julilili42/papers huggingface dataset:
Rhizosphere Microbial Community Composition Affects Cadmium and Zinc Uptake by the Metal-Hyperaccumulating Plant Arabidopsis halleri
2015-01-17

ABSTRACT The remediation of metal-contaminated soils by phytoextraction depends on plant growth and plant metal accessibility. Soil microorganisms can affect the accumulation of metals by plants either by directly or indirectly stimulating plant growth and activity or by (im)mobilizing and/or complexing metals. Understanding the intricate interplay of metal-accumulating plants with their rhizosphere microbiome is an important step toward the application and optimization of phytoremediation. We compared the effects of a “native” and a strongly disturbed (gamma-irradiated) soil microbial communities on cadmium and zinc accumulation by the plant Arabidopsis halleri in soil microcosm experiments. A. halleri accumulated 100% more cadmium and 15% more zinc when grown on the untreated than on the gamma-irradiated soil. Gamma irradiation affected neither plant growth nor the 1 M HCl-extractable metal content of the soil. However, it strongly altered the soil microbial community composition and overall cell numbers. Pyrosequencing of 16S rRNA gene amplicons of DNA extracted from rhizosphere samples of A. halleri identified microbial taxa ( Lysobacter , Streptomyces , Agromyces , Nitrospira , “ Candidatus Chloracidobacterium”) of higher relative sequence abundance in the rhizospheres of A. halleri plants grown on untreated than on gamma-irradiated soil, leading to hypotheses on their potential effect on plant metal uptake. However, further experimental evidence is required, and wherefore we discuss different mechanisms of interaction of A. halleri with its rhizosphere microbiome that might have directly or indirectly affected plant metal accumulation. Deciphering the complex interactions between A. halleri and individual microbial taxa will help to further develop soil metal phytoextraction as an efficient and sustainable remediation strategy.
Risk and outcomes of complications during and after MitraClip implantation: Experience in 828 patients from the German TRAnscatheter mitral valve interventions (TRAMI) registry
2015-01-19

Aims To analyze risk and outcomes of complications during and after MitraClip implantation using multicenter data from the prospective German Transcatheter Mitral Valve Interventions (TRAMI) registry. Methods and Results Data of 828 patients (mean age: 76.0 [71–81] years, 327 (40%) females) undergoing MitraClip implantation in Germany between 2010 and 2013 were analyzed. Most patients (85%) underwent elective procedures with on average implantation of 1.4 ± 0.6 clips. Emergent cardiac surgery was not required; a single patient died intraoperatively. During the in‐hospital period, complications occurred in 215 (25.9%) patients, of which 106 (12.8%) were considered major. Major bleeding complications were among the most frequent major complications (7.4%), while rates of pericardial tamponade (1.9%) and clip‐specific complications (embolization: 0%, partial clip detachment: 1.9%) were low. In‐hospital death, stroke or myocardial infarction (MACCE) occurred in 2.2, 0.9, and 0% patients, respectively. Patients with complications appeared to be older and more critically ill pre‐interventionally; in‐hospital mortality was significantly higher as compared to those without procedural complications. Conclusions MitraClip implantation appears to be a safe treatment option with low rates of MACCE and clip‐specific complications. Nevertheless, MitraClip therapy is not without complications. Careful patient selection and improvements in preventing peri‐procedural bleeding have the potential of reducing post‐procedural complications and improving outcomes. © 2015 Wiley Periodicals, Inc.
Impact induced surface heating by planetesimals on early Mars
2015-01-19

Aims. We investigate the influence of impacts of large planetesimals and small planetary embryos on the early Martian surface on the hydrodynamic escape of an early steam atmosphere that is exposed to the high soft X-ray and extreme-ultraviolet (EUV) flux of the young Sun. Methods. Impact statistics in terms of number, masses, velocities, and angles of asteroid impacts onto early Mars are determined via n-body integrations. Based on these statistics, smoothed particle hydrodynamics (SPH) simulations result in estimates of energy transfer into the planetary surface material and the resulting surface heating. For the estimation of the atmospheric escape rates we applied a soft X-ray and EUV absorption model and a 1D upper atmosphere hydrodynamic model to a magma ocean-related catastrophically outgassed steam atmosphere with surface pressure values of 52 bar H2O and 11 bar CO2. Results. The estimated impact rates and energy deposition onto an early Martian surface can account for substantial heating. The energy influx and conversion rate into internal energy is probably sufficient to keep a shallow magma ocean liquid for an extended period of time. Higher surface temperatures keep the outgassed steam atmosphere longer in vapor form and therefore enhance its escape to space within ~0.6 Myr after its formation.
Role of FXR in β-Cells of Lean and Obese Mice
2015-01-19

We have recently shown that the bile acid (BA) taurochenodeoxycholate (TCDC) acutely stimulates insulin secretion via activation of the farnesoid X receptor (FXR). Aims of the current investigation were to discriminate between nongenomic (≤1 h) and genomic effects (24-48 h) of BAs on β-cells and to evaluate whether FXR can modulate the adverse effects of a high-fat diet (HFD). TCDC (500 nM) as well as glycine-conjugated and unconjugated CDC (chenodeoxycholate) increased insulin secretion in acute incubations but did not evoke additional effects after 1-2 days of preincubation. The BAs did not stimulate β-cells of FXR-knockout (KO) mice and activation of the G protein-coupled BA receptor TGR5 was ineffective, suggesting that FXR is the sole BA receptor in β-cells activated by TCDC and its analogues. As opposed to lean mice, obese FXR-KO mice did not show HFD-induced glucose intolerance and increased fasting glucose. The beneficial impact of FXR-KO on glucose metabolism cannot be explained by an adaptive compensation of insulin secretion or β-cell mass. Interestingly, in contrast to its effect on islets from lean mice, the FXR agonist GW4064 was ineffective in stimulating insulin secretion of islets from wild type mice fed a HFD or isolated islets kept in a glucolipotoxic medium. Additional feeding of CDC restored the effect of GW4064. CDC prevented HFD-induced impairment of glucose tolerance and in vitro effects of glucolipotoxicity. The data show that the FXR is the most important BA receptor in β-cells and that FXR signaling in β-cells is impaired by overnutrition, which alters activatability of the FXR.
Do we have predictors of therapy responsiveness for a multimodal therapy concept and aerobic training in breast cancer survivors with chronic cancer-related fatigue?
2015-01-19

Cancer-related fatigue (CRF) is a burdensome symptom for breast cancer (BC) patients. In this pilot study, we tested several questionnaires as predictors for treatment responsiveness, along with the implementation of a multimodal therapy concept consisting of sleep, psycho-education, eurythmy, painting therapy and standard aerobic training. At the Community Hospital Havelhöhe and the Hannover Medical School, 31 BC patients suffering from CRF could be evaluated in a 10-week intervention study. CRF was assessed by the Cancer Fatigue Scale (CFS-D). Further questionnaires were the Pittsburgh Sleep Quality Index, the autonomic regulation scale, Self-Regulation Scale (SRS), the Internal Coherence Scale (ICS) and the European Organization of Research and Treatment Health-Related Quality of Life Core Questionnaire scale. We estimated the regression coefficients of all scales on CFS-D by simple and multiple linear regression analyses and compared regression slopes and variances between the different questionnaires on CFS-D at the end of treatment. We found a significant impact of SRS and ICS at baseline on CFS-D at the end of the intervention [absolute standardised multiple regression coefficient values ranging from 0.319 (SRS) to 0.269 (ICS)] but not for the other questionnaires. In conclusion, this study supports the hypothesis that the SRS or ICS measuring adaptive capacities could be more appropriate as outcome predictors than classical questionnaire measures in complex interventions studies.
Identification of hydroxyapatite spherules provides new insight into subretinal pigment epithelial deposit formation in the aging eye
2015-01-20

Significance Proteins and lipids accumulating in deposits external to the retinal pigment epithelium (RPE) represent a barrier to metabolic exchange between the retina and the choroidal capillaries. With time, these deposits can lead to age-related macular degeneration (AMD), the most common cause of blindness in the elderly in the developed world. It remains unclear how sub-RPE deposits are initiated and grow to clinically relevant features. Using a combination of high-resolution analytical techniques, we found that tiny hydroxyapatite (bone mineral) spherules with cholesterol-containing cores are present in all examined sub-RPE deposits, providing a scaffold to which proteins adhere. If the spherules are important in initiating sub-RPE deposit formation, this finding may provide attractive new approaches for early identification and treatment of AMD.
A new approach for the quantification of synchrony of multivariate non-stationary psychophysiological variables during emotion eliciting stimuli
2015-01-20

Emotion eliciting situations are accompanied by changes of multiple variables associated with subjective, physiological and behavioral responses. The quantification of the overall simultaneous synchrony of psychophysiological reactions plays a major role in emotion theories and has received increased attention in recent years. From a psychometric perspective, the reactions represent multivariate non-stationary intra-individual time series. In this paper, a new time-frequency based latent variable approach for the quantification of the synchrony of the responses is presented. The approach is applied to empirical data, collected during an emotion eliciting situation. The results are compared with a complementary inter-individual approach of Hsieh et al. (2011). Finally, the proposed approach is discussed in the context of emotion theories, and possible future applications and limitations are provided.
Workflows for automated downstream data analysis and visualization in large‐scale computational mass spectrometry
2015-01-20

MS‐based proteomics and metabolomics are rapidly evolving research fields driven by the development of novel instruments, experimental approaches, and analysis methods. Monolithic analysis tools perform well on single tasks but lack the flexibility to cope with the constantly changing requirements and experimental setups. Workflow systems, which combine small processing tools into complex analysis pipelines, allow custom‐tailored and flexible data‐processing workflows that can be published or shared with collaborators. In this article, we present the integration of established tools for computational MS from the open‐source software framework OpenMS into the workflow engine Konstanz Information Miner (KNIME) for the analysis of large datasets and production of high‐quality visualizations. We provide example workflows to demonstrate combined data processing and visualization for three diverse tasks in computational MS: isobaric mass tag based quantitation in complex experimental setups, label‐free quantitation and identification of metabolites, and quality control for proteomics experiments.
Failure to achieve disease control in acromegaly: cause analysis by a registry-based survey
2015-01-20

Context Disease control is a prime target in acromegaly treatment. This should be achievable in the vast majority of patients by available treatment options. For unknown reasons, however, a significant number of patients do not achieve disease control. Objective To investigate reasons for failure to achieve disease control in long-standing acromegaly. Design and methods Survey based on the German Acromegaly Registry database (1755 patients in 57 centres). Questionnaires were sent to 47 centres treating 178 patients with elevated disease markers (IGF1 and GH) at the last documented database visit out of 1528 patients with a diagnosis dated back ≥2 years. Thirty-three centres returned anonymised information for 120 patients (recall rate 67.4%). Results Median age of the 120 patients (58 females) was 57 years (range 17–84). Ninety-four patients had at least one operation, 29 had received radiotherapy and 71 had been previously treated medically. Comorbidities were reported in 67 patients. In 61 patients, disease activity had been controlled since the last documented database visit, while 59 patients still had biochemically active disease. Reasons were patients' denial to escalate therapy (23.3%), non-compliance (20.6%), fluctuating insulin-like growth factor 1 (IGF-1) and growth hormone (GH) levels with normal values at previous visits (23.3%) and modifications in pharmacotherapy (15.1%). Therapy resistance (9.6%), drug side effects (4.1%) and economic considerations (4.1%) were rare reasons. Conclusions Main reasons for long-standing active acromegaly were patients' lack of motivation to agree to therapeutic recommendations and non-compliance with medical therapy. Development of patient education programmes could improve long-term control and thus prognosis of acromegalic patients.
Maintenance therapy with the TLR-9 agonist MGN1703 in the phase II IMPACT study of metastatic colorectal cancer patients: A subgroup with improved overall survival.
2015-01-20

680 Background: Patients with mCRC and disease control after induction with first-line chemotherapy +/- bevacizumab were included in the double-blind placebo-controlled phase II IMPACT trial, aiming to assess the clinical efficacy, safety, and immunological effects of the immunomodulator MGN1703, a potent TLR9 agonist, given at the dose of 60 mg subcutaneously twice weekly as switch maintenance after first line induction therapy in mCRC. Methods: The trial was prematurely closed after randomization of 59 patients. The final analysis showed a superior effect of MGN1703 compared to placebo with hazard ratios (HR) for the primary endpoint PFS on maintenance of 0.55 (p=0.041) and 0.56 (p=0.070) by local investigator assessment or independent radiological review, respectively. Exploratory PFS analyses of pretreatment characteristics identified patients with normalized CEA, objective response, and the presence of activated NKT cells at the end of induction chemotherapy to benefit the most from maintenance with MGN1703. We analysed the impact of these factors on the secondary endpoint overall survival (OS). Results: At time of final study analysis, OS data were not mature. Only 35% of MGN1703 patients had an event, as opposed to 50% of placebo patients. The HR for OS of whole study population was 0.63 (median 22.6 vs. 15.1 months, p=NS). The subgroup of patients randomized into the study with confirmed RECIST response had a HR of 0.40 (median 24.5 vs. 15.1 months, p=NS), suggesting this may be the population with greater benefit. HR for patients with normalized CEA or with activated NKT cells were 0.69 and 0.43, respectively. Based on this evidence, in the phase III IMPALA study patients with objective response after standard induction therapy are randomized to standard treatment or switch maintenance with MGN1703. CEA and activated NKT cells are stratification factors for the study and will be prospectively assessed. Conclusions: The pretreatment characteristics predictive of a PFS benefit in the IMPACT study seem to retain their value also in exploratory analyses for OS. This information has been used to design the phase III IMPALA study, currently recruiting patients. Clinical trial information: NCT01208194.
New hope for the treatment of epilepsy
2015-01-20

This scientific commentary refers to ‘Targeting pharmacoresistant epilepsy and epileptogenesis with a dual-purpose antiepileptic drug’ by Doeser et al. (doi: 10.1093/brain/awu339). Compared to many other chronic neurological diseases, epilepsy can be regarded as relatively amenable to treatment, given that about two-thirds of patients become seizure-free with available medications. However, there are two major problems with current treatment using antiepileptic drugs. First, about one-third of patients with epilepsy are resistant to the available antiepileptic drugs, and second, the treatment is purely ‘symptomatic’, i.e. when the drugs are stopped, epileptic seizures usually recur, as the underlying cause of the seizures is still present. Epileptogenesis describes the process of development of epilepsy after an initial brain insult, such as trauma or a prolonged febrile seizure (Fig. 1) (Pitkanen and Lukasiuk, 2011). However, there are currently no treatments that target the process of epileptogenesis in an effort to prevent or at least modify the disease. There is only one possibility to cure epilepsy, namely epilepsy surgery, a treatment that can only be applied to selected patients in whom the epileptic focus can be surgically removed. Thus, new therapeutic approaches are urgently needed. In this issue of Brain , Doeser et al. (2014 a ) report that an existing AED, eslicarbazepine acetate (ESL), has unexpected effects with the potential to address both pharmacoresistance and epileptogenesis. Figure 1 Schematic of epileptogenesis. After an initial insult (such as status epilepticus, trauma or stroke), chronic epilepsy develops during a latent period without seizures. This process is called epileptogenesis. It is induced and maintained by many factors, some as yet unidentified, including inflammatory and epigenetic mechanisms. The goal of anti-epileptogenic treatment is to intervene as early as possible to stop or at least attenuate the process of epileptogenesis. This is in contrast to currently available anti-epileptic drugs, which only suppress ...
Traumatic Tracheobronchial Injuries - Incidence and Outcome among 68.216 Trauma Patients Derived from the TraumaRegister DGU®
2015-01-20

Objectives: Acute tracheobronchial injuries (TBI) resulting from blunt or penetrating trauma are rare, but potential life-threatening trauma sequelae. Up to now the incidence and mortality of these injuries are not well described. The aim of this study was to assess the incidence and outcome of traumatic TBI within the last decade.
Improving INTERMACS Level by Use of Extracorporeal Circulation Prior to Left Ventricular Assist Device Implantation Results in Favorable Outcome
2015-01-20

Objectives: Mechanical circulatory support has evolved during recent years, however a high mortality in INTERMACS I and II patients remains. We investigated the outcome of left ventricular assist device(LVAD) implantation following extracorporeal life support(ECLS).
Identification of Abdominal Swabs Exhibiting Procoagulant Potency Using a Novel Simple Clotting Test
2015-01-20

Objectives: Abdominal swabs are routinely used during surgical procedures to adsorb blood and other body fluids from the operation field. Consisting of cotton, abdominal swabs per se exhibit a slight procoagulant activity. This hemostyptic property is usually considered harmless. However, the induction of abnormal clot formation on the surface of abdominal swabs in the operation field during cardiac surgeries with heart-lung machine support, may, if the blood is retransfused to the extracorporeal circuit, lead to severe thromboembolic complications. Therefore, the aim of our study was to develop a simple clotting test (SCT) allowing the identification of abdominal swabs with increased procoagulant potency before clinical application.
A Single Herpesvirus Protein Can Mediate Vesicle Formation in the Nuclear Envelope
2015-01-21

Herpesviruses assemble capsids in the nucleus and egress by unconventional vesicle-mediated trafficking through the nuclear envelope. Capsids bud at the inner nuclear membrane into the nuclear envelope lumen. The resulting intralumenal vesicles fuse with the outer nuclear membrane, delivering the capsids to the cytoplasm. Two viral proteins are required for vesicle formation, the tail-anchored pUL34 and its soluble interactor, pUL31. Whether cellular proteins are involved is unclear. Using giant unilamellar vesicles, we show that pUL31 and pUL34 are sufficient for membrane budding and scission. pUL34 function can be bypassed by membrane tethering of pUL31, demonstrating that pUL34 is required for pUL31 membrane recruitment but not for membrane remodeling. pUL31 can inwardly deform membranes by oligomerizing on their inner surface to form buds that constrict to vesicles. Therefore, a single viral protein can mediate all events necessary for membrane budding and abscission.
Iron reduction by the deep-sea bacterium Shewanella profunda LT13a under subsurface pressure and temperature conditions
2015-01-21

Microorganisms influence biogeochemical cycles from the surface down to the depths of the continental rocks and oceanic basaltic crust. Due to the poor recovery of microbial isolates from the deep subsurface, the influence of physical environmental parameters, such as pressure and temperature, on the physiology and metabolic potential of subsurface inhabitants is not well constrained. We evaluated Fe(III) reduction rates (FeRRs) and viability, measured as colony-forming ability, of the deep-sea piezophilic bacterium Shewanella profunda LT13a over a range of pressures (0-125 MPa) and temperatures (4-37∘C) that included the in situ habitat of the bacterium isolated from deep-sea sediments at 4500 m depth below sea level. S. profunda LT13a was active at all temperatures investigated and at pressures up to 120 MPa at 30∘C, suggesting that it is well adapted to deep-sea and deep sedimentary environments. Average initial cellular FeRRs only slightly decreased with increasing pressure until activity stopped, suggesting that the respiratory chain was not immediately affected upon the application of pressure. We hypothesize that, as pressure increases, the increased energy demand for cell maintenance is not fulfilled, thus leading to a decrease in viability. This study opens up perspectives about energy requirements of cells in the deep subsurface.
Chemisorption, Morphology, and Structure of a n‐Type Perylene Diimide Derivative at the Interface with Gold: Influence on Devices from Thin Films to Single Molecules
2015-01-21

Abstract We have investigated thin films of a perylene diimide derivative with a cyano‐functionalized core (PDI‐8CN 2 ) deposited on Au(111) single crystals from the monolayer to the multilayer regime. We found that PDI‐8CN 2 is chemisorbed on gold. The molecules experience a thickness‐dependent reorientation, and a 2D growth mode with molecular stepped terraces is achieved adopting low deposition rates. The obtained results are discussed in terms of their impact on field effect devices, also clarifying why the use of substrate/contact treatments, decoupling PDI‐8CN 2 molecules from the substrate/contacts, is beneficial for such devices. Our results also suggest that perylene diimide derivatives with CN bay‐functionalization are very promising candidates for single‐molecule electronic devices.