julilili42/papers huggingface dataset:
Liquidity supply and adverse selection in a pure limit order book market
2007-12-31

This paper analyzes adverse selection costs and liquidity supply in a pure open limit order book market. We relax assumptions of the Glosten/Såndas modeling framework regarding marginal zero profit order book equilibrium and the parametric market order size distribution. We show that using average zero profit conditions considerably increases the empirical performance while a nonparametric specification for market order size combined with marginal zero profit conditions does not. A cross sectional analysis corroborates the finding that adverse selection costs are more severe for smaller capitalized stocks. We also find additional support for one of the central hypothesis put forth by the theory of limit order book markets, which states that liquidity supply and adverse selection costs are inversely related. Furthermore, adverse selection cost estimates based on our structural model and those obtained using popular model-free methods are strongly correlated. This indicates the robustness of the theory-based approach.
Guidelines for the use and interpretation of assays for monitoring autophagy in higher eukaryotes
2008-01-01

Research in autophagy continues to accelerate,1 and as a result many new scientists are entering the field. Accordingly, it is important to establish a standard set of criteria for monitoring macroautophagy in different organisms. Recent reviews have described the range of assays that have been used for this purpose.(2,3) There are many useful and convenient methods that can be used to monitor macroautophagy in yeast, but relatively few in other model systems, and there is much confusion regarding acceptable methods to measure macroautophagy in higher eukaryotes. A key point that needs to be emphasized is that there is a difference between measurements that monitor the numbers of autophagosomes versus those that measure flux through the autophagy pathway; thus, a block in macroautophagy that results in autophagosome accumulation needs to be differentiated from fully functional autophagy that includes delivery to, and degradation within, lysosomes (in most higher eukaryotes) or the vacuole (in plants and fungi). Here, we present a set of guidelines for the selection and interpretation of the methods that can be used by investigators who are attempting to examine macroautophagy and related processes, as well as by reviewers who need to provide realistic and reasonable critiques of papers that investigate these processes. This set of guidelines is not meant to be a formulaic set of rules, because the appropriate assays depend in part on the question being asked and the system being used. In addition, we emphasize that no individual assay is guaranteed to be the most appropriate one in every situation, and we strongly recommend the use of multiple assays to verify an autophagic response.
Eryptosis, a Window to Systemic Disease
2008-01-01

Similar to apoptosis of nucleated cells, suicidal erythrocyte death or eryptosis is characterized by cell shrinkage, membrane blebbing and membrane phospholipid scrambling with phosphatidylserine exposure at the cell surface. Signaling of eryptosis involves formation of prostaglandin E(2) with subsequent activation of cation channels and Ca(2+)-entry and/or release of platelet activating factor (PAF) with subsequent activation of sphingomyelinase and formation of ceramide. Ca(2+) and ceramide stimulate cell membrane scrambling. Ca(2+) further activates Ca(2+)-sensitive K(+)-channels leading to cellular KCl loss and cell shrinkage and stimulates the protease calpain resulting in degradation of the cytoskeleton. Injuries triggering eryptosis may similarly compromise survival of nucleated cells. The case is made that analysis of enhanced eryptosis may direct to the pathophysiology of systemic disease. Examples presented include drug side effects, sepsis, haemolytic uremic syndrome, Wilson's disease, phosphate depletion and a rare condition caused by a mutation in GLUT1 turning the carrier into a cation channel.
Ornithine-δ-aminotransferase is essential for Arginine Catabolism but not for Proline Biosynthesis
2008-01-01

Our findings indicate that deltaOAT feeds P5C exclusively into the catabolic branch of Pro metabolism, which yields Glu as an end product. Conversion of Orn to Glu is an essential route for recovery of nitrogen stored or transported as Arg. Pro biosynthesis occurs predominantly or exclusively via the Glu pathway in Arabidopsis and does not depend on Glu produced by Arg and Orn catabolism.
Platelet-vessel wall interactions in atherosclerotic disease
2008-01-01

Summary During the prolonged course of atherosclerotic disease,platelets are of central importance as they contribute to the initiation of the disease, to its progression and acute exacerbation but also provide potential regenerative mechanisms. Platelets secrete chemokines and cytokines that mediate vascular inflammation and are in turn activated by substances released from cells of the vascular wall.These interactions represent positive and negative feedback loops, which in case of dysregulation may lead to development and progression of disease. Furthermore, platelet adhesion to the endothelium is critical for the initiation of atherosclerotic lesion formation in vivo. Even prior to endothelial denudation, platelet adhesion governed by disturbed flow at predilection sites for atherosclerosis induces recruitment of proathe- rosclerotic cells and release of proinflammatory mediators from all involved cell types.Finally,the pathogenetic role of platelets for late atheroclerotic events including plaque rupture, microembolism or spasms within the microcirculation is well established. However, increasing evidence indicates that platelets mediate on the other hand potential regenerative mechanisms. Platelets recruit circulating progenitor cells to sites of vascular injury. Furthermore, they influence their biological activity and maturation. Therefore,platelets contribute at all stages of vascular disease by interfering with highly dynamic processes. Understanding interactions of platelets with other circulating cells and the vascular wall is a prerequisite to understand cardiovascular disease and to identify potential therapeutic targets.
Radiation-induced caveolin-1 associated EGFR internalization is linked with nuclear EGFR transport and activation of DNA-PK
2008-01-01

Src kinase activation following irradiation triggered caveolin-1 dependent EGFR internalization into caveolae. Subsequently EGFR shuttled into the nucleus. As a consequence, inhibition of internalization and nuclear transport of EGFR blocked radiation-induced phosphorylation of DNA-PK and hampered repair of radiation-induced double strand breaks.
Effects of coping-oriented couples therapy on depression: A randomized clinical trial.
2008-01-01

The aim of this study was to evaluate the effectiveness of treating depression with coping-oriented couples therapy (COCT) as compared with cognitive-behavioral therapy (CBT; A. T. Beck, C. Ward, & M. Mendelson, 1961) and interpersonal psychotherapy (IPT; M. M. Weissman, J. C. Markowitz, & G. L. Klerman, 2000). Sixty couples, including 1 clinically depressed partner, completed pre- and posttest questionnaires as well as follow-up assessments at 6-month intervals over the subsequent 1.5 years. Effects of the 3 treatments on depressive symptomatology assessed by the Beck Depression Inventory (A. T. Beck, A. J. Rush, B. L. Shaw, & G. Emery, 1979) and Hamilton Rating Scale for Depression (M. Hamilton, 1960); recovery rates; and relapse rates were examined. Additionally, changes in relationship quality were evaluated. Results suggest that the COCT is as effective in improving depressive symptomatology as are the well-established, evidenced-based CBT and IPT approaches. The COCT did not demonstrate a significantly better outcome with regard to self-reported relationship satisfaction or dyadic coping; however, it did produce significant improvements in partners' expressed emotion, changes that were not seen in other treatment conditions.
TRPC6 Contributes to the Ca<sup>2+</sup> Leak of Human Erythrocytes
2008-01-01

Human erythrocytes express cation channels which contribute to the background leak of Ca(2+), Na(+) and K(+). Excessive activation of these channels upon energy depletion, osmotic shock, Cl(-) depletion, or oxidative stress triggers suicidal death of erythrocytes (eryptosis), characterized by cell-shrinkage and exposure of phosphatidylserine at the cell surface. Eryptotic cells are supposed to be cleared from circulating blood. The present study aimed to identify the cation channels. RT-PCR revealed mRNA encoding the non-selective cation channel TRPC6 in erythroid progenitor cells. Western blotting indicated expression of TRPC6 protein in erythrocytes from man and wildtype mice but not from TRPC6(-/-) mice. According to flow-cytometry, Ca(2+) entry into human ghosts prepared by hemolysis in EGTA-buffered solution containing the Ca(2+) indicator Fluo3/AM was inhibited by the reducing agent dithiothreitol and the erythrocyte cation channel blockers ethylisopropylamiloride and amiloride. Loading of the ghosts with antibodies against TRPC6 or TRPC3/6/7 but neither with antibodies against TRPM2 or TRPC3 nor antibodies pre-adsorbed with the immunizing peptides inhibited ghost Ca(2+) entry. Moreover, free Ca(2+) concentration, cell-shrinkage, and phospholipid scrambling were significantly lower in Cl(-)-depleted TRPC6(-/-) erythrocytes than in wildtype mouse erythrocytes. In conclusion, human and mouse erythrocytes express TRPC6 cation channels which participate in cation leak and Ca(2+)-induced suicidal death.
Soluble NKG2D ligands: prevalence, release, and functional impact
2008-01-01

Natural Killer (NK) cells are capable to recognize and eliminate malignant cells. Anti-tumor responses of NK cells are promoted by the tumor-associated expression of cell stress-inducible ligands of the activating NK receptor NKG2D. Current evidence suggests that established tumors subvert NKG2D-mediated tumor immunosurveillance by releasing NKG2D ligands (NKG2DL). Release of NKG2DL has been observed in a broad variety of human tumor entities and is thought to interfere with NKG2D-mediated tumor immunity in several ways. Further, levels of soluble NKG2DL (sNKG2DL) were also found to be elevated under various non-malignant conditions, although the functional implications remain largely unclear. Here we review and discuss the available data on the prevalence, release, functional impact, and potential clinical value of sNKG2DL.
Modes of Action of the New Arylguanidine Abafungin beyond Interference with Ergosterol Biosynthesis and in vitro Activity against Medically Important Fungi
2008-01-01

&lt;i&gt;Background:&lt;/i&gt;In contrast to the increasing numbers of agents for the treatment of invasive fungal infections, discoveries of new antifungal agents with therapeutic value in dermatomycoses are reported only rarely. &lt;i&gt;Methods:&lt;/i&gt; Abafungin (chemical abstracts service registry No. 129639-79/8) is the first member of a novel class of synthetic antifungal compounds, the arylguanidines. It was first synthesized at Bayer AG, Leverkusen, Germany, and its antifungal action was discovered during the screening of H&lt;sub&gt;2&lt;/sub&gt;-receptor antagonists based on the structure of famotidine. To obtain insight into its mode of action and antifungal activity, various tests were carried out with different fungal pathogensin vitro. &lt;i&gt;Results:&lt;/i&gt; Abafungin was found to have potent antifungal activity. Furthermore, mode-of-action studies suggested that abafungin exerts its antifungal activity regardless of whether the pathogens are growing or in a resting state. One target of abafungin was found to be the inhibition of transmethylation at the C-24 position of the sterol side chain, catalyzed by the enzyme sterol-C-24-methyltransferase. A second action of abafungin seems to be a direct effect on the fungal cell membrane.&lt;i&gt;Conclusion:&lt;/i&gt; The observed characteristics of abafungin indicate that abafungin might be a promising antifungal agent defining a new class of antimycotics.
Drawing explicit phylogenetic networks and their integration into SplitsTree
2008-01-01

In this article, we presented an extension of SplitsTree 4 that incorporates explicit phylogenetic networks. The extension provides a set of core classes to handle explicit phylogenetic networks and a visualization of these networks.
Media Violence and Youth Violence
2008-01-01

The frequency of exposure to media violence and eight additional risk factors were path-analyzed in a 2-year longitudinal study. The exposure to media violence (total score) affected students’ later violence (β = .28) and later violent delinquency (β = .30) more strongly than other risk factors. Direct effects were also caused by risk factors assessed at Time 1, which in turn were reinforced by the remaining risk factors on the second or third stratum of analysis. Of particular importance are the findings that (1) playing violent electronic games is the strongest risk factor of violent criminality and (2) both media-stimulated and real experiences of aggressive emotions associated with the motive of revenge are core risk factors of violence in school and violent criminality. The results of our study show that the more frequently children view horror and violence films during childhood and the more frequently they play violent electronic games at the beginning of adolescence the higher will these students’ violence and delinquency be at the age of 14.
Influence of NO Synthase Inhibitor L-NAME on Parasitemia and Survival of <i>Plasmodium berghei</i> Infected Mice
2008-01-01

Accelerated suicidal death or eryptosis of infected erythrocytes may delay development of parasitemia in malaria. Eryptosis is inhibited by nitric oxide (NO). The present study has been performed to explore, whether inhibition of NO synthase by L-NAME modifies the course of malaria. We show here that L-NAME (>or=10 microM) increased phosphatidylserine exposure of Plasmodium falciparum infected human erythrocytes, an effect significantly more marked than in noninfected human erythrocytes. We further show that parasitemia in Plasmodium berghei infected mice was significantly decreased (from 50% to 18% of circulating erythrocytes 20 days after infection) by addition of 1 mg/ml L-NAME to the drinking water. According to CFSE labelling L-NAME treatment accelerated the clearance of both, noninfected and infected, erythrocytes from circulating blood, but did not significantly extend the life span of infected animals. In conclusion, treatment with L-NAME shortens the life span of circulating erythrocytes and thus delays development of parasitemia during malaria.
Positively and negatively excited random walks on integers, with branching processes
2008-01-01

We consider excited random walks on the integers with a bounded number of i.i.d. cookies per site which may induce drifts both to the left and to the right. We extend the criteria for recurrence and transience by M. Zerner and for positivity of speed by A.-L. Basdevant and A. Singh to this case and also prove an annealed central limit theorem. The proofs are based on results from the literature concerning branching processes with migration and make use of a certain renewal structure.
Capecitabine plus oxaliplatin as first-line treatment in patients with advanced biliary system adenocarcinoma: a prospective multicentre phase II trial
2008-01-01

This prospective multicentre phase II study characterises the toxicity and activity of first-line capecitabine and oxaliplatin combination therapy (CAPOX) in advanced biliary system adenocarcinomas. Patients received oxaliplatin (130 mg m(-2), day 1) plus capecitabine (1000 mg m(-2) b.i.d., days 1-14) every 3 weeks. Patients were stratified prospectively into two groups based on location of the primary (gallbladder carcinoma (GBC) or extrahepatic cholangiocarcinoma (ECC) versus intrahepatic mass-forming type cholangiocarcinoma (ICC)). Sixty-five patients were evaluable. The response rate in 47 patients with GBC/ECC was 27% (4% complete responses), and in 23 patients (49%) stable disease (SD) was encountered. In 18 patients with ICC, we observed no objective responses, but 6 patients (33%) had SD. Median survival was 12.8 months (95% CI, 10.0-15.6) for patients with GBC or ECC (GBC: 8.2 months; 95% CI, 4.3-11.7; ECC: 16.8 months; 95% CI, 12.7-20.5), and 5.2 months (95% CI, 0.6-9.8) for ICC patients. In both cohorts, therapy was well tolerated. The most common grade 3-4 toxicity was peripheral sensory neuropathy (11 patients). Our data suggest that the CAPOX regimen is a well-tolerated and active treatment option for advanced ECC and GBC but might produce poorer results for ICC.
Old Meets Modern: The Use of Traditional Cryoprobes in the Age of Molecular Biology
2008-01-01

&lt;i&gt;Background:&lt;/i&gt; Endobronchial forceps biopsies are often small and are associated with a relevant extent of artifacts. To overcome these limitations is an important task. Especially when considering predictive factors for pharmacological therapies of lung cancer (ERCC1, RRM1) a development of biopsy techniques seems to be essential. This is the first report on a new endobronchial biopsy technique called cryobiopsy. &lt;i&gt;Objectives:&lt;/i&gt; In this study the feasibility and the potential advantages of applying cryoprobes for harvesting samples for histological examination in flexible bronchoscopies will be focused on. &lt;i&gt;Methods:&lt;/i&gt; In 12 patients suffering from exophytic endobronchial malignancies, a modified flexible cryoprobe was used for immediate recanalization. The extracted tissue was examined histologically regarding sample quality and sample size. &lt;i&gt;Results:&lt;/i&gt; Tissue samples obtained using the cryoprobe showed an extraordinary good quality in terms of size (median diameter of 6.7 mm, range 4.2–13 mm) and artifact-free sample area (75% of the samples showed an artifact-free sample area of more than 75%). Additionally molecular markers were shown to be well preserved. &lt;i&gt;Conclusions:&lt;/i&gt; The new technique termed cryobiopsy might widen the chest physician’s range of tools for diagnostic bronchoscopies.
fMRI Brain-Computer Interfaces
2008-01-01

Brain-computer interfaces based on fMRI enable real-time feedback of circumscribed brain regions to learn volitional regulation of those regions. This is an emerging field of intense research, with potential for multiple applications in neuroscientific research in brain plasticity and reorganization, movement restoration due to stroke, clinical rehabilitation of emotional disorders, quality assurance of fMRI experiments, and teaching functional imaging. This article presents a general architecture of an fMRI-BCI, with descriptions of each of its subsystems, and factors influencing their performance. The study has attempted to describe and compare a variety of approaches toward signal acquisition, preprocessing, analysis, and feedback. Technological advancement in higher-field MRI scanners, data acquisition sequences and image reconstruction techniques, preprocessing algorithms to correct for artifacts, more intelligent and robust analysis and interpretation methods, and faster feedback and visualization technology are anticipated to make fMRI-BCI widely applicable. FMRI-BCI could potentially be used for training patients to learn self-regulation of specific brain areas for transferring them later on to a more portable EEG-BCI system. FMRI-BCI has the potential of establishing itself as a tool for neuroscientific research and experimentation and also as an aid for psychophysiological treatment.
Screening for trisomy 21 in twin pregnancies in the first trimester: an update of the impact of chorionicity on maternal serum markers
2008-01-01

Abstract Objective To examine the distribution of first‐trimester biochemical markers of aneuploidy in twin pregnancies, and to assess whether there are differences in the distributions between monochorionic and dichorionic twins. Methods Maternal serum‐free β‐hCG and PAPP‐A were measured between 11 + 0 and 13 + 6 weeks as part of a routine first‐trimester screening program in conjunction with fetal nuchal translucency (NT) performed at two sites. Data from twin pregnancies were extracted from the fetal databases along with information on the chorionicty. The individual marker concentrations were expressed as weight corrected, ethnicity corrected, smoking corrected and IVF corrected MoM using data from singleton pregnancies as the reference. The overall medians were compared to those in singleton pregnancies and between monochorionic and dichorionic twins. Results Data was available from 1914 sets of twins. Of these, 1214 had information with respect to chorionicity, with 1024 being dichorionic and 190 being monochorionic. The overall median weight corrected, ethnicity corrected, smoking corrected and IVF corrected MoM amongst twin pregnancies were 2.023 for free β‐hCG (sd log 10 MoM = 0.2611 and 2.121 for PAPP‐A (sd log 10 MoM = 0.2255)—both medians were significantly greater than the medians in singleton pregnancies (1.00 MoM). In the case of monochorionic and dichorionic twins the median weight corrected, ethnicity corrected, smoking corrected and IVF corrected, free β‐hCG MoM's were not significantly different (1.983 v 2.041), however for PAPP‐A the median weight corrected, ethnicity corrected, smoking corrected and IVF corrected MoM in monochorionic twins was significantly lower than in dichorionic twins (1.756 v 2.250) whilst the sd log 10 MoM's were not significantly different (0.2185 v 0.2167). Conclusion Screening in twin pregnancies requires adjustment of the calculated MoM to account for the presence of two fetuses. In general, for free β‐hCG, this should be by dividing the observed corrected MoM by 2.023. For PAPP‐A two different factors are required − 2.192 in dichorionic twins and 1.788 in monochorionic twins. Copyright © 2008 John Wiley &amp; Sons, Ltd.
Metabonomics in cancer diagnosis: mass spectrometry-based profiling of urinary nucleosides from breast cancer patients
2008-01-01

Modified nucleosides are formed post-transcriptionally in RNA. In cancer disease, the cell turnover and thus RNA metabolism is increased, yielding higher concentrations of excreted modified nucleosides. In the presented study, urinary ribonucleosides were used to differentiate between breast cancer patients and healthy volunteers. The nucleosides were extracted from urine samples using affinity chromatography and subsequently analyzed via liquid chromatography ion trap mass spectrometry (LC-IT-MS). The peak areas were related to the internal standard isoguanosine and to the urinary creatinine level. For bioinformatic pattern recognition we used the support vector machine. We examined 113 urine samples from breast cancer patients (stage Tis-T4) and 99 control samples from healthy volunteers. We achieved a sensitivity of 87.67% and a specificity of 89.90% when including 31 nucleosides. The medical metabonomics concept based on the urinary nucleoside profile reveals a significantly improved classification compared with currently applied breast cancer biomarkers such as CA15-3.
Adaptive, Fast, and Oblivious Convolution in Evolution Equations with Memory
2008-01-01

To approximate convolutions which occur in evolution equations with memory terms, a variable-step-size algorithm is presented for which advancing N steps requires only operations and active memory, in place of operations and memory for a direct implementation. A basic feature of the fast algorithm is the reduction, via contour integral representations, to differential equations which are solved numerically with adaptive step sizes. Rather than the kernel itself, its Laplace transform is used in the algorithm. The algorithm is illustrated on three examples: a blowup example originating from a Schrödinger equation with concentrated nonlinearity, chemical reactions with inhibited diffusion, and viscoelasticity with a fractional order constitutive law.