julilili42/papers huggingface dataset:
Upper ocean climate of the Eastern Mediterranean Sea during the Holocene Insolation Maximum – a model study
2011-10-21

Abstract. Nine thousand years ago (9 ka BP), the Northern Hemisphere experienced enhanced seasonality caused by an orbital configuration close to the minimum of the precession index. To assess the impact of this "Holocene Insolation Maximum" (HIM) on the Mediterranean Sea, we use a regional ocean general circulation model forced by atmospheric input derived from global simulations. A stronger seasonal cycle is simulated by the model, which shows a relatively homogeneous winter cooling and a summer warming with well-defined spatial patterns, in particular, a subsurface warming in the Cretan and western Levantine areas. The comparison between the SST simulated for the HIM and a reconstruction from planktonic foraminifera transfer functions shows a poor agreement, especially for summer, when the vertical temperature gradient is strong. As a novel approach, we propose a reinterpretation of the reconstruction, to consider the conditions throughout the upper water column rather than at a single depth. We claim that such a depth-integrated approach is more adequate for surface temperature comparison purposes in a situation where the upper ocean structure in the past was different from the present-day. In this case, the depth-integrated interpretation of the proxy data strongly improves the agreement between modelled and reconstructed temperature signal with the subsurface summer warming being recorded by both model and proxies, with a small shift to the south in the model results. The mechanisms responsible for the peculiar subsurface pattern are found to be a combination of enhanced downwelling and wind mixing due to strengthened Etesian winds, and enhanced thermal forcing due to the stronger summer insolation in the Northern Hemisphere. Together, these processes induce a stronger heat transfer from the surface to the subsurface during late summer in the western Levantine; this leads to an enhanced heat piracy in this region, a process never identified before, but potentially characteristic of time slices with enhanced insolation.
Understanding the risk factors of learning in adversarial environments
2011-10-21

Learning for security applications is an emerging field where adaptive approaches are needed but are complicated by changing adversarial behavior. Traditional approaches to learning assume benign errors in data and thus may be vulnerable to adversarial errors. In this paper, we incorporate the notion of adversarial corruption directly into the learning framework and derive a new criteria for classifier robustness to adversarial contamination.
Cerebrospinal fluid fatty acids in glucocerebrosidase‐associated Parkinson's disease
2011-10-21

Abstract Background: Heterozygous mutations in the glucocerebrosidase gene lead to an increased risk for and to more severe alpha‐synuclein‐associated pathology in Parkinson's disease. As both glucocerebrosidase and alpha‐synuclein interact with fatty acids, we hypothesized that cerebrospinal fluid fatty acid levels are altered in these Parkinson's disease patients. Methods: Cerebrospinal fluid levels of 13 fatty acids in 8 Parkinson's disease patients with a heterozygous glucocerebrosidase mutation were compared with those of 41 idiopathic Parkinson's disease patients and 30 controls using gas chromatography. Results: Parkinson's disease patients with a heterozygous glucocerebrosidase mutation had lower levels of palmitoleic ( P ≤ .007), oleic ( P ≤ .016), linoleic ( P ≤ .005), arachidonic ( P ≤ .003), eicosapentaenoic ( P ≤ .003) and decosahexaenoic ( P ≤ .03) acids and lower levels of total fatty acids ( P &lt; .005) compared with both idiopathic Parkinson's disease patients and control subjects. Conclusions: These results suggest that abnormalities of fatty acid metabolism are specifically involved in the pathogenesis of Parkinson's disease associated with a heterozygous glucocerebrosidase mutation. © 2011 Movement Disorder Society
Cosmic microwave background radiation in an inhomogeneous spherical space
2011-10-21

We analyse the CMB radiation in spherical 3-spaces with non-trivial topology. The focus is put on an inhomogeneous space which possesses observer dependent CMB properties. The suppression of the CMB anisotropies on large angular scales is analysed with respect to the position of the CMB observer. The equivalence of a lens space with a Platonic cubic space is shown and used for the harmonic analysis. We give the transformation of the CMB multipole radiation amplitude as a function of the position of the observer. General sum rules are obtained in terms of the squares of the expansion coefficients for invariant polynomials on the 3-sphere.
Acquired self‐control of insula cortex modulates emotion recognition and brain network connectivity in schizophrenia
2011-10-22

Abstract Real‐time functional magnetic resonance imaging (rtfMRI) is a novel technique that has allowed subjects to achieve self‐regulation of circumscribed brain regions. Despite its anticipated therapeutic benefits, there is no report on successful application of this technique in psychiatric populations. The objectives of the present study were to train schizophrenia patients to achieve volitional control of bilateral anterior insula cortex on multiple days, and to explore the effect of learned self‐regulation on face emotion recognition (an extensively studied deficit in schizophrenia) and on brain network connectivity. Nine patients with schizophrenia were trained to regulate the hemodynamic response in bilateral anterior insula with contingent rtfMRI neurofeedback, through a 2‐weeks training. At the end of the training stage, patients performed a face emotion recognition task to explore behavioral effects of learned self‐regulation. A learning effect in self‐regulation was found for bilateral anterior insula, which persisted through the training. Following successful self‐regulation, patients recognized disgust faces more accurately and happy faces less accurately. Improvements in disgust recognition were correlated with levels of self‐activation of right insula. RtfMRI training led to an increase in the number of the incoming and outgoing effective connections of the anterior insula. This study shows for the first time that patients with schizophrenia can learn volitional brain regulation by rtfMRI feedback training leading to changes in the perception of emotions and modulations of the brain network connectivity. These findings open the door for further studies of rtfMRI in severely ill psychiatric populations, and possible therapeutic applications. Hum Brain Mapp, 2013. © 2011 Wiley Periodicals, Inc.
Lack of CCR7 expression is rate limiting for lymphatic spread of pancreatic ductal adenocarcinoma
2011-10-23

Abstract CCR7 expression on tumor cells promotes lymphatic spread in several malignant tumors. However, a comprehensive characterization of the CCL19/CCL21–CCR7 axis in pancreatic ductal adenocarcinoma (PDAC), which is known for its high rates of lymph‐node metastases, is still lacking. CCR7 mRNA and CCR7 protein were found to be expressed in spheroid cultures of all six examined PDAC cell lines. In migration assays, CCR7 expressing PDAC cells showed enhanced migration toward CCL19 and CCL21, the two ligands of CCR7. In an orthotopic nude mouse model, CCR7‐transfected PT45P1 cells gave rise to significantly larger tumors and showed a higher frequency of lymph vessel invasion and lymph‐node metastases than mock‐transfected cells. In an analysis using quantitative real‐time PCR, CCR7 showed fourfold overexpression in microdissected PDAC cells compared to normal duct cells. Moderate‐to‐strong immunohistochemical CCR7 expression, found in 58 of 121 well‐characterized human PDACs, correlated with high rates of lymph vessel invasion. Conversely, PDACs completely lacking CCR7 expression showed only low rates of lymph vessel invasion and lymph‐node metastases. The evaluation of CCL21 expression by immunofluorescence staining revealed a significant upregulation of CCL21 in peritumoral and intratumoral lymph vessels compared to lymph vessels in disease‐free pancreata. In conclusion, our study revealed strong evidence that lack of CCR7 impairs the metastatic potential of PDAC. Lymph vessel invasion by CCR7 expressing PDAC cells may be additionally enhanced by upregulation of CCL21 in tumor‐associated lymph vessels, representing a previously unknown factor of lymphatic spread.
Simulation of Near-Infrared Light Absorption Considering Individual Head and Prefrontal Cortex Anatomy: Implications for Optical Neuroimaging
2011-10-24

Functional near-infrared spectroscopy (fNIRS) is an established optical neuroimaging method for measuring functional hemodynamic responses to infer neural activation. However, the impact of individual anatomy on the sensitivity of fNIRS measuring hemodynamics within cortical gray matter is still unknown. By means of Monte Carlo simulations and structural MRI of 23 healthy subjects (mean age: 25.0±2.8 years), we characterized the individual distribution of tissue-specific NIR-light absorption underneath 24 prefrontal fNIRS channels. We, thereby, investigated the impact of scalp-cortex distance (SCD), frontal sinus volume as well as sulcal morphology on gray matter volumes (V(gray)) traversed by NIR-light, i.e. anatomy-dependent fNIRS sensitivity. The NIR-light absorption between optodes was distributed describing a rotational ellipsoid with a mean penetration depth of (23.6±0.7) mm considering the deepest 5% of light. Of the detected photon packages scalp and bone absorbed (96.4±9.7)% and V(gray) absorbed (3.1±1.8)% of the energy. The mean V(gray) volume (1.1±0.4) cm3 was negatively correlated (r=-.76) with the SCD and frontal sinus volume (r=-.57) and was reduced by 41.5% in subjects with relatively large compared to small frontal sinus. Head circumference was significantly positively correlated with the mean SCD (r=.46) and the traversed frontal sinus volume (r=.43). Sulcal morphology had no significant impact on V(gray). Our findings suggest to consider individual SCD and frontal sinus volume as anatomical factors impacting fNIRS sensitivity. Head circumference may represent a practical measure to partly control for these sources of error variance.
Influence of implant geometry on primary insertion stability and simulated peri-implant bone loss: an in vitro study using resonance frequency analysis and damping capacity assessment.
2011-10-24

The results of this study clearly show that the outcome of implant stability assessment depends on environmental factors such as bone quality and implant geometry. While the authors do not recommend the use of the Periotest or Osstell devices for a comparison of the stability of two individual implants, both should be useful to monitor the state of an individual implant over time.
Intraoperator and interoperator repeatability of manual and semi‐automated measurement of increased fetal nuchal translucency according to the operator's experience
2011-10-24

Objective To compare the intraoperator and interoperator repeatability of manual and semi‐automated measurement of increased nuchal translucency (NT) in sonographers with different levels of experience. Methods One hundred NT images without measurements were selected from the digital database. Half had NT measurements between 2.5 and 3.5 mm, and half had NT measurements above 3.5 mm. Five operators (two experts, three general gynaecologist) measured fetal NT manually and automatically. Each operator was blinded to any pre‐existing measurements. Each image was measured twice by each operator. Intraoperator repeatability was assessed by standard deviation of within sonographer repeated measurement. Interoperator repeatability was assessed as difference towards the gold standard, which was defined as the mean measurement of experts. Results The overall standard deviation of the difference between the first and the second manual measurements was 0.14 and 0.10 mm for moderate and severely increased NT. It was 0.10 and 0.08 mm with the semi‐automated system. Mean difference between the manual measurement of nonexpert operators and the gold standard was −0.01 mm for moderately increased NT and 0.02 mm for severely increased NT. With the semi‐automated measurement, mean bias was similar. Conclusion The automated NT measurement leads to a further standardization of the NT assessment process. Especially inexperienced operators may benefit from this tool. Copyright © 2011 John Wiley &amp; Sons, Ltd.
Personalization in skipforward, an ontology-based distributed annotation system
2011-10-24

Abstract. Skipforward is a distributed annotation system allowing users to enter and browse statements about items and their features. Items can be things such as movies or books; item features are the genre of a movie or the storytelling pace of a book. Whenever multiple users annotate the same item with a statement about the same feature, these individual statements get aggregated by the system. For aggregation, individual user statements are weighted according to a competence metric based on the constrained Pearson correlation, adapted for Skipforward data: A user gets assigned high competence with regard to the feature in question if, for other items and the same feature type, he had a similar opinion to the current user. Since the competence metric is dependent on the user currently viewing the data, the user’s view of the data is completely personalized. In this paper, the personalization aspect as well as the item and expert recommender are presented. 1
Role of AMPK-mTOR-Ulk1/2 in the Regulation of Autophagy: Cross Talk, Shortcuts, and Feedbacks
2011-10-25

Living cells are adaptive self-sustaining systems. They strictly depend on the sufficient supply of oxygen, energy, and nutrients from the outside in order to sustain their internal organization. However, as autonomous entities they are able to monitor and appropriately adapt to any critical fluctuation in their environment. In the case of insufficient external nutrient supply or augmented energy demands, cells start to extensively digest their own interior. This process, known as macroautophagy, comprises the transport of cytosolic portions and entire organelles to the lysosomal compartment via specific double-membrane vesicles, called autophagosomes. Although extensively upregulated under nutrient restriction, a low level of basal autophagy is likewise crucial in order to sustain the cellular homeostasis. On the other hand, cells have to avoid excessive and enduring self-digestion. The delicate balance between external energy and nutrient supply and internal production and consumption is a demanding task. The complex protein network that senses and precisely reacts to environmental changes is thus mainly regulated by rapid and reversible posttranslational modifications such as phosphorylation. This review focuses on the serine/threonine protein kinases AMP-activated protein kinase, mammalian target of rapamycin (mTOR), and unc-51-like kinase 1/2 (Ulk1/2), three interconnected major junctions within the autophagy regulating signaling network.
First‐trimester ultrasound images using HDlive
2011-10-25

The image on the cover of this month's Journal shows a 7-week embryo obtained using a Voluson E8 (GE Medical Systems, Zipf, Austria) ultrasound machine equipped with a new surface render mode, ‘HDlive’ (Figure 1). Figure 2 shows another case at 10 weeks, obtained using the same technique. The HDlive system uses an adjustable light source, giving the operator the opportunity to create lighting and shadowing effects and thereby increasing depth perception. In both images it is clear to see that this capacity to adjust lighting, combined with use of new skin-like colors, gives the fetus a natural and anatomically realistic appearance. Three-dimensional HDlive rendered image showing a cross-section through a gestational sac with a 7-week embryo (crown–rump length, 12 mm) visible inside the amniotic cavity. The patient was a 33-year-old primigravida, who was referred for ultrasound due to lower abdominal pain. Three-dimensional HDlive rendered image showing a 10-week fetus with crown–rump length of 35 mm. The patient was a 30-year-old primigravida, who presented with vaginal bleeding.
Contemporary microsurgical concept for the treatment of Cushing’s disease: endocrine outcome in 83 consecutive patients
2011-10-25

Summary Background Evidence suggests that occult adenoma remnants are responsible for persistent Cushing’s disease (CD) following transsphenoidal surgery (TSS). To optimize the outcome, we have adapted our microsurgical concept. The influence of our surgical strategy on remission rate and pituitary function is presented. Design and patients 83 patients undergoing TSS for newly diagnosed CD. An enlarged resection was performed in 36 patients. A modified exploration technique with radial incisions was performed in 19 patients in whom an adenoma was not readily detectable. Results The overall remission rate of primary surgery was 84·3% (70/83). A remission rate of 87·5% (63/72) was achieved in microadenomas. Six patients with microadenomas were re‐operated for persistence, and hypercortisolism was corrected in five of them. With re‐operation included, the overall remission rate for microadenomas was 94·4%. No procedure‐related complications occurred in primary surgery. Of the patients in remission, 72·5% had early postoperative random cortisol levels below 2 μg/dl, 17·4% had cortisol levels between 2 and 5 μg/dl, and 10·1% had cortisol levels &gt;5 μg/dl. 15·2% of the patients with microadenomas developed postoperative partial hypopituitarism and 3% diabetes insipidus. No increased rate of hypopituitarism was found with enlarged adenomectomy compared to selective adenomectomy. Only a slightly higher rate of partial hypopituitarism (23·1%) was found if extensive exploration was required. Conclusion With our microsurgical concept, a high initial cure rate is achievable with minimal surgical morbidity. Enlarged adenomectomy has no adverse effect on the rate of postoperative hypopituitarism. Early repeat surgery is a successful option if CD persists.
A cardiac pathway of cyclic GMP-independent signaling of guanylyl cyclase A, the receptor for atrial natriuretic peptide
2011-10-25

Cardiac atrial natriuretic peptide (ANP) regulates arterial blood pressure, moderates cardiomyocyte growth, and stimulates angiogenesis and metabolism. ANP binds to the transmembrane guanylyl cyclase (GC) receptor, GC-A, to exert its diverse functions. This process involves a cGMP-dependent signaling pathway preventing pathological [Ca 2+ ] i increases in myocytes. In chronic cardiac hypertrophy, however, ANP levels are markedly increased and GC-A/cGMP responses to ANP are blunted due to receptor desensitization. Here we show that, in this situation, ANP binding to GC-A stimulates a unique cGMP-independent signaling pathway in cardiac myocytes, resulting in pathologically elevated intracellular Ca 2+ levels. This pathway involves the activation of Ca 2+ ‐permeable transient receptor potential canonical 3/6 (TRPC3/C6) cation channels by GC-A, which forms a stable complex with TRPC3/C6 channels. Our results indicate that the resulting cation influx activates voltage-dependent L-type Ca 2+ channels and ultimately increases myocyte Ca 2 + i levels. These observations reveal a dual role of the ANP/GC-A–signaling pathway in the regulation of cardiac myocyte Ca 2+ i homeostasis. Under physiological conditions, activation of a cGMP-dependent pathway moderates the Ca 2+ i -enhancing action of hypertrophic factors such as angiotensin II. By contrast, a cGMP-independent pathway predominates under pathophysiological conditions when GC-A is desensitized by high ANP levels. The concomitant rise in [Ca 2+ ] i might increase the propensity to cardiac hypertrophy and arrhythmias.
A Novel Metagenomic Short-Chain Dehydrogenase/Reductase Attenuates Pseudomonas aeruginosa Biofilm Formation and Virulence on Caenorhabditis elegans
2011-10-26

In Pseudomonas aeruginosa, the expression of a number of virulence factors, as well as biofilm formation, are controlled by quorum sensing (QS). N-Acylhomoserine lactones (AHLs) are an important class of signaling molecules involved in bacterial QS and in many pathogenic bacteria infection and host colonization are AHL-dependent. The AHL signaling molecules are subject to inactivation mainly by hydrolases (Enzyme Commission class number EC 3) (i.e. N-acyl-homoserine lactonases and N-acyl-homoserine-lactone acylases). Only little is known on quorum quenching mechanisms of oxidoreductases (EC 1). Here we report on the identification and structural characterization of the first NADP-dependent short-chain dehydrogenase/reductase (SDR) involved in inactivation of N-(3-oxo-dodecanoyl)-L-homoserine lactone (3-oxo-C(12)-HSL) and derived from a metagenome library. The corresponding gene was isolated from a soil metagenome and designated bpiB09. Heterologous expression and crystallographic studies established BpiB09 as an NADP-dependent reductase. Although AHLs are probably not the native substrate of this metagenome-derived enzyme, its expression in P. aeruginosa PAO1 resulted in significantly reduced pyocyanin production, decreased motility, poor biofilm formation and absent paralysis of Caenorhabditis elegans. Furthermore, a genome-wide transcriptome study suggested that the level of lasI and rhlI transcription together with 36 well known QS regulated genes was significantly (≥10-fold) affected in P. aeruginosa strains expressing the bpiB09 gene in pBBR1MCS-5. Thus AHL oxidoreductases could be considered as potent tools for the development of quorum quenching strategies.
Modulation of Microsaccades in Monkey during a Covert Visual Attention Task
2011-10-26

The use of awake, fixating monkeys in neuroscience has allowed significant advances in understanding numerous brain functions. However, fixation is an active process, with the occurrence of incessant eye movements, including rapid ones called microsaccades. Even though microsaccades have been shown to be modulated by stimulus and cognitive processes in humans, it is not known to what extent these results are similar in monkeys or why they occur. Here, we analyzed the stimulus-, context-, and attention-related changes in microsaccades while monkeys performed a challenging visual attention task. The distributions of microsaccade times were highly stereotypical across thousands of trials in the task. Moreover, in epochs of the task in which animals anticipated the occurrence of brief stimulus probes, microsaccade frequency decreased to a rate of less than one movement per second even on long multisecond trials. These effects were explained by the observation that microsaccades occurring at the times of the brief probes were sometimes associated with reduced perceptual performance. Microsaccade directions also exhibited temporal modulations related to the attentional demands of the task, like earlier studies in humans, and were more likely to be directed toward an attended location on successfully performed trials than on unsuccessfully completed ones. Our results show that microsaccades in nonhuman primates are correlated with the allocation of stimulus-evoked and sustained covert attention. We hypothesize that involvement of the superior colliculus in microsaccade generation and attentional allocation contributes to these observations. More importantly, our results clarify the potential role of these eye movements in modifying behavior and neural activity.