julilili42/papers huggingface dataset:
Increased copper levels inhibit denitrification in urban soils
2018-09-01

ABSTRACT The consequences of urbanisation for Earth's biogeochemical cycles are largely unexplored. Copper (Cu) in urban soils is being accumulated mainly due to anthropogenic activities under rapid urbanisation. The increasing Cu concentrations may contribute to altering soil nitrogen (N) cycling in urban ecosystems through modulating denitrification processes. This research aims to identify how Cu impacts urban soil denitrification functions and denitrifier abundance. An urban park soil with a background total Cu concentration of 7.9μgg –1 was incubated anaerobically with different Cu amendments (10, 20, 40, 80 and 160μg Cu g –1 soil), similar to prevalent Cu contents in urban soils. We evaluated the soil denitrification functions using the acetylene (C 2 H 2 ) inhibition method and assessed the denitrifier abundance by quantitative polymerase chain reaction (qPCR) analyses of denitrifying marker genes ( nirK , nirS and nosZ ). At the function level, we observed that both the potential soil denitrification activity and the N 2 O emission rate due to denitrification were significantly ( P &lt;0.05) inhibited by Cu; even the lowest Cu addition (10μg Cu g –1 soil) drastically affected the denitrification function. Moreover, Cu significantly ( P &lt;0.05) decreased the abundance of nirK and nirS genes at the additions of 160μg Cu g –1 soil and 40μg Cu g –1 soil, respectively, whereas it had no clear impact on nosZ gene copies. Further correlation analyses revealed that the potential denitrification activity was positively correlated to the copy numbers of nirK and nirS genes, but it was not correlated to nos Z gene abundance. These findings indicate that Cu additions inhibited soil denitrification function and decreased denitrifier abundance in the investigated urban park soil. Our results suggest that Cu accumulation in urban soils, resulting from urbanisation, may generally influence denitrification in urban ecosystems.
F63 Preliminary results from Q-MOTOR/Q-COG analyses in the repair-hd study
2018-09-01

<h3>Background</h3> The Q-Motor assessment battery has been designed to quantitatively measure motor deficits and progression for use in clinical studies. The assessments have shown to be able to detect subtle motor changes reliably and with absence of rater induced bias. The Q-Cog assessment battery adds assessments with an increased cognitive share, with the goal to achieve a comparable level of sensitivity for cognitive deficits of participants. The EUFP 7 funded Repair-HD (www.repair-hd.eu) study is the first to implement the Q-Cog assessments for exploratory analyses. <h3>Aims</h3> To identify sensitive and robust measures to quantitatively track cognitive progression in HD. <h3>Methods</h3> The analyzed data set includes 128 participants (52 controls, 76 HD manifest TFC stage I or II, mean age: 51 (22–78), female: 54). Statistical analyses were performed using generalized linear mixed models in R. Motor and cognitive tests were included in the assessment battery. Cognitive Assessments: Force Matching: To match a visually presented force by applying pressure on a force transducer. Blinded Force Matching: Reproduction of presented force by memory (without visual feedback). Morse Code Mimicry: To tap an acoustically presented Morse code (series of short and long beeps) on a force transducer. Trail Making: Connect dots numbered from 1 to 25 (test A) or alternating digits and letters 1,A,2,B ... to 13 (test B), using a 6-axis motion tracker pen. Motor Assessments: Speeded Finger Tapping, Metronome Tapping, Grasping &amp; Lifting, Spiral Drawing. <h3>Results</h3> Highly significant differences between control and manifest group could be found for various variables in all performed tests. Assessment of of cognitive function using the tests described is feasible and test-retest assessment shows low variability. <h3>Conclusion</h3> While results from motor tasks reproduce previous findings, the cognitive assessments, too, are able to discriminate control groups from manifest population robustly. The long-term longitudinal performance, robustness and possible redundancy of the novel variables is yet to be explored. Further analysis is required to separate motor and cognitive effects through ratios of variables of the different assessments.
CBT-I and HT-I group therapy for adults with insomnia in comparison to those with insomnia and comorbid depression &ndash; a pilot study
2018-09-01

Combining CBT-I and HT-I is effective in reducing depressive symptoms and improving sleep. Therefore, nonresponders to other forms of therapy, eg, pharmacological, interpersonal, or cognitive-behavioral therapy, might benefit from the combined CBT-I/HT-I intervention.
The Monotone Satisfiability Problem with Bounded Variable Appearances
2018-09-01

The prominent Boolean formula satisfiability problem SAT is known to be [Formula: see text]-complete even for very restricted variants such as 3-SAT, Monotone 3-SAT, or Planar 3-SAT, or instances with bounded variable appearance. We settle the computational complexity status for two variants with bounded variable appearance: We show that Planar Monotone Sat — the variant of Monotone Sat in which the incidence graph is required to be planar — is [Formula: see text]-complete even if each clause consists of at most three distinct literals and each variable appears exactly three times, and that Monotone Sat is [Formula: see text]-complete even if each clause consists of three distinct literals and each variable appears exactly four times in the formula. The latter confirms a conjecture stated in scribe notes [7] of an MIT lecture by Eric Demaine. In addition, we provide hardness results with respect to bounded variable appearances for two variants of Planar Monotone Sat.
Factors influencing the contamination rates of the conjunctival swabs and organ culture media of human donor eyes
2018-09-01

This study assessed the influence of donor, environmental, and logistical factors on the contamination rates of the conjunctival swabs and organ culture media of human donor eyes.In total, 1008 conjunctival swabs and 418 organ culture media samples from 504 consecutive human donor eyes were analyzed. Cross-tabulation, chi-squared tests, and Fisher's exact tests were used to assess the influence of the different factors on the contamination rates of the conjunctival swabs and organ culture media.The overall contamination rates were 28.4% for the conjunctival swabs and 1.0% for the organ culture media. A prolonged time between death and the conjunctival swab collection was associated with an increased conjunctival swab contamination rate [odds ratio (OR) = 1.9, 95% confidence interval (CI) = 1.2-3.0, P = .007]. The highest conjunctival swab contamination rate was found in the corneas procured in external institutions (outside the university hospital) (44.1%, OR = 3.6, 95%CI = 1.5-8.4, P = .003). Hospitalization times of 2 to 7 days prior to death were associated with an increased conjunctival swab contamination risk (OR = 2.6, 95%CI = 1.1-5.8, P = .021). However, the sex, age, cause of donor death, differentiation between septic and aseptic donors, differentiation between heart-beating brain-dead multiorgan donors and cadaveric donors, a warmer mean monthly temperature, and death to corneoscleral disc excision time did not significantly increase the conjunctival swab contamination risk. In addition, none of these factors affected the organ culture media contamination risk. Moreover, a positive conjunctival swab did not significantly increase the media contamination risk (P = .08). Surprisingly, the microorganisms causing media contamination were present at 50% of the amount detected on the conjunctival surface of the respective donor eye.A prolonged time between death and the conjunctival swab collection, a hospitalization time of 2 to 7 days prior to death, and corneal collection outside the university hospital seemed to be the main factors responsible for an increased conjunctival swab contamination risk. In addition, our investigation illustrated that a positive conjunctival swab is not a strong indicator for organ culture media contamination. Critical discussion is necessary regarding the validity of conjunctival swabs as prognostic parameters for organ culture media contamination.
Pediatric Growth Hormone Deficiency (GHD) in the Recombinant Human GH (rhGH) Era.
2018-09-01

During the phase of using hGH extracted from pituitaries (pit hGH) - 1958-1985 - fundamental experience related to the diagnosis and treatment was accumulated. However, since recombinant hGH (rhGH) had become available diagnosis and treatment of GHD were conducted world-wide in a more standardized way. Treatment with rhGH was also accompanied by documentations in large international pharmaco-epidemiological surveys, which provided new insight. Despite of this development the treatment of children and adolescents with GHD raises still issues related to the most effective and efficacious as well as safe use of rhGH. This brief review attempts to discuss a few aspects related to these topics as they have developed during the rhGH era.
Heterotrimeric G-protein subunit Gα i2 contributes to agonist-sensitive apoptosis and degranulation in murine platelets
2018-09-01

Gα<sub>i2</sub> , a heterotrimeric G-protein subunit, regulates various cell functions including ion channel activity, cell differentiation, proliferation and apoptosis. Platelet-expressed Gα<sub>i2</sub> is decisive for the extent of tissue injury following ischemia/reperfusion. However, it is not known whether Gα<sub>i2</sub> plays a role in the regulation of platelet apoptosis, which is characterized by caspase activation, cell shrinkage and cell membrane scrambling with phosphatidylserine (PS) translocation to the platelet surface. Stimulators of platelet apoptosis include thrombin and collagen-related peptide (CoRP), which are further known to enhance degranulation and activation of α<sub>II</sub><sub>b</sub> β3-integrin and caspases. Using FACS analysis, we examined the impact of agonist treatment on activation and apoptosis in platelets drawn from mice lacking Gα<sub>i2</sub> and their wild-type (WT) littermates. As a result, treatment with either thrombin (0.01 U/mL) or CoRP (2 μg/mL or 5 μg/mL) significantly upregulated PS-exposure and significantly decreased forward scatter, reflecting cell size, in both genotypes. Exposure to CoRP triggered a significant increase in active caspase 3, ceramide formation, surface P-selectin, and α<sub>II</sub><sub>b</sub> β3-integrin activation. These molecular alterations were significantly less pronounced in Gα<sub>i2</sub> -deficient platelets as compared to WT platelets. In conclusion, our data highlight a previously unreported role of Gα<sub>i2</sub> signaling in governing platelet activation and apoptosis.
Polyelectrolyte Coatings for Surface Modification of Medical Implants
2018-09-01

Abstract Polyelectrolyte multi-layer (PEM) coatings are prepared by alternative deposition of single polyelectrolyte monolayers on charged surfaces using the Layer-by-Layer (LbL) dip coating procedure. These are nanometre scaled coatings which allow fulfilling of different technical or biological requirements. The build-up process is based on selfassembly and self-organization of polycations and polyanions on different substrates including complex geometrical structures and even closed volumes, forming homogeneous layer without defects. Depending on the proper selection of the applied polyelectrolytes, coatings with different stabilities can be prepared. Some of the coatings are stable and cannot be removed from the surface. Others are degradable and can be used as systems for controlled local drug delivery. Here we summarise the results of our experience in preparation of PEM coatings with different functionalities. PEM coatings can be used as controllable delivery system for siRNA polyplexes. They can be used to control the adhesion of different cell types on the surfaces and support e.g. the endothelialisation process on cardio-vascular medical devices as e.g. stents or reduce the immunological response of the tissue after implantation. We summarise results from physical characterisation of the coatings (e.g. film thickness, roughness, electrical charge and hydrophilicity) combined with in-vitro biological studies on adhesion of HUVEC cells.
Comparing the ability of humans and DNNs to recognise closed contours in cluttered images
2018-09-01

Given the recent success of machine vision algorithms in solving complex visual inference tasks, it becomes increasingly challenging to find tasks for which machines are still outperformed by humans. We seek to identify such tasks and test them under controlled settings. Here we compare human and machine performance in one candidate task: discriminating closed and open contours. We generated contours using simple lines of varying length and angle, and minimised statistical regularities that could provide cues. It has been shown that DNNs trained for object recognition are very sensitive to texture cues (Gatys et al., 2015). We use this insight to maximize the difficulty of the task for the DNN by adding random natural images to the background. Humans performed a 2IFC task discriminating closed and open contours (100 ms presentation) with and without background images. We trained a readout network to perform the same task using the pre-trained features of the VGG-19 network. With no background image (contours black on grey), humans reach a performance of 92% correct on the task, dropping to 71% when background images are present. Surprisingly, the model's performance is very similar to humans, with 91% dropping to 64% with background. One contributing factor for why human performance drops with background images is that dark lines become difficult to discriminate from the natural images, whose average pixel values are dark. Changing the polarity of the lines from dark to light improved human performance (96% without and 82% with background image) but not model performance (88% without to 64% with background image), indicating that humans could largely ignore the background image whereas the model could not. These results show that the human visual system is able to discriminate closed from open contours in a more robust fashion than transfer learning from the VGG network. Meeting abstract presented at VSS 2018
Effect of BDNFVal66Met on disease markers in dominantly inherited Alzheimer's disease
2018-09-01

Previous studies suggest that the brain-derived neurotrophic factor (BDNF) Val66Met (rs6265) polymorphism may influence symptom onset in Alzheimer's disease (AD). Our recent cross-sectional findings suggest that Met66 may influence clinical expression in dominantly inherited AD (DIAD) through its effects on tau. However, it remains unclear whether carriage of Met66 in DIAD results in faster increases in cerebrospinal fluid (CSF) tau and ptau181 , and whether these increases are associated with accelerated brain volume loss and memory decline.A total of 211 subjects (101 mutation noncarriers, 110 mutation carriers), who were cognitively normal, as defined by a Clinical Dementia Rating global score of 0, completed assessments of cognitive function, neuroimaging, and CSF sampling over 3.5 years as part of the Dominantly Inherited Alzheimer's Network.In mutation carriers, Met66 carriers showed faster memory decline (4×), hippocampal volume loss (16×), and CSF tau and ptau181 increases (6×) than Val66 homozygotes. BDNF did not influence rates of cortical β-amyloid accumulation or change in CSF Aβ42 levels in mutation carriers. In mutation noncarriers, BDNF genotype had no effect on change in cognition, brain volume, cortical β-amyloid accumulation, or change in any CSF measures of tau, ptau181 , and CSF Aβ42 .As in sporadic AD, the deleterious effects of β-amyloid on cognitive function, brain volume loss, and CSF tau in DIAD mutation carriers are less in Val66 homozygotes. The BDNF Val66Met polymorphism should be considered as a potential moderator of clinical trial outcomes in current treatment and prevention trials in DIAD and sporadic AD. Ann Neurol 2018;84:424-435.
Pain Inhibition Through Transplantation of Fetal Neuronal Progenitors into the Injured Spinal Cord in Rats
2018-09-01

Neuropathic pain after spinal cord injury (SCI) is a complex condition which responds poorly to usual treatments. Cell transplantation represents a promising therapy; nevertheless, the ideal cell type in terms of neurogenic potential and effectiveness against pain remains largely controversial. Thus, the objective of the present study was to evaluate the ability of fetal neural stem cells (fNSC) to relieve chronic pain and, secondarily, evaluate the effects on motor recovery. For this purpose, Wistar rats were immunosuppressed with cyclosporine and submitted to traumatic SCI using the NYU Impactor at 9–10th thoracic level. After 10 days, the animals received four intra-spinal injections of culture medium (sham) or fNSC extracted from telencephalic vesicle (TV group) or ventral medulla (VM group) of E14 embryos. Behavioral and pain assessment were performed weekly for 8 weeks. Thereafter, spinal cords were processed for immunofluorescence, and transplanted vital cells were quantified by stereology. The results showed improvement of thermal hyperalgesia in TV group after the fifth week of transplantation (p < 0.01) and in VM group after the fourth week (p < 0.01). Moreover, mechanical allodynia improved in both TV and VM groups at the 8th week (p < 0.01). No significant motor recovery was observed in TV and VM groups when compared to sham group. Stereological analyses showed that ~70% of TV and VM cells differentiated into NeuN+ neurons, with high proportion of enkephalinergic and GABAergic cells in the TV group, and enkephalinergic and Serotoninergic cells in the VM group. Our study suggests that neuronal precursors from the TV and VM, once implanted into the injured spinal cord, maturate into different neuronal subtypes, mainly GABAergic, serotoninergic, and enkephalinergic, and all subtypes were able to alleviate pain, despite no significant motor recovery.
OS6.4 NOA-16: A first-in-man multicenter phase I clinical trial of the German Neurooncology Working Group evaluating a mutation-specific peptide vaccine targeting IDH1R132H in patients with newly diagnosed malignant astrocytomas
2018-09-01

In preclinical studies we have defined IDH1R132H as a clonal neoantigen presented on MHC class II. A peptide vaccine encompassing IDH1R132H induces tumor-specific T helper cell responses effective in controlling syngeneic IDH1R132H-mutant tumors in humanized mouse models. NOA-16 (NCT02454634) is a first-in-man, multicenter, phase I trial testing the safety and immunogenicity of an IDH1R132H peptide in incomplete Freund’s adjuvant in patients with newly diagnosed, IDH1R132H mutant WHO °III and °IV astrocytomas. Between September 2015 and October 2016, 32 patients were enrolled in seven German sites. 23 patients (71.9%) received radiochemotherapy with temozolomide, six patients (18.8%) received radiotherapy alone and three patients (9.4%) received temozolomide alone. 249 vaccines were administered, 29 (90.6%) of the patients of the safety set (N=32) and 27 (90.0%) patients of the immunogenicity set (N=30) received all eight vaccines. No regime-limiting toxicity was observed. The majority of the patients (N=29, 90.6%) experienced treatment related adverse events (trAE), 1 (3.1%) of them had treatment related SAE. None of the reported AEs were severe. 28/30 (93.3%) patients, who were evaluable for immunogenicity, displayed mutation-specific T cellular (24/30 (80%)) or humoral (26/30 patients (87%)) immune responses not detectable before vaccination. Until end of study no deaths were observed. 4/32 (12.5 %) patients had PD according to RANO criteria, all other patients (N=28, 87.5%) had SD. 12/32 (37.5%) patients displayed pseudoprogressions after the initiation of the vaccine. Single-cell T cell receptor (TCR) sequencing allowed for the identification of IDH1R132H-specific TCRs. NOA-16 met its primary endpoints by demonstrating safety and immunogenicity of a mutation-specific IDH1R132H peptide vaccine given with standard of care in patients with newly diagnosed IDH1R132H mutant malignant astrocytoma.
A demonstrator for a flexible active microelectrode array with high electrode number
2018-09-01

Abstract The integration of dies is a possibility to reduce the number of conducting tracks within electrical active implants. For passive microelectrode arrays the number of conducting tracks limits the number of electrodes. By embedding an array of small dies (250 μm edge length) employed to amplify and multiplex the signals of 25 electrodes each into a flexible foil we create a flexible active microelectrode array with more than 1000 electrodes. A fabrication process was developed containing a transfer process for the dies as well as an embedding procedure. Here a non-functional Dummy-System is presented as a demonstrator proving the feasibility of the proposed microelectrode array.
Variable slope of the psychometric function for different spatial frequencies measured by the Tuebingen Contrast Sensitivity Test
2018-09-01

Introduction: The threshold contrast and the slope of the psychometric function can be determined by using computer-based stimulus presentations and an adaptive staircase, like the TuebingenCSTest (TueCST). The TueCST assesses contrast sensitivity with high repeatability and reliability, using a fixed slope. The slope of the psychometric function is the measure of change in performance with changing stimulus intensity, which reflects the variability of the estimated threshold contrast. The slope relies on several factors, like finger errors, eye artefacts due to e.g. blinks, observers' attention or motivation. The aim of the study was to estimate individual slopes for each participant in order to increase the accuracy of the threshold contrast assessment. Methods: In this study, the slope of the psychometric function was estimated with the TueCST, using 250 trials for different spatial frequencies in eight experienced (0.5, 1.5, 3, 6 and 12 cycle per degree – cpd) and eight naïve participants (1.5, 3, 6, 12, 20 and 30cpd). The stimulus was a Gabor Patch grating with four possible orientations to identify. Results: Repeated ANOVA returned a significant effect for spatial frequency in experienced participants (F(4,28)=30.9, p< 0.001, ω2=0.78) and naïve participants (F(5,35)=62.4, p< 0.001, ω2=0.88). Largest slopes were estimated for lower spatial frequencies (≤6cpd) and smallest slopes for higher spatial frequencies (≥12cpd) in both subgroups. In naïve participants, the threshold contrast was significantly lower for a first measurement with a fixed slope compared to the second measurement for slope estimation (p< 0.05). Comparing the slopes of naïve and experienced participants, there was no significant difference (p=0.7). Conclusion: When using the TueCST, the estimated slopes of the psychometric function showed a difference between higher and lower spatial frequencies. These results revealed that naïve participants were sufficiently trained after one measurement with the TueCSTest, resulting in indistinguishable slopes between naïve and experienced participants. Meeting abstract presented at VSS 2018