gebhart/patrepeval huggingface dataset:
An Algorithm for the Design of Low-Power Hardware-Efficient FIR Filters (2008)

<para xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink"> <?Pub Dtl=""?>A novel algorithm for designing low-power and hardware-efficient linear-phase finite-impulse response (FIR) filters is presented. The algorithm finds filter coefficients with reduced number of signed-power-of-two (SPT) terms given the filter frequency response characteristics. The algorithm is a branch-and-bound-based algorithm that fixes a coefficient to a certain value. The value is determined by finding the boundary values of the coefficient using linear programming. Although the worst case run time of the algorithm is exponential, its capability to find appreciably good solutions in a reasonable amount of time makes it a desirable CAD tool for designing low-power and hardware-efficient filters. The superiority of the algorithm on existing methods in terms of SPT term count, design time, hardware complexity, and power performance is shown with several design examples. Up to 30% reduction in the number of SPT terms is achieved over unoptimized Remez coefficients, which is 20% better than compared optimization methods. The average power saving is 20% over unoptimized coefficients, which is up to 14% better than optimized coefficients obtained with existing methods. </para>
Molecular Sensing and Computing Systems (2015)

Advances in the field of synthetic biology have been key to demonstration of molecular computing systems in general and DNA in particular. This paper presents an overview of how continuous-time, discrete-time, and digital signal processing systems can be implemented using molecular reactions and DNA. In this paper, discrete-time systems refer to sampled signals with continuous signal amplitude. Signals that are sampled in discrete time steps with digital amplitude are referred to as digital signals. Delay elements in sampled signals are implemented using molecular reactions in the form of molecular transfer reactions. Completion of all phases of transfer reactions once corresponds to a computation cycle. These molecular systems can be implemented in a fully-synchronous, globally-synchronous locally-asynchronous or fully-asynchronous manner. The paper also presents molecular sensing systems where molecular reactions are used to implement analog-to-digital converters (ADCs) and digital-to-analog converters (DACs). Molecular implementations of digital logic systems are presented. A complete example of the addition of two molecules using digital implementation is described where the concentrations of two molecules are converted to digital by two 3-bit ADCs, and the 4-bit output of the digital adder is converted to analog by a 4-bit DAC. This system is demonstrated using both molecular reactions and DNA. A brief comparison of molecular and electronic systems is also presented.
High-k materials for nonvolatile memory applications (2005)

The paper proposes solutions for the future scaling of tunnel and interpoly dielectrics (IPD) in flash memories based on high-k materials. The concept of engineered barriers is reviewed as well as the main reliability issues associated with the introduction of these materials in nonvolatile memory (NVM) devices. For completeness, the application of high-k materials in charge trapping devices is also addressed.
Factors Influencing Absorbent Properties of Saponified Starch‐g‐Polyacrylonitrile Isolated by Methanol Precipitation (1984)

Abstract The method by which methanol is added to precipitate saponified starch‐g‐polyacrylonitrile (HSPAN) from an alkaline saponification mixture will influence the particle size of the polymer and thus the properties of the absorbent. Slow methanol addition, coupled with thorough mixing to ensure complete absorption of methanol by the reaction mass, will separate individual micron‐sized fragments of HSPAN gel and will yield a product with a small enough particle size to produce a smooth, tree‐flowing gel dispersion when added to water. This product is perhaps more suitable as a thickener than as a water absorbent. More rapid addition of methanol results in incomplete absorption by the reaction mass and causes individual gel fragments to coalesce to form millimeter‐sized chunks of water‐swollen HSPAN. Subsequent dewatering with excess methanol produces a granular product with good absorption properties. Gel‐blocking was reduced by adding either stearic acid or poly(vinyl acetate) to methanol‐precipitated HSPAN.
유집분석에 의한 한국산 나리속 ( Lilum L. ) 식물의 분류 : 나문재속 한반도 미기록식물 1종 (2001)

One unrecorded species of Suaeda is found from the western and southern coast of Korea. The morphological characteristics and habitat of the plant are described. The species is distinguished from the other Korean species in the genus by its thin and broad leaves and the stellate shape of fruits.
Using Pulsed Neutron Decay-Spectrum Data and Multi-inflatable Packer Plugdown Assemblies Improve Oil Production Rates in a Mature CO2 Flood (1996)

Abstract A gravity-stable, vertical C02 miscible injection flood was implemented in the 824 feet thick Wellman Unit Wolfcamp reef reservoir in July 1983. C02 is being injected in the crest of the reservoir to displace the oil vertically downward. The producing wells areconstantly being plugged down out of the "gassed out" interval into the oil bank. The purpose of this paper is to present the results of the PND®-S through tubing logging tool as a method to determine the C02/oil/water contacts and the use of multiple inflatable packers/sliding sleeve plugdown assemblies to achieve zonal isolation between "gassed out" intervals and producing intervals.
Non-acute (residual) neurocognitive effects of cannabis use: A meta-analytic study (2003)

The possible medicinal use of cannabinoids for chronic diseases emphasizes the need to understand the long-term effects of these compounds on the central nervous system. We provide a quantitative synthesis of empirical research pertaining to the non-acute (residual) effects of cannabis on the neurocognitive performance of adult human subjects. Out of 1,014 studies retrieved using a thorough search strategy, only 11 studies met essential a priori inclusion criteria, providing data for a total of 623 cannabis users and 409 non- or minimal users. Neuropsychological results were grouped into 8 ability domains, and effect sizes were calculated by domain for each study individually, and combined for the full set of studies. Using slightly liberalized criteria, an additional four studies were included in a second analysis, bringing the total number of subjects to 1,188 (i.e., 704 cannabis users and 484 non-users). With the exception of both the learning and forgetting domains, effect size confidence intervals for the remaining 6 domains included zero, suggesting a lack of effect. Few studies on the non-acute neurocognitive effects of cannabis meet current research standards; nevertheless, our results indicate that there might be decrements in the ability to learn and remember new information in chronic users, whereas other cognitive abilities are unaffected. However, from a neurocognitive standpoint, the small magnitude of these effect sizes suggests that if cannabis compounds are found to have therapeutic value, they may have an acceptable margin of safety under the more limited conditions of exposure that would likely obtain in a medical setting.
The EGF receptor: structure, regulation and potential role in malignancy. (1985)

Retroviral onc genes are derived from cellular proto-oncogenes that may function in normal cellular growth control. The epidermal growth factor (EGF) receptor is the proto-oncogene of erbB; both possess intrinsic protein tyrosine kinase activity, a property shared by several retroviral onc genes. The EGF receptor is a transmembrane glycoprotein with an external EGF binding domain and a cytoplasmic region that is homologous with other tyrosine kinases. erbB lacks the EGF binding and carboxyl terminal regions, which are thought to be important in regulation. The EGF receptor is regulated by several mechanisms: stimulation by ligand binding and self-phosphorylation, inhibition by heterologous phosphorylation and downregulation by ligand. EGF binding stimulates several early events, including phosphatidylinositol (PI) turnover in A431 cells. A PI kinase activity copurifies with the EGF receptor and some other tyrosine kinases, but this is a contaminant as it can be separated from the EGF receptor. Although the role of proto-onc genes in human malignancy is incompletely defined, increased numbers of EGF receptors are present in several types of human tumours. Overexpression of EGF receptors, as occurs in human epidermoid carcinoma A431 cells, can augment cell growth because of increased formation of active ligand:receptor complexes. Gene amplification is the mechanism underlying overexpression of EGF receptors in A431 cells and in some glioblastoma multiforme tumours.
Complete primary structure of the triple-helical region and the carboxyl-terminal domain of a new type IV collagen chain, alpha 5(IV). (1990)

We have isolated and characterized overlapping cDNA clones which code for a previously unidentified human collagen chain. Although the cDNA-derived primary structure of this new polypeptide is very similar to the basement membrane collagen alpha 1(IV) and alpha 2(IV) chains, the carboxyl-terminal collagenous/non-collagenous junction sequence does not correspond to the junction sequence in either of the newly described alpha 3(IV) or alpha 4(IV) chains (Butkowski, R.J., Langeveld, J.P.M., Wieslander, J., Hamilton, J., and Hudson, B. G. (1987) J. Biol. Chem. 262, 7874-7877). Thus the protein presented here has been designated the alpha 5 chain of type IV collagen. Four clones encode an open reading frame of 1602 amino acids that cover about 95% of the entire chain including half of the amino-terminal 7S domain and all of the central triple-helical region and carboxyl-terminal NC1 domain. The collagenous region of the alpha 5(IV) chain contains 22 interruptions which are in most cases identical in distribution to those in both the alpha 1(IV) and alpha 2(IV) chains. Despite the relatively low degree of conservation among the amino acids in the triple-helical region of the three type IV collagen chains, analysis of the sequences clearly showed that alpha 5(IV) is more related to alpha 1(IV) than to alpha 2(IV). This similarity between the alpha 5(IV) and alpha 1(IV) chains is particularly evident in the NC1 domains where the two polypeptides are 83% identical in contrast to the alpha 5(IV) and alpha 2(IV) identity of 63%. In addition to greatly increasing the complexity of basement membranes, the alpha 5 chain of type IV collagen may be responsible for specialized functions of some of these extracellular matrices. In this regard, it is important to note that we have recently assigned the alpha 5(IV) gene to the region of the X chromosome containing the locus for a familial type of hereditary nephritis known as Alport syndrome (Myers, J.C., Jones, T.A., Pohjalainen, E.-R., Kadri, A.S., Goddard, A.D., Sheer, D., Solomon, E., and Pihlajaniemi, T. (1990) Am. J. Hum. Genet. 46, 1024-1033). Consequently, the newly discovered alpha 5(IV) collagen chain may have a critical role in inherited diseases of connective tissue.
Skin regeneration using keratinocytes and dermal fibroblasts cultured on biodegradable microspherical polymer scaffolds (2005)

Bioartificial skin sheet grafts have been utilized to treat large burns and chronic ulcers. However, the trypsinization step to harvest cultured skin grafts from culture dishes damages the cells by breaking the anchoring proteins and lowers their uptake ratio after transplantation. In addition, epidermal sheet grafts require a long fabrication period. To overcome these limitations, we utilized biodegradable poly(lactide-co-glycolide) (PLGA) microspheres as both cell culture matrix and transplantation vehicle of skin cells for skin regeneration in this study. This method could avoid the trypsinization step and have a relatively short preparation period. Human keratinocytes and dermal fibroblasts cultured on PLGA microspheres in spinner flasks proliferated by 3.0-fold and 9.4-fold, respectively, after 10 days. When both types of cells cultured on PLGA microspheres were reinoculated onto culture dishes, the cells migrated from the PLGA microspheres to the culture dish surface, grew, and formed a confluent cell layer within 5 days, showing the growth and migration abilities of the cells cultured on PLGA microspheres. Full-thickness skin wounds created on the back of athymic mice were either treated with transplantation of keratinocytes and dermal fibroblasts cultured on microspheres (cell-transplanted group), treated with PLGA microspheres alone (microsphere-implanted group), or covered with dressing materials without treatment (untreated group). Three weeks after the treatments, differentiated epithelium that stained positively for cytokeratin, a marker of epidermis, was observed in the cell-transplanted group, while the microsphere-implanted group and untreated group showed incomplete reepithelialization. Dermal regeneration with positive staining for vimentin, a marker of dermal fibroblast, was observed in the cell-transplanted group. Regenerated dermis with positive staining for vimentin was partly observed in the microsphere-implanted group and untreated group. These results suggest that transplantation of keratinocytes and dermal fibroblasts cultured on PLGA microspheres could be potentially useful as an alternative to bioartificial skin grafts for the treatment of skin wounds.
Complex Formation of NiII, CuII, PdII, and CoIII with 1,2,3,4-Tetraaminobutane (2001)

Complex formation of the two tetraamine ligands (2S,3S)-1,2,3,4-tetraaminobutane (threo-tetraaminobutane, ttab) and (2R,3S)-1,2,3,4-tetraaminobutane (erythro-tetraaminobutane, etab) with Co(III), Ni(II), Cu(II), and Pd(II) was investigated in aqueous solution and in the solid state. For Ni(II) and Cu(II), the pH-dependent formation of a variety of species [Mn(II)xLyHz](2x+z)+ was established by potentiometric titrations and UV/Vis spectroscopy. In sufficiently acidic solutions the divalent cations formed a mononuclear complex with the doubly protonated ligand of composition [M(H2L)]4+. An example of such a complex was characterized in the crystal structure of [Pd(H2ttab)Cl2]Cl2.H2O. If the metal cation was present in excess, increase of pH resulted in the formation of dinuclear complexes [M2L]4+. Such a species was found in the crystal structure of [Cu2(ttab)Br4].H2O. Excess ligand, on the other hand, lead to the formation of a series of mononuclear bis-complexes [Mq(HxL)(HyL)](q+x+y)+. The crystal structure of [Co(Hetab)2][ZnCl4]2Cl. H2O with the inert, trivalent Co(III) center served as a model to illustrate the structural features of this class of complexes. By using an approximately equimolar ratio of the ligand and the metal cation, a variety of polymeric aggregates both in dilute aqueous solution and in the solid state were observed. The crystal structure of Cu2(ttab)3Br4, which exhibits a two-dimensional, infinite network, and that of [Ni8(ttab)12]Br16.17.5H2O, which contains discrete chiral [Ni8(ttab)12]16+ cubes with approximate T symmetry, are representative examples of such polymers. The energy of different diastereomeric forms of such complexes with the two tetraamine ligands were analyzed by means of molecular mechanics calculations, and the implications of these calculations for the different structures are discussed.
Neurodevelopmental Schizophrenia: Obstetric Complications, Birth Weight, Premorbid Social Withdrawal and Learning Disabilities (2001)

Neurodevelopmental schizophrenia seems to be caused by impaired cerebral development and is supposed to be associated with obstetric complications (OCs), poor premorbid adjustment, schizotypal or schizoid personality traits and negative symptoms. In the present study, 36 schizophrenic and schizoaffective patients and their same-sex, healthy siblings were recruited. They were diagnosed according to DSM-III-R, using structured psychiatric interviews and a consensus of 2 psychiatrists. Information on OCs, birth weight, premorbid social and learning functioning was obtained from their mothers. The main results show significant differences in OCs, birth weight, premorbid social and learning functioning between patients and their same-sex, healthy siblings. Using multivariate analyses, both premorbid variables were again identified to discriminate well between affected and unaffected siblings. Our findings seem to confirm the concept of schizophrenia as a neurodevelopmental process.
Mechanisms of Resistance of Human Glioma Cells to Apo2 Ligand/TNF-Related Apoptosis-Inducing Ligand (2007)

These data challenge the view that specific cell lines harbour specific mechanisms of resistance to Apo2L/TRAIL. Weak expression of DR5 in primary glioma might limit the therapeutic application of Apo2L/TRAIL in human glioblastoma patients.
The integrin alphavbeta3 is a receptor for the latency-associated peptides of transforming growth factors beta1 and beta3 (2003)

The integrins alpha(v)beta(1), alpha(v)beta(5), alpha(v)beta(6) and alpha(v)beta(8) have all recently been shown to interact with the RGD motif of the latency-associated peptide (LAPbeta(1)) of transforming growth factor beta(1) (TGFbeta(1)), with binding to alpha(v)beta(6) and alpha(v)beta(8) leading to TGFbeta(1) activation. Previously it has been suggested that the remaining alpha(v) integrin, alpha(v)beta(3,) does not interact with LAPbeta(1). However, here we show clearly that alpha(v)beta(3) does indeed interact with the LAPbeta(1) RGD motif. This interaction is similar to other alpha(v)beta(3) ligands in terms of the cations required for adhesion, the concentrations of LAPbeta(1) required for binding and the ability of a small-molecule inhibitor of alpha(v)beta(3), SB223245, to block the interaction. Using glutathione S-transferase fusion proteins we have mapped a minimal integrin-binding loop in LAPbeta(1) and then used this approach to probe the integrin-binding properties of the equivalent loops in LAPbeta(2) and LAPbeta(3). We show that the RGD motif of LAPbeta(3) also interacts with alpha(v)beta(3), in addition to alpha(v)beta(6), alpha(v)beta(1) and alpha(v)beta(5), whereas the corresponding loop in LAPbeta(2) does not interact with these integrins. These observations therefore correct a previously reported inaccuracy in the literature. Furthermore, they are important as they link alpha(v)beta(3) and TGFbeta, which may have implications in cancer and a number of inflammatory and fibrotic diseases where expression of both proteins has been documented.
Sindbis virus nucleocapsid assembly: RNA folding promotes capsid protein dimerization (2003)

In Sindbis virus, initiation of nucleocapsid core assembly begins with recognition of the encapsidation signal of the viral RNA genome by capsid protein. This nucleation event drives the recruitment of additional capsid proteins to fully encapsidate the genome, generating an icosahedral nucleocapsid core. The encapsidation signal of the Sindbis virus genomic RNA has previously been localized to a 132-nucleotide region of the genome within the coding region of the nsP1 protein, and the RNA-binding activity of the capsid was previously mapped to a central region of the capsid protein. It is unknown how capsid protein binding to encapsidation signal leads to ordered oligomerization of capsid protein and nucleocapsid core assembly. To address this question, we have developed a mobility shift assay to study this interaction. We have characterized a 32 amino acid peptide capable of recognizing the Sindbis virus encapsidation signal RNA. Using this peptide, we were able to observe a conformational change in the RNA induced by capsid protein binding. Binding is tight (K(d)(app) = 12 nM), and results in dimerization of the capsid peptide. Mutational analysis reveals that although almost every predicted secondary structure within the encapsidation signal is required for efficient protein binding, the identities of the bases within the helices and hairpin turns of the RNA do not need to be maintained. In contrast, two purine-rich loops are essential for binding. From these data, we have developed a model in which the encapsidation signal RNA adopts a highly folded structure and this folding process directs early events in nucleocapsid assembly.
Hydrocarbon‐stapled lipopeptides exhibit selective antimicrobial activity (2017)

Antimicrobial peptides (AMPs) occur widely in nature and have been studied for their therapeutic potential. AMPs are of interest due to the large number of possible chemical structural combinations using natural and unnatural amino acids, with varying effects on their biological activities. Using physicochemical properties from known naturally occurring amphipathic cationic AMPs, several hydrocarbon-stapled lipopeptides (HSLPs) were designed, synthesized, and tested for antimicrobial properties. Peptides were chemically modified by N-terminal acylation, C-terminal amidation, and some were hydrocarbon stapled by intramolecular olefin metathesis. The effects of peptide length, amphipathic character, and stapling on antimicrobial activity were tested against Escherichia coli, three species of Gram-positive bacteria (Staphylococcus aureus, Bacillus megaterium, and Enterococcus faecalis), and two strains of Candida albicans. Peptides were shown to disrupt liposomes of different phospholipid composition, as measured by leakage of a fluorescent compound from vesicles. Peptides with (S)-2-(4'-pentenyl)-alanine substituted for l-alanine in a reference peptide showed a marked increase in antimicrobial activity, hemolysis, and membrane disruption. Stapled peptides exhibited slightly higher antimicrobial potency; those with greatest hydrophobic character showed the greatest hemolysis and liposome leakage, but lower antimicrobial activity. The results support a model of HSLPs as membrane-disruptive AMPs with potent antimicrobial activity and relatively low hemolytic potential at biologically active peptide concentrations.
Transposon-facilitated recombination in classical biotypes of Vibrio cholerae (1981)

Transposon-facilitated recombination (Tfr) donors of classical Vibrio cholerae strain 162 were constructed by introducing the ampicillin transposon Tn1 into the P conjugative plasmid and the bacterial chromosome. The improved donors mediated high-frequency, polarized transfer of chromosomal genes from origins to confirm the gene orders of the previous classical strain 162 genetic map and to establish its circularity. Significant transfer of linked genes from E1 Tor Tfr donors to classical recipients was demonstrated, and other evidence for genetic relatedness of these two V. cholerae biotypes is discussed.