obtained from an execution of the application. However, this "measure and modify" approach is not feasible when the applications have a dynamic behavior. In this case, another approach is required to accomplish performance expectations. This paper presents a solution based on the dynamic tuning approach that addresses these issues. In this approach, an application is monitored, its performance bottlenecks are detected and the application is modified automatically during the execution, without stopping, recompiling or re-running it. The introduced modifications adapt the behavior of the application to dynamic variations.
LOCAL INFLAMMATORY RESPONSE AROUND DIFFUSION CHAMBERS CONTAINING XENOGRAFTS (1996)

Immunoisolation of xenogeneic pancreatic islets within membrane-bound devices has been proposed as an approach to cure diabetes. We examined the local response to implanted xenografts and allografts in comparison with isografts in diffusion chambers with 0.4-microm pore membranes when implanted into epididymal fat pads of rats. These membranes prevented host cell entry into the device but did not prevent passage of large molecules such as IgG and IgM. Well-differentiated allogeneic tissues (Sprague-Dawley rat embryonic lung implanted into Lewis rats) survived for 1 year when implanted in intact devices, but similar tissues were destroyed within 3 weeks when implanted within devices with holes poked in the membrane to allow host cell contact. In contrast, xenografts (CF1 mouse embryonic lung implanted into Lewis rats) were destroyed within 3 weeks even when implanted in devices with intact membranes. The death of the xenogeneic tissues was accompanied by a severe local accumulation of inflammatory cells and a decrease in local vascularization. When isogeneic tissues (Lewis rat embryonic lung implanted in Lewis rats) were mixed with xenogeneic tissues, a local inflammatory response occurred and both iso- and xenogeneic tissues were destroyed within 5 weeks. These results suggest the possibility that xenografts are killed by local accumulation of inflammatory cells, perhaps mediated by the release of antigens from the tissues within the device and presentation by an indirect pathway. The observation that the local response to xenografts is sufficient to kill isografts complicates issues of immunoprotection, suggesting that successful immunoisolation will require membranes that not only provide protection of the encapsulated tissues from the host immune system but also have properties that diminish the release of xenogeneic antigens.
EFFECT OF FUEL IMPURITIES ON FUEL CELL PERFORMANCE AND DURABILITY (2010)

A fuel cell is an electrochemical energy conversion device that produces electricity during the combination of hydrogen and oxygen to produce water. Proton exchange membranes fuel cells are favored for portable applications as well as stationary ones due to their high power density, low operating temperature, and low corrosion of components. In real life operation, the use of pure fuel and oxidant gases results in an impractical system. A more realistic and cost efficient approach is the use of air as an oxidant gas and hydrogen from hydrogen carriers (i.e., ammonia, hydrocarbons, hydrides). However, trace impurities arising from different hydrogen sources and production increases the degradation of the fuel cell. These impurities include carbon monoxide, ammonia, sulfur, hydrocarbons, and halogen compounds. The International Organization for Standardization (ISO) has set maximum limits for trace impurities in the hydrogen stream; however fuel cell data is needed to validate the assumption that at those levels the impurities will cause no degradation. This report summarizes the effect of selected contaminants tested at SRNL at ISO levels. Runs at ISO proposed concentration levels show that model hydrocarbon compound such as tetrahydrofuran can cause serious degradation. However, the degradation is only temporary as when the impurity is removed from the hydrogen stream the performance completely recovers. Other molecules at the ISO concentration levels such as ammonia don't show effects on the fuel cell performance. On the other hand carbon monoxide and perchloroethylene shows major degradation and the system can only be recovered by following recovery procedures.
OUTCOME AFTER REPLACEMENT OF FAILING HEARTMATE XVE LVAD WITH HEARTMATE II LVAD (2006)

Purpose: Long-term left ventricular assist devices (LVADs) are increasingly used to bridge end-stage heart failure patients to cardiac transplantation. In some cases, however, the LVAD requires replacement because of primary pump failure, infection, or other complications. Replacement with a new pump is the method of choice to provide further bridging to transplantation. New-generation nonpulsatile pumps can be used for this purpose. In comparison to pulsatile devices, nonpulsatile ones are smaller, are less noisy, [and have only a single moving part.] Methods: In 6 patients who had a failing HeartMate XVE pulsatile LVAD (Thoratec Corp., Pleasanton, Calif.) and indications for LVAD replacement, we replaced the failing device with a HeartMate II nonpulsatile LVAD (Thoratec). We analyzed mortality and morbidity data from the postoperative hospital stay and ensuing follow-up period. Results: In all 6 cases, the reason for LVAD removal was pump failure. Bleeding from the LVAD (n=1) and LVAD infection (n=1) were further complications. The median duration of support with the HeartMate XVE LVAD was 545±399 days. One patient had 2 replacement HeartMate XVEs before receiving the HeartMate II. Four patients were discharged home after a median hospital stay of 22±32 days and are awaiting transplantation. Conclusion: Use of the HeartMate II as a replacement device in patients with HeartMate XVE failure is a valuable option with an acceptable survival rate.
The selectivity of Cathepsin D Suggests an Involvement of the Enzyme in the Generation of T-cell Epitopes (1989)

The selectivity of cathepsin D, a mammalian intracellular aspartyl proteinase involved in the degradation of endocytosed proteins, was studied. For this purpose, several proteins of known primary structure were subjected to mild proteolysis by the enzyme, and the preferentially cleaved peptide bonds were identified. Comparison of the primary structures around these sites indicates that cathepsin D shows a strong preference for peptide bonds within a distinct sequence pattern of amino acids extending over 7 residues. In general, this pattern is most likely to occur within amphipathic alpha-helical structures. These findings and their possible implications are discussed together with additional evidence suggesting an important role for cathepsin D in the processing of protein antigens, an essential step for their recognition by T-cells. Accordingly, it is proposed that the proteolytic activity of cathepsin D is crucial in selecting processing sites and hence the location and structural context of T-cell epitopes for the majority of protein antigens.
Interaction of Collagen-Like Peptide Models of Asymmetric Acetylcholinesterase with Glycosaminoglycans:  Spectroscopic Studies of Conformational Changes and Stability (2000)

The effect of heparin on the conformation and stability of triple-helical peptide models of the collagen tail of asymmetric acetylcholinesterase expands our understanding of heparin interactions with proteins and presents an opportunity for clarifying the nature of binding of ligands to collagen triple-helix domains. Within the collagen tail of AChE, there are two consensus sequences for heparin binding of the form BBXB, surrounded by additional basic residues. Circular dichroism studies were used to determine the effect of the addition of increasing concentrations of heparin on triple-helical peptide models for the heparin binding domains, including peptides in which the basic residues within and surrounding the consensus sequence were replaced by alanine residues. The addition of heparin caused an increased triple-helix content with saturation properties for the peptide modeling the C-terminal site, while precipitation, with no increased helix content resulted from heparin addition to the peptide modeling the N-terminal site. The results suggest that the two binding sites with a similar triple-helical conformation have distinctive ways of interacting with heparin, which must relate to small differences in the consensus sequence (GRKGR vs GKRGK) and in the surrounding basic residues. Addition of heparin increased the thermal stability of all peptides containing the consensus sequence. Heparan sulfate produced conformational and stabilization effects similar to those of heparin, while chondroitin sulfate led to a cloudy solution, loss of circular dichroism signal, and a smaller increase in thermal stability. Thus, specificity in both the sequence of the triple helix and the type of glycosaminoglycan is required for this interaction.
Flame‐retardancy and anti‐dripping effects of intumescent flame retardant incorporating montmorillonite on poly(lactic acid) (2009)

Abstract In the present study, the effects of intumescent flame retardant (IFR) incorporating organically modified montmorillonite (O‐MMT) on the flame retardancy and melt stability of PLA were investigated. The flame‐retardant PLA was prepared using a twin‐screw extruder and a two roll mill. Then, the influence of IFR and MMT on flame retardancy and melt stability was thoroughly investigated by means of limiting oxygen index (LOI), vertical burning test, thermogravimetric analysis, scanning electronic microscopy, melt flow index (MFI), and parallel plate rheological experiments. The experimental results show that the IFR system in combination with MMT has excellent fire retardancy, i.e. the sample could achieve a UL94 V‐0 rating and LOI value increases from 20.1 for pristine PLA to 27.5 for the flame‐retarded PLA. MFI and rheological measurement indicate that O‐MMT significantly enhances the melt stability and suppresses the melt dripping. Copyright © 2009 John Wiley &amp; Sons, Ltd.
Cooperative Interception of Neuronal Apoptosis by BCL‐2 and BAG‐1 Expression: Prevention of Caspase Activation and Reduced Production of Reactive Oxygen Species (1997)

Neuronally differentiated PC12 cells undergo synchronous apoptosis when deprived of nerve growth factor (NGF). Here we show that NGF withdrawal induces actinomycin D- and cycloheximide-sensitive caspase (ICE-like) activity. The peptide inhibitor of caspase activity, N-acetyl-Asp-Glu-Val-Asp-aldehyde, was more potent than acetyl-Tyr-Val-Ala-Asp-chloromethyl ketone in preventing NGF withdrawal-induced apoptosis, suggesting an important role for caspase-3 (CPP32)-like proteases. We observed a peak of reactive oxygen species (ROS) 6 h after NGF withdrawal. ROS appear to be required for apoptosis, because cell death is prevented by the free radical spin trap, N-tert-butyl-alpha-phenylnitrone, and the antioxidant, N-acetylcysteine. ROS production was blocked by actinomycin D, cycloheximide, and caspase protease inhibitors, suggesting that ROS generation is downstream of new mRNA and protein synthesis and activation of caspases. Forced expression of either BCL-2 or the BCL-2-binding protein BAG-1 blocked NGF withdrawal-induced apoptosis, activation of caspases, and ROS generation, showing that they function upstream of caspases. Coexpression of BCL-2 and BAG-1 was more protective than expression of either protein alone.
Ultrasensitivity in biochemical systems controlled by covalent modification. Interplay between zero-order and multistep effects. (1984)

A previous analysis of covalent modification systems (Goldbeter, A., and Koshland, D. E., Jr. (1981) Proc. Natl. Acad. Sci. U. S. A. 78, 6840-6844) showed that steep transitions in the amount of modified protein can occur when the converter enzymes are saturated by their protein substrate. This "zero-order ultrasensitivity" can further be amplified when an effector acts at more than one step in a monocyclic or multicyclic cascade of covalent modification. We analyze the limitations of the latter "multistep ultrasensitivity" and show how it can combine with the zero-order effect to enhance the sensitivity of biochemical systems controlled by covalent modification.
Coenzyme Q10 and nicotinamide block striatal lesions produced by the mitochondrial toxin malonate (1994)

A potential mechanism of neuronal injury in neurodegenerative diseases is a defect in energy metabolism that may lead to slow excitotoxic neuronal death. Consistent with this possibility, we showed that specific inhibitors of the electron transport chain produce excitotoxic lesions in vivo. In the present study we examined whether agents that improve energy metabolism can block lesions produced by the mitochondrial toxin malonate. Striatal lesions produced by the complex II inhibitor malonate were blocked in a dose-dependent manner by oral pretreatment with coenzyme Q10. Administration of nicotinamide by Alzet pump for 1 week attenuated malonate-induced lesions, but riboflavin had no effect. Administration of nicotinamide intraperitoneally just prior to and following induction of the lesions produced dose-dependent neuroprotection. A combination of coenzyme Q10 with nicotinamide was more effective than either compound alone, as shown by both lesion size and magnetic resonance imaging in vivo. Both coenzyme Q10 and nicotinamide blocked adenosine triphosphate depletions and lactate increases. These results confirm that mitochondrial toxins produce striatal excitotoxic lesions by a mechanism involving energy depletion in vivo. Furthermore, they suggest novel neuroprotective strategies that may be useful in the treatment of both mitochondrial encephalopathies and neurodegenerative diseases.