Miracle-dz/UniFAR-FTUs huggingface dataset:
Antibodies against the fibrin beta-chain amino-terminus detect active canine venous thrombi.

BACKGROUND This study was performed to determine whether antibodies against the amino-terminus of the beta-chain of fibrin (anti-beta) could noninvasively distinguish actively enlarging thrombi from thrombi stabilized with anticoagulants. METHODS AND RESULTS Dogs with unilateral femoral vein thrombi were allocated into three groups: (1) no anticoagulation, (2) intravenous heparin maintained in the "therapeutic" range (0.2 to 0.5 U/mL plasma), and (3) "excess" heparin, maintained at >1.0 U/mL plasma. Thrombolysis was suppressed with tranexamic acid. (111)In-labeled anti-beta was infused, and gamma scans of the legs were performed at regular intervals for 24 hours. Scans were interpreted in a blinded fashion. In addition, for each scan, the number of gamma counts from the femoral area on the thrombosed side was compared with the contralateral side. Clot/blood isotope density was determined postmortem. Leg thrombi in the no-anticoagulation group were 100% detectable, mean (+/-SD) relative count in the thrombosed femoral area was 186% (+/-30%) of the contralateral side, and clot/blood ratio was 14.7 (+/-2.0). Thrombi in the therapeutic heparin group were only 75% detectable, relative counts in the thrombosed femoral areas decreased to 125% (+/-20%), and clot/blood ratio declined to 11.3 (+/-3.5). In the "excess heparin" group, leg thrombi were only 50% detectable, the thrombosed femoral area had relative counts of 118%+/-17%, and the clot/blood ratio fell to 7.8+/-1.9. CONCLUSIONS Radiolabeled anti-beta noninvasively distinguishes propagating thrombi from those stabilized by anticoagulants. They may be useful for detecting thrombosis clinically as well as for monitoring the efficacy of anticoagulation.
Estimation of Force and Extensor Moment Contributions of the Disc and Ligaments at L4-L5

An anatomic-mathematical representation of the individual ligaments and disc at L4-L5 was used in a model to examine their role in joint behavior. Geometry of the anatomic components was obtained from cadaveric dissection and the anatomic literature; mechanical properties were obtained from various literature sources. Resistance to flexion of the L4-L5 joint was simulated using various ligament cross-sectional areas, and combined loading modes of compression coupled with bending in an attempt to understand physiologic conditions that may occur during activities such as lifting. Results suggest that the interspinous ligament sustains the greatest stress during flexion at L4-L5, is the dominant component in resistance to flexion, and also creates large shear components that must be resisted by the facet complex. Simulated compressive loads of 6300 N were noted to allow an additional 2° of flexion at the joint.
Pterygium surgery: conjunctival rotation autograft versus conjunctival autograft.

BACKGROUND AND OBJECTIVES To compare the safety and efficacy of conjunctival rotation autograft to conjunctival autograft in primary pterygium surgery. PATIENTS AND METHODS A prospective randomized study was performed of 39 eyes in 31 patients who had undergone pterygium surgery. Nineteen eyes were treated by conjunctival rotation autograft (Group A). Twenty eyes were treated by conjunctival autograft (Group B). Follow up ranged from 8 to 12 months (mean 11 months). Recurrence was defined as postoperative regrowth of 2 mm fibrovascular tissue onto clear cornea in the area of previous pterygium excision. Four eyes were excluded from the study. Delayed wound healing occurred in 11.76% of eyes, and 5.88% of eyes had persistent congestion in Group A. A loose graft was present in 5.55% of eyes, and 5.55% of eyes had dellen formation in Group B. CONCLUSION We conclude that conjunctival rotation autograft and conjunctival autograft are both equally effective methods to reduce the recurrence rate after pterygium surgery. Conjunctival rotation autograft can be tried as an alternative attractive procedure for pterygium surgery to reduce the chances of recurrence. However, a larger, randomized, prospective double masked study with more patients and a longer follow up will eventually demonstrate the superiority of one procedure over the other.
Interaction of microbes with mucus and mucins

Due to the recent rapid expansion in our understanding of the composition of the gut microflora and the consequences of altering that composition the question of how bacteria colonise mucus layers and interact with components of mucus, such as mucin, is now receiving widespread attention. Using a combination of mucus secreting cells, and a novel mucin microarray platform containing purified native mucins from different sources we recently demonstrated that two gastrointestinal pathogens, Helicobacter pylori and Campylobacter jejuni, colonise mucus by different mechanisms. This result emphasizes the potential for even closely related bacteria to interact with mucus in divergent ways to establish successful infection. Expanding the use of the mucin arrays described in the study to other microorganisms, both pathogenic and commensal, should lead to the discovery of biologically important motifs in bacterial-host interactions and complement the use of novel in vitro cell models, such as mucus secreting cell lines.
Human T-cell leukemia virus type I Tax activation of NF-kappa B/Rel involves phosphorylation and degradation of I kappa B alpha and RelA (p65)-mediated induction of the c-rel gene

The tax gene product of human T-cell leukemia virus type I (HTLV-I) is a potent transcriptional activator that both stimulates viral gene expression and activates an array of cellular genes involved in T-cell growth. Tax acts indirectly by inducing or modifying the action of various host transcription factors, including members of the NF-kappa B/Rel family of enhancer-binding proteins. In resting T cells, many of these NF-kappa B/Rel factors are sequestered in the cytoplasm by various ankyrin-rich inhibitory proteins, including I kappa B alpha. HTLV-I Tax expression leads to the constitutive nuclear expression of biologically active NF-kappa B and c-Rel complexes; however, the biochemical mechanism(s) underlying this response remains poorly understood. In this study, we demonstrate that Tax-stimulated nuclear expression of NF-kappa B in both HTLV-I-infected and Tax-transfected human T cells is associated with the phosphorylation and rapid proteolytic degradation of I kappa B alpha. In contrast to prior in vitro studies, at least a fraction of the phosphorylated form of I kappa B alpha remains physically associated with the NF-kappa B complex in vivo but is subject to rapid degradation, thereby promoting the nuclear translocation of the active NF-kappa B complex. We further demonstrate that Tax induction of nuclear c-Rel expression is activated by the RelA (p65) subunit of NF-kappa B, which activates transcription of the c-rel gene through an intrinsic kappa B enhancer element. In normal cells, the subsequent accumulation of nuclear c-Rel acts to inhibit its own continued production, indicating the presence of an autoregulatory loop. However, the pathologic action HTLV-I Tax leads to the deregulated and sustained nuclear expression of both NF-kappa B and c-Rel, a response that may contribute to HTLV-I-induced T-cell transformation.
Expansion and Contraction of the NK Cell Compartment in Response to Murine Cytomegalovirus Infection1

NK cells are capable of responding quickly to infectious challenge and contribute to the early defense against a wide variety of pathogens. Although the innate NK cell response to murine CMV (MCMV) has been extensively characterized, its resolution and the fate of the activated NK cell population remains unexplored. Herein, we characterize both the expansion and contraction phases of the NK cell response to MCMV. We demonstrate that NK cell recruitment into the immune response to MCMV infection is restricted to the first 3 days of infection and as the peripheral NK cell compartment expands, NK cells undergo accelerated phenotypic maturation. During the resolution of the immune response, NK cell compartmental contraction is marked by the selective death of responding NK cells. Additionally, throughout the infection, a naive NK cell pool that remains responsive to additional stimuli is actively maintained. These findings illustrate the plasticity of the NK cell compartment in response to pathogens and underscore the homeostatic maintenance of the resting peripheral NK cell pool.
A Human Proteome Microarray Identifies that the Heterogeneous Nuclear Ribonucleoprotein K (hnRNP K) Recognizes the 5′ Terminal Sequence of the Hepatitis C Virus RNA*

Stem-loop I (SL1) located in the 5′ untranslated region of the hepatitis C virus (HCV) genome initiates binding to miR-122, a microRNA required for hepatitis HCV replication. However, proteins that bind SL1 remain elusive. In this study, we employed a human proteome microarray, comprised of ∼17,000 individually purified human proteins in full-length, and identified 313 proteins that recognize HCV SL1. Eighty-three of the identified proteins were annotated as liver-expressing proteins, and twelve of which were known to be associated with hepatitis virus. siRNA-induced silencing of eight out of 12 candidate genes led to at least 25% decrease in HCV replication efficiency. In particular, knockdown of heterogeneous nuclear ribonucleoprotein K (hnRNP K) reduced HCV replication in a concentration-dependent manner. Ultra-violet-crosslinking assay also showed that hnRNP K, which functions in pre-mRNA processing and transport, showed the strongest binding to the HCV SL1. We observed that hnRNP K, a nuclear protein, is relocated in the cytoplasm in HCV-expressing cells. Immunoprecipitation of the hnRNP K from Huh7.5 cells stably expressing HCV replicon resulted in the co-immunoprecipitation of SL1. This work identifies a cellular protein that could have an important role in the regulation of HCV RNA gene expression and metabolism.
Procedure complications of carotid angioplasty and stent placement without cerebral protection devices.

OBJECT The goal in this retrospective study was to examine the procedural complication rate for carotid angioplasty and stent placement performed without cerebral protection devices. METHODS Between March 1996 and December 2003, 167 carotid angioplasty and/or stent placement procedures were performed without cerebral protection devices in 152 patients (57 women and 95 men whose mean age was 64 years, range 19-92 years). Seven of these patients underwent angioplasty alone. Eighty-nine patients presented with focal neurological symptoms. Indications for surgery included atherosclerosis, radiation-associated stenosis, dissection, pseudoaneurysm, and stretched endovascular coils from aneurysm treatment. In this study, the patients' medical records were reviewed for clinical characteristics, techniques used, and resulting intraprocedural and 30-day complication rates. The intraprocedural stroke rate was four (2.4%) of 167; this included three hemispheric strokes and one retinal embolus. All events occurred in patients who had symptomatic stenosis. The procedural transient ischemic complication rate was six (3.6%) of 167, as was the procedural nonneurological complication rate. During the 30 days postprocedure, one patient had died and three had suffered permanent ischemic events (two cerebral and one ocular). The composite 30-day postprocedural stroke and death rate was eight (5%) of 160. The rate of asymptomatic angiographically confirmed abnormalities was 0.6% (one treated vessel that was occluded but asymptomatic). The 30-day rate of nonneurological complications was 2.5%. A strong association between intraprocedural thromboembolic events (eight cases) and prior ischemic symptoms was found (p = 0.01). CONCLUSIONS Carotid angioplasty and stent placement without cerebral protection devices is safe, particularly in patients without symptomatic stenosis.
A biomechanical comparison of four different cementless press-fit stems used in revision surgery for total knee replacements

Few biomechanical studies exist on femoral cementless press-fit stems for revision total knee replacement (TKR) surgeries. The aim of this study was to compare the mechanical quality of the femur–stem interface for a series of commercially available press-fit stems, because this interface may be a ‘weak link’ which could fail earlier than the femur–TKR bond itself. Also, the femur–stem interface may become particularly critical if distal femur bone degeneration, which may necessitate or follow revision TKR, ever weakens the femur–TKR bond itself. The authors implanted five synthetic femurs each with a Sigma Short Stem (SSS), Sigma Long Stem (SLS), Genesis II Short Stem (GSS), or Genesis II Long Stem (GLS). Axial stiffness, lateral stiffness, ‘offset load’ torsional stiffness, and ‘offset load’ torsional strength were measured with a mechanical testing system using displacement control. Axial (range = 1047–1461 N/mm, p = 0.106), lateral (range = 415–462 N/mm, p = 0.297), and torsional (range = 115–139 N/mm, p > 0.055) stiffnesses were not different between groups. The SSS had higher torsional strength (863 N) than the other stems (range = 167–197 N, p < 0.001). Torsional failure occurred by femoral ‘spin’ around the stem’s long axis. There was poor linear correlation between the femur–stem interface area versus axial stiffness (R = 0.38) and torsional stiffness (R = 0.38), and there was a moderate linear correlation versus torsional strength (R = 0.55). Yet, there was a high inverse linear correlation between interfacial surface area versus lateral stiffness (R = 0.79), although this did not result in a statistical difference between stem groups (p = 0.297). These press-fit stems provide equivalent stability, except that the SSS has greater torsional strength.
Sustained Activation of N-Methyl-d-Aspartate Receptors in Podoctyes Leads to Oxidative Stress, Mobilization of Transient Receptor Potential Canonical 6 Channels, Nuclear Factor of Activated T Cells Activation, and Apoptotic Cell Death

Atypical N-methyl-d-aspartate (NMDA) receptors are expressed in podocytes. Sustained (≥24 h) application of 50 to 100 μM NMDA to immortalized mouse podocytes evoked a marked increase in the production of reactive oxygen species (ROS) such as H2O2. This effect of NMDA was associated with increased cell-surface expression of p47(phox), a cytosolic regulatory subunit of the NADPH oxidase NOX2. NMDA-evoked generation of ROS drove an increase in steady-state surface expression of transient receptor potential canonical (TRPC) 6 channels, which was blocked by the NMDA antagonist dizocilpine (MK-801) and by a membrane-permeable scavenger of ROS. The effect of NMDA on TRPC6 was observed using cell surface biotinylation assays and also with whole-cell recordings made under conditions designed to facilitate detection of current through TRPC6. NMDA mobilization of TRPC6 channels was blocked by concurrent treatment with the NMDA antagonist MK-801 and by a membrane-permeable scavenger of ROS. Mobilization of TRPC6 was also evoked by l-homocysteic acid. NMDA treatment also increased nuclear localization of endogenous nuclear factor of activated T cells, which could be blocked by MK-801, by scavenging ROS, by the calcineurin inhibitor cyclosporine, and by the TRPC channel inhibitor 1-[2-(4-methoxyphenyl)-2-[3-(4-methoxyphenyl)propoxy]ethyl]imidazole (SKF-96365). NMDA treatment also evoked robust activation of Rho but not Rac, consistent with previous studies of downstream effectors of TRPC6 activation. Exposing cells to NMDA for 24 h reduced total and cell surface expression of the podocyte markers nephrin and podocin, but there was no loss of cells. With longer NMDA exposure (72 h), we observed loss of cells associated with nuclear fragmentation and increased expression of caspase-3, caspase-6, and Bax, suggesting an apoptotic process.
New scalable microfabrication method for surface ion traps and experimental results with trapped ions

This paper presents a new microfabrication method for surface ion traps and experimental results with trapped ions. Fabricating ion trap chips is a very formidable task because the top electrodes are vertically spaced more than 10 μm from the bottom electrodes with an indented dielectric layer in the middle. Previous ion traps were fabricated using TEOS timed etch or tungsten sacrificial etch techniques. This paper presents a new microfabrication method, using copper as a sacrificial material for an aluminum-oxide-aluminum ion trap structure. Using the developed method the overhang dimensions of the top aluminum electrodes can be accurately controlled. Fabricated ion trap chips are installed in a 1 × 10-11 Torr vacuum environment for ion trapping experiments. Successful results in trapping strings of 171Yb+ and 174Yb+ ions as well as manipulating 171Yb+ ions for qubit operation are demonstrated.
eU-OFDM based multiple access for visible light communication networks

In this paper, we propose a novel protocol for cooperative multiple access in visible light communication (VLC) networks. The proposed protocol exploits the features of enhanced unipolar orthogonal frequency division multiplexing (eU-OFDM) scheme in order to enable user terminals to sequentially access the multi-hop network. The signal-to-noise ratios (SNRs) for user terminals within the network are derived and the individual bit-error-rate (BER) expressions are presented. We evaluate the BER performances of each user in the network through Monte Carlo simulation. The theoretical results validates the simulation results.
Rapid detection and identification of avian infectious bronchitis virus

A rapid and sensitive method for the detection and unambiguous typing of infectious bronchitis virus (IBV) is described. RNA was isolated from IBV-infected allantoic fluid and was transcribed into cDNA. This cDNA was amplified by the polymerase chain reaction. The polymerase chain reaction products were subsequently analyzed on an agarose gel. The presence of IBV-specific RNA in the allantoic fluid then allowed the amplification of a 438-bp DNA fragment from the nucleocapsid (N) gene. For the typing of IBV isolates, we used amplified double-stranded DNA as a template in a sequencing reaction. We report 360 bases of the N gene of 18 IBV isolates. The sequence of the N gene was different between serologically indistinguishable IBV strains and may be a valuable tool in epidemiologic studies. A phylogenetic tree that was based on the sequences obtained did not agree with trees that were based on other parts of the sequence, illustrating the high frequency of recombination between IBV strains.
Self‐assembly of coiled‐coil tetramers in the 1.40 Å structure of a leucine‐zipper mutant

The hydrophobic core of the GCN4 leucine‐zipper dimerization domain is formed by a parallel helical association between nonpolar side chains at the a and d positions of the heptad repeat. Here we report a self‐assembling coiled‐coil array formed by the GCN4‐pAe peptide that differs from the wild‐type GCN4 leucine zipper by alanine substitutions at three charged e positions. GCN4‐pAe is incompletely folded in normal solution conditions yet self‐assembles into an antiparallel tetraplex in crystals by formation of unanticipated hydrophobic seams linking the last two heptads of two parallel double‐stranded coiled coils. The GCN4‐pAe tetramers in the lattice associate laterally through the identical interactions to those in the intramolecular dimer–dimer interface. The van der Waals packing interaction in the solid state controls extended supramolecular assembly of the protein, providing an unusual atomic scale view of a mesostructure.
β-Amyloid Induces Paired Helical Filament-like Tau Filaments in Tissue Culture*

Paired helical filaments (PHF) are the principal pathologic components of neurofibrillary tangles in Alzheimer's disease (AD). To reproduce the formation of PHF in tissue culture, we stably expressed human tau with and without pathogenic mutations in human SH-SY5Y cells and exposed them for 5 days to aggregated synthetic β-amyloid peptide (Aβ42). This caused a decreased solubility of tau along with the generation of PHF-like tau-containing filaments. These were 20 nm wide and had periodicities of 130-140 nm in the presence of P301L mutant tau or 150-160 nm in the presence of wild-type tau. Mutagenesis of the phosphoepitope serine 422 of tau prevented both the Aβ42-mediated decrease in solubility and the generation of PHF-like filaments, suggesting a role of serine 422 or its phosphorylation in tau filament formation. Together, our data underscore a role of Aβ42 in the formation of PHF-like filaments. Our culture system will be useful to map phosphoepitopes of tau involved in PHF formation and to identify and characterize modifiers of the tau pathology. Further adaptation of the system may allow the screening and validation of compounds designed to prevent PHF formation.
Nuclear imaging of thrombosis in small animal

Abstract Thromboembolic disorders are a major cause of morbidity and mortality worldwide. The progress in noninvasive imaging techniques has led to the development of radionuclide imaging based on SPECT and PET approaches to observe molecular and cellular processes that may underlie the onset and progression of disease. The advantages of using normal and genetically modified small animal research have spurred the development of dedicated small animal imaging systems. Animal models of venous and arterial thrombosis are largely used and have improved our understanding of the etiology and pathogenesis of thrombosis. Here, we review the literature regarding nuclear imaging of thrombosis in mice and rats.
RNA Interference towards the Potato Psyllid, Bactericera cockerelli, Is Induced in Plants Infected with Recombinant Tobacco mosaic virus (TMV)

The potato/tomato psyllid, Bactericera cockerelli (B. cockerelli), is an important plant pest and the vector of the phloem-limited bacterium Candidatus Liberibacter psyllaurous (solanacearum), which is associated with the zebra chip disease of potatoes. Previously, we reported induction of RNA interference effects in B. cockerelli via in vitro-prepared dsRNA/siRNAs after intrathoracic injection, and after feeding of artificial diets containing these effector RNAs. In order to deliver RNAi effectors via plant hosts and to rapidly identify effective target sequences in plant-feeding B. cockerelli, here we developed a plant virus vector-based in planta system for evaluating candidate sequences. We show that recombinant Tobacco mosaic virus (TMV) containing B. cockerelli sequences can efficiently infect and generate small interfering RNAs in tomato (Solanum lycopersicum), tomatillo (Physalis philadelphica) and tobacco (Nicotiana tabacum) plants, and more importantly delivery of interfering sequences via TMV induces RNAi effects, as measured by actin and V-ATPase mRNA reductions, in B. cockerelli feeding on these plants. RNAi effects were primarily detected in the B. cockerelli guts. In contrast to our results with TMV, recombinant Potato virus X (PVX) and Tobacco rattle virus (TRV) did not give robust infections in all plants and did not induce detectable RNAi effects in B. cockerelli. The greatest RNA interference effects were observed when B. cockerelli nymphs were allowed to feed on leaf discs collected from inoculated or lower expanded leaves from corresponding TMV-infected plants. Tomatillo plants infected with recombinant TMV containing B. cockerelli actin or V-ATPase sequences also showed phenotypic effects resulting in decreased B. cockerelli progeny production as compared to plants infected by recombinant TMV containing GFP. These results showed that RNAi effects can be achieved in plants against the phloem feeder, B. cockerelli, and the TMV-plant system will provide a faster and more convenient method for screening of suitable RNAi target sequences in planta.