julilili42/papers huggingface dataset:
Separating the role of biotic interactions and climate in determining adaptive response of plants to climate change
2015-05-01

Altered rainfall regimes will greatly affect the response of plant species to climate change. However, little is known about how direct effects of changing precipitation on plant performance may depend on other abiotic factors and biotic interactions. We used reciprocal transplants between climatically very different sites with simultaneous manipulation of soil, plant population origin, and neighbor conditions to evaluate local adaptation and possible adaptive response of four Eastern Mediterranean annual plant species to climate change. The effect of site on plant performance was negligible, but soil origin had a strong effect on fecundity, most likely due to differential water retaining ability. Competition by neighbors strongly reduced fitness. We separated the effects of the abiotic and biotic soil properties on plant performance by repeating the field experiment in a greenhouse under homogenous environmental conditions and including a soil biota manipulation treatment. As in the field, plant performance differed among soil origins and neighbor treatments. Moreover, we found plant species‐specific responses to soil biota that may be best explained by the differential sensitivity to negative and positive soil biota effects. Overall, under the conditions of our experiment with two contrasting sites, biotic interactions had a strong effect on plant fitness that interacted with and eventually overrode climate. Because climate and biotic interactions covary, reciprocal transplants and climate gradient studies should consider soil biotic interactions and abiotic conditions when evaluating climate change effects on plant performance.
Signal integration by the CYP1A1 promoter -- a quantitative study
2015-05-01

Genes involved in detoxification of foreign compounds exhibit complex spatiotemporal expression patterns in liver. Cytochrome P450 1A1 (CYP1A1), for example, is restricted to the pericentral region of liver lobules in response to the interplay between aryl hydrocarbon receptor (AhR) and Wnt/β-catenin signaling pathways. However, the mechanisms by which the two pathways orchestrate gene expression are still poorly understood. With the help of 29 mutant constructs of the human CYP1A1 promoter and a mathematical model that combines Wnt/β-catenin and AhR signaling with the statistical mechanics of the promoter, we systematically quantified the regulatory influence of different transcription factor binding sites on gene induction within the promoter. The model unveils how different binding sites cooperate and how they establish the promoter logic; it quantitatively predicts two-dimensional stimulus-response curves. Furthermore, it shows that crosstalk between Wnt/β-catenin and AhR signaling is crucial to understand the complex zonated expression patterns found in liver lobules. This study exemplifies how statistical mechanical modeling together with combinatorial reporter assays has the capacity to disentangle the promoter logic that establishes physiological gene expression patterns.
On Tracking Dynamic Objects with Long Range Passive UHF RFID Using a Mobile Robot
2015-05-01

Service robots have shown an impressive potential in providing assistance and guidance in various environments, such as supermarkets, shopping malls, homes, airports, and libraries. Due to the low cost and contactless way of communication, radiofrequency identification (RFID) technology provides a solution to overcome the difficulties (e.g., occlusions) that the traditional line-of-sight sensors (e.g., cameras and laser range finders) face. In this paper, we address the applications of using passive ultrahigh frequency (UHF) RFID as a sensing technology for mobile robots to track dynamic objects. 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. The state estimation from the particle filter is used in combination with the VFH+ (Vector Field Histogram) to guide the robot towards the target. This is then integrated into a framework, which allows the robot to search for both static and dynamic tags, follow them, and maintain the distance between them. We finally tested our approach on a SCITOS G5 service robot through various experiments.
Salient regions detection for indoor robots using RGB-D data
2015-05-01

The goal of saliency detection is to highlight objects in image data that stand out relative to their surrounding. Therefore, saliency detection aims to capture regions that are perceived as important. The most recent bottom-up approaches for saliency detection measure contrast based on visual features in 2D scenes, ignoring depth value. This work presents an effective method to measure saliency by mapping pixels into foreground and background regions in RGB-D images. Namely, we first segment an image into regions to evaluate the object uniqueness and consistency using graph-based segmentation. Then, we utilize the region color, depth, layout and boundary information to produce robust foreground and background saliency measures. Finally, we combine the two saliency maps based on Gaussian weights. As a result, our approach produces high-quality saliency maps, which may be used for further processing like object detection or recognition. Experimental results on two datasets compare our method with the state of the art and highlight its effectiveness.
Microfluidic chip system for the selection and enrichment of cell binding aptamers
2015-05-01

Aptamers are promising cell targeting ligands for several applications such as for the diagnosis, therapy, and drug delivery. Especially, in the field of regenerative medicine, stem cell specific aptamers have an enormous potential. Using the combinatorial chemistry process SELEX (Systematic Evolution of Ligands by Exponential enrichment), aptamers are selected from a huge oligonucleotide library consisting of approximately 1015 different oligonucleotides. Here, we developed a microfluidic chip system that can be used for the selection of cell specific aptamers. The major drawbacks of common cell-SELEX methods are the inefficient elimination of the unspecifically bound oligonucleotides from the cell surface and the unspecific binding/uptake of oligonucleotides by dead cells. To overcome these obstacles, a microfluidic device, which enables the simultaneous performance of dielectrophoresis and electrophoresis in the same device, was designed. Using this system, viable cells can be selectively assembled by dielectrophoresis between the electrodes and then incubated with the oligonucleotides. To reduce the rate of unspecifically bound sequences, electrophoretic fields can be applied in order to draw loosely bound oligonucleotides away from the cells. Furthermore, by increasing the flow rate in the chip during the iterative rounds of SELEX, the selection pressure can be improved and aptamers with higher affinities and specificities can be obtained. This new microfluidic device has a tremendous capability to improve the cell-SELEX procedure and to select highly specific aptamers.
The positivist dispute in German sociology: A scientific or a political controversy?
2015-05-01

In 1914 the dispute about scientific value judgments in economics reached its climax. In the 1960s it was followed by the positivist dispute in German sociology. In both controversies one party pretended to provide ethical knowledge and questioned the distinction between what is and what should be. In 1961, at a conference of the German Sociological Association, Karl Popper and Theodor W. Adorno gave lectures on “the Logic of the Social Sciences”. While Popper tried to contribute to methodology, Adorno pleaded for a dialectical philosophy of society. In 1963 Jürgen Habermas criticized Popper’s contribution and Hans Albert made a counterplea. At this time Habermas assumed that critical theory, i.e. neomarxist dialectical theory of society, provided ethical knowledge. Instead of seriously defending this assumption he attacked the self-understanding of the empirical social sciences, in particular the idea of the value freedom of research. Albert showed that Habermas’ criticism of the methodology of Popper’s critical rationalism was completely untenable. So the positivist dispute was not a scientific dispute. Nevertheless Habermas’ version of a critical theory of society was politically immensely influential. It provided the illusion that leftist political programs could be known to be ethically right. In 1981 Habermas admitted that his critical theory was due to ‘confusions in fundamental concepts’. Meanwhile he had proposed a consensus theory of the rightness of norms and his ethics of discourse. Both proved to be untenable as well. Finally Habermas turned to religion and advocated the political influence of religious organizations.
Communication in locked-in state after brainstem stroke: a brain-computer-interface approach.
2015-05-01

In a recent study by Sellers et al. (1) a patient in locked-in state after brainstem stroke was able to successfully communicate via electroencephalography (EEG) based brain computer interface (BCI) employing a P300 speller paradigm.
Management of patients with type 2 diabetes and mild/moderate renal impairment: profile of linagliptin
2015-05-01

Dipeptidyl-peptidase-IV (DPP-4) inhibitors are oral antidiabetic agents that can be administered as monotherapy in patients with contraindications to metformin or metformin intolerance, and in combination with other oral compounds and/or insulin. DPP-4 inhibitors act in a glucose-dependent manner and only increase insulin secretion and inhibit glucagon secretion under hyperglycemic conditions. Renal impairment is frequent in type 2 diabetes as a result of microvascular complications and diabetes treatment, and options in these patients are limited. Linagliptin is a DPP-4 inhibitor with a hepatobiliary route of elimination. In comparative studies, it was noninferior to metformin and sulfonylureas in lowering glycated hemoglobin (HbA1c) and improving glycemic parameters. It can be used throughout all stages of renal impairment without dose adjustments. This review gives an overview of linagliptin in various stages of chronic kidney disease and has a focus on efficacy and safety parameters from clinical studies in patients with impaired renal function. These data are interpreted in the context of type 2 diabetes therapy in general.
Alteration of Biomechanical Properties of Skin During the Course of Healing of Partial-thickness Wounds.
2015-05-01

The alteration of biomechanical properties of skin is a function of tissue structure. The presented results demonstrate the complex changes of skin biomechanical properties in the course of healing of partial-thickness wounds. This study could serve as a model to compare the effectiveness of different wound dressings in regard to skin elasticity.
Abstract P5-19-12: Subgroup analysis on efficacy in the routine treatment - Results of the 2nd interim analysis of BRAWO, the non-interventional trial "Breast Cancer Treatment with Everolimus and Exemestane for HR+ Women"
2015-05-01

Abstract Introduction BRAWO is a German non-interventional study of 3000 patients (pts) with advanced or metastatic, hormone-receptor-positive, HER2-negative breast cancer treated with everolimus (EVE) and exemestane (EXE). We report results of the 2nd preplanned interim analysis (IA) with a data cut-off on 8th July 2014. Methods BRAWO collects data on the routine clinical treatment with EVE and EXE at about 400 sites. Main objectives are to extend the knowledge on a) the efficacy in the clinical routine and the impact of physical activity on efficacy and quality of life, b) prophylaxis and management of stomatitis, and c) the sequence of therapy in the clinical routine. The 2nd IA was defined to take place 12 months after the inclusion of the 500. patient into the documentation. Results Efficacy data will be reported for the first 500 documented pts. Apart from data on the total study population we will present the PFS results for subgroups including pts with or without prior EXE therapy, with or without prior chemotherapy for the advanced setting, with or without visceral metastasis and with regard to the line of treatment in the advanced setting and the extent of physical activity. The respective summary of adverse events for these patients will be presented as well as results on treatment compliance and dosing. Baseline characteristics and medical history as well as insights into treatment sequences before EVE and EXE will further be shown for all enrolled patients with valid baseline documentation (approx. 1200). Conclusion This subgroup analysis will provide insights into the treatment efficacy in the clinical routine and will add to a more comprehensive understanding of the treatment with EVE/EXE. Citation Format: Christian Jackisch, Eva-Maria Grischke, Andreas Schneeweiss, Thomas Decker, Christoph Uleer, Frank Förster, Oliver Tomé, Pauline Wimberger, Christian M Kurbacher, Bettina Mueller, Nadia Harbeck, Christoph Mundhenke, Sherko Kuemmel, Mathias Muth, Julia Kreuzeder, Wilhelm Bloch, Hans Tesch, Diana Lüftner, Florian Schütz, Peter A Fasching. Subgroup analysis on efficacy in the routine treatment - Results of the 2nd interim analysis of BRAWO, the non-interventional trial "Breast Cancer Treatment with Everolimus and Exemestane for HR+ Women" [abstract]. In: Proceedings of the Thirty-Seventh Annual CTRC-AACR San Antonio Breast Cancer Symposium: 2014 Dec 9-13; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2015;75(9 Suppl):Abstract nr P5-19-12.
Adenylyl cyclases 5 and 6 underlie PIP3-dependent regulation
2015-05-01

Many different neurotransmitters and hormones control intracellular signaling by regulating the production of the second messenger cAMP. The function of the broadly expressed adenylyl cyclases (ACs) 5 and 6 is regulated by either stimulatory or inhibitory G proteins. By analyzing a well-known rebound stimulation phenomenon after withdrawal of Gi protein in atrial myocytes, we discovered that AC5 and -6 are tightly regulated by the second messenger PIP3. By monitoring cAMP levels in real time by means of Förster resonance energy transfer (FRET)-based biosensors, we reproduced the rebound stimulation in a heterologous expression system specifically for AC5 or -6. Strikingly, this cAMP rebound stimulation was completely blocked by the PI3K inhibitor wortmannin, both in atrial myocytes and in transfected human embryonic kidney cells. Similar effects were observed by heterologous expression of the PIP3 phosphatase and tensin homolog (PTEN). However, general kinase inhibitors or inhibitors of Akt had no effect, suggesting a PIP3-dependent mechanism. These findings demonstrate the existence of a novel general pathway for regulation of AC5 and -6 activity via PIP3 that leads to pronounced alterations of cytosolic cAMP levels.
Abstract 349: Sgk1 Is a Pivotal Player in Vascular Inflammation and Atherogenesis
2015-05-01

Objective: Atherosclerosis, an inflammatory disease of arterial vessel wall, requires migration and MMP-9-dependent invasion of macrophages into the vascular wall. MMP-9 expression is stimulated by transcription factor NF-κB, which is regulated by IκB and thus IκB-kinase IKK. Regulators of NF-κB include SGK1. The present study explored involvement of SGK1 in vascular inflammation and atherogenesis. Approach and Results: Gene-targeted ApoE-deficient mice without (apoe-/-sgk1+/+) or with (apoe-/-sgk1-/-) additional SGK1 knockout received 16-weeks cholesterol-rich diet. Atherosclerotic lesions in aorta and carotid artery, vascular CD45+ leukocyte infiltration, Mac-3+ macrophage infiltration, VSMC content, MMP-2 and MMP-9 positive areas in atherosclerotic tissue were significantly less in apoe-/-sgk1-/-mice. Migration of SGK1-deficient CD11b+F4/80+ macrophages was significantly diminished in vitro and in vivo. Zymographic MMP-2 and MMP-9 production, MMP-9 activity and invasion through matrigel in vitro were significantly less in sgk1-/- than in sgk1+/+ macrophages and in control plasmid- or inactive K127NSGK1-transfected than in constitutively active S422DSGK1-transfected THP-1 cells. Plaques of apoe-/-sgk1-/- mice displayed reduced macrophage number and macrophage MMP-9 content. In THP-1 cells MMP-inhibitor GM6001 abrogated S422DSGK1-induced MMP-9 production and invasion. MMP-9 transcript levels were significantly reduced in sgk1-/- macrophages and strongly upregulated in S422DSGK1-transfected THP-1 cells compared to control plasmid- or K127NSGK1-transfected THP-1 cells. Phosphorylation of IKK and IκB and nuclear translocation of p50 were significantly lower in sgk1-/- macrophages than in sgk1+/+ macrophages and significantly higher in S422DSGK1-transfected THP-1 cells than in control plasmid- or K127NSGK1-transfected THP-1 cells. Treatment of S422DSGK1-transfected THP-1 cells with IKK-inhibitor BMS-345541 abolished S422DSGK1-induced increase of MMP-9 transcription and gelatinase activity. Conclusions: SGK1 plays a pivotal role in vascular inflammation during atherogenesis. SGK1 participates in the regulation of macrophage migration and MMP-9 transcription via regulation of NF-κB.
Influence of injection technique on detection of sentinel lymph nodes by SPECT/CT in endometrial cancer
2015-05-01

342 Objectives Scintigraphic mapping of sentinel lymph nodes (SLN) is increasingly performed in endometrial cancer although its routine clinical use is still under investigation. Previous studies have compared intraoperative detection rates after pericervical injection or hysteroscopic application without imaging1,2. The aim of our study was to analyze preoperative SLN detection by SPECT/CT. Methods We reviewed 139 consecutive patients with endometrial cancer who underwent surgery and SLN SPECT/CT at Tuebingen University Hospital between 2006 and 2013. 70 patients received hysteroscopic-peritumoral application (200-300 MBq Technetium-99m-nanocolloide) and 69 received pericervical injection at 3, 6, 9 and 12 o9clock positions. Each patient underwent SPECT/CT 3-5 h p.i. and total hysterectomy with lymphadenectomy the next day. Results 324 SLN were detected by SPECT/CT (mean 3 per patient, range 0-9). The detection rate was significantly better with pericervical injection (84%) as compared to hysteroscopic injection (69%; Pearson9s χ2 test, p = 0.031), however hysteroscopic injection detected para-aortic SLN more frequently (43% vs. 32%, p = 0.18). In negative scans after hysteroscopic injection minor to failing injection depot was detectable in 7/22 patients (32%). With pericervical injection, this was only observed in 1/11 cases (9%). Often there was a strong uptake in the reticuloendothelial system of liver and spleen (12/22 vs. 6/11, 55%) and also in bone marrow (8/22 vs. 3/11, 27% vs. 36%). Conclusions Pericervical injection leads to a significantly better scintigraphic detection of SLN while reducing invasiveness. Failure to detect SLNs is associated with major venous drainage. Research Support 1. Int J Gynecol Cancer. 2009 Apr;19(3):391-4. doi: 10.1111/IGC.0b013e3181a1c0b1. Lymphatic mapping in endometrial cancer: comparison of hysteroscopic and subserosal injection and the distribution of sentinel lymph nodes. Robova H, Charvat M, Strnad P, Hrehorcak M, Taborska K, Skapa P, Rob L. 2. Gynecol Oncol. 2013 Nov;131(2):299-303. doi: 10.1016/j.ygyno.2013.08.018. Epub 2013 Aug 27. Tracer injection sites and combinations for sentinel lymph node detection in patients with endometrial cancer. Niikura H, Kaiho-Sakuma M, Tokunaga H, Toyoshima M, Utsunomiya H, Nagase S, Takano T, Watanabe M, Ito K, Yaegashi N.
Evaluation of Cartilaginous End Plate and Annulus Fibrosus in Lumbar Disc Degeneration using OFF Resonant Saturation Ratios Assessed by a 3D Ultra Short Echo Time Sequence at 3 Tesla
2015-05-01

Introduction Ultrashort echo time (UTE) imaging in combination with off-resonant saturation ratios (OSR) is increasingly used for characterization of tissue with fast signal decay, such as the annulus fibrosus (AF) as well as the upper and lower cartilaginous end plate (EP). The aim of this study was to assess effects of age, gender, and location of OSR measurement on evaluation of lumbar disc degeneration. Materials and Methods A total of 35 lumbar intervertebral discs of 12 fresh-frozen cadaveric specimens (median age 66 years, range 49–75 years) were examined in a whole-body MR scanner using a sagittal 3D UTE sequence with an isotropic submillimeter resolution of 0.7 mm (TE 0.07 milliseconds, TR 10.3 milliseconds, FoV 128 mm, and FA 10 degrees) with and without off-resonant saturation preparation pulse at 3 T. The off-resonance frequency varied between 1 and 5 kHz. OSRs of images with and without preparation pulse were calculated for upper and lower EP as well as for AF. Intervertebral discs were classified healthy (CO, n = 20), mild degeneration (MIL, n = 7), and severe degeneration (SEV, n = 8) concerning morphology and signal alteration in conventional MR sequences and UTE imaging. A nonparametric U-test reports level of significance. Correlation between age and OSRs is calculated using Spearman rank correlation coefficient. Effects of different off-resonance frequencies and measurement locations on lumbar disc degeneration are investigated using logistic regression and ROC analysis. Cut-off values, sensitivity, and specificity are given. Results Best differentiation between mild and severe degeneration was seen at an off-resonance frequency of 1 kHz for AF (sensitivity 87.5%/specificity 87.5%/cut-off 0.34) and the lower EP at 1.5 kHz (sensitivity 100%/specificity 85.7%/cut-off 0.29). Comparison of CO and MIL groups revealed best differentiation at 1 kHz for upper EP (sensitivity 100%/specificity 80%/cut-off 0.35). A reasonable correlation between age and OSRs in healthy lumbar discs was seen in AF for all investigated frequencies, ρ = 0.49 (5 kHz) to 0.61 (2 kHz), and in lower EP for frequencies above 2 kHz, ρ = 0.51 (3 kHz) to 0.71 (5 kHz). Significant differences between OSR measurements were seen in AF of healthy female and male lumbar discs for all investigated sequences and in upper EP at 1 kHz. Conclusion OSR assessment might be a suitable method for detection of early stage lumbar disc degeneration and should be preferably performed using off-resonance frequencies between 1 and 2 kHz. Age might influence OSR measurement in AF and lower EP. Gender seems to influence results of OSRs, especially in evaluation of AF. [Figure: see text]
Guidelines for the standardization of preanalytic variables for blood-based biomarker studies in Alzheimer's disease research
2015-05-01

Abstract The lack of readily available biomarkers is a significant hindrance toward progressing to effective therapeutic and preventative strategies for Alzheimer's disease (AD). Blood-based biomarkers have potential to overcome access and cost barriers and greatly facilitate advanced neuroimaging and cerebrospinal fluid biomarker approaches. Despite the fact that preanalytical processing is the largest source of variability in laboratory testing, there are no currently available standardized preanalytical guidelines. The current international working group provides the initial starting point for such guidelines for standardized operating procedures (SOPs). It is anticipated that these guidelines will be updated as additional research findings become available. The statement provides (1) a synopsis of selected preanalytical methods utilized in many international AD cohort studies, (2) initial draft guidelines/SOPs for preanalytical methods, and (3) a list of required methodological information and protocols to be made available for publications in the field to foster cross-validation across cohorts and laboratories.