gebhart/patrepeval huggingface dataset:
Shape-based object recognition in videos using 3D synthetic object models (2009)

In this paper we address the problem of recognizing moving objects in videos by utilizing synthetic 3D models. We use only the silhouette space of the synthetic models making thus our approach independent of appearance. To deal with the decrease in discriminability in the absence of appearance, we align sequences of object masks from video frames to paths in silhouette space. We extract object silhouettes from video by an integration of feature tracking, motion grouping of tracks, and co-segmentation of successive frames. Subsequently, the object masks from the video are matched to 3D model silhouettes in a robust matching and alignment phase. The result is a matching score for every 3D model to the video, along with a pose alignment of the model to the video. Promising experimental results indicate that a purely shape-based matching scheme driven by synthetic 3D models can be successfully applied for object recognition in videos.
Specific Extraction of Antigen in Vivo by Extracorporeal Circulation Over Antibody Immobilized in Collodion-Charcoal (1976)

A novel extracorporeal immunoadsorbent is described in which anti-bovine serum albumin (anti-BSA) was entrapped in collodion membranes adherent to activated charcoal particles. This immunoadsorbent was capable of specifically removing circulating BSA in vitro and in vivo in an extracorporeal system in dogs. In preparation of the immunoadsorbent, up to 81.2% of added anti-BSA was retained on collodion-charcoal. In vitro circulation studies demonstrated that anti-BSA collodion-charcoal removed 812% more 125I-BSA than control colloidon-charcoal. For in vivo studies, an extracorporeal circulation system was established and arterial blood was passaged through a continuous flow celltrifuge wherein plasma which was separated from formed elements of the blood was circulated over anti-BSA and control rabbit gamma-globulin collodion-charcoal. 125I-BSA was passively infused into mongrel dogs, and plasma was then circulated over extracorpeal immunoadsorbents for 2 hr. Results showed up to 896% greater uptake of circulating 125I-BSA on the charcoal containing immobilized anti-BSA compared to control charcoal. There was no evidence of release of anti-BSA from the immunoadsorbent since 125I-anti-BSA cpm on the charcoal before and after the experiments were unchanged. In addition, there were no significant alterations in hematocrit, leukocyte counts, serum sodium, potassium, calcium, magnesium, or creatinine levels before and after in vivo procedures. These data suggest that this immunoadsorbent consisting of anti-BSA immobilized in collodion membranes adherent to charcoal particles may specifically withdraw circulating antigens in vivo with minimal release of entrapped antibodies and no significant alteration in the host hematologic and biochemical status.
Virtual Reality: Concepts and Technologies (2011)

A manual for both designers and users, comprehensively presenting the current state of experts' knowledge on virtual reality (VR) in computer science, mechanics, optics, acoustics, physiology, psychology, ergonomics, ethics, and related area. Designed as a reference book and design guide to help the reader develop a VR project, it presents the read
Protein crystallization using incomplete factorial experiments. (1979)

We have studied the crystallization of Bacillus ste- arothermophilus tryptophan tRNA synthetase. Exper- imental conditions used in 35 different crystallization trials were chosen by systematic assignment of varia- bles in accordance with the two principles of randomi- zation and balance, which are characteristic of incom- plete factorial experiments. Polymorphism in the re- sulting precipitated, microcrystalline, or crystalline protein samples was identified and rated numerically on a rough but quantitative scale. Correlations between these estimates of crystal quality and all experimental variables were identified by stepwise multiple regres- sion analysis. Several variables proved to be signifi- cantly correlated with crystal quality. Having established a favorable precipitation proce- dure and ionic composition within broad limits, we next carried out a complete factorial experiment with four factors using two pH values and two temperatures in the presence or absence of two low molecular weight substrates, tryptophan and ATP. These experiments clearly established a favorable pH and produced large (0.5 mm) single crystals with each of the four possible substrate permutations. At least one crystal form, en- zyme plus tryptophan, is suitable for structural studies by x-ray diffraction. The factorial approach appears to be an advantageous alternative to classical controlled single factor and full factorial designs for establishing cause and effect relationships in protein crystallization. Rational exploration of cause and effect relationships gov- erning the crystallization of proteins has traditionally been eschewed, owing to the potentially very large number of controlled experiments required for a systematic study. The essential difficulty is that a number of different experimental conditions, pH, temperature, various mono- and divalent ions, and different organic solutes, may interact in apparently ca- pricious ways to provide a favorable environment in which crystals will eventually grow (an excellent review is Mc- Pherson, 1976a). Despite this seemingly overwhelming difficulty, small quan- tities of protein can be used quite efficiently by using the factorial approach to experimental design (Fisher, 1942). This approach is counter-intuitive: no attempt is made to identify the effects of varying individual factors by controlled experi- ments in which other factors remain constant. Rather, effi- ciency in a factorial experiment arises from two rather differ- * This work was supported by Research Grant GM21991 from the National Institutes of Health and by a fellowship in academic medi- cine from the Jefferson Pilot Corporation (C!. W. C. Jr.). The costs of publication of this article were defrayed in part by the payment of
Control of pH alters the type of cross-linking produced by 1-ethyl-3-(3-dimethylaminopropyl)-carbodiimide (EDC) treatment of acellular matrix vascular grafts (2001)

Carbodiimide cross-linking of bioprosthetic materials has been shown to provide tissue stabilization equivalent to that of glutaraldehyde cross-linking, but without the risk of the release of unreacted or depolymerized cytotoxic reagent after implantation. In this study, the effects of 1-ethyl-3-(3-dimethylaminopropyl)-carbodiimide (EDC) treatment on acellularized ovine carotid arteries were studied under two different pH conditions: (i) pH controlled at an optimal value of 5.5; and (ii) a simpler, but industrially significant, uncontrolled pH system. A multimode approach was employed involving biochemical assays, thermomechanical, tensile, and shear mechanical testing, and in vitro enzyme degradation analyses. EDC treatment decreased the hoop tangent modulus of acellular matrix (ACM) arterial grafts measured at 20 kPa of stress regardless of pH control. Extensibility of ACM arterial grafts measured at 20 kPa of stress was reduced after EDC treatment with pH control only. In contrast, shear stiffness of ACM arterial grafts increased to a greater degree under cross-linking without pH control (21 x compared to 14 x with pH control). Thermomechanical analyses revealed that EDC cross-linking with pH control also increased the collagen denaturation temperature of ACM arteries to a greater degree (a rise of 24.3 +/- 0.6 degrees C vs. 21.7 +/- 0.7 degrees C for no pH control), whereas cross-linking without pH control consumed a larger amount of lysine residues after 3 h of treatment. Most interestingly, both EDC treatments were equally effective in stabilizing ACM arteries against multiple degradative enzymes in vitro. The observed differences between EDC treatments under different pH conditions are attributed to differences in the location and types of the exogenous cross-links formed. The absence of pH control may have favored the formation of interfibrillar or intermolecular cross-links in collagen as well as involvement of other extracellular matrix components (proteoglycans and glycosaminoglycans). Furthermore, it may be emphasized that the location or type of cross-links differentially affected the mechanical behavior of treated materials without affecting the increase in resistance to enzymatic degradation.
PEG-ing down (and preventing?) the cause of pegloticase failure (2014)

Pegloticase is a powerful but underutilized weapon in the rheumatologist's armamentarium. The drug's immunogenicity leads to neutralizing antibody formation and rapid loss of efficacy in roughly one-half of all patients, which remains an impediment to broader use. New data, however, suggest that drug survival might improve with concomitant immunosuppressive agent (s), which merits further study. Efficacy appears to be unchanged when pegloticase is infused at 3-week (rather than 2-week) intervals. Stretching the time between infusions may also improve patient adherence and allow for earlier identification of transient responders.
Extracellular signal-regulated kinase 2 is necessary for mesoderm differentiation (2003)

The extracellular signal-regulated kinase (ERK) is a component of the mitogen-activated protein kinase cascade. Exon 2 of erk2 was deleted by homologous recombination and resulted in embryonic lethality at embryonic day 6.5. erk2 mutant embryos did not form mesoderm and showed increased apoptosis but comparable levels of BrdUrd incorporation, indicating a defect in differentiation. erk2 null embryonic stem (ES) cells exhibited reduced total ERK activity upon serum stimulation, augmented ERK1 phosphorylation, and decreased downstream p90Rsk phosphorylation and activity; yet ES cell proliferation was unaffected. Mutant ES cells were capable of forming mesoderm; however, treatment of mutant ES cells with the mitogen-activated protein kinase kinase inhibitor PD184352 decreased total ERK activity and expression of the mesodermal marker brachyury, suggesting that ERK1 can compensate for ERK2 in vitro. Normal embryos at embryonic day 6.5 expressed activated ERK1/2 in the extraembryonic ectoderm, whereas erk2 mutant embryos had no detectable activated ERK1/2 in this region, suggesting that activated ERK1 was not expressed, and therefore cannot compensate for loss of ERK2 in vivo. These data indicate that ERK2 plays an essential role in mesoderm differentiation during embryonic development.
Protective Effects of B2 Preservation Solution in Comparison to a Standard Solution (Histidine-Tryptophan-Ketoglutarate/Bretschneider) in a Model of Isolated Autologous Hemoperfused Porcine Kidney (2004)

Reperfusion injuries after organ transplantation affect graft function and influence long-term graft survival. As hypothermic storage, which minimizes the extent of unspecific tissue injury after ischemia and reperfusion, is significantly influenced by the composition of preservation solutions, strategies to optimize the different components may lead to longer graft survival. In the present study the effects of the preservation solution B2 on early renal function and histopathological changes were compared to histidine-tryptophan-ketoglutarate solution (HTK, Bretschneider) in a model of isolated blood-perfused porcine kidneys. B2-preserved kidneys displayed a lower renal resistance and significantly better creatinine clearance as compared to HTK. Mean differences were also found for filtration fraction and sodium fraction reabsorption. The functional data were also related to histopathological changes. Together, these data indicate that the recently developed preservation solution B2 offers new principles of preservation and is a useful preservation solution for experimental isolated perfused kidney models. B2 may also be an interesting model for optimizing preservation within other organ perfusion models.
CXCR4: a key receptor in the crosstalk between tumor cells and their microenvironment (2005)

Signals from the microenvironment have a profound influence on the maintenance and/or progression of hematopoietic and epithelial cancers. Mesenchymal or marrow-derived stromal cells, which constitute a large proportion of the non-neoplastic cells within the tumor microenvironment, constitutively secrete the chemokine stromal cell-derived factor-1 (SDF-1/CXCL12). CXCL12 secretion by stromal cells attracts cancer cells, acting through its cognate receptor, CXCR4, which is expressed by both hematopoietic and nonhematopoietic tumor cells. CXCR4 promotes tumor progression by direct and indirect mechanisms. First, CXCR4 is essential for metastatic spread to organs where CXCL12 is expressed, and thereby allows tumor cells to access cellular niches, such as the marrow, that favor tumor-cell survival and growth. Second, stromal-derived CXCL12 itself can stimulate survival and growth of neoplastic cells in a paracrine fashion. Third, CXCL12 can promote tumor angiogenesis by attracting endothelial cells to the tumor microenvironment. CXCR4 expression is a prognostic marker in various types of cancer, such as acute myelogenous leukemia or breast carcinoma. Promising results in preclinical tumor models indicate that CXCR4 antagonists may have antitumor activity in patients with various malignancies. Collectively, these observations reveal that CXCR4 is an important molecule involved in the spread and progression of a variety of different tumors. As such, CXCR4 antagonists, although initially developed for treatment of AIDS, actually may become effective agents for the treatment of neoplastic disease.
20S proteasomes and protein degradation “by default” (2006)

The degradation of the majority of cellular proteins is mediated by the proteasomes. Ubiquitin-dependent proteasomal protein degradation is executed by a number of enzymes that interact to modify the substrates prior to their engagement with the 26S proteasomes. Alternatively, certain proteins are inherently unstable and undergo "default" degradation by the 20S proteasomes. Puzzlingly, proteins are by large subjected to both degradation pathways. Proteins with unstructured regions have been found to be substrates of the 20S proteasomes in vitro and, therefore, unstructured regions may serve as signals for protein degradation "by default" in the cell. The literature is loaded with examples where engagement of a protein into larger complexes increases protein stability, possibly by escaping degradation "by default". Our model suggests that formation of protein complexes masks the unstructured regions, making them inaccessible to the 20S proteasomes. This model not only provides molecular explanations for a recent theoretical "cooperative stability" principle, but also provokes new predictions and explanations in the field of protein regulation and functionality.
ChemInform Abstract: Addition of Grignard Reagents to 1‐Acyl‐4‐methoxypyridinium Salts. An Approach to the Synthesis of Quinolizidinones. (1987)

Abstract 4‐Methoxy‐pyridine (I) reacts with the chloroformates (II) and the Grignard compounds (III) to produce the N‐acyloxypyridines (IV) which are hydrolyzed to form the dihydropyridones (V).
When Is Parenteral Nutrition Appropriate? (2017)

Parenteral nutrition (PN) represents one of the most notable achievements of modern medicine, serving as a therapeutic modality for all age groups across the healthcare continuum. PN offers a life-sustaining option when intestinal failure prevents adequate oral or enteral nutrition. However, providing nutrients by vein is an expensive form of nutrition support, and serious adverse events can occur. In an effort to provide clinical guidance regarding PN therapy, the Board of Directors of the American Society for Parenteral and Enteral Nutrition (ASPEN) convened a task force to develop consensus recommendations regarding appropriate PN use. The recommendations contained in this document aim to delineate appropriate PN use and promote clinical benefits while minimizing the risks associated with the therapy. These consensus recommendations build on previous ASPEN clinical guidelines and consensus recommendations for PN safety. They are intended to guide evidence-based decisions regarding appropriate PN use for organizations and individual professionals, including physicians, nurses, dietitians, pharmacists, and other clinicians involved in providing PN. They not only support decisions related to initiating and managing PN but also serve as a guide for developing quality monitoring tools for PN and for identifying areas for further research. Finally, the recommendations contained within the document are also designed to inform decisions made by additional stakeholders, such as policy makers and third-party payers, by providing current perspectives regarding the use of PN in a variety of healthcare settings.
Activity and Distribution of Binding Sites in Brain of a Nonpeptide Substance P (NK 1 ) Receptor Antagonist (1991)

CP-96,345, a nonpeptide substance P antagonist, is selective for the tachykinin NK1 receptor. The compound binds to a single population of sites in guinea pig brain and potently inhibits substance P-induced excitation of locus ceruleus neurons. CP-96,345 should be a useful tool for studying the action of substance P in the central nervous system.
Identification of Naturally Processed HLA-A2—Restricted Proinsulin Epitopes by Reverse Immunology (2005)

Type 1 diabetes is thought to result from the destruction of beta-cells by autoantigen-specific T-cells. Observations in the NOD mouse model suggest that CD8+ cytotoxic T-cells play an essential role in both the initial triggering of insulitis and its destructive phase. However, little is known about the epitopes derived from human beta-cell autoantigens and presented by HLA class I molecules. We used a novel reverse immunology approach to identify HLA-A2-restricted, naturally processed epitopes derived from proinsulin, an autoantigen likely to play an important role in the pathogenesis of type 1 diabetes. Recombinant human proinsulin was digested with purified proteasome complexes to establish an inventory of potential COOH-terminals of HLA class I-presented epitopes. Cleavage data were then combined with epitope predictions based on the SYFPEITHI and BIMAS algorithms to select 10 candidate epitopes; 7 of these, including 3 with a sequence identical to murine proinsulin, were immunogenic in HLA-A2 transgenic mice. Moreover, six of six tested peptides were processed and presented by proinsulin-expressing cells. These results demonstrate the power of reverse immunology approaches. Moreover, the novel epitopes may be of significant interest in monitoring autoreactive T-cells in type 1 diabetes.
GaN HBT: toward an RF device (2001)

This paper reviews efforts to develop growth and fabrication technology for the GaN HBT. Conventional devices are grown by plasma assisted MBE on MOCVD GaN templates on sapphire. HBTs were fabricated on LEO material identifying threading dislocations as the primary source of collector-emitter leakage which was reduced by four orders of magnitude for devices on nondislocated material. Base doping studies show that the mechanism of this leakage is localized punch-through caused by compensation near the dislocation. High contact and lateral resistance in the base cause large parasitic common emitter offset voltages (from 1 to 5 V) in GaN HBTs. The effect of this voltage drop on common emitter characteristics is discussed. The combination of this voltage drop and the emitter collector leakage make Gummel and common base characteristics unreliable without verification with common emitter characteristics. The selectively regrown emitter bipolar transistor is presented with a DC current gain of 6 and early voltage greater than 400 V. The transistor operated to voltages over 70 V. This device design reduces base contact resistance, and circumvented difficulties associated with the emitter mesa etch process. The Mg memory effect in MOCVD grown GaN HBTs is discussed, and MBE grown device layers are shown to produce sharp doping profiles. The low current gain of these devices is discussed, and an HBT with a compositionally graded base is presented, as well as simulations predicting further current gain improvements with base grading.
The Escherichia coli K99 periplasmic chaperone FanE is a monomeric protein (1996)

The monomeric or dimeric nature of the K99 periplasmic chaperone FanE was examined. The gene encoding FanE was subcloned in a pINIIIA1 derivative expression vector. A complementation experiment showed that the subcloned FanE was biologically functional. The protein was purified from the periplasm of cells harbouring the constructed plasmid. Automated Edman degradation experiments confirmed the predicted N-terminal amino acid sequence of FanE. A polyclonal mouse antiserum was raised against the FanE chaperone. The monomeric or oligomeric nature of the protein in the periplasm was studied by gel filtration, immunoblotting and chemical cross-linking experiments. The results indicated that FanE is a monomeric protein, in contrast to the K88 periplasmic chaperone.
Cloning of Drosophila choline acetyltransferase cDNA. (1986)

Choline acetyltransferase (EC 2.3.1.6) is the biosynthetic enzyme for the neurotransmitter acetylcholine. To isolate choline acetyltransferase cDNA clones, a cDNA library was constructed from poly(A)+ RNA of Drosophila melanogaster heads, these being one of the richest known sources of the enzyme. By screening the cDNA library with a mixture of three different monoclonal antibodies to Drosophila choline acetyltransferase, we isolated 14 positive clones. Only 1 of these clones was identified to be a Drosophila choline acetyltransferase cDNA clone based on the following evidence. (i) The amino acid sequence deduced from the nucleotide sequence of the cDNA insert completely corresponded to that of several tryptic peptides from choline acetyltransferase. (ii) The cDNA insert hybridized specifically to only the region on Drosophila polytene chromosomes that had been identified as the site of the choline acetyltransferase (Cha) gene by cytogenetic analysis. The cDNA insert consisted of a coding region 2190 nucleotides long, a 3'-noncoding region 284 nucleotides long, and EcoRI linkers. RNA analysis of Drosophila head poly(A)+ RNA with the cDNA insert as a probe showed the choline acetyltransferase mRNA to be approximately equal to 4700 nucleotides long.
Alpha 1,3‐Galactosyltransferase Deficiency in Pigs Increases Sialyltransferase Activities That Potentially Raise Non‐Gal Xenoantigenicity (2011)

We examined whether deficiency of the GGTA1 gene in pigs altered the expression of several glycosyltransferase genes. Real-time RT-PCR and glycosyltransferase activity showed that 2 sialyltransferases [α2,3-sialyltransferase (α2,3ST) and α2,6-sialyltransferase (α2,6ST)] in the heterozygote GalT KO liver have higher expression levels and activities compared to controls. Enzyme-linked lectin assays indicated that there were also more sialic acid-containing glycoconjugate epitopes in GalT KO livers than in controls. The elevated level of sialic-acid-containing glycoconjugate epitopes was due to the low level of α-Gal in heterozygote GalT KO livers. Furthermore, proteomics analysis showed that heterozygote GalT KO pigs had a higher expression of NAD+-isocitrate dehydrogenase (IDH), which is related to the CMP-N-acetylneuraminic acid hydroxylase (CMAH) enzyme reaction. These findings suggest the deficiency of GGTA1 gene in pigs results in increased production of N-glycolylneuraminic acid (Neu5Gc) due to an increase of α2,6-sialyltransferase and a CMAH cofactor, NAD+-IDH. This indicates that Neu5Gc may be a critical xenoantigen. The deletion of the CMAH gene in the GalT KO background is expected to further prolong xenograft survival.