julilili42/papers huggingface dataset:
Three‐dimensional models of cancer for pharmacology and cancer cell biology: Capturing tumor complexity in vitro/ex vivo
2014-09-01

Abstract Cancers are complex and heterogeneous pathological “organs” in a dynamic interplay with their host. Models of human cancer in vitro, used in cancer biology and drug discovery, are generally highly reductionist. These cancer models do not incorporate complexity or heterogeneity. This raises the question as to whether the cancer models' biochemical circuitry (not their genome) represents, with sufficient fidelity, a tumor in situ. Around 95% of new anticancer drugs eventually fail in clinical trial, despite robust indications of activity in existing in vitro pre‐clinical models. Innovative models are required that better capture tumor biology. An important feature of all tissues, and tumors, is that cells grow in three dimensions. Advances in generating and characterizing simple and complex (with added stromal components) three‐dimensional in vitro models (3D models) are reviewed in this article. The application of stirred bioreactors to permit both scale‐up/scale‐down of these cancer models and, importantly, methods to permit controlled changes in environment (pH, nutrients, and oxygen) are also described. The challenges of generating thin tumor slices, their utility, and potential advantages and disadvantages are discussed. These in vitro/ex vivo models represent a distinct move to capture the realities of tumor biology in situ, but significant characterization work still remains to be done in order to show that their biochemical circuitry accurately reflects that of a tumor.
The Jabal Akhdar dome in the Oman Mountains: Evolution of a dynamic fracture system
2014-09-01

Acknowledgments: This study was carried out within the framework of DGMK (German Society for Petroleum and Coal Science and Technology) research project 718 “Mineral Vein Dynamics Modelling,” which is funded by the companies ExxonMobil Production Deutschland GmbH, GDF SUEZ E&P Deutschland GmbH, RWE Dea AG and Wintershall Holding GmbH, within the basic research program of the WEG Wirtschaftsverband Erdo ̈l- und Erdgasgewinnung e.V. We thank the companies for their financial support and their permission to publish these results. The German University of Technology in Oman (GU-Tech) is acknowledged for its logistic support. We gratefully acknowledge the reviewers Andrea Billi and Jean-Paul Breton, whose constructive reviews greatly improved the manuscript
No effect of odor-induced memory reactivation during REM sleep on declarative memory stability
2014-09-01

Memory reactivations in hippocampal brain areas are critically involved in memory consolidation processes during sleep. In particular, specific firing patterns of hippocampal place cells observed during learning are replayed during subsequent sleep and rest in rodents. In humans, experimentally inducing hippocampal memory reactivations during slow-wave sleep (but not during wakefulness) benefits consolidation and immediately stabilizes declarative memories against future interference. Importantly, spontaneous hippocampal replay activity can also be observed during rapid eye movement (REM) sleep and some authors have suggested that replay during REM sleep is related to processes of memory consolidation. However, the functional role of reactivations during REM sleep for memory stability is still unclear. Here, we reactivated memories during REM sleep and examined its consequences for the stability of declarative memories. After 3 h of early, slow-wave sleep (SWS) rich sleep, 16 healthy young adults learned a 2-D object location task in the presence of a contextual odor. During subsequent REM sleep, participants were either re-exposed to the odor or to an odorless vehicle, in a counterbalanced within subject design. Reactivation was followed by an interference learning task to probe memory stability after awakening. We show that odor-induced memory reactivation during REM sleep does not stabilize memories against future interference. We propose that the beneficial effect of reactivation during sleep on memory stability might be critically linked to processes characterizing SWS including, e.g., slow oscillatory activity, sleep spindles, or low cholinergic tone, which are required for a successful redistribution of memories from medial temporal lobe regions to neocortical long-term stores.
Wildcard Compression of Inter-Domain Routing Tables for OpenFlow-Based Software-Defined Networking
2014-09-01

In this paper we consider carrier networks using only OpenFlow switches instead of IP routers. Accommodating the full forwarding information base (FIB) of IP routers in the switches is difficult because the BGP routing tables in the default-free zone currently contain about 500,000 entries and switches have only little capacity in their fast and expensive TCAM memory. The objective of this paper is the compression of the FIB in acceptable time to minimize the TCAM requirements of switches. The benchmark is simple prefix aggregation as it is common in IP networks where longest-prefix matching is applied. In contrast, OpenFlow-based switches can match general wildcard expressions with priorities. Starting from a minimum-size prefix-based FIB, we further compress that FIB by allowing general wildcard expressions utilizing the Espresso heuristic that is commonly used for logic minimization. As the computation time of Espresso is challenging for large inputs, we provide means to trade computation time against compression efficiency. Our results show that today's FIB sizes can be reduced by 17% saving up to 40,000 entries and the compression time can be limited to 1 - 2s sacrificing only 1% -- 2% compression ratio.
Integrating hydrogeochemical, hydrogeological, and environmental tracer data to understand groundwater flow for a karstified aquifer system
2014-09-01

Abstract For karstified aquifer systems, numerical models of groundwater flow are difficult to setup and parameterize. However, a system understanding useful for groundwater management may be obtained without applying overly complicated models. In this study, we demonstrate for a karstified carbonate aquifer in south‐western Germany that a combination of methods with moderate data requirements can be used to infer flowpaths and transit times of groundwater to production wells.
Coping With Growth in Adolescent Elite Sport
2014-09-01

Growing up in elite sport represents a challenging project. Young athletes must negotiate a career-defining transitional period while in the midst of adolescence. In this context, notably, the growth process can lead to health problems such as overloading and injuries. In this article, we investigate how adolescent elite athletes cope with problematic growth experiences. Taking a Bourdieusian perspective, we consider coping to be a socioculturally-located practice. Drawing on qualitative interviews and participant observation in German elite sport, our conversational analysis reveals five typical coping strategies among young athletes: (a) distancing, (b) rationalization, (c) active agency, (d) self-disciplining, and (e) responsibility transfer. We reflect on the health-compromising side effects of these strategies as well as the implications for the sporting community’s handling of growth problems.
Towards plug and play filling of microfluidic devices by utilizing networks of capillary stop valves
2014-09-01

Robust bubble-free priming of complex microfluidic chips represents a critical, yet often unmet prerequisite to enable their practical and widespread application. Towards this end, the usage of a network of capillary stop valves as a generic design feature is proposed. Design principles, numerical simulations, and their application in the development of a microfluidic cell culture device are presented. This chip comprises eight parallel chambers for the assembly and cultivation of human hepatocytes and endothelial cells. The inlet channel divides into cell chambers, after which the flows are reunited to a single chip outlet. Dimensions and geometry of channels and cell chambers are designed to yield capillary burst pressures sequentially increasing towards the chip outlet. Thus, progress of liquid flow through the device is predefined by design and enclosure of air bubbles inside the microfluidic structures is efficiently avoided. Capillary stop valves were designed using numerical simulations. Devices were fabricated in cyclic olefin polymer. Pressure during filling was determined experimentally and is in good agreement with data obtained from simulation.
Dynamic objects tracking with a mobile robot using passive UHF RFID tags
2014-09-01

Recent research deals more and more with the application of ultra high frequency (UHF) radio-frequency identification (RFID) on mobile robots. However, the sensing characteristics between the reader and the tag (i.e. detections and signal strength) are challenging to model due to the influence of environmental effects (e.g. tag density, reflection, diffraction, or absorption). In this paper, we address the problem of dynamic objects tracking with a mobile agent using the signal strength from UHF RFID tags attached to objects. Our solution estimates the positions of RFID tags under a Bayesian framework. More precisely, we combine a two stage dynamic motion model with the dual particle filter, to capture the dynamic motion of the object and to quickly recover from failures in tracking. This approach is then tested on a Scitos G5 mobile robot through various experiments.
Facial markers in second‐ and third‐trimester fetuses with trisomy 18 or 13, triploidy or Turner syndrome
2014-09-01

ABSTRACT Objective To examine the effectiveness of nasal bone ( NB ) evaluation (including NB length ( NBL )), prenasal thickness ( PT ) measurement, the PT : NBL ratio and the prefrontal space ratio ( PFSR ) in the identification of fetuses with trisomy 18 or 13, triploidy or Turner syndrome. Methods This was a retrospective study using stored midsagittal two‐dimensional images of the facial profile of fetuses with trisomy 18 or 13, triploidy or Turner syndrome in the second and third trimesters. For images of acceptable quality, measurements were obtained of NBL (where NB was present), PT , the PT : NBL ratio and PFSR , and these measurements were compared with previously published normal ranges. Results The search of databases identified 189 fetuses that met the study criteria: 132 (69.8%) with trisomy 18, 40 (21.2%) with trisomy 13, 10 (5.3%) with triploidy and seven (3.7%) with Turner syndrome. The NB was either absent or its measurement was below the 5 th centile in 67 (50.8%), 20 (50.0%), five (50.0%) and two (28.6%) of the fetuses with trisomy 18, trisomy 13, triploidy and Turner syndrome, respectively. The PT measurement was above the 95 th centile in 24 (18.2%), six (15.0%), one (10.0%) and one (14.3%) of the affected fetuses, respectively. The PFSR was abnormal in 72 (54.5%), 29 (72.5%), seven (70%) and four (57.1%) of the cases and the PT : NBL ratio was above the 95 th centile or the nasal bone was absent in 72 (54.5%), 20 (50.0%), six (60.0%) and four (57.1%) cases, respectively. Conclusion Although each of the facial markers considered provides some useful information in screening for trisomy 18, trisomy 13, triploidy and Turner syndrome, the performance of none of the markers appears to be as good as that in screening for trisomy 21. Copyright © 2014 ISUOG. Published by John Wiley &amp; Sons Ltd.
Effects of 12 weeks of once-daily tiotropium and olodaterol fixed-dose combination on exercise endurance in patients with COPD
2014-09-01

Background : Both tiotropium (T) and olodaterol (O) monotherapies improve exercise endurance in patients with chronic obstructive pulmonary disease (COPD). Objective: To evaluate the effects of T+O fixed-dose combination on exercise endurance in patients with GOLD 2–3 COPD after 12 weeks. Methods: TORRACTO (NCT01525615) was a 12-week, double-blind, parallel-group, placebo-controlled, Phase III study. Patients with GOLD 2–3 COPD received T+O (5/5 or 2.5/5 μg) once daily via Respimat Soft Mist inhaler, or placebo. Primary end point was endurance time (ET) during constant work-rate cycle ergometry to symptom limitation after 12 weeks. ET during endurance shuttle walking (ESW) to symptom limitation after 12 weeks was also assessed in a subset of 165 patients. Other end points included pre-exercise inspiratory capacity (IC). Results: 404 patients (269 men) were randomised (full analysis set n=385). Mean post-bronchodilator FEV 1 was 1.66 L (58.6% predicted). ET during cycle ergometry was significantly increased with T+O 5/5 μg vs placebo at 12 weeks. Increases in ET during ESW were observed for both T+O doses vs placebo at 12 weeks (21% increase, nominal p=0.06 for each dose). Both T+O doses increased pre-exercise IC vs placebo (nominal p Conclusions: T+O 5/5 μg improved ET during cycle ergometry vs placebo. Funding: Boehringer Ingelheim.
The Kraken: when myth encounters science
2014-09-01

Hundreds of years ago, sailors were terrified by the Kraken, a dreadful sea monster capable of sinking ships and with a taste for human flesh. Today we know the legends of this monster were based on sightings of giant squids. This animal belongs to the genus Architeuthis and was the subject of many scientific studies. Despite its enormous size (up to 18m), the giant squid is astoundingly elusive and much of its biology remains unknown. Thus shrouded in mystery, Architeuthis is almost a mythological creature and has a place both in science and in myth: the very last of the legends to persist to this day.
Reappraisal of Testudo antiqua (Testudines, Testudinidae) from the Miocene of Hohenhöwen, Germany
2014-09-01

Testudo antiqua is one of the few fossil turtle names to have survived the past 200 years of taxonomic reshuffling with its original genus and specific epithet intact. The nine currently known specimens were collected from the middle Miocene Hohenhöwen locality in southern Germany. Because the available Hohenhöwen material was never fully described, we here completely document all known specimens. It is unclear which of these specimens formed the original T. antiqua type series, so we herein selected the best preserved representative as the neotype. A phylogenetic analysis places T. antiqua in a basal polytomy within the clade Testudo , indicating that T. antiqua may represent the ancestral morphology of Testudo . As with a number of other published studies, ours was unable to resolve relationships between the three extant Testudo lineages (the hermanni -group, the graeca / kleinmanni / marginata group, and the horsfieldii -group). Finally, with a view toward locating more turtles and in order to better understand the geological and ecological context of these tortoises, we visited Hohenhöwen several times to search for the original collection sites, but we were unable to locate the original fossil quarries described in the literature.
Building local terrain maps using spatio-temporal classification for semantic robot localization
2014-09-01

The correct classification of the surrounding terrain is an important ability of a mobile robot that drives in outdoor environments. Our robot uses a 3D LIDAR and a camera to classify terrain as either asphalt, cobblestones, grass, or gravel. We build on previous work where we modeled the terrain as a Conditional random field to account for spatial dependencies, which improved results substantially. We now show how to speed up the spatial classification by defining a new energy term for neighborhood relations. Moreover, we now also consider temporal dependencies as the robot moves. This not only further improves the results, but makes it possible to build local terrain maps of the environment. We describe how to efficiently integrate the classification results of each time step into the map in a probabilistic manner. By also detecting obstacles with the LIDAR, the robot can build combined terrain and elevation maps. We show that these maps can be used for semantic robot localization.
A new species of Leiostracus (Gastropoda, Pulmonata, Orthalicoidea) from Espírito Santo, Brazil
2014-09-01

A remarkable new species of pulmonate land snail was found in the collection of the Senckenberg Forschungninstitut und Naturmuseum Frankfurt (Frankfurt am Main, Germany) and is described here as Leiostracus faerie sp. nov. It can be easily identified by its small and translucent shell with fine axial light brown bands and its protoconch sculpture. It was collected in the Rio Doce ("Doce River") region in Espírito Santo, Brazil, an area known for a high diversity and endemicity of land snails. This discovery shows how little this fauna is known and reinforces the importance of museum collections in the study of biodiversity and conservation.
ReMax – A MaxSAT aided Product (Re-)Configurator
2014-09-01

Abstract. We introduce a product configurator with the ability of optimal re-configuration built on MaxSAT as the background engine. A product configurator supported by a SAT solver can provide an an-swer at any time about which components are selectable and which are not. But if a user wants to select a component which has already been disabled, a purely SAT based configurator does not support a guided re-configuration process. With MaxSAT we can compute the minimal number of changes of component selections to enable the desired component again. We implemented a product configurator — called ReMax — using state-of-the-art MaxSAT algorithms. Be-sides the demonstration of handmade examples, we also evaluate the performance of our configurator on problem instances based on real configuration data of the automotive industry. 1
Recurrence and Transience of Critical Branching Processes in Random Environment with Immigration and an Application to Excited Random Walks
2014-09-01

We establish recurrence and transience criteria for critical branching processes in random environments with immigration. These results are then applied to the recurrence and transience of a recurrent random walk in a random environment on Z disturbed by cookies inducing a drift to the right of strength 1.
Once-daily tiotropium and olodaterol fixed-dose combination via the respimat improves outcomes vs mono-components in COPD in two 1-year studies
2014-09-01

Introduction: Tiotropium (T), a once-daily long-acting muscarinic antagonist, is a well-established first-line maintenance treatment in chronic obstructive pulmonary disease (COPD); olodaterol (O) is a once-daily long-acting β 2 -agonist that has recently gained approval in several countries. Two Phase III replicate pivotal studies assessed the efficacy and safety of fixed-dose combinations of T and O (T+O) delivered via Respimat Soft Mist inhaler in patients with GOLD Stage 2–4 COPD. Methods: Two 52-week, double-blind, parallel-group studies randomised 5162 patients to O 5 μg, T 2.5 μg, T 5 μg, T+O 2.5/5 μg or T+O 5/5 μg. Primary efficacy end points were trough FEV 1 response (ie change from baseline), FEV 1 area under the curve from 0–3 hours and SGRQ total score after 24 weeks. Pooled data from the two studies are presented here; lung function from the individual studies will subsequently be provided. Results: All treatments resulted in clinically relevant improvements in lung function, with significant increases with both T+O doses over the individual components (p 1 responses were 0.055 L (O 5 μg), 0.073 L (T 2.5 μg), 0.080 L (T 5 μg), 0.118 L (T+O 2.5/5 μg) and 0.140 L (T+O 5/5 μg). SGRQ total scores improved by 5.1 (O 5 μg), 5.7 (T 2.5 μg), 5.6 (T 5 μg), 6.2 (T+O 2.5/5 μg) and 6.8 points (T+O 5/5 μg); differences between T+O 5/5 μg and O 5 μg and T 5 μg were statistically significant (p Conclusions: T+O 5/5 μg significantly improved lung function and provided symptomatic benefit over O 5 μg and T 5 μg. Funding: Boehringer Ingelheim.
Microbial aetiology of community-acquired pneumonia and it's relation with ICS use in patients with COPD – Results from the German competence network CAPNETZ
2014-09-01

Background: Community-Acquired Pneumonia (CAP) is a major cause of mortality worldwide. While COPD is a common co-morbidity in CAP, its impact remains relatively unknown. Objectives: 1) To assess potential differences in microbial aetiology of CAP between subjects with and without COPD in a well-characterized cohort of CAP patients; 2) To study the association between microbiology, ICS use and mortality. Methods: 1307 patients with CAP (57.0% males, age 59.0±18.5 y) were included and followed for 180 days. 264 of these (20.2%) fulfilled diagnostic criteria for COPD. Differences in microbial aetiology and ICS use were investigated by univariate analyses. Logistic regression analysis was performed to study the association between microbial aetiology and mortality. Results: H. influenzae and S. pneumoniae were the most common pathogens in CAP-COPD, whereas S. pneumoniae was most frequently identified in CAP-only. Enterobacteriaceae significantly predicted mortality risk in all CAP-patients ( p =0.045), while COPD was not identified as independent risk factor. ICS use of ≥1000μg Fluticason-equivalent was associated with 180-day mortality in COPD ( p =0.043). ICS use was not associated with different microbial aetiology. Conclusion: Microbial aetiology differs between CAP patients with and without COPD. Enterobacteriaceae impacts on mortality risk, highlighting the importance of microbiological sampling in CAP. The role of ICS use in CAP mortality requires further investigation, as there might be a dose-related association.
L-type calcium channels in the auditory system
2014-09-01

The voltage-activated L-type calcium channels Cav1.2 and Cav1.3 mediate Ca2+ influx into neurons at the soma or at dendrites, whereas they are not observed at the presynapse. Surprisingly, in the inner ear, Cav1.3 is indispensable for signal transmission from the presynaptic cochlear inner hair cells to the postsynaptic auditory nerve fibers. Due to Cav1.3 channel clustering at ribbons, i.e., specific presynaptic structures of the hair cells, they promote Ca2+ influx, which triggers calcium-dependent fusion of synaptic vesicles with the plasma membrane. Mutations in Cacna1d, a gene that encodes Cav1.3, result in deafness because release of the neurotransmitter glutamate at the synapses is abolished. Moreover, studies of the auditory pathway have revealed that Cav1.3 plays an important part in the central auditory system as well. Absence of the channel results in severe changes in auditory pathway cytoarchitecture and in abnormal electrophysiological performance of auditory neurons. Furthermore, developmental refinement of tonotopic inhibitory projections in sound localization circuits is disrupted. These aberrations are associated with abnormal sound processing in the auditory pathway. This goes to show that the Cav1.3 channel is essential for inner ear functioning as well as auditory pathway development and performance. Cacna1d therefore represents a prototypal deafness-associated gene, in which mutations result in both peripheral and central auditory deficiencies. This, in turn, has implications for auditory rehabilitation using cochlear implants that address only peripheral dysfunctions. Exploratory research into the closely related Cav1.2 isoform points to an important role of this channel in acoustic trauma. Cav1.2 is mainly expressed in the auditory nerve, but apparently not essential for normal auditory function. Loss of function of the channel, however, does influence the effects of traumatic noise exposure. Loss of this channel induced by noise trauma results in reduced auditory threshold increase—as compared with the control group. This phenomenon points to the fact that Cav1.2-mediated Ca2+ influx is involved in noise trauma-induced damage. Deeper insight into this function might result in new therapeutic approaches.
Dual-State Quantum Dot Laser Self-Interferometric Sensing
2014-09-01

We demonstrate dual-state quantum dot laser self-interferometry. A low-frequency Doppler signal originating from the coupled emission-states bears the potential of high-velocity-detection of diffuse reflecting objects. Modeling confirms the experiments and identify the carrier-coupling as the relevant mechanism.