gebhart/patrepeval huggingface dataset:
Capillary Deposition of Complement Split Product C4d in Renal Allografts is Associated with Basement Membrane Injury in Peritubular and Glomerular Capillaries (2002)

Endothelial deposition of the complement split product C4d is an established marker of antibody-mediated acute renal allograft rejection. A contribution of alloantibody-dependent immune reactions to chronic rejection is under discussion. In this study, the association of immunohistochemically detected endothelial C4d deposition in peritubular capillaries (PTC) with morphologic features of chronic renal allograft injury was investigated in a large study cohort. C4d deposits in PTC were detected in 73 (34%) of 213 late allograft biopsies performed in 213 patients more than 12 mo after transplantation (median, 4.9 yr) because of chronic allograft dysfunction. Endothelial C4d deposition was found to be associated with chronic transplant glomerulopathy (CG) (P < 0.0001), with basement membrane multilayering in PTC (P = 0.01), and with an accumulation of mononuclear inflammatory cells in PTC (P < 0,001). Furthermore, C4d deposits in PTC (in biopsies with normal glomerular morphology) were associated with development of CG in follow-up biopsies. Other morphologic features of chronic allograft nephropathy (with exception of tubular atrophy) were not associated with C4d deposits in PTC. Analyses of previous and follow-up biopsies revealed that C4d deposits may occur de novo and may also disappear at any time after transplantation. In conclusion, the data suggest that complement activation in renal microvasculature, indicating humoral alloreactivity, contributes to chronic rejection characterized by chronic transplant glomerulopathy and basement membrane multilayering in PTC.
Effect of Linker Length on DNA Duplexes Containing a Mismatched O6-2'-Deoxyguanosine-Alkyl Interstrand Cross-Link (2008)

DNA duplexes containing a directly opposed O(6)- alkyl-2'-deoxyguanosine interstrand cross-link were synthesized to serve as structural mimics of lesions formed by the bifunctional chemotherapeutic alkylating agents busulfan and hepsulfam. One of the key steps to prepare the necessary bis-phosphoramidites involved the Mitsunobu reaction between a diol linking two protected 2'-deoxyguanosine nucleosides at the O(6) position. These bis-phosphoramidites were incorporated into 11-bp DNA duplexes by solid phase synthesis to produce cross-linked DNA probes in high yields. UV thermal denaturation studies revealed that these interstrand cross-linked containing oligonucleotides were stabilized compared to a DNA duplex containing a central 2'-deoxyguanosine mismatch. The duplex containing the four carbon cross-link was stabilized by 10 degrees C relative to the seven carbon linker. Molecular models of these duplexes that were geometry optimized by the AMBER force field suggest that the seven carbon cross-link was less efficiently accommodated in the major groove of the duplex relative to the four carbon linker, accounting for the observed destabilization.
Relative Contributions of Chemistry and Topography to the Osseointegration of Hydroxyapatite Coatings (2002)

The purpose of the current study was to ascertain the relative contributions of surface chemistry and topography to the osseointegration of hydroxyapatite-coated implants. A canine femoral intramedullary implant model was used to compare the osseous response to commercially pure titanium implants that were either polished, grit-blasted, plasma-sprayed with hydroxyapatite, or plasma-sprayed with hydroxyapatite and masked with a very thin layer of titanium using physical vapor deposition (titanium mask). The titanium mask isolated the chemistry of the underlying hydroxyapatite layer without functionally changing its surface topography and morphologic features. At 12 weeks, the bone-implant specimens were prepared for undecalcified thin section histologic evaluation and serial transverse sections were quantified with backscattered scanning electron microscopy for the percentage of bone apposition to the implant surface. Bone apposition averaged 3% for the polished implants and 23% for the grit-blasted implants. Bone apposition to the hydroxyapatite-coated implants averaged 74% whereas bone apposition to the titanium mask implants averaged 59%. Although there was significantly greater osseointegration with the hydroxyapatite-coated implants, 80% of the maximum bone forming response to the implant surfaces developed with the titanium mask implants. This simple, controlled experiment revealed that topography is the dominant factor governing bone apposition to hydroxyapatite-coated implants.
Magnetic anisotropies and exchange coupling in ultrathin fcc Co(001) structures (1991)

Metastable fcc structures using ultrathin layers of metastable fcc Co(001) and fcc Cu(001) were grown by molecular-beam epitaxy. The growth was studied using reflection high-energy electron-diffraction (RHEED) patterns and RHEED intensity oscillations. The magnetic properties were investigated by employing ferromagnetic-resonance (FMR) and surface magneto-optic Kerr effect (SMOKE) techniques. A detailed discussion of the underlying physical mechanisms in FMR and SMOKE studies is presented. The temperature and thickness dependences of the perpendicular uniaxial and fourfold in-plane anisotropies are given and discussed. The role of lattice strains in magnetic anisotropies is demonstrated. FMR measurements revealed that the magnetic properties of single Co layers are different from those in Co/Cu/Co trilayers becuase of a lattice-strain relaxation in the multilayer samples. The exchange coupling between fcc Co(001) layers separated by a fcc Cu(001) interlayer was studied for several structures. The exchange coupling in Co structures was found to be anisotropic. Hysteresis loops were measured by means of SMOKE. Magnetic-trilayer hysteresis loops are complex. Micromagnetic calculations were carried out to explain their main features.
Human Milk Oligosaccharides: Next-Generation Functions and Questions (2019)

Human milk oligosaccharides (HMOs) are the third most abundant component of human milk. So far, more than 150 different and structurally distinct HMOs have been identified. HMO composition varies substantially between women, but remains fairly constant over the course of lactation in the same woman. Which maternal genetic and environmental factors drive the interindividual variations in HMO composition remains poorly understood, and it is currently unknown whether or not a woman's characteristic HMO composition has evolved to match her own infant's specific needs. A combination of preclinical, cohort, and clinical studies is required to fully assess the many effects, functions, and potential claims associated with HMOs. In some cases, individual HMOs exert a certain effect and, while there might be some redundancy, the effects are often highly structure-specific. In other cases, a combination of different HMOs in specific ratios to each other is required to be effective, and future research needs to assess whether or not the administration of individual HMOs alone may be counterproductive and potentially harmful to the infant's short- and long-term health. Overall, the personalized complexity of HMOs cannot be mimicked in artificial infant formula and provides yet another powerful reason to protect, promote, and support breastfeeding.
REVIEW OF B. F. SKINNER'S THE BEHAVIOR OF ORGANISMS<sup>1</sup> (1988)

As I reread my review nearly 50 years later, I think of the circumstances. I had heard a paper by Fred at the Ithaca meeting of the APA in 1932, and recall the praise by Edna Heidbreder, who was sitting next to me, whose remark was that "He has a clean mind." The year before his book appeared, I had already cited eight of his published papers in a review of the conditioned response in relation to conventional learning experiments that appeared in the Psychological Bulletin (1937, 34, 61-102). It may be because of that the editor sent me Fred's book to review.When I received the copy of his new book to review, I read it carefully, and soon reported on it orally before Lewis Terman's weekly seminar to get comments and questions before revising my review. I was pleased by Terman's excitement over the originality of Fred's approach.
A 1 watt, 38 GHz monolithic grid oscillator (2002)

We have demonstrated a monolithic grid oscillator that shows 1 watt of effective transmitter power at 38 GHz. Use of a wire twist reflector as an external feedback element added to a successful monolithic grid amplifier allows a tuning range from 37.5 GHz to 41 GHz. Impedance matching is accomplished by a double-slug tuner and the movable back-short of the twist reflector.
Swelling of Wood. Part II. Swelling in Organic Liquids (1994)

The rate and maximum swelling of several North American wood species in 40 organic liquids have been obtained with a computer interfaced linear variable displacement transformer. Since wood swells very fast in some organic liquids, even at room temperature, this apparatus made it possible to obtain accurate rate data on the swelling of wood in organic liquids. It was found that many similarities existed between wood and cellulose maximum swelling within various solvent chemical classes. Hence, it appears that cellulose is the primary wood polymer responsible for the major amount of swelling of wood (...)
A motion estimator for low bit-rate video codec (1992)

A novel component performing motion estimation is presented. This chip is designed based on the three-step hierarchical search block-matching algorithm and can be applied to image communication on ISDN (integrated services digital network) (H.261 standard), MPEG, TV transmission, HDTV (high-definition television), etc. The practical architectural design techniques and the chip features are discussed. This component has the following features: unified execution steps, low latency delay, low I/O bandwidth, regular hardware structure, and single-chip or cascaded configurations.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Inflammation and pregnancy: the role of the immune system at the implantation site (2011)

The concept that pregnancy is associated with immune suppression has created a myth of pregnancy as a state of immunological weakness and, therefore, of increased susceptibility to infectious diseases. A challenging question is whether the maternal immune system is a friend or a foe of pregnancy. In this review, we discuss data associated to the role of the immune system during pregnancy. We propose a new paradigm in terms of the fetal-maternal immune interaction as well as the immunological response of the mother to microorganism. Our challenge is to better understand the immunology of pregnancy in order to deliver the appropriate treatment to patients with pregnancy complications as well as to determine public policies for the protection of pregnant women during pandemics.
Characteristics of Long-Term Cultures of Avian Primordial Germ Cells and Gonocytes1 (2013)

Avian cell lines derived from germinal crescent primordial germ cells and gonadal gonocytes with long-term proliferative capacity in vitro and their subsequent rates of colonization and germline transmission are described. In general, male cultures proliferate more rapidly than female cultures although both can be developed into cell lines of >2 × 10(6) cells, at which time, they can be grown indefinitely and a cell bank can be established. All the cell lines injected into embryos transmitted through the germline with the percentage of germline transmission of both male and female cell lines varying from single digits to the high 90s. The derivation of these primordial germ cell and gonadal cell lines and the subsequent robustness of germline transmission validates these cells as suitable for establishment of lines of chickens bearing novel genetic modifications.
Interplay between interferon and other cytokine systems in bone metabolism (2005)

Interferons (IFNs) play crucial roles in the regulation of a wide variety of innate and adaptive immune responses. Type I interferons (IFN-alpha/beta) are central to the host defense against pathogens such as viruses, whereas type II interferon (IFN-gamma) mainly contributes to the T-cell-mediated regulation of the immune responses. Studies of bone destruction associated with rheumatoid arthritis have highlighted the importance of the interaction between the immune and skeletal systems. Recently, a new research area, termed osteoimmunology, has been spawned by a series of studies focusing on the signaling networks between IFN and other cytokines in bone metabolisms. It has been revealed that IFN-gamma interferes with the osteoclast differentiation induced by receptor activator of nuclear factor-kappaB ligand (RANKL), and this mechanism is critical for the suppression of pathological bone resorption associated with inflammation. In addition, RANKL induces the IFN-beta gene in osteoclast precursor cells, and this induction constitutes a critical aspect of the negative feedback regulation mechanisms of RANKL signaling to suppress excessive osteoclastogenesis. Furthermore, a novel function of signal transducer and activator of transcription 1 (Stat1), the essential transcription factor for both type I and type II IFN responses, was revealed in the regulation of osteoblast differentiation. Collectively, these studies unveil novel aspects of the IFN system and indicate the operation of the intricate signaling network among IFN and other cytokine systems in bone remodeling, which might offer a molecular basis for the treatment of bone diseases.
A Helium Densitometer for Use with Powdered Materials (1943)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTA Helium Densitometer for Use with Powdered MaterialsWalter C. Schumb and Edmund S. RittnerCite this: J. Am. Chem. Soc. 1943, 65, 9, 1692–1695Publication Date (Print):September 1, 1943Publication History Published online1 May 2002Published inissue 1 September 1943https://pubs.acs.org/doi/10.1021/ja01249a010https://doi.org/10.1021/ja01249a010research-articleACS PublicationsRequest reuse permissionsArticle Views120Altmetric-Citations15LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-Alertsclose Get e-Alerts
Impact of delivery method on antiviral activity of phosphodiester, phosphorothioate, and phosphoryl guanidine oligonucleotides in MDCK cells infected with H5N1 bird flu virus (2017)

We have previously described nanocomposites containing conjugates or complexes of native oligodeoxyribonucleotides with poly-L-lysine and TiO2 nanoparticles. We have shown that these nanocomposites efficiently suppressed influenza A virus reproduction in MDCK cells. Here, we have synthesized previously undescribed nanocomposites that consist of TiO2 nanoparticles and polylysine conjugates with oligonucleotides that contain phosphoryl guanidine or phosphorothioate internucleotide groups. These nanocomposites have been shown to exhibit antiviral activity in MDCK cells infected with H5N1 influenza A virus. The nanocomposites containing phosphorothioate oligonucleotides inhibited virus replication ~130-fold. More potent inhibition, i.e., ~5000-fold or ~4600-fold, has been demonstrated by nanocomposites that contain phosphoryl guanidine or phosphodiester oligonucleotides, respectively. Free oligonucleotides have been nearly inactive. The antiviral activity of oligonucleotides of all three types, when delivered by Lipofectamine, has been significantly lower compared to the oligonucleotides delivered in the nanocomposites. In the former case, the phosphoryl guanidine oligonucleotide has appeared to be the most efficient; it has inhibited the virus replication by a factor of 400. The results make it possible to consider phosphoryl guanidine oligonucleotides, along with other oligonucleotide derivatives, as potential antiviral agents against H5N1 avian flu virus.
HML-1 antigen on mucosa-associated T cells, activated cells, and hairy leukemic cells is a new integrin containing the beta 7 subunit. (1991)

The monoclonal antibodies HML-1, B-ly7 and Ber-ACT8 recognize intramucosal gut T lymphocytes, activated cells, and hairy cell leukemia. The antigen on hairy cells consists of three glycoproteins (160 kappa D, 130 kappa D and 105 kappa D unreduced; 145 kappa D and 120 kappa D reduced). These peptides have biochemical features reminiscent of integrins but we have shown by immunoprecipitation that they are not known integrin subunits. We have used a newly produced antibody (BP6) to purify this molecule and shown by N-terminal sequence analysis that the smallest subunit is the product of integrin beta 7 cDNA. This molecule is thus a new member of the integrin family of leucocyte adhesion proteins. Immunoprecipitation experiments indicate that the two larger subunits are recognized by HML-1, B-ly7 and Ber-ACT8.
Mycobacterium avium complex in water, food, and soil samples collected from the environment of HIV-infected individuals. (1995)

As part of an epidemiologic study of Mycobacterium avium complex (MAC) infection in San Francisco, water, food and soil samples were collected from the home environment of 290 persons with human immunodeficiency virus (HIV) infection and cultured for mycobacteria. Isolates recovered from the environment were compared with isolates cultured from study patients. Although mycobacteria were recovered from numerous environmental samples, isolates reactive with MAC-specific DNA probes were recovered from only four of 528 (0.76%) water samples and one of 397 (0.25%) food samples. The species M. avium was recovered from one water (0.19%) and one food sample. In contrast, MAC was recovered from 55% and M. avium from 27% of soil samples taken from potted plants in patients' home. Speciation of 76 MAC isolates from study patients showed all isolates belonged to the species M. avium. With use of serotype and multilocus enzyme electrophoresis analysis, some of the soil isolates were found to be similar to isolates recovered from study patients. The results of this study suggest that soil, rather than water, may be a significant reservoir of organisms causing MAC infection in San Francisco.
Orphan selenoproteins (1999)

Selenoproteins contain selenium in stoichiometric amounts. Most are synthesized by a process that decodes UGA codons as selenocysteine. Twelve animal selenoproteins have been characterized, and biochemical functions have been described for all but three. Two of these "orphan" selenoproteins are discussed in this paper. Selenoprotein P is an extracellular glycoprotein that contains multiple selenocysteines. It binds heparin and associates with endothelial cells. Two isoforms have been identified. Plasma concentration of selenoprotein P correlates with protection against diquat liver injury, suggesting that the protein protects against oxidant injury. Selenoprotein W is a small intracellular protein that contains one selenocysteine. It binds glutathione and has been suggested to function in oxidant defense. The postulated oxidant defense properties of these selenoproteins are consistent with the facile thiol-redox properties of selenocysteine. It can be predicted that more proteins will be discovered that take advantage of the chemical properties of selenium.
Nanometer thickness laser ablation for spatial control of cell attachment (2002)

We demonstrate here a new method to control the location of cells on surfaces in two dimensions, which can be applied to a number of biomedical applications including diagnostic tests and tissue engineered medical devices. Two-dimensional control over cell attachment is achieved by generation of a spatially controlled surface chemistry that allows control over protein adsorption, a process which mediates cell attachment. Here, we describe the deposition of thin allylamine plasma polymer coatings on silicon wafer and perfluorinated poly(ethylene-co-propylene) substrates, followed by grafting of a protein resistant layer of poly(ethylene oxide). Spatially controlled patterning of the surface chemistry was achieved in a fast, one-step procedure by nanometer thickness controlled laser ablation using a 248 nm excimer laser. X-ray photoelectron spectroscopy and atomic force microscopy were used to confirm the production of surface chemistry patterns with a resolution of approximately 1 µm, which is significantly below the dimensions of a single mammalian cell. Subsequent adsorption of the extracellular matrix proteins collagen I and fibronectin followed by cell culture experiments using bovine corneal epithelial cells confirmed that cell attachment is controlled by the surface chemistry pattern. The method is an effective tool for use in a number of in vitro and in vivo applications.
High-Throughput Screening for Inhibitors of the SARS-CoV-2 Protease Using a FRET-Biosensor (2020)

The global SARS-CoV-2 pandemic started late 2019 and currently continues unabated. The lag-time for developing vaccines means it is of paramount importance to be able to quickly develop and repurpose therapeutic drugs. Protein-based biosensors allow screening to be performed using routine molecular laboratory equipment without a need for expensive chemical reagents. Here we present a biosensor for the 3-chymotrypsin-like cysteine protease from SARS-CoV-2, comprising a FRET-capable pair of fluorescent proteins held in proximity by a protease cleavable linker. We demonstrate the utility of this biosensor for inhibitor discovery by screening 1280 compounds from the Library of Pharmaceutically Active Compounds collection. The screening identified 65 inhibitors, with the 20 most active exhibiting sub-micromolar inhibition of 3CL<sup>pro</sup> in follow-up EC<sub>50</sub> assays. The top hits included several compounds not previously identified as 3CL<sup>pro</sup> inhibitors, in particular five members of a family of aporphine alkaloids that offer promise as new antiviral drug leads.
Professing Australian Literature: The Webby Way (2007)

Elizabeth Webby's retirement in 2007 from the Chair of Australian Literature at The University of Sydney to which she was appointed in 1990 rounds out a career in which she has, in the fullest sense, professed Australian literature. Her identification with her subject is extra - ordinarily complete, succinctly spelled out in the citation for the award of Membership of the Order of Australia (in the 2004 Australia Day Honours), for 'service to the study, teaching and promotion of Australian literature, for supporting Australian authors and for fostering links between the academic and general reading communities'. This embracing commitment at once characterises her achievement and provides the score for the chorus of appreciation that has attended her retirement...
Using TCAD for fast analysis of misprocessed wafers and yield excursions (2005)

So far, TCAD simulation has been extensively used for process development, but its application for manufacturing control and corrective action was very limited. In this paper we show that TCAD can also be very beneficially used for identifying manufacturing accidents like missing or doubled implants without involving process integration or device physics experts