Miracle-dz/UniFAR-FTUs huggingface dataset:
The common gene variants of CYP2C19 affect pharmacokinetics and pharmacodynamics in an active metabolite of clopidogrel in healthy subjects

EG, Mumford AD. Pharmacodynamic resistance to warfarin associated with a Val66Met substitution in vitamin K epoxide reductase complex subunit 1. Thromb Haemost 2005; 93: 23–6. 17 Wilms EB, Touw DJ, Conemans JM, Veldkamp R, Hermans M. A new VKORC1 allelic variant (p.Trp59Arg) in a patient with partial resistance to acenocoumarol and phenprocoumon. J Thromb Haemost 2008; 6: 1224–6. 18 Tie JK, Nicchitta C, von Heijne G, Stafford DW.Membrane topology mapping of vitamin K epoxide reductase by in vitro translation/ cotranslocation. J Biol Chem 2005; 280: 16410–6. 19 Goodstadt L, Ponting CP. Vitamin K epoxide reductase : homology, active site and catalytic mechanism. Trends Biochem Sci 2004; 29: 289–92.
Cannabis constituent synergy in a mouse neuropathic pain model

Abstract Cannabis and its psychoactive constituent &Dgr;9-tetrahydrocannabinol (THC) have efficacy against neuropathic pain, however, this is hampered by their side effects. It has been suggested that co-administration with another major constituent cannabidiol (CBD) might enhance the analgesic actions of THC and minimise its deleterious side effects. We examined the basis for this phytocannabinoid interaction in a mouse chronic constriction injury (CCI) model of neuropathic pain. Acute systemic administration of THC dose-dependently reduced CCI-induced mechanical and cold allodynia, but also produced motor incoordination, catalepsy, and sedation. Cannabidiol produced a lesser dose-dependent reduction in allodynia, but did not produce the cannabinoid side effects. When co-administered in a fixed ratio, THC and CBD produced a biphasic dose-dependent reduction in allodynia. At low doses, the THC:CBD combination displayed a 200-fold increase in anti-allodynic potency, but had lower efficacy compared with that predicted for an additive drug interaction. By contrast, high THC:CBD doses had lower potency, but greater anti-allodynic efficacy compared with that predicted for an additive interaction. Only the high dose THC:CBD anti-allodynia was associated with cannabinoid side effects and these were similar to those of THC alone. Unlike THC, the low dose THC:CBD anti-allodynia was not cannabinoid receptor mediated. These findings demonstrate that CBD synergistically enhances the pain-relieving actions of THC in an animal neuropathic pain model, but has little impact on the THC-induced side effects. This suggests that low dose THC:CBD combination treatment has potential in the treatment of neuropathic pain.
Protein kinase C‐δ mediates von Willebrand factor secretion from endothelial cells in response to vascular endothelial growth factor (VEGF) but not histamine

Summary. Background: Vascular endothelial growth factor (VEGF) and histamine induce von Willebrand factor (VWF) release from vascular endothelial cells. Protein kinase C (PKC) is involved in the control of exocytosis in many secretory cell types. Objectives: We investigated the role of PKC and the interactions between PKC and Ca2+ signaling in both VEGF‐induced and histamine‐induced VWF secretion from human umbilical vein endothelial cells (HUVECs). Results: Several PKC inhibitors (staurosporine, Ro31‐8220, myristoylated PKC peptide inhibitor and Go6983) block VEGF‐induced but not histamine‐induced VWF secretion. PKC‐α and novel PKCs (PKC‐δ, PKC‐ε, and PKC‐η), but not PKC‐β, are expressed in HUVECs. Both VEGF and histamine activate PKC‐δ. However, gene inactivation experiments using small interfering RNA indicate that PKC‐δ (but not PKC‐α) is involved in the regulation of VEGF‐induced but not histamine‐induced secretion. Both VEGF and histamine induce a rise in cytosolic free Ca2+ ([Ca2+]c), but the response to VEGF is weaker and even absent in a significant subset of cells. Furthermore, VEGF‐induced secretion is largely preserved when the rise in [Ca2+]c is prevented by BAPTA‐AM. Conclusions: Our study identifies striking agonist specificities in signal–secretion coupling. Histamine‐induced secretion is dependent on [Ca2+]c but not PKC, whereas VEGF‐induced secretion is largely dependent on PKC‐δ and significantly less on [Ca2+]c. Our data firmly establish the key role of PKC‐δ in VEGF‐induced VWF release, but suggest that a third, VEGF‐specific, signaling intermediate is required as a PKC‐δ coactivator.
Induction of chronic migraine phenotypes in a rat model after environmental irritant exposure

Abstract Air pollution is linked to increased emergency department visits for headache and migraine patients frequently cite chemicals or odors as headache triggers, but the association between air pollutants and headache is not well understood. We previously reported that chronic environmental irritant exposure sensitizes the trigeminovascular system response to nasal administration of environmental irritants. Here, we examine whether chronic environmental irritant exposure induces migraine behavioral phenotypes. Male rats were exposed to acrolein, a transient receptor potential channel ankyrin-1 (TRPA1) agonist, or room air by inhalation for 4 days before meningeal blood flow measurements, periorbital cutaneous sensory testing, or other behavioral testing. Touch-induced c-Fos expression in trigeminal nucleus caudalis was compared in animals exposed to room air or acrolein. Spontaneous behavior and olfactory discrimination was examined in open-field testing. Acrolein inhalation exposure produced long-lasting potentiation of blood flow responses to a subsequent TRPA1 agonist and sensitized cutaneous responses to mechanical stimulation. C-Fos expression in response to touch was increased in trigeminal nucleus caudalis in animals exposed to acrolein compared with room air. Spontaneous activity in an open-field and scent preference behavior was different in acrolein-exposed compared with room air–exposed animals. Sumatriptan, an acute migraine treatment blocked acute blood flow changes in response to TRPA1 or transient receptor potential vanilloid receptor-1 agonists. Pretreatment with valproic acid, a prophylactic migraine treatment, attenuated the enhanced blood flow responses observed after acrolein inhalation exposures. Environmental irritant exposure yields an animal model of chronic migraine in which to study mechanisms for enhanced headache susceptibility after chemical exposure.
Bevacizumab immune complexes activate platelets and induce thrombosis in FCGR2A transgenic mice

Summary. Background: Treatment with Bevacizumab has been associated with arterial thromboembolism in colorectal cancer patients. However, the mechanism of this remains poorly understood, and preclinical testing in mice failed to predict thrombosis. Objective: We investigated whether thrombosis might be the result of platelet activation mediated via the FcγRIIa (IgG) receptor – which is not present on mouse platelets – and aimed to identify the functional roles of heparin and platelet surface localization in Bev‐induced FcγRIIa activation. Methods and results: We found that Bev immune complexes (IC) activate platelets via FcγRIIa, and therefore attempted to reproduce this finding in vivo using FcγRIIa (hFcR) transgenic mice. Bev IC were shown to be thrombotic in hFcR mice in the presence of heparin. This activity required the heparin‐binding domain of Bev’s target, vascular endothelial growth factor (VEGF). Heparin promoted Bev IC deposition on to platelets in a mechanism similar to that observed with antibodies from patients with heparin‐induced thrombocytopenia. When sub‐active amounts of ADP or thrombin were used to prime platelets (simulating hypercoagulability in patients), Bev IC‐induced dense granule release was significantly potentiated, and much lower (sub‐therapeutic) heparin concentrations were sufficient for Bev IC‐induced platelet aggregation. Conclusions: The prevailing rationale for thrombosis in Bev therapy is that VEGF blockade leads to vascular inflammation and clotting. However, we conclude that Bev can induce platelet aggregation, degranulation and thrombosis through complex formation with VEGF and activation of the platelet FcγRIIa receptor, and that this provides a better explanation for the thrombotic events observed in vivo.
Activated thrombin activatable fibrinolysis inhibitor levels are associated with the risk of cardiovascular death in patients with coronary artery disease: the AtheroGene study

Summary. Background: Thrombin activatable fibrinolysis inhibitor (TAFI) attenuates fibrinolysis. Results on the association between TAFI levels and the risk of coronary artery disease (CAD) are inconsistent. Objectives: We investigated the association between TAFI levels and the risk of cardiovascular events in CAD. Patients/Methods: 1668 individuals with angiographically proven CAD at baseline were followed for a median of 2.3 years, as part of the prospective AtheroGene cohort. Fifty‐six deaths from cardiovascular (CV) causes and 35 non‐fatal CV events were observed. Results: At baseline, three TAFI measurements were available: one evaluating the total amount of TAFI (t‐TAFI), one measuring the TAFIa/TAFIai amount, and the last the released activated peptide (TAFI‐AP). TAFIa/TAFIai levels were associated with increased risk of CV death [hazard ratio (HR) for one tertile increase, 2.38 (1.56–3.63); P < 10−4]. This association remained significant after adjustment for conventional risk factors, CRP levels, white blood count and markers of thrombin generation and fibrinolysis [HR = 1.69 (1.07–2.67); P = 0.01]. In addition, CPB2 gene polymorphisms explained 12%, 6%, and 3% of t‐TAFI, TAFIa/TAFIai and TAFI‐AP levels, respectively, but none was associated with CV events. Conclusions: The amount of activated TAFI, measured by TAFIa/TAFIai ELISA, but not of the t‐TAFI is independently associated with the risk of CV death.
A human monoclonal antibody inhibiting partially factor VIII activity reduces thrombus growth in baboons

Summary. Background: The inhibitory activity of an anti‐factor VIII (FVIII) antibody can be modulated through glycosylation of the antigen binding site, as has recently been described. This offers the opportunity to develop an optimized anticoagulant agent targeting partial FVIII inhibition. Objectives: We investigated in non‐human primates the antithrombotic activity, pharmacokinetics,and pharmacodynamics of a human monoclonal antibody, Mab‐LE2E9Q, inhibiting FVIII activity partially. Methods: The ability of Mab‐LE2E9Q to prevent thrombosis was evaluated in baboons after administration of 1.25 and 5 mg kg−1 antibody or saline as a single intravenous (i.v.) bolus. Thrombus development was recorded in expansion (‘venous’) and in Dacron® (‘arterial’) thrombosis chambers incorporated in an extracorporeal arteriovenous shunt implanted between the femoral vessels 1 h, 24 h and 7 days after the administration of Mab‐LE2E9Q. Results: Mab‐LE2E9Q reduced thrombus growth to a similar extend 1 h, 1 day and 1 week after administration of the antibody. Ex vivo pharmacodynamic analysis indicated that the evaluation of the residual FVIII activity was strongly dependent on the type of FVIII assay and on the phospholipid concentration in the assay. No significant difference in bleedings was observed between animals treated with Mab‐LE2E9Q or with saline. Conclusions: Understanding the role of glycosylation in FVIII inhibition by a human monoclonal antibody allowed selection of an antibody inhibiting only moderately FVIII activity while significantly reducing thrombus development in a baboon extracorporeal model. As that antibody did not increase the bleeding tendency, it may represent a novel type of a long‐acting antithrombotic agent with an optimal safety/efficacy profile.
Elevated d‐dimer levels predict recurrence in patients with idiopathic venous thromboembolism: a meta‐analysis

Summary. Background : The evidence on the optimal duration of treatment in patients with an idiopathic venous thromboembolic event (VTE) is inconclusive. d‐dimer testing to predict recurrent VTE has been evaluated in several studies. Objectives: We performed a meta‐analysis of studies of patients with idiopathic VTE treated with oral anticoagulation therapy (OAT) to assess the prognostic value of elevated d‐dimer levels 1 month after discontinuation of OAT for VTE recurrence. Patients/Methods: The MEDLINE, EMBASE and Cochrane databases were searched to identify relevant studies. Studies were eligible for inclusion if they included patients with idiopathic VTE and in addition reported results for this group separately, had measured d‐dimer approximately 1 month after discontinuation of OAT and had reported on recurrence of VTE. A random‐effects model was used to pool study results. Results: Data from four studies (1539 patients) were included in the current analysis. All studies reported on the number of recurrent events in the normal and elevated d‐dimer groups. Overall, 125 of 751 patients (16.6%) with elevated d‐dimer levels experienced recurrent VTE during the period of follow‐up compared with 57 of 788 patients (7.2%) with normal d‐dimer levels. Elevated d‐dimer levels were significantly associated with recurrent VTE (odds ratio , 2.36; 95% CI, 1.65 to 3.36). Conclusions: Elevated d‐dimer levels measured 1 month after discontinuation of OAT identify patients with idiopathic VTE at higher risk of recurrence.
The Relationship of Carotid Plaque, Intima Media Thickness (IMT), Resistivity Index (RI) and Pulsatility Index(PI) in Asian-Indian Patients with Acute Ischemic Stroke with and without Type2 DM

Aim: To determine the relationship of carotid plaque, intima media thickness (IMT), resistivity index (RI) and pulsatility index (PI) and prevalence of different risk factors with acute ischemic stroke and stroke subtypes in both diabetic and non-diabetic subjects. Materials and methods: 80 cases of acute ischemic strokes and 40 healthy controls were included in the study. The plaque, IMT, RI and PI were measured by carotid duplex ultrasound. Results: 31 subjects were Type 2 diabetic, 54 hypertensive while 25 were both diabetic and hypertensive. 23 cases (28.75%) had lacunar stroke (LACI), 32 (40%) stroke involving partial anterior circulation(PACI), 10(12.5%) stroke in posterior circulation (PACI) and 15(18.75%) stroke involving total anterior circulation(TACI) respectively. The mean IMT (0.88 ± 0.19mm), RI(0.76 ± 0.05) and PI(1.71 ± 0.19) of patients and mean IMT (0.6±0.09mm), RI (0.61 ± 0.06) and PI (1.53 ± 0.11) of controls were statistically significant (p-0.000). The mean values of IMT, PI and RI were significantly higher in diabetics (IMT-0.90 ± 0.16 VS 0.64 ± 0.11, p-0.013; PI-1.76 ± 0.20 VS 1.49 ± 0.09, P-0.000 and RI-0.76 ± 0.04 VS 0.59 ± 0.06, P-0.000) and similarly the mean values for IMT, PI and RI in hypertensives as compared to controls (IMT-0.88 ± 0.16 vs 0.65 ± 0.10, P-0.006; PI1.69 ± 0.18 vs 1.49 ± 0.09, P-0.000 and RI 0.76 ± 0.04 vs 0.59 ± 0.06, P-0.000). The mean IMT, PI and RI were increased significantly in smokers compared to controls (IMT-0.93 ± 0.20 vs 0.63 ± 0.06, P-0.000; PI-1.82 ± 0.22 vs 1.49 ± 0.09, P-0.000 and RI-0.77 ± 0.04 vs 0.59 ± 0.06, P-0.000). Type 3 plaque accounted for 27 (56.2%) cases and Type 2 plaque 12 (25%) cases. The total number of plaques in patients as compared to controls were significantly more (P-0.0034) and the mean plaque area was 46 mm2 for cases and 20 mm2 for control (P-0.0001). TACI was the most common type of ischemic stroke seen in DM (60%), HTN (66.6%) and smokers (66.7%). Plaques (73.3%), IMT (0.90 ± 0.12), PI(1.72 ± 0.14) and RI (0.76 ± 0.13) were more commonly associated with TACI subtype. On multivariate analysis using ANOVA, the mean PI was highly significant (0.000) in relation to types of plaque. Summary and Conclusions: IMT, RI, PI and plaque type are useful diagnostic parameters for acute ischemic stroke and its subtypes. They can be used as noninvasive tools for predicting and preventing ischemic stroke in smokers as well as subjects with DM and hypertension.
Results of a worldwide survey on the assessment of platelet function by light transmission aggregometry: a report from the platelet physiology subcommittee of the SSC of the ISTH

Background: Light transmission aggregometry (LTA) is the most common method used in clinical and research laboratories to assess platelet function. However, the method has never been standardized. Objectives: As the first step towards development of methodological guidelines, the Platelet Physiology Subcommittee of the Scientific and Standardization Committee of the International Society on Thrombosis and Haemostasis (ISTH) undertook a large, detailed, global survey of LTA practices. Methods: Members of ISTH and of External Quality Assurance in Thrombosis and Haemostasis organizations were invited to complete a 129 item, online questionnaire. Results were analyzed anonymously to participant identities. Results: The online supplement for this article (http://www.isth.org/Publications/OfficialCommunications/PlateletPhysiology/LightTransmissionAggregometry/tabid/201/Default.aspx) contains the full details of the study findings. 359 (244 clinical, 115 research) laboratories from 48 countries participated in the survey. LTA was widely used to assess inherited or acquired bleeding disorders. Common practices were identified in sample collection, processing and analysis and although some are generally considered acceptable, others are not ideal. The agonist concentrations used for LTA varied, and many laboratories used ADP, collagen, epinephrine and Ristocetin, at more than one concentration, in addition to arachidonic acid. The parameters commonly used to assess LTA responses were maximal amplitude or % aggregation, which was considered particularly important, in addition to the presence of a ‘secondary wave’, deaggregation, shape change and a measure of the lag phase. However, many laboratories did not have appropriate reference intervals. Conclusions: This is the largest and most detailed survey of LTA practices ever undertaken. It shows a very high variability in LTA practices worldwide, and, as a consequence, methodological standardization is necessary. The information gathered in this survey will be helpful in the development of ISTH methodological guidelines for LTA.
Contamination of synthetic HuD protein spanning peptide pools with a CMV‐encoded peptide

To detect HuD‐specific T cells in patients with Hu‐antibody associated paraneoplastic neurological syndromes (Hu‐PNS), we used short‐term stimulation assays with HuD protein spanning peptide pools (PSPP) with purities of at least 70% and found reproducible false‐positive CD8+ T‐cell responses in three of 127 individuals (two healthy controls and one Hu‐PNS patient), which all shared HLA‐A*2402 and HLA‐B*1801. After testing the 15‐mer peptides of the HuD antigen separately, we discovered that the same three 15‐mers yielded the CD8+ T cell response in those three individuals. This highly unusual result could not be reproduced when using new batches of peptides with a higher level of purity (>82% and >95%). Therefore, we assumed this response was not directed against the HuD peptides and analyzed the HuD 15‐mers by Fourier transform ion cyclotron resonance (FT‐ICR) tandem mass spectrometry (MS/MS), which showed the presence of a cytomegalovirus (CMV)‐encoded peptide (AIAEESDEEEAIVAY) as a contaminant. The three responding individuals all were CMV‐seropositive and the contaminating peptide appeared to fit in the binding groove of HLA‐B*18. Our data reveal that synthetic PSPP may contain immunogenic contaminations which may cause false positive results in T‐cell stimulation assays. © 2008 International Society for Advancement of Cytometry
GFP: From humble beginnings to Nobel winnings—The color that changed cytometry

CONGRATULATIONS to the 2008 Nobel Prize winners in Chemistry, Martin Chalfie, Osamu Shimomura, and Rodger Y. Tsien ‘‘for the discovery and development of the green fluorescent protein, GFP’’. In the field of live cell cytometry, no single discovery has had such a dramatic and lasting impact as the use of fluorescent proteins. No matter the model system (bacteria, insect, plants, or animals) (1), or the areas of interest (cancer research, neurosciences, immunology, or developmental biology), there is not a field that has not been touched and transformed by the ability to visualize biological processes in real time. Prior to the use of GFP and its derivatives, the ability to monitor gene expression, protein trafficking and localization was limited. Bulk methods for isolation of sub-cellular compartments followed by Northern and Southern blotting, immunohistochemistry or in situ hybridization were the standard techniques of the day, all of which gave a brief snapshot of what was happening in the cell because the cells had to be fixed and permeablized to get the target probes into place. In the 1960s, Dr. Shimomura first characterized the fluorescent protein that would become known as GFP from the humble jellyfish Aequorea victoria (2–4). It was not until the early 1990s that the gene encoding this protein was characterized by Douglas Prasher (5). Because of Dr. Prasher’s generosity, Martin Chalfie and Rodger Y. Tsien both obtained the gene for GFP, leading to their seminal work and the Nobel award. Dr. Chalfie was the first to use this gene for monitoring real time changes in gene expression during development (6), ushering in the ability to monitor—in real time—biological processes as they happened, and to provide a crucial new element ‘‘time’’ into our understanding. For the first time it became relatively simple to watch how a protein behaved in a cell in real time. Researchers could poke and prod a cell, getting near instantaneous feedback as to the effect on the cell. Of course, there were other hurdles to overcome, including designing appropriate cloning vectors and getting the protein expressed in the cell, but those technical hurdles were overcome one by one. GFP’s usefulness was not just in monitoring protein expression and cellular events by microscopy. It became an essential tool in the identification and isolation of cells by flow cytometry. From transgenic mice expressing proteins in unique cell lineages, or at different stages of development to the introduction of novel genes into cells, investigators were able to isolate these cells that were previously difficult (and sometimes impossible) to isolate in a prospective manner. Progenitor cells were no longer a mystery, but could be seen glowing green in the microscope and on the flow cytometer. All to be isolated and studied, the deepest secrets revealed because of the green glow of GFP. Not to be limited, fluorescent proteins from other organisms were isolated, characterized, and utilized. Based in large
The decrease in procarboxypeptidase U (TAFI) concentration in acute ischemic stroke correlates with stroke severity, evolution and outcome

See also Willemse JL, Brouns R, Heylen E, De Deyn PP, Hendriks DF. Carboxypeptidase U (TAFIa) activity is induced in vivo in ischemic stroke patients receiving thrombolytic therapy. J Thromb Haemost 2008; 6: 200–2.
Consistency of QSAR models: Correct split of training and test sets, ranking of models and performance parameters†

Recent implementations of QSAR modelling software provide the user with numerous models and a wealth of information. In this work, we provide some guidance on how one should interpret the results of QSAR modelling, compare and assess the resulting models, and select the best and most consistent ones. Two QSAR datasets are applied as case studies for the comparison of model performance parameters and model selection methods. We demonstrate the capabilities of sum of ranking differences (SRD) in model selection and ranking, and identify the best performance indicators and models. While the exchange of the original training and (external) test sets does not affect the ranking of performance parameters, it provides improved models in certain cases (despite the lower number of molecules in the training set). Performance parameters for external validation are substantially separated from the other merits in SRD analyses, highlighting their value in data fusion.