gebhart/patrepeval huggingface dataset:
Mechanistic Studies of the Transfer Dehydrogenation of Cyclooctane Catalyzed by Iridium Bis(phosphinite)p-XPCP Pincer Complexes (2004)

Reaction of bis(phosphinite) PCP iridium pincer complexes (p-XPCP)IrHCl (5a-f) [X = MeO (5a), Me (5b), H (5c), F (5d), C(6)F(5) (5e), Ar(F)(= 3,5-bis(trifluoromethyl)phenyl) (5f)] with NaOtBu in neat cyclooctane (COA) generates 1:1 mixtures of the respective (p-XPCP)IrH(2) complexes 4a-f and the cyclooctene (COE) olefin complexes (p-XPCP)Ir(COE) (6a-f) at 23 degrees C. At higher temperatures, complexes 4 and 6 are equilibrated because of the degenerate transfer dehydrogenation of COA with free COE (6 + COA right harpoon over left harpoon 4 + 2COE), as was shown by temperature-dependent equilibrium constants and spin saturation transfer experiments at 80 degrees C. At this temperature, the COE complexes 6 exchange with free COE on the NMR time scale with the more electron-deficient complexes 6 exchanging COE faster. The exchange is dissociative and zero order in [COE]. Further analysis reveals that the stoichiometric hydrogenation of COE by complex 4f, and thus the separated back reaction 4f + 2COE --> 6f + COA proceeds at temperatures as low as -100 degrees C with the intermediacy of two isomeric complexes (p-Ar(F)PCP)Ir(H)(2)(COE) (8f, 8f'). COE deuteration with the perdeuterated complex 4f-d(38) at -100 degrees C results in hydrogen incorporation into the hydridic sites of complexes 8f,8f'-d(38) but not in the hydridic sites of complex 4f-d(38), thus rendering COE migratory insertion in complexes 8f,8f' reversible and COE coordination by complex 4f rate-determining for the overall COE deuteration.
Regulation of BAD by cAMP-dependent protein kinase is mediated via phosphorylation of a novel site, Ser155 (2000)

The interaction of BAD (Bcl-2/Bcl-XL-antagonist, causing cell death) with Bcl-2/Bcl-XL is thought to neutralize the anti-apoptotic effects of the latter proteins, and may represent one of the mechanisms by which BAD promotes apoptosis. A variety of survival signals are reported to induce the phosphorylation of BAD at Ser112 or Ser136, triggering its dissociation from Bcl-2/Bcl-XL. Ser136 is thought to be phosphorylated by protein kinase B (PKB, also called Akt), which is activated when cells are exposed to agonists that stimulate phosphatidylinositol 3-kinase (PI3K). In contrast, Ser112 is reported to be phosphorylated by mitogen-activated protein (MAP) kinase-activated protein kinase-1 (MAPKAP-K1, also called RSK) and by cAMP-dependent protein kinase (PKA). Here we identify Ser155 as a third phosphorylation site on BAD. We find that Ser155 is phosphorylated preferentially by PKA in vitro and is the only residue in BAD that becomes phosphorylated when cells are exposed to cAMP-elevating agents. The phosphorylation of BAD at Ser155 prevents it from binding to Bcl-XL and promotes its interaction with 14-3-3 proteins. We also provide further evidence that MAPKAP-K1 mediates the phosphorylation of Ser112 in response to agonists that activate the classical MAP kinase pathway. However insulin-like growth factor 1, a potent activator of PI3K and PKB does not increase the phosphorylation of Ser136 in BAD-transfected HEK-293 cells, and nor is the basal level of Ser136 phosphorylation suppressed by inhibitors of PI3K.
Core–shell Si1−xGex nanowires with controlled structural defects for phonon scattering enhancement (2014)

Core–shell Si<sub>1−x</sub>Ge<sub>x</sub> alloy nanowires can suppress the phonon propagation without reducing the electrical conductivity.
CONCLUSION (2005)

This concluding chapter offers a balance sheet for this experience and what it reveals about slavery, secession, the Southern war effort, and the connections binding these things together. It suggests the significance of this episode for subsequent Southern history — and especially for the Southern elite's attempt to regain its footing in a postwar, post-slavery nation.
Multimaterial Magneto-Structural Topology Optimization of Wound Field Synchronous Machine Rotors (2020)

A combined magneto-structural topology optimization approach based on the solid isotropic with material penalization method is proposed for wound field synchronous machines (WFSMs) to optimally distribute multiple materials including electrical steel, copper, and air in a rotor design domain. Magnetic topology optimization is simultaneously combined with structural topology optimization to ensure rotors, which are mechanically feasible. A topology optimization approach does not require the use of a geometric template where dimensions are controlled by parameters. Example designs of salient pole WFSM rotors are used to demonstrate the proposed technique. The proposed topology optimization technique is compared with a multiobjective optimization with the rotor geometry defined by a geometric template. For the same torque level the topology optimized rotor has lower copper losses.
Sequence Analysis of the ank Gene of Granulocytic Ehrlichiae (2000)

The ank gene of the agent of human granulocytic ehrlichiosis (HGE) codes for a protein with a predicted molecular size of 131.2 kDa that is recognized by serum from both dogs and humans infected with granulocytic ehrlichiae. As part of an effort to assess the phylogenetic relatedness of granulocytic ehrlichiae from different geographic regions and in different host species, the ank gene was PCR amplified and sequenced from a variety of sources. These included 10 blood specimens from patients with confirmed human granulocytic ehrlichiosis (three from New York, four from Wisconsin, two from Slovenia, and one from Sweden). Also examined was a canine granulocytic ehrlichia sample obtained from Minnesota, Ehrlichia equi from California, Ehrlichia phagocytophila from Sweden, and the granulocytic ehrlichia isolate USG3. The sequences showed a high level of homology (>95.5% identity), with the lowest homology occurring between a New York HGE agent and the Swedish E. phagocytophila. Several 3-bp deletions and a variable number of 51- and 81-bp direct repeats were noted. Although the North American HGE sequences showed the highest conservation (>98.1% identity), phylogenetic analyses indicated that these samples represent two separate clades, one including the three New York HGE samples and the USG3 strain and another with the Wisconsin HGE and Minnesota canine sequences. Two of the New York samples and the USG3 strain showed 100% identity over the entire 3,696-bp product. Likewise, three of the Wisconsin human samples and the Minnesota dog sample were identical (3,693 bp). Whereas phylogenetic analysis showed that the E. equi sequence was most closely related to the Upper Midwest samples, analysis of the repeat structures showed it to be more similar to the European samples. Overall, the genetic analysis based on the ank gene showed that the granulocytic ehrlichiae are closely related, appear to infect multiple species, and can be grouped into at least three different clades, two North American and one European.
Biosensor‐based characterisation of a single chain variable fragment with specificity to IgE as a candidate molecule for the therapy of IgE‐mediated diseases (2008)

Aim of our project is the development of an adsorber based on mAb12, a murine monoclonal anti‐IgE antibody, for the selective depletion of IgE by immunoadsorption to treat patients with severe manifestations of type I allergy. As the serum concentration of IgE (100ng/ml) is very low (100.000fold lower than IgG), adsorption of IgE requires rapid binding with high stability and affinity. MAb12, ScFv12 (a mAb12‐derived non‐anaphylactic single chain variable fragment) and recombinant α‐chain of the human high‐affinity IgE‐receptor, FcεRI, were immobilised on a BIACore C1 chip. Monoclonal human IgE was injected to determine affinities and rate constants. To investigate the impact of mAb12 and ScFv12 on the interaction of IgE with FcεRI, sequential injection of IgE and mAb12 or ScFv12 as well as injection after preincubation of IgE with mAb12 or ScFv12 into the cell containing immobilised α‐chain were carried out. 1 IgE associates with mAb12, ScFv12 and α‐chain with equally high affinities. Both mAb12 and ScFv12 stably bind to α‐chain‐bound IgE without actively detaching it from the receptor and either molecule prevents binding of IgE to immobilised α‐chain almost completely. Due to its highly affine and stable interaction with human IgE, we consider ScFv12 a candidate for the construction of an adsorber for the specific extracorporeal depletion of IgE. Supported by grant F1815 of the Austrian Science Fund (FWF). 1
Stabilization of Monomeric Tau Protein by All D-Enantiomeric Peptide Ligands as Therapeutic Strategy for Alzheimer’s Disease and Other Tauopathies (2023)

Alzheimer's disease and other tauopathies are the world's leading causes of dementia and memory loss. These diseases are thought to be caused by the misfolding and aggregation of the intracellular tau protein, ultimately leading to neurodegeneration. The tau protein is involved in a multitude of different neurodegenerative diseases. During the onset of tauopathies, tau undergoes structural changes and posttranslational modifications and aggregates into amyloid fibrils that are able to spread with a prion-like behavior. Up to now, there is no therapeutic agent which effectively controls or reverses the disease. Most of the therapeutics that were developed and underwent clinical trials targeted misfolded or aggregated forms of tau. In the current manuscript, we present the selection and characterization of two all D-enantiomeric peptides that bind monomeric tau protein with a low nanomolar K<sub>D</sub>, stabilize tau in its monomeric intrinsically disordered conformation, and stop the conversion of monomers into aggregates. We show that the effect of the two all D-enantiomeric peptides is strong enough to stop ongoing tau aggregation in vitro and is able to significantly reduce tau fibril assembly in cell culture. Both compounds may serve as new lead components for the development of therapeutic agents against Alzheimer's disease and other tauopathies.
A Neurotoxic Phosphoform of Elk-1 Associates with Inclusions from Multiple Neurodegenerative Diseases (2010)

Neurodegenerative diseases are characterized by a number of features including the formation of inclusions, early synaptic degeneration and the selective loss of neurons. Molecules serving as links between these shared features have yet to be identified. Identifying candidates within the diseased microenvironment will open up novel avenues for therapeutic intervention. The transcription factor Elk-1 resides within multiple brain areas both in nuclear and extranuclear neuronal compartments. Interestingly, its de novo expression within a single dendrite initiates neuronal death. Given this novel regionalized function, we assessed whether extranuclear Elk-1 and/or phospho-Elk-1 (pElk-1) protein might be associated with a spectrum of human neurodegenerative disease cases including Lewy body Disease (e.g. Parkinson's), Alzheimer's disease, and Huntington's Disease. We first determined the importance of Elk-1 post-translational modifications on its ability to initiate regionalized cell death. We next screened human cases from three major neurodegenerative diseases to look for remarkable levels of Elk-1 and/or pElk-1 protein as well as their association with inclusions characteristic of these diseases. We compared our findings to age-matched control cases. We find that the ability of Elk-1 to initiate regionalized neuronal death depends on a specific phosphosite, T417. Furthermore, we find that T417(+) Elk-1 uniquely associates with several types of inclusions present in cases of human Lewy body Disease, Alzheimer's disease, and Huntington's Disease. These results suggest a molecular link between the presence of inclusions and neuronal loss that is shared across a spectrum of neurodegenerative disease.
Supplementary Table 2 from <i>Intersex-like</i> (<i>IXL</i>) Is a Cell Survival Regulator in Pancreatic Cancer with 19q13 Amplification (2023)

Supplementary Table 2 from &lt;i&gt;Intersex-like&lt;/i&gt; (&lt;i&gt;IXL&lt;/i&gt;) Is a Cell Survival Regulator in Pancreatic Cancer with 19q13 Amplification
Sequence sorting in secondary storage (2002)

We investigate the I/O complexity of the problem of sorting sequences (or strings of characters) in external memory, which is a fundamental component of many large-scale text applications. In the standard unit-cost RAM comparison model, the complexity of sorting K strings of total length N is /spl Theta/(K log/sub 2/ K+N). By analogy, in the external memory (or I/O) model, where the internal memory has size M and the block transfer size is B, it would be natural to guess that the I/O complexity of sorting sequences is /spl Theta/((K/B)log/sub M/B/(K/B)+(N/B)), but the known algorithms do not come even close to achieving this bound. Our results show, somewhat counterintuitively, that the I/O complexity of string sorting depends upon the length of the strings relative to the block size. We first consider a simple comparison I/O model, where the strings are not allowed to be broken into their individual characters, and we show that the I/O complexity of string sorting in this model is /spl Theta/((N/sub 1//B)log/sub M/B/(N/sub 1//B)+K/sub 2/+(N/B)), where N/sub 1/ is the total length of all strings shorter than B and K/sub 2/ is the number of strings longer than B. We then consider two more general I/O comparison models in which string breaking is allowed. We obtain improved algorithms and in several cases lower bounds that match their I/O bounds. Finally, we develop more practical algorithms outside the comparison model.
Linear Programming Algorithms for Sparse Filter Design (2009)

In designing discrete-time filters, the length of the impulse response is often used as an indication of computational cost. In systems where the complexity is dominated by arithmetic operations, the number of nonzero coefficients in the impulse response may be a more appropriate metric to consider instead, and computational savings are realized by omitting arithmetic operations associated with zero-valued coefficients. This metric is particularly relevant to the design of sensor arrays, where a set of array weights with many zero-valued entries allows for the elimination of physical array elements, resulting in a reduction of data acquisition and communication costs. However, designing a filter with the fewest number of nonzero coefficients subject to a set of frequency-domain constraints is a computationally difficult optimization problem. This paper describes several approximate polynomial-time algorithms that use linear programming to design filters having a small number of nonzero coefficients, i.e., filters that are sparse. Specifically, we present two approaches that have different computational complexities in terms of the number of required linear programs. The first technique iteratively thins the impulse response of a non-sparse filter until frequency-domain constraints are violated. The second minimizes the 1-norm of the impulse response of the filter, using the resulting design to determine the coefficients that are constrained to zero in a subsequent re-optimization stage. The algorithms are evaluated within the contexts of array design and acoustic equalization.
Vector based speed control of permanent magnet AC servomotor with FEA and experimental verification (2012)

In this paper, real time vector control implementation for an AC servomotor is presented. Matlab-Simulink and dSpace control board were used. Speed control on desired reference using vector control technique is accomplished in the paper. Experimental results are provided for different speed conditions.
Combinatorial Libraries of Metal-Ligand Assemblies with an Encapsulated Guest Molecule (2001)

The combination of two different biscatecholate ligands with GaIII ions gives rise to twelve different assemblies (shown schematically), which are all simultaneously present in solution. These were characterized by ESI-FTICR mass spectrometry and NMR spectroscopy. Even larger libraries are obtained by using an increasing number of components.
NFI in the development of the olfactory neuroepithelium and the regulation of olfactory marker protein gene expression. (2000)

Nuclear factor I (NFI) proteins are DNA-binding transcription factors that participate in the tissue specific expression of various genes. They are encoded by four different genes (NFI-A, B, C, and X) each of which generates multiple isoforms by alternative RNA splicing. NFI-like binding sites have been identified in several genes preferentially expressed in olfactory receptor neurons. Our prior demonstration that NFI binds to these elements led to the hypothesis that NFI is involved in the regulation of these genes. To analyse the role of NFI in the regulation of olfactory neuron gene expression we have performed transient transfection experiments in HEK 293 cells using constructs that place luciferase expression under the control of an olfactory marker protein (OMP)-promoter fragment containing the NFI binding site. In vitro mutagenesis of this site revealed a negative modulation of luciferase expression by endogenous NFI proteins in HEK 293 cells. In addition, we have used in situ hybridization to analyse the tissue and cellular distribution of the four NFI gene transcripts during pre- and postnatal mouse development. We have simultaneously characterized the expression of Pax-6, and O/E-1, transcription factors known to regulate the phenotype of olfactory receptor neurons. We demonstrate that all of these transcription factors vary in specific spatio-temporal patterns during the development of the olfactory system. These data on NFI activity, and on transcription factor expression, provide a basis to understand the role of NFI in regulating gene expression in olfactory receptor neurons.
DNA content and other factors associated with ten‐year survival after resection of pancreatic carcinoma (1998)

Background and Objectives: The 5-year survival rates after resection of pancreatic carcinoma have recently increased and are predicted by tumor size, DNA content, and lymph node metastases at the time of resection. However, whether the 10-year survival rates have also increased and are similarly predicted by these factors is not known. Methods The influence of preoperative imaging tests, alcohol consumption, cigarette smoking, K-ras mutations, anatomic location, details of surgical resection, pathologic findings, and tumor DNA content on survival was tested for 96 patients after a successful resection of a pancreatic carcinoma with 17 patients being followed for more than 5 years. Results The 5- and 10-year patient survival rates were 18% and 3%, respectively. Univariate and multivariable analyses showed that tumor DNA content, pathologic tumor size, and lymph node metastases were the strongest prognostic indicators for long-term patient survival, although the importance of tumor size may diminish 2 or more years after resection. Surprisingly, the 11 patients with diploid carcinomas ⩾4 cm had an estimated 10-year survival rate of 36%. Conclusion These results show that the 10-year survival rate for pancreatic carcinoma remains very low, although the subset of patients with biologically favorable tumors has a prolonged survival and possible cure after resection. J. Surg. Oncol. 1998;67:151–159. © 1998 Wiley-Liss, Inc.
Tunable Inter-Resonator Coupling Structure With Positive and Negative Values and Its Application to the Field-Programmable Filter Array (FPFA) (2011)

In this paper, we show a tunable inter-resonator coupling structure capable of varying the coupling coefficient between resonators from positive to negative values, including values that approach zero. The presented inter-resonator coupling structure can be tuned to generate large isolation between two resonators as well as the required coupling for filter responses. Using the inter-resonator coupling structure, this paper demonstrates the concept of a field-programmable filter array (FPFA). The proposed array is composed of tunable resonators and can have multiple functionalities by routing signals from input ports to output ports. Signal routing can be achieved by controlling the inter-resonator coupling with a wide tuning ratio of coupling coefficients. A unit cell of the proposed FPFA was fabricated to prove the proposed concept. It is shown that the unit cell can be adjusted to have filter array responses with two second-order bandpass responses, third-order bandpass responses, and fourth-order bandpass responses. The unit cell can also be operated as a switchable filter bank without a switch. All operation modes are verified by measurements. This paper also demonstrates, for the first time, a reconfigurable filter that can be tuned to have both elliptic and self-equalized responses using the presented inter-resonator coupling structure.
Synthesis of All Four Stereoisomers of (E)‐Vitamin KT (Phylloquinone), Analysis of Their Diastereoisomeric and Enantiomeric Purities and Determination of Their Biopotencies (1990)

Abstract All four stereoisomers of ( E )‐vitamin Kb i. e. (2 1 E, 7 R, 11 1 R)‐l (= 1a), (2 1 E, 7 1 R, l1 1 S)‐1 (= 1b), (2 1 E, 7 1 S, 11 1 S) 1 ( = 1c), and (2 1 E, 7 1 S, 11 1 R)‐l ( = Id), have been synthesized in a state of high chemical and stereoisomeric purity. The synthesis of stereoisomers lb‐d relied on the use of the optically active Cf 1 * and C* 10 ‐building blocks ( R )‐ or ( S )‐4‐(benzyloxy)‐3‐methylbutanal (( R )‐ or ( S )‐2) and ( R )‐ or ( S )‐citronellal (( R )‐ or ( S )‐ 3 ) which had been secured by the Rh 1 ‐catalyzed allylamine‐to‐enamine isomerization technology. For the synthesis of the natural ( E )‐vitamin‐K1 stereoisomer 1a , a new route starting from natural phylol was developed, based on an O ‐alkylation/rearrangement procedure. A HPLC method was developed which separates with remarkable efficiency all four stereoisomers of (E) ‐ as well as three out of the four stereoisomers of ( Z )‐vitamin K 1 on optically active poly(trityl methacrylate) as the chiral stationary phase supported on Nucleosil. By this method, the stereoisomeric content of the stereoisomers 1b‐d synthesized was shown to be in the range of 96‐98 %, while the natural isomer 1a was configurationally uniform. The biological activity of the four ( E )‐vitamin‐K 1 stereoisomers was determined by means of the curative prothrombin time test with vitamin‐K‐depleted chicks. A high precision of the results was obtained with the recently introduced up‐and‐down organization of the test and the statistical evaluation according to an estimation procedure. With the natural ( E )‐vitamin‐K 1 stereoisomer 1a as standard (set at 1. 0), activities of 0. 93, 1. 19, and 0. 99 were found for stereoisomers 1b, 1c , and 1d , respectively. Within the confidence limits, these activity ratios can be regarded as identical, A very similar efficacy was obtained by comparison of ( E , all‐rac )‐vitamin K 1 ((2 1 E , RS , 11′ RS )‐ 1 ; equimolar mixture of the four stereoisomers 1a‐d) with the natural ( E )‐vitamin‐K 1 stereoisomer 1a ). A synergistic effect was not detectable, as was the case with the eight α‐tocopheryl‐acetate stereoisomers.