gebhart/patrepeval huggingface dataset:
Enhanced Oligodendrocyte Survival after Spinal Cord Injury in Bax-Deficient Mice and Mice with Delayed Wallerian Degeneration (2003)

Mechanisms of oligodendrocyte death after spinal cord injury (SCI) were evaluated by T9 cord level hemisection in wild-type mice (C57BL/6J and Bax+/+ mice), Wlds mice in which severed axons remain viable for 2 weeks, and mice deficient in the proapoptotic protein Bax (Bax-/-). In the lateral white-matter tracts, substantial oligodendrocyte death was evident in the ipsilateral white matter 3-7 mm rostral and caudal to the hemisection site 8 d after injury. Ultrastructural analysis and expression of anti-activated caspase-3 characterized the ongoing oligodendrocyte death at 8 d as primarily apoptotic. Oligodendrocytes were selectively preserved in Wlds mice compared with C57BL/6J mice at 8 d after injury, when severed axons remained viable as verified by antereograde labeling of the lateral vestibular spinal tract. However, 30 d after injury when the severed axons in Wlds animals were already degenerated, the oligodendrocytes preserved at 8 d were lost, and numbers were then equivalent to control C57BL/6J mice. In contrast, oligodendrocyte death was prevented at both time points in Bax-/- mice. When cultured oligodendrocytes were exposed to staurosporine or cyclosporin A, drugs known to stimulate apoptosis in oligodendrocytes, those from Bax-/- mice but not from Bax+/+ or Bax+/- mice were resistant to the apoptotic death. In contrast, the three groups were equally vulnerable to excitotoxic necrosis death induced by kainate. On the basis of these data, we hypothesize that the Wallerian degeneration of white matter axons that follows SCI removes axonal support and induces apoptotic death in oligodendrocytes by triggering Bax expression.
ChemInform Abstract: Some Carbazole and Carboline Quinones and an Unexpected Demethoxylation Reaction. (1990)

Abstract The tetrahydrodimethoxycarbazole (I), readily prepared from 2‐chlorocyclohexanone and 2,5‐dimethoxyaniline, and the known triazolopyridine (IV) are used as starting materials for the syntheses of the carbazole quinones (II)/(III) and the carboline quinone (VII) respectively.
Direct Inkjet Printing of Dental Prostheses Made of Zirconia (2009)

CAD/CAM milling systems provide a rapid and individual method for the manufacturing of zirconia dental restorations. However, the disadvantages of these systems include limited accuracy, possible introduction of microscopic cracks, and a waste of material due to the principle of the 'subtractive process'. The hypothesis of this study was that these issues can be overcome by a novel generative manufacturing technique, direct inkjet printing. A tailored zirconia-based ceramic suspension with 27 vol% solid content was synthesized. The suspension was printed on a conventional, but modified, drop-on-demand inkjet printer. A cleaning unit and a drying device allowed for the build-up of dense components of the size of a posterior crown. A characteristic strength of 763 MPa and a mean fracture toughness of 6.7 MPam(0.5) were determined on 3D-printed and subsequently sintered specimens. The novel technique has great potential to produce, cost-efficiently, all-ceramic dental restorations at high accuracy and with a minimum of materials consumption.
Angiogenesis (2005)

T he concept of modulating blood vessel growth-stimu- lation or inhibition-to serve a desired clinical goal has an enormous intellectual appeal.It can be used to relieve ischemia in tissues with compromised arterial blood supply, improve edema in areas of impaired lymphatic drainage, and inhibit the growth of tumors.Other applications involve facilitating reendothelialization and inhibiting neointima formation after vascular injury, preventing the progression of atherosclerotic plaque, and promoting "vascular health" in general.The least-explored application of this concept involves modulating body and organ size by regulating the endothelial cell mass.All of these areas received a significant, albeit varied, amount of attention in past decades but only recently have we begun approaching clinical applications.Indeed, the first antiangiogenic agent has been approved by the US Food and Drug Administration for the treatment of certain types of cancer, and it is hoped that the emergence of therapeutically useful angiogenesis-promoting agents is not far behind.This article examines some of our current understanding of the regulation of blood vessel growth in mature adult tissues and the various therapeutic applications of this knowledge.Obviously, a review of this size cannot cover such a vast field in any amount of detail, and the author regrets not citing primary references for many of the facts and concepts that are mentioned.
Gemini's protected silver coatings: first two years in operation (2006)

The Gemini twins were the first large modern telescopes to receive protected Silver coatings on their mirrors in 2004. We report the performance evolution of these 4-layer coatings in terms of reflectivity and emissivity. We evaluate the durability of these thin films by comparison to the evolution of some samples that we have produced and exposed since 2002. Finally, we will explain our maintenance plan.
General framework for developing and evaluating database scoring algorithms using the TANDEM search engine (2006)

Source code for the scoring functions is available from http://proteomics.fhcrc.org
ATP-Citrate Lyase Controls a Glucose-to-Acetate Metabolic Switch (2016)

Mechanisms of metabolic flexibility enable cells to survive under stressful conditions and can thwart therapeutic responses. Acetyl-coenzyme A (CoA) plays central roles in energy production, lipid metabolism, and epigenomic modifications. Here, we show that, upon genetic deletion of Acly, the gene coding for ATP-citrate lyase (ACLY), cells remain viable and proliferate, although at an impaired rate. In the absence of ACLY, cells upregulate ACSS2 and utilize exogenous acetate to provide acetyl-CoA for de novo lipogenesis (DNL) and histone acetylation. A physiological level of acetate is sufficient for cell viability and abundant acetyl-CoA production, although histone acetylation levels remain low in ACLY-deficient cells unless supplemented with high levels of acetate. ACLY-deficient adipocytes accumulate lipid in vivo, exhibit increased acetyl-CoA and malonyl-CoA production from acetate, and display some differences in fatty acid content and synthesis. Together, these data indicate that engagement of acetate metabolism is a crucial, although partial, mechanism of compensation for ACLY deficiency.
The effects of tissue factor pathway inhibitor and anti-beta-2-glycoprotein-I IgG on thrombin generation. (2006)

Our findings support the hypothesis that anti-beta2GPI IgG antibodies accelerate thrombin generation in the presence of TFPI and may contribute to hypercoagulability in patients with aPS.
Double-strand gap repair in a mammalian gene targeting reaction. (1991)

To better understand the mechanism of homologous recombination in mammalian cells that facilitates gene targeting, we have analyzed the recombination reaction that inserts a plasmid into a homologous chromosomal locus in mouse embryonic stem cells. A partially deleted HPRT gene was targeted with various plasmids capable of correcting the mutation at this locus, and HPRT+ recombinants were directly selected in HAT medium. The structures of the recombinant loci were then determined by genomic Southern blot hybridizations. We demonstrate that plasmid gaps of 200, 600, and 2,500 bp are efficiently repaired during the integrative recombination reaction. Targeting plasmids that carry a double-strand break or gap in the region of DNA homologous to the target locus produce 33- to 140-fold more hypoxanthine-aminopterin-thymidine-resistant recombinants than did these same plasmids introduced in their uncut (supercoiled) forms. Our data suggest that double-strand gaps and breaks may be enlarged prior to the repair reaction since sequence heterologies carried by the incoming plasmids located close to them are often lost. These results extend the known similarities between mammalian and yeast recombination mechanisms and suggest several features of the insertional (O-type) gene targeting reaction that should be considered when one is designing mammalian gene targeting experiments.
Control of Flow Past a Wing Section with Plasma-based Body Forces (2005)

Abstract : The response of the flow past a stalled NACA 0015 airfoil at 15 deg angle of attack and Reynolds number of 45, 000 to body forces originating from radio-frequency asymmetric dielectric-barrier-discharge actuators is described via direct numerical simulations. The theoretical model couples a phenomenologically derived averaged body force with a high-order 3-D compressible Navier-Stokes solver. The body force distribution is assumed to vary linearly, diminishing away from the surface until the critical electric field limit is reached. Various magnitudes and orientations of the force field are explored, ranging from vertically upwards (away from the body) to vertically downwards (towards the body). The imposed body forces couple to the non-linear inertial terms and the pressure gradients to engender a complex sequence of events. A significant streamwise component assures the reduction or elimination of stall with the formation of a stable wall-jet. When the only component of the force vector is pointed normal to and away from the surface, no control effect is achieved. On the other hand, when the force vector is directed towards the surface, a shallower separation region is observed, accompanied by unsteady boundary layer development. At the low Mach number considered (0.1), the work done by the force has little impact on the solution, and density variations remain less than 5%. Relaxation effects are explored by abruptly switching off the force, and estimates of response times are noted. The lack of a proper spanwise breakdown mechanism for the separated shear layer in 2-D simulations results in large coherent structures, whose response in transient and unsteady asymptotic states differ significantly from those observed in 3-D. Nonetheless, if the force is sufficiently effective to eliminate separation, the flowfield becomes generally two-dimensional and steady in the vicinity of the airfoil, and the overall results from 2-D and 3-D analyses yield similar results.
Diabetes mellitus and impaired pancreatic β‐cell proliferation (1996)

The factors that normally regulate the proliferation of the insulin-producing pancreatic beta-cell largely remain elusive although several factors have been identified that influence beta-cell growth in vitro. The adult beta-cell is normally virtually quiescent, but its replicatory activity can be enhanced in vitro by certain nutrients and growth factors, and long-term alterations in beta-cell mass constitute an important means to accommodate an increased demand for insulin. Likewise, expansion of the beta-cell mass by recruitment of beta-cells to proliferate may constitute a means by which the organism can compensate for the loss or dysfunction of beta-cells occurring in diabetes. However, neither in human or animal models for type-1 diabetes, nor in type-2 diabetes, is beta-cell regeneration a noteworthy feature. Thus, if beta-cells could be induced to replicate at a higher rate, this may prove beneficial in maintaining normoglycaemia, since the beta-cell mass is a major determinant of the total amount of insulin that can be secreted by the pancreas. The present review will focus on the normal regulation of beta-cell mitogenesis and hormones production in vitro and in vivo, and furthermore, will present evidence for an insufficient extent of beta-cell regeneration in different forms of diabetes mellitus. Additionally, the possibility of manipulating beta-cell proliferation by peptides and genetic engineering, and the significance of beta-cell mitogenesis in islet transplantation will be discussed in relation to treatments of diabetes mellitus.
Hyperplasia of Type II Pneumocytes in Pulmonary Lymphangioleiomyomatosis Immunohistochemical and Electron Microscopic Study (2000)

c Background.—Little is known of the morphology of the pneumocytes lining the parenchymal cysts in lymphangioleiomyomatosis (LAM). Objective.—To evaluate the structural characteristics of the alveolar epithelial cells in LAM. Methods.—Immunohistochemical and electron microscopic studies were performed on lung tissue from 22 women with pulmonary LAM. Results.—Epithelial cells that reacted with PE-10 (a mouse monoclonal antibody that recognizes the surfactant apoprotein A in type II pneumocytes) and TTF-1 (an antibody that identifies nuclear transcription factor found in type II pneumocytes) were the predominant cell type lining the surfaces of lesions of LAM and normal areas of lung. Scanning and transmission electron microscopic studies confirmed that these cells were type II pneumocytes as demonstrated by (1) apical microvilli, (2) electron-dense lamellar bodies, and (3) cytoplasmic projections that extended from the basal surfaces into the underlying connective tissue, where they made extensive contact with interstitial connective tissue cells. A few cells had morphologic characteristics of type I pneumocytes, including large flat surfaces lacking microvilli. Cells that appeared intermediate between type I and type II pneumocytes were observed occasionally. Conclusions.—These observations and the reactivity of these cells with antibody to proliferating cell nuclear antigen demonstrate that extensive hyperplasia of type II pneumocytes is a major characteristic of LAM. (Arch Pathol Lab Med. 2000;124:1642‐1648)
Design and synthesis of wire-actuated universal-joint wrists for surgical applications (2009)

This paper presents synthesis methods and performance measures for wire-actuated wrists using a universal-joint constraining linkage. Performance measures based on the isotropy of the wrench-closure workspace are derived and used in generating design atlases as a function of non-dimensional design parameters. The performance indices that are optimized include wrench-closure workspace, isotropy of the wrench-closure workspace, and kinematic conditioning index. Stiffness is used to define a safety margin from singularities of wrench closure. A design example of a wire-actuated surgical wrist is presented and validated through simulation. The methods presented in this paper are useful for quick dimensional synthesis of wire-actuated wrists with predefined wrench-closure workspaces.
THE DECOMPENSATED DETRUSOR III: IMPACT OF BLADDER OUTLET OBSTRUCTION ON SARCOPLASMIC ENDOPLASMIC RETICULUM PROTEIN AND GENE EXPRESSION (2000)

Regulation of calcium ion homeostasis has a significant role in smooth muscle contractility. The sarcoplasmic endoplasmic reticulum, calcium, magnesium, adenosine triphosphatase (SERCA) is a regulatory ion pump that may have a role in the functional outcome after outlet obstruction. We investigate what correlation if any existed between SERCA protein and gene expression, and the contractile properties in the same bladder.Standardized partial bladder outlet obstructions were created in adult New Zealand white rabbits, which were divided into control, sham operated and obstructed groups. Muscle strip studies subcategorized the obstructed group into compensated (force greater than 50% of control) and decompensated (force less than 50% of control). Microsomal membrane and total RNA fractions were prepared from the same bladder tissue. Membrane proteins were used for Western blot analysis using a SERCA specific monoclonal antibody, and total RNA was assessed with Northern blot analysis.The relative intensities of signals for the Western and Northern blots demonstrated a strong correlation between protein and gene expression. Furthermore there was a strong association between the loss of SERCA messenger RNA and protein expression and loss of bladder function.Bladder contractility after outlet obstruction is influenced in part by smooth muscle cell ability to maintain calcium homeostasis via SERCA. The loss of SERCA protein expression is mediated by down-regulation in gene expression in the same bladder. These data suggest that smooth muscle ion pump gene expression is in part mechanically (pressure work) regulated.
Universal oligonucleotides for the detection of infectious bronchitis virus by the polymerase chain reaction (1996)

The universality of seven pairs of oligonucleotides for detection of the coronavirus infectious bronchitis virus (IBV) by reverse-transcription polymerase chain reaction (RT-PCR) was examined using 41 isolates of IBV collected over five decades from Europe, Japan and the USA. Oligonucleotides specific for sequences within the S2 region of the spike (S) gene (Lin et al., 1991a) and nucleocapsid (N) gene (Zwaagstra et al., 1992) gave the appropriate products with all 41 isolates. Oligonu-cleotide pair UTR1 - UTR2 +, corresponding to sequences within the 3 untranslated region (UTR) of the genome, also gave the predicted product with all the isolates. Oligonucleotide pair UTR3 - /UTR4 + was internal to oligonucleotides UTR1 - /UTR2 + and was used in a nested-set arrangement for greater specificity and sensitivity, giving the correct product with the 39 isolates examined. Oligonucleotide pair S1Unil - /S1Uni2 + was used to produce a 1.6 kb cDNA, corresponding to most of the S1 region of the S gene, with 24/24 isolates tested. This oligonucleotide pair was less suited than the others for routine detection of IBV but is recommended for the amplification of the S1 region of the S gene of new isolates for subsequent analysis. Other oligonucleotide pairs, yielding cDNA corresponding to the variable region of the IBV genome where genes 3 and 4 (M) overlap, were selected to be largely specific for Massachusetts serotype isolates, in the context of European strains. RT-PCR analysis using these oligonucleotide pairs showed that a number of field isolate preparations also contained a small amount of Massachusetts serotype virus, probably of vaccine origin and indicative of low level persistent infection. These results suggest that any strain of IBV is likely to be detectable by RT-PCR with at least one of our primer pairs.
Effects of bradykinin on signal transduction, cell proliferation, and cytokine, prostaglandin E2 and collagenase‐1 release from human corneal epithelial cells (1998)

1. We recently demonstrated the presence of phospholipase C-coupled bradykinin (BK) B2-receptors in human primary and SV40 virus-immortalized corneal epithelial (CEPI) cells. 2. The aims of the present studies were to demonstrate the specific binding of [3H]-BK to CEPI cell membranes and to study its pharmacological characteristics. In addition, we wished to study the functional coupling of the BK receptors to various physiological and pathological mechanisms in the CEPI cells, including phosphoinositide (PI) turnover, intracellular Ca2+-mobilization ([Ca2+]i), cell proliferation (via [3H]-thymidine incorporation), and the release of various cytokines, collagenase-1 (matrix metalloproteinase-1) and prostaglandin E2 (PGE2). 3. Specific [3H]-BK binding comprised 83 +/- 2% of the total binding, and was of high affinity (Kd = 1.66 +/- 0.52 nM, n = 5), saturable (Bmax = 640 +/- 154 fmol g(-1) wet weight) and reversible. Competition studies yielded the following affinity values for BK and a number of BK-related peptides: Hoe-140 (D-Arg-[Hyp3,Thi5,D-Tic7,Oic8]BK; icatibant): Ki = 0.17 +/- 0.07 nM; BK: Ki = 1.0 +/- 0.11 nM; [Tyr8]-BK: Ki = 12.9 +/- 2.3 nM; [des-Arg9]-BK: Ki > 9,200 nM (all n = 3-5)). 4. BK potently stimulated PI turnover (EC50 = 2.3 +/- 0.3 nM; n = 7) and [Ca2+]i mobilization (EC50 = 8-20 nM) in CEPI cells and both responses were inhibited in a concentration-dependent manner by 100 nM-10 microM Hoe-140, a selective B2-receptor antagonist, and also inhibited by the selective phospholipase C (PLC) inhibitor, U73122 (1-(6-((17beta-3-methoxyestra-1,3,5(10)-trien-17-yl)amino)hexyl)-1 H-pyrrole-2,5-dione) (IC50 = 3.0 +/- 1.6 microM). BK-induced [Ca2+]i mobilization was reduced by about 30% in the presence of 4 mM EGTA, but was not significantly affected by 100 nM nifedipine. 5. BK (0.1 nM-10 microM) significantly (P<0.05-0.001) stimulated [3H]-thymidine incorporation into CEPI cellular DNA. However, while interleukin-1alpha (IL-1alpha; 10 ng ml(-1)) potently stimulated the release of IL-6, IL-8 and granulocyte macrophage colony-stimulating factor from CEPI cells, BK (0.1 nM-10 microM) was without effect. 6. Whilst phorbol-12-myristate-13-acetate (PMA; 3 microg ml(-1)) and 10% foetal bovine serum (positive control agents) significantly stimulated the release of both MMP-1 and PGE2 from CEPI cells, BK (0.1 nM-10 microM) was without any significant effect under these conditions. 7. In conclusion, these data indicate that the CEPI cells express high-affinity [3H]-BK binding sites representing B2-subtype BK receptors coupled to PI turnover and [Ca2+]i mobilization which appear to stimulate [3H]-thymidine incorporation into cellular DNA. In contrast, BK failed to elicit the release of PGE2, various cytokines and MMP-1 from CEPI cells. These results suggest that BK may have a potential role in corneal epithelium wound healing by stimulating cell proliferation.
Brittle IV Mouse Model for Osteogenesis Imperfecta IV Demonstrates Postpubertal Adaptations to Improve Whole Bone Strength (2004)

Our findings parallel the currently unexplained clinical observation of decreased fractures in human OI patients after puberty. The Brtl mouse remains an important tool for investigating therapeutic interventions for OI.
Prospects and perspectives for development of a vaccine against herpes simplex virus infections (2014)

Herpes simplex viruses 1 and 2 are human pathogens that lead to significant morbidity and mortality in certain clinical settings. The development of effective antiviral medications, however, has had little discernible impact on the epidemiology of these pathogens, largely because the majority of infections are clinically silent. Decades of work have gone into various candidate HSV vaccines, but to date none has demonstrated sufficient efficacy to warrant licensure. This review examines developments in HSV immunology and vaccine development published since 2010, and assesses the prospects for improved immunization strategies that may result in an effective, licensed vaccine in the near future.
Bit-interleaved coded modulation with shaping (2010)

The performance of bit-interleaved coded modulation (BICM) with shaping (i.e., non-equiprobable bit probabilities) is studied. For the AWGN channel, the rates achievable with BICM and shaping are practically identical to those of coded modulation or multilevel coding, virtually closing the gap that made BICM suboptimal in terms of information rates.
Does a fish-oil-containing lipid emulsion improve liver function in comparison with a soybean oil lipid emulsion? (2010)

Liver function disturbances have been of concern in parenteral nutrition. The aim of the post hoc analyses of two pooled studies was to compare liver function parameters using fish-oil-containing vs soybean oil lipid emulsions.