gebhart/patrepeval huggingface dataset:
The Lorentz-Polarization Factor and Preferred Orientation in Oriented Clay Aggregates (1986)

Abstract A closed-form equation was derived that describes the powder-ring distribution factor as a function of 2 θ , soller slit collimation, and σ *, which is defined as the standard deviation of an axially symmetrical Gaussian orientation function. Methods were developed for measuring σ * in the reflection mode by means of a θ /2 θ diffractometer. Six experimental arrangements for a sedimentary chlorite showed widely different intensity ratios of the 001/005 reflections and gave a standard deviation of ±5.8% when corrected by the theory. The absolute integrated intensities of the 003 reflection from eleven illite samples provided an eight-fold maximum range which, when corrected, yielded a standard deviation of ±7.7%. The intensity distributions within each of two X-ray powder diffraction patterns obtained from instruments with different soller-slit configurations could not be directly compared at low diffraction angles unless corrections, based on σ *, were introduced to allow for the differences in axial divergence.
Ohmic contact formation mechanism of nonalloyed Pd contacts to p-type GaN observed by positron annihilation spectroscopy (1999)

The change of the Fermi energy level at the interface of Pd/p-type GaN by surface treatment was investigated using positron annihilation spectroscopy, and the results were used to provide interpretation of the electrical properties of the contact. Changes in the positron parameters at the interface in the aqua regia-treated GaN are more pronounced than that in the HCl-treated one. This provides evidence that the surface treatment with aqua regia prior to Pd metal deposition removes surface oxides, resulting in the shift of the Fermi level position from a middle of the bandgap to near the valence band. Thus, the barrier for hole injection from metal to p-type GaN is lowered, subsequent to the decrease of contact resistivity by two orders of magnitude.
Genomic organization of human JAK2 and mutation analysis of its JH2-domain in leukemia (1999)

The Janus kinase family of proteins, with four mammalian members (JAK1, JAK2, JAK3 and TYK2), plays an essential role in the signal transduction pathway from non-catalytic cytokine receptors to the nucleus. We recently reported the involvement of ETV6-JAK2 fusion genes in the development of leukemia of both lymphoid and myeloid origin. Dominant missense mutations of hopscotch, a Drosophila JAK homologue, causing leukemia-like defects were described. One of these mutations affected a conserved residue of the kinase- like JH2 domain and the introduction of this mutation in murine Jak2 resulted in the constitutional activation of its kinase activity. In order to further analyze its role in leukemogenesis, we cloned human JAK2 and determined its genomic organization. Twenty-four exons spanning a region of approximately 150 kb were identified. A mutation analysis of the exons 13 to 19, encoding the kinase-like JH2 domain failed to detect activating mutations in leukemia samples, suggesting that this is a rare event in human leukemia.
Photocrosslinkable poly(ethylene oxide) and poly(vinyl alcohol) hydrogels for tissue engineering cartilage (2003)

Photopolymerizable hydrogels are attractive for tissue-engineered applications because of their high water content, tissue-like mechanical properties, and ability to be polymerized in vivo under physiological conditions. We are interested in using photocrosslinkable macromers of poly(ethylene oxide) (PEG) and poly(vinyl alcohol) (PVA) to encapsulate chondrocytes for cartilage tissue regeneration. Our aim is to optimize the network composition and structure to facilitate regeneration of type-specific cartilage in a hydrogel that will temporarily withstand the normal loads of natural cartilage. We have demonstrated that cartilage produced in two hydrogel systems resulted in 6.7/spl plusmn/1.2% (PVA) and 1.5/spl plusmn/0.8% (PEG) total glycosaminoglycans and 2.5/spl plusmn/2% (PVA) and 6.5/spl plusmn/0.7% (PEG) total collagen per wet weight of cartilage after 6 and 7 weeks, respectively.
Novel phase transition in two-dimensional xy-models with long-range interaction (2005)

The purpose of this article is to give an overview of results concerning ordering and critical properties of two-dimensional ferromagnets including the dipolar interaction. We investigate a two-dimensional xy-model extended by the dipolar interaction. Describing our system by a nonlinear -model and using renormalization group methods we predict a phase transition to an ordered state. This transition is due to the long-range dipolar interaction. The ferromagnetic phase is governed by a low temperature fixed-point with infinite dipolar coupling. In the critical regime we find exponential behavior for the correlation length and the order parameter in contrast to the usual power laws. The nature of the transition shows a striking similarity to the Kosterlitz-Thouless transition. We show that there is a whole class of longrange xy-models leading to such non-standard behavior. Parameterizing the divergencies in terms of the correlation length we are able to calculate the critical exponents. These exponents are correct in any loop order.
Renal function in patients with non-dialysis chronic kidney disease receiving intravenous ferric carboxymaltose: an analysis of the randomized FIND-CKD trial (2017)

ClinicalTrials.gov NCT00994318 (first registration 12 October 2009).
Extrathymic Pathways of T-cell Differentiation in the Liver and Other Organs (1994)

Key Words: extrathymic T cellsintraepithelial lymphocytesliverthymic medullaT cell receptorintestineautoimmunity
Wound drains in proximal femoral fracture surgery: a randomized prospective trial of 177 patients. (1995)

We report on a prospective randomized trial on the effect of wound drains on wound healing following surgery for proximal femoral fractures. One hundred and seventy-seven consecutive patients admitted to Queen's Medical Centre Nottingham, undergoing AO dynamic hip screw (DHS) or hemiarthroplasty were randomized whether or not to receive wound drainage. Wound healing was assessed in terms of ultrasound examination, the ASEPSIS wound score system and overt infection rates. All patients were followed up at 6 weeks and 6 months. Ultrasound examinations showed that drains were indeed ineffective in preventing haematoma formation, the first time this has been demonstrated objectively. However, using drains failed to prevent late seroma formation. Patients who received wound drainage showed statistically better wound healing on the ASEPSIS wound scoring system and a reduced infection rate. The ASEPSIS scores on day 2 and 5 postoperatively proved an accurate predictor of poor wound healing. This study conflicts with previous smaller studies which failed to show an effect of wound drainage upon wound healing, and strongly supports the use of wound drains.
Unique Physical Properties and Interactions of the Domains of Methylated DNA Binding Protein 2 (2010)

Methylated DNA binding protein 2 (MeCP2) is a methyl CpG binding protein whose key role is the recognition of epigenetic information encoded in DNA methylation patterns. Mutation or misregulation of MeCP2 function leads to Rett syndrome as well as a variety of other autism spectrum disorders. Here, we have analyzed in detail the properties of six individually expressed human MeCP2 domains spanning the entire protein with emphasis on their interactions with each other, with DNA, and with nucleosomal arrays. Each domain contributes uniquely to the structure and function of the full-length protein. MeCP2 is approximately 60% unstructured, with nine interspersed alpha-molecular recognition features (alpha-MoRFs), which are polypeptide segments predicted to acquire secondary structure upon forming complexes with binding partners. Large increases in secondary structure content are induced in some of the isolated MeCP2 domains and in the full-length protein by binding to DNA. Interactions between some MeCP2 domains in cis and trans seen in our assays likely contribute to the structure and function of the intact protein. We also show that MeCP2 has two functional halves. The N-terminal portion contains the methylated DNA binding domain (MBD) and two highly disordered flanking domains that modulate MBD-mediated DNA binding. One of these flanking domains is also capable of autonomous DNA binding. In contrast, the C-terminal portion of the protein that harbors at least two independent DNA binding domains and a chromatin-specific binding domain is largely responsible for mediating nucleosomal array compaction and oligomerization. These findings led to new mechanistic and biochemical insights regarding the conformational modulations of this intrinsically disordered protein, and its context-dependent in vivo roles.
Sequence and analysis of a swinepox virus homologue of the vaccinia virus major envelope protein P37 (F13L) (2000)

P37 (F13L gene product), the most abundant protein in the envelope of the extracellular virus form of the prototype poxvirus, vaccinia virus (VV), is a crucial player in the process leading to acquisition of the envelope, virus egress and transmission. We have cloned and sequenced a swinepox virus (SPV) gene homologous to VV F13L. The SPV gene product, termed P42, was 54% identical to P37, the VV F13L gene product, and, among the poxviruses, was most similar (73% identity) to the myxoma virus homologue. The SPV P42 gene contained late transcription signals and was expressed only at late times during infection. The protein was palmitylated, and showed an intracellular distribution similar to that of VV P37, both by immunofluorescence and by subcellular fractionation. As with VV P37, SPV P42 was incorporated in extracellular enveloped SPV particles, but was absent from the intracellular mature virus form. To check the ability of SPV P42 to function in the context of VV infection, we inserted the SPV gene into a VV deficient in P37, which is severely blocked in virus envelopment and cell-to-cell transmission. Despite correct expression of SPV P42, the resulting recombinant VV showed no rescue of extracellular virus formation or cell-to-cell virus spread. The lack of function of SPV P42 in the VV genetic background suggests that specific interactions between SPV P42 or VV P37 and other viral proteins is required to drive the envelopment process.
Harnessing the heart’s resistance to malignant tumors: cardiac-derived extracellular vesicles decrease fibrosarcoma growth and leukemia-related mortality in rodents (2017)

The heart is known for its resistance to cancer. Although different conjectures have been proposed to explain this phenomenon, none has been tested. We propose that the heart microenvironment may exert anti-cancer properties. So, our objective was to test the anti-oncogenic potential of cardiac-derived extracellular vesicles (EVs). For that EVs secreted by cardiosphere-derived cells (CDCs, heart progenitor cells) were tested <i>in vitro</i> on fibrosarcoma HT1080. <i>In vivo</i> models comprised the xenograft HT1080 fibrosarcoma in athymic mice (n=35), and spontaneous acute lymphocyte leukemia in old rats (n=44). CDC-EVs were compared with two control groups: EVs secreted by bone-marrow derived mesenchymal stem cells (MSC-EVs) and phosphate-buffered saline (PBS). Injection of CDC-EVs led to a 2.5-fold decrease of fibrosarcoma growth in mice (p<0.01 and p<0.05 for human and rat EVs, respectively) vs PBS group. The effect was associated with 2-fold decrease of tumor cells proliferation (p<0.001) and 1.5-fold increase of apoptosis (p<0.05) in CDC-EV vs PBS mice. Salutary changes in tumor gene and protein expression were observed in CDC-EV animals. CDC-EVs reduced tumor vascularization compared with PBS (p<0.05) and MSC-EVs (p<0.01). Moreover, CDC-EVs increased leukemia-free survival (p<0.05) in old rats vs PBS. MiR-146, highly enriched in CDC-EVs, may be implicated in part of the observed effects. In conclusion, this study presents the first evidence that ties together the long-recognized enigma of the "heart immunity to cancer" with an antioncogenic effect of heart-derived EVs. These findings open up cancer as a new therapeutic target for CDC-EVs.
Targeted DNA methylation in vivo using an engineered dCas9-MQ1 fusion protein (2017)

Comprehensive studies have shown that DNA methylation plays vital roles in both loss of pluripotency and governance of the transcriptome during embryogenesis and subsequent developmental processes. Aberrant DNA methylation patterns have been widely observed in tumorigenesis, ageing and neurodegenerative diseases, highlighting the importance of a systematic understanding of DNA methylation and the dynamic changes of methylomes during disease onset and progression. Here we describe a facile and convenient approach for efficient targeted DNA methylation by fusing inactive Cas9 (dCas9) with an engineered prokaryotic DNA methyltransferase MQ1. Our study presents a rapid and efficient strategy to achieve locus-specific cytosine modifications in the genome without obvious impact on global methylation in 24 h. Finally, we demonstrate our tool can induce targeted CpG methylation in mice by zygote microinjection, thereby demonstrating its potential utility in early development.
Deficient expression of NCR in NK cells from acute myeloid leukemia: evolution during leukemia treatment and impact of leukemia cells in NCRdull phenotype induction (2006)

Natural killer (NK) cells play an important role in tumor-cell clearance, particularly against leukemia, as shown by killer cell inhibitory receptor (KIR)-mismatched allogeneic stem cell transplantation. Analysis of in vitro IL-2-expanded NK cells from patients with myelocytic/monocytic acute myeloid leukemia (AML-NK cells) has revealed poor cytolytic functions because of deficient expression of pivotal activation molecules-the natural cytotoxicity receptors (NCRs) NKp30, NKp44, and NKp46. To exclude the possibility that this observation was caused by the in vitro amplification of a small NCR(dull) population, we analyzed the AML-NK phenotype directly, without any in vitro expansion. We first confirmed that the NCR(dull) phenotype was not an in vitro artifact. Moreover, analysis of a large population of AML patients allowed us to demonstrate that phenotype was not restricted to a French-American-British (FAB) subtype and was not associated with a particular cytogenetic abnormality. Our longitudinal study of AML patients showed that the NCR(dull) phenotype was acquired during leukemia development because we observed its complete (for NKp46) or partial (for NKp30) reversibility in patients achieving complete remission (CR). Reversibility of the NCR(dull) phenotype after CR suggested that leukemia cells might be involved in NCR down-regulation. In agreement with this hypothesis, direct contact between leukemic blasts and NK cells (but not leukemia-cell supernatants) induced loss or decrease in NKp30 and NKp46 expression while impeding NKp44 induction by IL-2. We excluded the major implication of TGF-beta in NCR down-regulation. Although the clinical antitumor value of NK cells is clearly demonstrated in allogeneic stem cell transplantation, the role of NK cells in autologous transplantation is not proved. Interestingly, we observed a correlation between the NCR(dull) phenotype and poor survival in AML patients, suggesting that NK-deficient activation caused by NCR down-regulation could play a role in patient outcome. The prognostic value of NCR expression is discussed, and pathophysiologic implication of the NCR phenotype will be further investigated in a larger study.
Attraction between Surfaces in a Polymer Melt Containing Telechelic Chains:  Guidelines for Controlling the Surface Separation in Intercalated Polymer−Clay Composites (1999)

Using numerical and analytical self-consistent field (SCF) calculations, we investigate the interactions between two closely spaced surfaces and the surrounding polymer melt, which contains a volume fraction of end-functionalized polymers. The functionalized polymers contain two reactive “stickers”, one at each end of the chain, that are highly attracted to the surfaces. The surfaces model clay crystallites, or sheets. Through the calculations, we determine the free energy profiles as the surfaces are pried apart and the polymer fills the gap. The free energy vs distance plots reveal a distinctive minimum, even at very small volume fractions of the end-functionalized chains. Thus, the presence of these telechelic polymers promotes the formation of thermodynamically stable intercalated composites, where the polymers enhance the separation between the silicate sheets. However, the telechelic chains prohibit the creation of the more desirable exfoliated structures, where the sheets are uniformly dispersed throughout the polymer matrix. The results provide guidelines for significantly enhancing the separation between the sheets, thus possibly making properties of the intercalated composites more like the exfoliated material.
Crystal structure of a thermostable type B DNA polymerase from Thermococcus gorgonarius (1999)

Most known archaeal DNA polymerases belong to the type B family, which also includes the DNA replication polymerases of eukaryotes, but maintain high fidelity at extreme conditions. We describe here the 2.5 A resolution crystal structure of a DNA polymerase from the Archaea Thermococcus gorgonarius and identify structural features of the fold and the active site that are likely responsible for its thermostable function. Comparison with the mesophilic B type DNA polymerase gp43 of the bacteriophage RB69 highlights thermophilic adaptations, which include the presence of two disulfide bonds and an enhanced electrostatic complementarity at the DNA-protein interface. In contrast to gp43, several loops in the exonuclease and thumb domains are more closely packed; this apparently blocks primer binding to the exonuclease active site. A physiological role of this "closed" conformation is unknown but may represent a polymerase mode, in contrast to an editing mode with an open exonuclease site. This archaeal B DNA polymerase structure provides a starting point for structure-based design of polymerases or ligands with applications in biotechnology and the development of antiviral or anticancer agents.
Quantitative and Qualitative Differences in the In Vivo Response of NKT Cells to Distinct α- and β-Anomeric Glycolipids (2004)

NKT cells represent a unique subset of immunoregulatory T cells that recognize glycolipid Ags presented by the MHC class I-like molecule CD1d. Because of their immunoregulatory properties, NKT cells are attractive targets for the development of immunotherapies. The prototypical NKT cell ligand alpha-galactosylceramide (alpha-GalCer), originally isolated from a marine sponge, has potent immunomodulatory activities in mice, demonstrating therapeutic efficacy against metastatic tumors, infections, and autoimmune diseases, but also has a number of adverse side effects. In vivo administration of alpha-GalCer to mice results in the rapid activation of NKT cells, which is characterized by cytokine secretion, surface receptor down-regulation, expansion, and secondary activation of a variety of innate and adaptive immune system cells. In this study, we have evaluated the in vivo immune response of mice to a set of structural analogues of alpha-GalCer. Our results show that, contrary to current thinking, beta-anomeric GalCer can induce CD1d-dependent biological activities in mice, albeit at lower potency than alpha-anomeric GalCer. In addition, we show that the response of NKT cells to distinct GalCer differs not only quantitatively, but also qualitatively. These findings indicate that NKT cells can fine-tune their immune responses to distinct glycolipid Ags in vivo, a property that may be exploited for the development of effective and safe NKT cell-based immunotherapies.
A Back-Illuminated Time-of-Flight Image Sensor with SOI-Based Fully Depleted Detector Technology for LiDAR Application (2018)

A back-illuminated time-of-flight (ToF) image sensor based on a 0.2 µm silicon-on-insulator (SOI) CMOS detector technology using fully-depleted substrate is developed for the light detection and ranging (LiDAR) applications. A fully-depleted 200 µm-thick bulk silicon is used for the higher quantum efficiency (QE) in a near-infrared (NIR) region. The developed SOI pixel structure has a 4-tapped charge modulator with a draining function to achieve a higher range resolution and to cancel background light signal. A distance is measured up to 27 m with a range resolution of 12 cm at the outdoor and average light power density is 150 mW/m2@30 m.
An active covalently linked dimer of human interferon-gamma. Subunit orientation in the native protein. (1992)

We have constructed and expressed a covalently linked head to tail dimer of human interferon-gamma (IFN-gamma) in which two monomers are joined head to tail via a rigid peptide hinge using genetic engineering techniques. The hinge was derived from the human immunoglobin IgA1 sequence (Hallewell, R.A., Laria, I., Tabrizi, A., Carlin, G., Getzoff, E.D., Tainer, J.A., Cousens, L.S., and Mullenbach, G.T. (1989) J. Biol. Chem. 264, 5260-5268). Analysis by sodium dodecyl sulfate-polyacrylamide gel electrophoresis shows that the polypeptide produced by this construction migrates as a 30,000 polypeptide species. The protein elutes as a single species by molecular sieve chromatography under native conditions. The covalently linked dimer exhibits one-half the antiviral activity of native dimeric IFN-gamma; receptor binding assays show the covalently linked dimer binds to the IFN-gamma receptor with one-half the avidity of native IFN-gamma. This difference is not due to conformational differences between the two molecules, as the aromatic region of the NMR spectrum of the purified covalently linked dimer is identical with that of the wild type protein. From these data, we suggest that human IFN-gamma associates in a head to tail dimer in its active configuration. Regions of IFN-gamma are contiguous with the amino and carboxyl termini and are obscured by the hinge peptide in the covalently linked dimer. Our studies demonstrate that these regions may be important for receptor-ligand interaction.
Growth process conditions of vertically aligned carbon nanotubes using plasma enhanced chemical vapor deposition (2001)

The growth of vertically aligned carbon nanotubes using a direct current plasma enhanced chemical vapor deposition system is reported. The growth properties are studied as a function of the Ni catalyst layer thickness, bias voltage, deposition temperature, C2H2:NH3 ratio, and pressure. It was found that the diameter, growth rate, and areal density of the nanotubes are controlled by the initial thickness of the catalyst layer. The alignment of the nanotubes depends on the electric field. Our results indicate that the growth occurs by diffusion of carbon through the Ni catalyst particle, which rides on the top of the growing tube.