gebhart/patrepeval huggingface dataset:
Interaction of Mitochondrial F1ATPase with Trinitrophenyl Derivatives of ATP. Photoaffinity Labeling of Binding Sites with 2-azido-2',3'-O-(4,6-trinitrophenyl)adenosine 5'-Triphosphate (1995)

It was shown recently that ATP present at near saturating concentrations did not prevent binding and hydrolysis of submicromolar concentration of trinitrophenyl adenosine triphosphate (Tnp-ATP) by F1-ATPase [Murataliev, M. B. & Boyer, P. O. (1994) J. Biol. Chem. 269, 15431–15439]. To explore F1-ATPase binding sites that bind Tnp-ATP a new photoreactive analog of ATP, 2-azido-trinitrophenyl adenosine triphosphate (2-N3-Tnp-ATP) has been synthesized and used for photoaffinity labeling of mitochondrial F1- ATPase. The analog shares many properties of the parent non-azido Tnp-ATP as shown from spectral characteristics, binding with F1-ATPase, and kinetic and inhibition studies. 500 μM ATP does not prevent binding and hydrolysis of low concentrations of 2-N3,-Tnp-ATP by F1-ATPase. Photoirradiation of the enzyme-analog complex formed under such conditions results in the labeling of the catalytic-site peptide. This shows that in the presence of near saturating ATP, Tnp-ATP can enter the catalytic cycle and inhibit ATP hydrolysis by initial binding at a third catalytic site. The results give strong evidence that only two catalytic sites need to have bound substrate for near maximal turnover rate, and that three catalytic sites of F1-ATPase participate equally in catalysis. When F1-ATPase binds substoichiometric 2-N3-Tnp-ATP in the presence of Mg2+, illumination of the inactive complex formed results in the covalent labeling of a catalytic site. This shows that F1-ATPase forms similar inactive complexes when ADP or Tnp-ADP is bound at a catalytic site in the presence of Mg2+. Exposure of the nucleotide-depleted F1-ATPase to 20 μM 2-N3-Tnp-ATP followed by a short incubation with excess of Tnp-ATP results in binding, and, upon illumination, in a covalent labeling of a non-catalytic-site peptide.
Separation of independent sources from correlated inputs (1992)

The characterization of independent stationary stochastic components (sources), is generally achieved by using the spectral matrix of partially correlated measurements, which are linearly related to the components of interest. In the general case where no assumptions are made concerning the way the sources are mixed on the measurements, the spectral matrix is not able to extract the true sources. While spectral analysis only uses second-order properties of independent stochastic sources, a procedure based on higher-order analysis (fourth-order cross cumulants) is developed. This approach leads to a complete identification of the sources.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
The Clustering of Axonal Sodium Channels during Development of the Peripheral Nervous System (1996)

The distribution of Na+ channels in rat peripheral nerve was measured during development by using immunofluorescence. Small segments of sciatic nerve from postnatal day 0-13 (P0-P13) pups were labeled with an antibody raised against a well conserved region of the vertebrate Na+ channel. At day P0 axons contained almost no Na+ channel aggregates. The number of clusters increased dramatically throughout the first week. In almost all cases Na+ channels clustered in the vicinity of Schwann cell processes. At least four classes of aggregates were noted. Clusters formed singly at Schwann cell edges, in pairs or in broad regions between neighboring Schwann cells, and in more focal zones at presumptive nodes. Almost all Na+ channel aggregates had reached the latter stage by the end of the first week. Histograms plotting the frequency of occurrence of each cluster type suggested a sequence of events in node formation involving the initiation of channel aggregation by Schwann cell processes. The requirement for Schwann cells during sodium channel clustering was tested by blocking proliferation of these cells with the antimitotic agent mitomycin C. Na+ channel clustering was sharply reduced, whereas node formation was normal at a distal site along the same nerve. Immunocytochemical detection of myelin-associated glycoprotein (MAG) indicated that Schwann cells must begin to ensheathe axons before inducing Na+ channel clustering.
The power of patient ownership: The path from engagement to equity (2015)

Understanding patient engagement from the lens of a person who is suffering, who is in pain and anguish, who is wracked with fear of the impact of this pain on their body, their family, their career, and their mortality, is a complex undertaking. The authors provide an important patient perspective in acknowledging and highlighting efforts to shift the conversation on experience from one about patients and families to one with patients and families. They challenge us to consider the power that can be found in creating ownership for patients and suggest it may be the one true path to moving beyond a mindset of engagement to real equity in healthcare.
Rhizopus raw-starch-degrading glucoamylase: Its cloning and expression in yeast. (1986)

A glucoamylase gene has been cloned from a Rhizopus genomic DNA library using synthetic oligonucleotides corresponding to the amino acid sequence of the glucoamylase. Since this glucoamylase gene was not expressed in yeast cells, we have cloned a glucoamylase gene from a cDNA library prepared from Rhizopus mRNA. Sequence analysis of both glucoamylase genes revealed that the genomic gene contained 4 intervening sequences and the cDNA gene lacked 145 nucleotides corresponding to the N-terminal region. The glucoamylase consists of 604 amino acids including a putative signal peptide and its molecular weight was calculated to be 65, 000. The glucoamylase gene to be expressed in yeast cells was constructed by recombination of both genes. The yeast cells containing this constructed glucoamylase gene secreted the glucoamylase into the culture fluid and grew at almost the normal rate on a medium containing starch as the sole carbon source.
Surgical Treatment of Wolff-Parkinson-White Syndrome: Epicardial Approach Without the Use of Cardiopulmonary Bypass (1993)

Epicardial dissection without the use of cardiopulmonary bypass (CPB) was performed in 88 patients (56 males and 32 females, mean age 31.9 years). With intraoperative epicardial mapping, 101 accessory pathways were detected, with multiple pathways in 11 patients. CPB was avoided in all but one patient due to frequent onset of atrial fibrillation with rapid ventricular rate. Surgical ablation was successful in 86 patients (97.6%). Three patients required multiple surgical procedures because of persistence of conduction along a component of the original pathway. All but two patients were discharged without antiarrhythmic medication; these two patients were given quinidine therapy because of atrial fibrillation, but had normal early and late electrophysiological studies. Surgical ablation of Kent bundles by the epicardial approach for the treatment of Wolff-Parkinson-White syndrome can be achieved without the use of CPB. Optimal and steady exposure of the area are mandatory for the procedure, and dissection is eased by avoidance of heparin required for CPB.
Characterization of Native Outer Membrane Vesicles fromlpxLMutant Strains ofNeisseria meningitidisfor Use in Parenteral Vaccination (2005)

Native outer membrane vesicles (NOMV) of Neisseria meningitidis consist of intact outer membrane and contain outer membrane proteins (OMP) and lipooligosaccharides (LOS) in their natural conformation and membrane environment. NOMV have been safely used intranasally in P1 studies with encouraging results, but they are too toxic for parenteral vaccination. We now report the preparation and characterization of lpxL mutants that express LOS with reduced toxicity, and the evaluation of the potential of NOMV from these strains for use as a parenteral vaccine. A series of deletion mutants were prepared with knockouts of one or more of the lpxL1, lpxL2, or synX genes. The deltalpxL2 mutants had a reduced growth rate, reduced level of LOS expression, and increased sensitivity to surfactants. In addition, deltasynX deltalpxL2 double mutants had reduced viability in stationary phase. The deltalpxL1 deltalpxL2 double mutant behaved essentially the same as the deltalpxL2 single mutant. LOS from both lpxL mutant strains exhibited altered migration on polyacrylamide gels. The LOS of deltalpxL2 mutants of L3,7 strains were fully sialylated. NOMV prepared from lpxL2 mutants was about 200-fold less active than wild-type NOMV in rabbit pyrogen tests and in tumor necrosis factor alpha release assays. Bactericidal titers induced in animals by deltalpxL2 mutant NOMV were lower than those induced by deltalpxL1 or wild-type NOMV. However, immunogenicity could be largely restored by use of an adjuvant. These results provide evidence that NOMV from deltalpxL2 mutant strains will be safe and immunogenic in humans when given parenterally.
Expression and Characterization of Recombinant Human UDP-glucuronosyltransferases (UGTs) (2003)

Eight human liver UDP-glucuronosyltransferases (UGTs) were expressed in baculovirus-infected insect cells as fusion proteins carrying a short C-terminal extension that ends with 6 histidine residues (His tag). The activity of recombinant UGT1A1, UGT1A3, UGT1A4, UGT1A6, UGT2B4, UGT2B7, and UGT2B15 was almost fully inhibited by 0.2% Triton X-100. In the case of UGT1A9, however, glucuronidation of alpha-naphthol and scopoletin was resistant to such inhibition, whereas glucuronidation of entacapone and several other aglycones was sensitive. His-tagged UGT1A9 was purified by immobilized metal-chelating chromatography (IMAC). Purified UGT1A9 glucuronidated scopoletin at a high rate, whereas its glucuronidation activity toward entacapone was low and largely dependent on phospholipid addition. Recombinant UGT1A9 in which the His tag was replaced by hemagglutinin antigenic peptide (HA tag) was also prepared. Insect cells were co-infected with baculoviruses encoding both HA-tagged and His-tagged UGT1A9. Membranes from the co-infected cells, or a mixture of membranes from separately infected cells, were subjected to detergent extraction and IMAC, and the resulting fractions were analyzed for the presence of each type of UGT1A9 using tag-specific antibodies. In the case of separate infection, the HA-tagged UGT1A9 did not bind to the column. When co-infected with His-tagged UGT1A9, however, part of the HA-tagged enzyme was bound to the column and was eluted by imidazole concentration gradient together with the His-tagged UGT1A9, suggesting the formation of stable dimers that contain one His-tagged and one HA-tagged UGT1A9 monomers.
Role of caspase‐3 in tau truncation at D421 is restricted in transgenic mouse models for tauopathies (2009)

Truncated tau is widely detected in Alzheimer's disease brain, and caspase-3 has been considered as a major executioner for tau truncation at aspartate421 (D421), according to its capability of cleaving recombinant tau in vitro. Here we investigated the relationship between D421 truncated tau and caspase-3 in two transgenic mouse models for tauopathies. In adult transgenic mice, activated caspase-3 could not be detected in neurons containing truncated tau, with the exception of a few glia-like cells or neurons in postnatal mice. Caspase-3 expression exhibited a dramatic decrease at the early development stage, and kept at constantly low levels during adult stages in both wild type and transgenic mice. On the other hand, co-incubating brain homogenates from adult tau transgenic mice and ethanol-treated postnatal mice promoted tau truncation at D421, which was mildly reduced by caspase inhibitor, but completely suppressed by phosphatase inhibitor, indicating that hyperphosphorylated tau becomes a poor substrate for truncation at D421. Taken together, our study shows that insufficient caspase-3 expression and hyperphosphorylated status of tau in the adult transgenic mouse brain restrict caspase-3 as an efficient enzyme for tau truncation in vivo. Clearly, there is a caspase-3 independent mechanism responsible for tau truncation at D421 in these models.
Methylation profiles of genomic DNA of mouse developmental brain detected by restriction landmark genomic scanning (RLGS) method (1993)

Restriction landmark genomic scanning using methylation-sensitive endonucleases (RLGS-M) is a newly developed powerful method for systematic detection of DNA methylation. Using this method, we scanned mouse brain genomic DNAs from various developmental stages to detect the transcriptionally active regions. This approach is based on the assumption that CpG methylation, particularly of CpG islands, might be associated with gene transcriptional regulation. Genomic DNAs were prepared from telencephalons of 9.5-, 13.5- and 16.5-day embryos, 1- and 10-day neonates and adults, followed by subjecting them to RLGS-M and comparing their patterns with each other or with that of the adult liver. We used NotI as a methylation-sensitive restriction enzyme and surveyed the methylation states of 2,600 NotI sites, almost of which should correspond to gene loci. Although almost all RLGS spots (98%) were present constantly at every developmental stages, only a few percent of spots reproducibly appeared and disappeared at different developmental stages of the brain (44 spots, 1.7%) and some were tissue-specific (10 spots, 0.7%). These data suggest that DNA methylation associated with gene transcription is a well-programmed event during the central nervous system (CNS) development. Thus, RLGS-M can offer a means for detecting systematically the genes in which the state of DNA methylation changes during development of the higher organism.
Crystal structures of peptides and modified peptides (1996)

The X-ray diffraction experiments on peptides and related molecules which have been carried out in Western Europe, except Italy, in the last eight years are reviewed. The crystal structures of some bioactive peptides such as Leu-enkephalin (a neurotransmitter), cyclosporin A (an immunomodulator in both the free and protein-bound state), balhimycin (an antibiotic) and octreotide (a somatostatin analogue) are briefly presented. Crystallized N- and C-protected model peptides have given an insight into the folding tendency and folding modes depending on the peptide sequences. The crystal structures of various pseudopeptide molecules reveal how the three-dimensional structure of peptide analogues can be modulated by substituting non-peptide groups for the peptide bond. A few examples of structural mimetics of the beta- and gamma-turns, and of templates for alpha-helix induction are also presented.
Smooth Muscle–Specific Expression of the Smooth Muscle Myosin Heavy Chain Gene in Transgenic Mice Requires 5′-Flanking and First Intronic DNA Sequence (1998)

The smooth muscle myosin heavy chain (SM-MHC) gene encodes a major contractile protein whose expression exclusively marks the smooth muscle cell (SMC) lineage. To better understand smooth muscle differentiation at the transcriptional level, we have initiated studies to identify those DNA sequences critical for expression of the SM-MHC gene. Here we report the identification of an SM-MHC promoter-intronic DNA fragment that directs smooth muscle-specific expression in transgenic mice. Transgenic mice harboring an SM-MHC-lacZ reporter construct containing approximately 16 kb of the SM-MHC genomic region from -4.2 to + 11.6 kb (within the first intron) expressed the lacZ transgene in all smooth muscle tissue types. The inclusion of the intronic sequence was required for transgene expression, since 4.2 kb of the 5'-flanking region alone was not sufficient for expression. In the adult mouse, transgene expression was observed in both arterial and venous smooth muscle, in airway smooth muscle of the trachea and bronchi, and in the smooth muscle layers of all abdominal organs, including the stomach, intestine, ureters, and bladder. During development, transgene expression was first detected in airway SMCs at embryonic day 12.5 and in vascular and visceral SMC tissues by embryonic day 14.5. Of interest, expression of the SM-MHC transgene was markedly reduced or absent in some SMC tissues, including the pulmonary circulation. Moreover, the transgene exhibited a heterogeneous pattern between individual SMCs within a given tissue, suggesting the possibility of the existence of different SM-MHC gene regulatory programs between SMC subpopulations and/or of episodic rather than continuous expression of the SM-MHC gene. To our knowledge, results of these studies are the first to identify a promoter region that confers complete SMC specificity in vivo, thus providing a system with which to define SMC-specific transcriptional regulatory mechanisms and to design vectors for SMC-specific gene targeting.
Growth and nutritional trials on transgenic Nile tilapia containing an exogenous fish growth hormone gene (2001)

In a long‐term growth trial, transgenic tilapia Oreochromis niloticus L. showed a 2·5‐fold increase in growth compared with non‐transgenic siblings. At 7 months, mean mass of transgenic tilapia was 653 g compared with 260 g for non‐transgenic siblings. A significant increase ( P &gt;0·01) in head: total length ratio, viscera‐somatic index and hepato‐somatic index was observed in transgenic fish. Female gonado‐somatic index ( I G) was found to be lower in transgenics than non‐transgenic siblings in both mixed and separate culture conditions. Transgenic male I G values were found to be higher in mixed culture and lower in separate culture than that of their non‐transgenic siblings. Food conversion efficiency was more than 20% greater in the transgenic fish. In a second shorter‐term growth performance trial, the transgenic fish grew to about four times the size of their non‐transgenic siblings. A digestibility trial suggested that transgenic tilapia were more efficient utilizers of protein, dry matter and energy. Apparent digestibility of protein and apparent energy digestibility were higher in the transgenic fish.
Isolation and characterization of the c-fos(rat) cDNA and analysis of post-translational modification in vitro. (1987)

c-fos mRNA accumulates to a level of 0.2% of cellular poly(A)-containing RNA 45 min after treatment of rat pheochromocytoma (PC12) cells with 1 mM barium chloride. Several clones of the c-fos(rat) cDNA were isolated from a cDNA library constructed from this RNA population. Nucleotide sequence analysis of a full-length cDNA clone reveals striking conservation among the c-fos genes isolated from rat, mouse and human cells, and confirms the c-fos gene structure predicted from an analysis of c-fos genomic clones. Translation of an SP6-derived transcript of the c-fos(rat) cDNA in a messenger-dependent rabbit reticulocyte lysate yields the complete c-fos protein. It undergoes extensive post-translational modification in the lysate, particularly in the presence of additional cAMP. The c-fos protein synthesized in vitro appears to be phosphorylated by the cAMP-dependent protein kinase.
Serum Amyloid P Component Binding to C4b-binding Protein (1995)

Human C4b-binding protein (C4BP), which is a regulator of the classical complement pathway C3 convertase, forms high affinity complexes with anticoagulant protein S and with the pentraxin serum amyloid P component (SAP). SAP is a plasma protein present in all amyloid deposits. Recently, SAP was shown to inhibit the complement regulatory functions of C4BP. In this investigation, we have studied the structural requirements for the C4BP-SAP interaction. C4BP was subjected to chymotrypsin digestion, which yielded two major fragments corresponding to the central core (160 kDa) and to the cleaved-off tentacles (48 kDa). SAP-Sepharose specifically bound the 160-kDa fragment, suggesting that the central core of C4BP contains the binding site for SAP. In a quantitative affinity chromatography assay, the dissociation constants for binding of intact C4BP and of the 160-kDa central core fragment to SAP were found to be 30 and 70 nM, respectively. Recombinant C4BP composed of only alpha-chains bound SAP with similar affinity (Kd = 22 nM), whereas nonglycosylated recombinant alpha-chain C4BP (synthesized in the presence of tunicamycin) bound SAP with lower affinity (Kd = 126 nM). This suggests that the carbohydrate moiety of the central core of C4BP is important for binding of C4BP to SAP in contrast to the C4BP beta-chain, which is not required. EDTA, heparin, and phosphorylethanolamine as well as a peptide comprising amino acids 27-39 of SAP were found to completely displace C4BP from the SAP matrix. Moreover, the immobilized SAP peptide bound C4BP in a reaction that, in contrast to the C4BP-SAP interaction, was not dependent on calcium.
Design Framework for Social Wearables (2019)

Wearables are integrated into many aspects of our lives, yet, we still need further guidance to develop devices that truly enhance in-person interactions, rather than detract from them by taking people's attention away from the moment and one another. The value of this paper is twofold: first, we present an annotated portfolio of 'social wearables', namely technology designs worn on the body that augment co-located interaction. The design work described can serve as inspiration for others. Then we propose a design framework for social wearables grounded in prior work, as well as our own design research, that can help designers to ideate by raising valuable questions to begin their inquiry with and use to evaluate their designs. We illustrate the evaluative value of this framework through two social wearable designs, each tested in the appropriate social setting.
Large spontaneous spin splitting in gate-controlled two-dimensional electron gases at normal In0.75Ga0.25As/In0.75Al0.25As heterojunctions (2001)

Amounts of spontaneous spin splittings were estimated from low-temperature magnetoresistances in two-dimensional electron gases created at In0.75Ga0.25As/In0.75Al0.25As heterojunctions under a gate bias. Typical sheet electron densities and mobilities in the raw wafers were ∼1.0×1012/cm2 and 2–5×105 cm2/V s at 1.5 K, respectively. A maximum spin-orbit coupling constant αzero of ∼30(×10−12 eV m) was obtained for the van der Pauw sample. In gated Hall-bar samples, a decrease in the αzero value with decreasing gate voltage (Vg) was first confirmed in a normal heterojunction. The main origin for such a large αzero, which is a few times larger than any previously reported, was found to be a structure-dependent so-called interface contribution in the Rashba term.
TGF-β2, a Protective Intestinal Cytokine, Is Abundant in Maternal Human Milk and Human-Derived Fortifiers but Not in Donor Human Milk (2013)

Pasteurization decreases concentrations of most cytokines and lactoferrin in DHM. TGF-β2, a protective intestinal cytokine, has comparable concentrations in HDMF to MHM despite pasteurization.
Single-crystalline (100) Ge networks on insulators by rapid-melting growth along hexagonal mesh-pattern (2011)

Single-crystalline-Ge (c-Ge) networks on insulator films formed on Si substrates are essential for integrating high-speed and multifunctional devices onto the Si-platform. Rapid-melting-growth of mesh-patterned amorphous-Ge is examined over large areas (500×250 μm2). For squared-mesh-pattern, polycrystalline-Ge forms throughout most of the mesh, though c-Ge is obtained near (&amp;lt;100 μm) Si-seed. Based on the consideration of geometric-effects, mesh-patterns are changed to hexagonal. This realizes c-Ge networks over the entire insulator area. These results indicate that Ge growth initiated from Si-seed propagates laterally over the hexagonal-mesh-pattern though bending and branching. These unique c-Ge-networks on insulators facilitate Ge-based advanced-devices on the Si-platform.