gebhart/patrepeval huggingface dataset:
Thyroid hormone-induced gene expression program for amphibian tail resorption (1993)

The changes in gene expression leading to tail resorption that are initiated by thyroid hormone (TH) were studied in Xenopus laevis. Four of the less than 10 genes that are down-regulated during this period have been isolated; their mRNAs decay with identical kinetics. Twenty of the approximately 35 genes that are up-regulated in the first 48 h have been isolated. The up-regulated genes fall into two kinetic patterns. After a lag of several hours, the direct response genes (including thyroid hormone receptor beta) increase their mRNA level steadily for 24-48 h. The delayed genes respond mainly in the second 24 h after TH addition. The importance of these genes for tail resorption is supported by the fact that they are all regulated developmentally during normal metamorphosis in tail and respond to hormone induction when the tail becomes competent to respond to TH. The relatively simple gene expression program leading to tail resorption is contrasted with the complex and multiple periods of gene expression during limb development. The gene expression screen defines the tail resorption program and has isolated the majority of TH-regulated genes.
Pace‐Termination and Pacing for Prevention of Atrial Tachyarrhythmias: Results from a Multicenter Study with an Implantable Device for Atrial Therapy (2001)

DDDRP pacing with a new system for AT therapy was safe and associated with successful pace-termination of AT in 53% of episodes. Preventive pacing and atrial ATP algorithms represent two new functions that can be implemented safely into pacemaker systems for nonpharmacologic treatment of ATs in patients requiring pacemaker therapy.
Critical Roles of Toll-Like Receptors in Host Defense (2000)

Drosophila Toll is involved not only in dorsoventral patterning of embryos but also in immune responses to microbial infection. Several Toll-like receptors (TLRs) have also been identified in mammals. They are expressed on macrophages or dendritic cells (DCs), which are essential sentinels for innate immunity. These cells utilize TLRs as a recognition and signal transducing receptor for microbial molecular components. The most characterized mammalian TLR, TLR4, is a receptor for lipopolysaccharides (LPS). TLR2 recognizes other components, such as peptideglycans (PGN). This recognition, called pattern recognition, is essential for the establishment of innate immunity, which is the basis for host defense. In this article, we review recent findings about this expanding receptor family.
Nutritional Significance and Metabolism of Very Long Chain Fatty Alcohols and Acids from Dietary Waxes (2004)

Very long chain fatty alcohols obtained from plant waxes and beeswax have been reported to lower plasma cholesterol in humans. This review discusses nutritional or regulatory effects produced by wax esters or aliphatic acids and alcohols found in unrefined cereal grains, beeswax, and many plant-derived foods. Reports suggest that 5-20 mg per day of mixed C24-C34 alcohols, including octacosanol and triacontanol, lower low-density lipoprotein (LDL) cholesterol by 21%-29% and raise high-density lipoprotein cholesterol by 8%-15%. Wax esters are hydrolyzed by a bile salt-dependent pancreatic carboxyl esterase, releasing long chain alcohols and fatty acids that are absorbed in the gastrointestinal tract. Studies of fatty alcohol metabolism in fibroblasts suggest that very long chain fatty alcohols, fatty aldehydes, and fatty acids are reversibly inter-converted in a fatty alcohol cycle. The metabolism of these compounds is impaired in several inherited human peroxisomal disorders, including adrenoleukodystrophy and Sjögren-Larsson syndrome. Reports on dietary management of these diseases confirm that very long chain fatty acids (VLCFA) are normal constituents of the human diet and are synthesized endogenously. Concentrations of VLCFA in blood plasma increase during fasting and when children are placed on ketogenic diets to suppress seizures. Existing data support the hypothesis that VLCFA exert regulatory roles in cholesterol metabolism in the peroxisome and also alter LDL uptake and metabolism.
Revisiting the specificity of the MHC class II transactivator CIITA in classical murine dendritic cells in vivo (2017)

Ciita was discovered for its role in regulating transcription of major histocompatibility complex class II (MHCII) genes. Subsequently, CIITA was predicted to control many other genes based on reporter and ChIP-seq analysis but few such predictions have been verified in vivo using Ciita<sup>-/-</sup> mice. Testing these predictions for classical dendritic cells (cDCs) has been particularly difficult, since Ciita<sup>-/-</sup> mice lack MHCII expression required to identify cDCs. However, recent identification of the cDC-specific transcription factor Zbtb46 allows the identification of cDCs independently of MHCII expression. We crossed Zbtb46<sup>gfp</sup> mice onto the Ciita<sup>-/-</sup> background and found that all cDC lineages developed in vivo in the absence of Ciita. We then compared the complete transcriptional profile of wild-type and Ciita<sup>-/-</sup> cDCs to define the physiological footprint of CIITA for both immature and activated cDCs. We find that CIITA exerts a highly restricted control over only the MHCII, H2-DO and H2-DM genes, in DC1 and DC2 cDC subsets, but not over other proposed targets, including Ii. These findings emphasize the caveats needed in interpreting transcription factor binding sites identified by in-vitro reporter analysis, or by ChIP-seq, which may not necessarily indicate their functional activity in vivo.
Two Fibonacci P-code based image scrambling algorithms (2008)

Image scrambling is used to make images visually unrecognizable such that unauthorized users have difficulty decoding the scrambled image to access the original image. This article presents two new image scrambling algorithms based on Fibonacci p-code, a parametric sequence. The first algorithm works in spatial domain and the second in frequency domain (including JPEG domain). A parameter, p, is used as a security-key and has many possible choices to guarantee the high security of the scrambled images. The presented algorithms can be implemented for encoding/decoding both in full and partial image scrambling, and can be used in real-time applications, such as image data hiding and encryption. Examples of image scrambling are provided. Computer simulations are shown to demonstrate that the presented methods also have good performance in common image attacks such as cutting (data loss), compression and noise. The new scrambling methods can be implemented on grey level images and 3-color components in color images. A new Lucas p-code is also introduced. The scrambling images based on Fibonacci p-code are also compared to the scrambling results of classic Fibonacci number and Lucas p-code. This will demonstrate that the classical Fibonacci number is a special sequence of Fibonacci p-code and show the different scrambling results of Fibonacci p-code and Lucas p-code.
Metal oxide semiconductor 3D printing: preparation of copper(<scp>ii</scp>) oxide by fused deposition modelling for multi-functional semiconducting applications (2017)

A CuO semiconductor was fabricated by FDM printing and sintering technique. The obtained CuO can be used as a multifunctional semiconductor.
Identification of the Key Residue of Calcitonin Gene Related Peptide (CGRP) 27−37 to Obtain Antagonists with Picomolar Affinity at the CGRP Receptor (2005)

Calcitonin gene related peptide (CGRP) plays an important role in the CNS and in the cardiovascular system. To identify high-affinity antagonists in competitive binding studies, we identified a novel radioactive tracer, [(3)H-propionyl-K(24)]-halphaCGRP 8-37, which was labeled in solution by a recently developed strategy using photolabile protecting groups at reactive side chains. This tracer was shown to be as potent as commercially available (125)I-tracers for the determination of agonists and to have increased sensitivity for antagonists. We applied it to investigate the predicted turn structures centered at Pro(29) and Pro(34). The substitution at positions 29 and 34 by turn-inducing amino acid mimetica showed that these turns are highly diverse. At position 29, a hydrophobic residue is preferred that constricts the secondary structure, whereas position 34 is required to stabilize the conformation of the backbone. All high-affinity analogues showed antagonistic properties with potency similar to CGRP 8-37.
Giant magnetic Kerr rotation for MnSbPt films with NiAs structure (1994)

Magnetic and magneto-optical properties, Kerr rotation angle, Kerr ellipticity and reflectance, were investigated for Pt substituted MnSb compound films with film thickness of about 1000 /spl Aring/ by RF sputtering in the concentration range of 44 at%<Mn<55at%, 37 at%<Sb<44 at%, 4 at%<Pt<15 at%. MnSbPt films with the concentration of 50 at%Mn, 44 at%Sb and 6 at%Pt annealed at 300/spl deg/C showed giant Kerr rotation angle of about 0.9/spl deg/ at short wavelength of /spl lambda/=500 nm. The results of structural analysis with X-ray and NMR revealed that the giant Kerr rotation angle observed in present films is closely related to the MnSb compound including Pt atom in NiAs structure.<<ETX>>
Enhancing moisture resistance of PBGA (2002)

One of the main package reliability limitations of PBGA is its moisture sensitivity performance, i.e. popcorn failure. The objective of this work is to enhance the moisture resistance of a 35/spl times/35 mm overmolded PBGA by matching its material combination. The approach taken is to correlate the package moisture sensitivity performance with the packaging material properties. JEDEC level 2 moisture sensitivity performance was achieved with two different combinations of materials. The best combination was close to achieving level 1 performance, thereby reinforcing the importance of material matching. Mold compound moisture absorption property has the strongest correlation with package moisture performance. A low value is favourable. For die attach material, the hot and wet adhesion shear strength showed the strongest correlation with package moisture performance. High adhesion shear strength is preferred. Unlike mold compound, the moisture absorption property of die attach material has a significantly weaker correlation.
Pathophysiological Role of Autophagy: Lesson from Autophagy-Deficient Mouse Models (2011)

Autophagy is a cellular degradation system in which cytoplasmic components including organelles are sequestered by double membrane structures called autophagosomes and sequestered materials are degraded by lysosomal hydrolases for supply of amino acids and for cellular homeostasis. The autophagy induced in response to nutrient deprivation is executed in a nonselective fashion, and adaptation to nutrient-poor conditions is the main purpose of autophagy. On the other hand, recent studies have shed light on another indispensable role for starvation-independent or constitutive autophagy in cellular homeostasis, which is mediated by selective degradation of a specific substrate(s). Herein, we introduce pathophysiological roles of starvation-induced, constitutive, and selective autophagy (in particular, selective turnover of p62 through autophagy) disclosed by autophagy-deficient mouse models.
Molecular and Expression Analysis of Cowpea Trypsin Inhibitor (CpTI) Gene in Transgenic 'Elaeis guineensis' Jacq Leaves (2010)

Cowpea trypsin inhibitor (CpTI) has been reported to have insecticidal properties against a wide range of insects. An 8year-old insect resistant oil palm, Elaeis guineensis Jacq. variety Tenera assigned as CpTI P8 was the first transgenic oil palm tree generated by the co-transformation of pDM 402 and pCAMBIA 1301 plasmids into the immature embryos of the oil palm via particle bombardment. PCR analyses had confirmed that 100% of the tested CpTI P8 frond leaves and root tissue genomic samples showed the presence of the CpTI transgene. The partial pDM 402 expression cassette consisting of the actin promoter sequence ( Act1-5’ ), the whole CpTI coding sequence and the Nos-3’ terminator sequence was fully recovered from the CpTI P8 genome using the Act1F1/NosTR1 primer pair in subsequent PCR analysis. Moreover, Southern blotting analysis showed the presence of two hybridized fragments, 0.96 kb and 1.2 kb in size in the Bam HI-digested genomic DNA and also demonstrated the stable integration of the transgene into the CpTI P8 genome. The amplification of a 425 bp RT-PCR product using the CpTI gene-specific primer pair has clearly implicated the expression of CpTI transcript. Quantitative study on the expression of CpTI gene was carried out using SYBR Green Quantitative Real Time-Polymerase Chain Rection (QRT-PCR) assay and revealed a remarkably higher expression of CpTI in the CpTI P8 tree compared to non-transformed oil palm tree. Together, these data have proven the successful gene transfer and a 7-fold increase in CpTI transcript accumulation in the leaves of CpTI P8 tree which could ultimately confer greater resistance against insect pest invasion. Interestingly, the data in present study also suggest that a simple integration pattern contributes significantly to the stability and high transgene expression in transgenic plants.
Oxysulfide Sm<sub>2</sub>Ti<sub>2</sub>S<sub>2</sub>O<sub>5</sub> as a Stable Photocatalyst for Water Oxidation and Reduction under Visible Light Irradiation (λ ≤ 650 nm) (2002)

A Ti-based oxysulfide, Sm(2)Ti(2)S(2)O(5), was studied as a visible light-driven photocatalyst. Under visible light (440 nm < or = lambda < or = 650 nm) irradiation, Sm(2)Ti(2)S(2)O(5) with a band gap of approximately 2 eV evolved H(2) or O(2) from aqueous solutions containing a sacrificial electron donor (Na(2)S-Na(2)SO(3) or methanol) or acceptor (Ag(+)) without any noticeable degradation. This oxysulfide is, therefore, a stable photocatalyst with strong reduction and oxidation abilities under visible-light irradiation. The electronic band structure of Sm(2)Ti(2)S(2)O(5) was calculated using the plane-wave-based density functional theory (DFT) program. It was elucidated that the S3p orbitals constitute the upper part of the valence band and these orbitals make an essential contribution to the small band gap energy. The conduction and valence bands' positions of Sm(2)Ti(2)S(2)O(5) were also determined by electrochemical measurements. It indicated that conduction and valence bands were found to have satisfactory potentials for the reduction of H(+) to H(2) and the oxidation of H(2)O to O(2) at pH = 8. This is consistent with the results of the photocatalytic reactions.
Enhancing Children's Rights to Protection from Violence and Neglect in Aotearoa New Zealand (2003)

This article offers comment on New Zealand's performance over the last five years in protecting its children from violence with reference to the United Nations Convention on the Rights of the Child. We draw from the care and protection paper released by Action for Children and Youth Aotearoa (ACYA), a coalition of non-government organisations in New Zealand. Barriers to improvement are identified, along with the changes required if the barriers are to be overcome. We argue that significant reduction of violence to children requires long-term comprehensive initiatives, including changes in macro-level policies, as well as a combination of universal and targeted community-based prevention programmes. This involves action to reduce child poverty, a holistic inter-departmental approach to policy and planning for children, an increased focus on evidence-based primary prevention and early intervention initiatives, and repeal of Section 59 of the Crimes Act 1961.
Architecture for self-clocked self-routing photonic bit switching (2002)

Optical signal processing will be widely used in future photonic switches, because it can remove the bottleneck at electrooptic interfaces and offer an ultrahigh throughput. Self-clocked self-routing photonic switching with optical pulse-interval time-division address encoding (OPI-TDAE) has been recently demonstrated, which is useful to build broadband communication networks. In order to effectively implement photonic bit switching with OPI-TDAE, a modified architecture is presented in this paper. It is based on the two-wavelength scheme.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Characterization of glutaryl 7-ACA acylase from Pseudomonas diminuta KAC-1 (2001)

The glutaryl 7-aminocephalosporanic acid (glutaryl 7-ACA) acylase was purified from Pseudomonas diminuta KAC-1 cells isolated from soil, and characterized. The acylase was purified by procedures including ammonium sulfate fractionation and column chromatographies on DEAE-Sepharose, Phenyl-Sepharose, Q-Sepharose, and Superose 12H/R. The native acylase was found to be composed of two subunits with molecular masses of approximately 55 kDa and 17 kDa, respectively. The isoelectric point of the enzyme was 4.0. The specific activities of the purified acylase were 8.0 and 7.0 U/mg on glutaryl 7-ACA and glutaryl 7-aminodesacetoxy cephalosporanic acid (glutaryl 7-ADCA), respectively, and K m values were 0.45 mM for glutaryl 7-ACA and 0.67 mM for glutaryl 7-ADCA. The enzyme had a pH optimum at 8.0 and a temperature optimum at 40 °C. The acylase catalyzed the synthesis of glutaryl 7-ACA from glutaric acid and 7-ACA as well as the hydrolysis of glutaryl 7-ACA, although the reaction rate of the synthesis was slower than that of the hydrolysis. In addition, it was found that the enzyme had a glutaryl transferase activity, thereby transferring the glutaryl group from one cephalosporin nucleus to another.
Properties and performance of regenerated cellulose thermoset biocomposites (2015)

Biocomposites have been developed to address the sustainability issues of nonrenewableresource based materials. These composites are often produced by reinforcing natural fibres in petroleum based ...
Optimum Light Intensity Distribution for Growing Large Si Grains by Phase-Modulated Excimer-Laser Annealing (2004)

Characteristics have been investigated for both KrF excimer-laser light and KrF excimer-laser crystallization of Si thin films. The results were applied to design an optical system for growing densely packed and large grains. A high-resolution beam profiler confirmed that the laser light intensity distribution on the sample surface had a nearly ideal triangular form with a maximum-to-minimum intensity ratio of approximately 2, as designed. This distribution could grow 5-µm-long grains with a packing efficiency close to 100% by a single laser light pulse.
Identifying a two-state Hamiltonian in the presence of decoherence (2006)

Mapping the system evolution of a two-state system allows the determination of the effective system Hamiltonian directly. We show how this can be achieved even if the system is decohering appreciably over the observation time. A method to include various decoherence models is given and the limits of this technique are explored. This technique is applicable both to the problem of calibrating a control Hamiltonian for quantum computing applications and for precision experiments in two-state quantum systems. The accuracy of the results obtained with this technique are ultimately limited by the validity of the decoherence model used.
Differential Localization of T-bet and Eomes in CD8 T Cell Memory Populations (2013)

In mice, two T-box transcription factors, T-box expressed in T cells (T-bet) and eomesodermin (Eomes), drive the differentiation of CD8 T cell lineages; however, little is known regarding their role in human CD8 T cell differentiation. In this study, we characterized T-bet and Eomes expression and localization within human CD8 memory T cell populations. We find that T-bet and Eomes are broadly expressed in human memory CD8 T cells, with increasing levels of T-bet and Eomes strongly correlating with differentiation from central memory to effector memory and effector subpopulations. In resting T cells, T-bet levels directly correlate to subcellular localization, with a higher propensity for nuclear expression of T-bet within T-bet(hi) cells and predominantly cytoplasmic expression in T-bet(lo) cells. In addition, Eomes is also localized to either the nucleus or the cytoplasm. Upon TCR stimulation, the percentage of T cells that express T-bet dramatically increases, whereas the percentage of cells expressing Eomes remains largely unchanged across all memory populations. Of interest, T-bet, but not Eomes, relocalizes to the nucleus in the majority of cells across all populations within 24 h post stimulation. These data indicate that T-bet and Eomes are likely regulated at the level of subcellular localization, potentially via different mechanisms. Together, these findings suggest a novel model for CD8 T cell differentiation in humans that is based on the localization of T-bet and Eomes.
Structure and mechanism of chromatin remodeler SWI/SNF (2019)

University of Minnesota M.S. thesis.December 2019. Major: Biochemistry, Molecular Bio, and Biophysics. Advisor: Aaron Goldstrohm. 1 computer file (PDF); x, 91 pages.
Protransglutaminase (Factor XIII) Mediated Crosslinking of Fibrinogen and Fibrin* (2001)

Plasma factor XIII (plasma protransglutaminase) circulates as an A2B2 tetramer bound to the gamma' variant chains of fibrinogen "2". During clotting the A subunits of fXIII are cleaved by thrombin to form fXIIIa (transglutaminase) and in the presence of calcium ions, activated A2* subunits dissociate from the B subunits. When purified plasma fXIII or recombinant cellular factor XIII (A2) was incubated with fibrinogen in the presence of calcium ions (> or =50 microM) a non-synerizing gel formed concomitant with formation of gamma dimers, followed by Agamma polymers, and eventually gamma trimers and gamma tetramers. As is the case of fXIIIa, the fXIII-mediated crosslinking rate was enhanced in the presence of thiols. After an initial lag period, fXIII catalyzed fibrinogen crosslinking at approximately 75% of the rate of fXIIIa under typical crosslinking conditions (100 Loewy u/ml, 5 mM CaCl2 & 500 microM DTT). Fibrin was crosslinked about 8 times more rapidly by fXIII than was fibrinogen, and after an initial lag period fXIII crosslinked fibrin at nearly the same rate as fXIIIa. Substituting plasma for purified fXIII as the source for fXIII resulted in robust fibrinogen crosslinking activity. In contrast to the high level of fXIII-mediated crosslinking activity observed with fibrinogen or fibrin as substrates, when transglutamination was measured using cadaverine incorporation into casein, fXIII was 30-fold less active than fXIIIa. Thus, factor XIII displays constitutive enzymatic activity with respect to fibrinogen and fibrin. The results further indicate that uncleaved fXIII in plasma provides a potent source of readily available crosslinking activity in clotting blood. Fibrinogen 2, whose gamma'chains bind fXIII B subunits, was crosslinked 3.5 times more slowly by fXIII than was fibrinogen 1 (lacking gamma' chains), suggesting that complex formation between fibrinogen 2 and plasma fXIII plays a significant role in down-regulating potential plasma fXIII-mediated crosslinking activity. Since fibrin is a considerably better substrate for fXIII than is fibrinogen, the rate at which crosslinking takes place in a fibrinogen-containing plasma environment is much lower than it would be if fibrin were present.