LLukas22/scidocs huggingface dataset:
An in vitro evaluation of graphene oxide reduced by Ganoderma spp. in human breast cancer cells (MDA-MB-231)

BACKGROUND
Recently, graphene and graphene-related materials have attracted much attention due their unique properties, such as their physical, chemical, and biocompatibility properties. This study aimed to determine the cytotoxic effects of graphene oxide (GO) that is reduced biologically using Ganoderma spp. mushroom extracts in MDA-MB-231 human breast cancer cells.


METHODS
Herein, we describe a facile and green method for the reduction of GO using extracts of Ganoderma spp. as a reducing agent. GO was reduced without any hazardous chemicals in an aqueous solution, and the reduced GO was characterized using a range of analytical procedures. The Ganoderma extract (GE)-reduced GO (GE-rGO) was characterized by ultraviolet-visible absorption spectroscopy, X-ray diffraction, Fourier-transform infrared spectroscopy, X-ray photoelectron spectroscopy, dynamic light scattering, scanning electron microscopy, Raman spectroscopy, and atomic force microscopy. Furthermore, the toxicity of GE-rGO was evaluated using a sequence of assays such as cell viability, lactate dehydrogenase leakage, and reactive oxygen species generation in human breast cancer cells (MDA-MB-231).


RESULTS
The preliminary characterization of reduction of GO was confirmed by the red-shifting of the absorption peak for GE-rGO to 265 nm from 230 nm. The size of GO and GE-rGO was found to be 1,880 and 3,200 nm, respectively. X-ray diffraction results confirmed that reduction processes of GO and the processes of removing intercalated water molecules and the oxide groups. The surface functionalities and chemical natures of GO and GE-rGO were confirmed using Fourier-transform infrared spectroscopy and X-ray photoelectron spectroscopy. The surface morphologies of the synthesized graphene were analyzed using high-resolution scanning electron microscopy. Raman spectroscopy revealed single- and multilayer properties of GE-rGO. Atomic force microscopy images provided evidence for the formation of graphene. Furthermore, the effect of GO and GE-rGO was examined using a series of assays, such as cell viability, membrane integrity, and reactive oxygen species generation, which are key molecules involved in apoptosis. The results obtained from cell viability and lactate dehydrogenase assay suggest that GO and GE-rGO cause dose-dependent toxicity in the cells. Interestingly, it was found that biologically derived GE-rGO is more toxic to cancer cells than GO.


CONCLUSION
We describe a simple, green, nontoxic, and cost-effective approach to producing graphene using mushroom extract as a reducing and stabilizing agent. The proposed method could enable synthesis of graphene with potential biological and biomedical applications such as in cancer and angiogenic disorders. To our knowledge, this is the first report using mushroom extract as a reducing agent for the synthesis of graphene. Mushroom extract can be used as a biocatalyst for the production of graphene.
Integrated Morphological and Syntactic Disambiguation for Modern Hebrew

Current parsing models are not immediately applicable for languages that exhibit strong interaction between morphology and syntax, e.g., Modern Hebrew (MH), Arabic and other Semitic languages. This work represents a first attempt at modeling morphological-syntactic interaction in a generative probabilistic framework to allow for MH parsing. We show that morphological information selected in tandem with syntactic categories is instrumental for parsing Semitic languages. We further show that redundant morphological information helps syntactic disambiguation.
STRUM: structure-based prediction of protein stability changes upon single-point mutation

MOTIVATION
Mutations in human genome are mainly through single nucleotide polymorphism, some of which can affect stability and function of proteins, causing human diseases. Several methods have been proposed to predict the effect of mutations on protein stability; but most require features from experimental structure. Given the fast progress in protein structure prediction, this work explores the possibility to improve the mutation-induced stability change prediction using low-resolution structure modeling.


RESULTS
We developed a new method (STRUM) for predicting stability change caused by single-point mutations. Starting from wild-type sequences, 3D models are constructed by the iterative threading assembly refinement (I-TASSER) simulations, where physics- and knowledge-based energy functions are derived on the I-TASSER models and used to train STRUM models through gradient boosting regression. STRUM was assessed by 5-fold cross validation on 3421 experimentally determined mutations from 150 proteins. The Pearson correlation coefficient (PCC) between predicted and measured changes of Gibbs free-energy gap, ΔΔG, upon mutation reaches 0.79 with a root-mean-square error 1.2 kcal/mol in the mutation-based cross-validations. The PCC reduces if separating training and test mutations from non-homologous proteins, which reflects inherent correlations in the current mutation sample. Nevertheless, the results significantly outperform other state-of-the-art methods, including those built on experimental protein structures. Detailed analyses show that the most sensitive features in STRUM are the physics-based energy terms on I-TASSER models and the conservation scores from multiple-threading template alignments. However, the ΔΔG prediction accuracy has only a marginal dependence on the accuracy of protein structure models as long as the global fold is correct. These data demonstrate the feasibility to use low-resolution structure modeling for high-accuracy stability change prediction upon point mutations.


AVAILABILITY AND IMPLEMENTATION
http://zhanglab.ccmb.med.umich.edu/STRUM/ CONTACT: qiang@suda.edu.cn and zhng@umich.edu


SUPPLEMENTARY INFORMATION
Supplementary data are available at Bioinformatics online.
Automatic Nepali Number Plate Recognition with Support Vector Machines

Automatic number plate recognition is the task of extracting vehicle registration plates and labeling it for its underlying identity number. It uses optical character recognition on images to read symbols present on the number plates. Generally, numberplate recognition system includes plate localization, segmentation, character extraction and labeling. This research paper describes machine learning based automated Nepali number plate recognition model. Various image processing algorithms are implemented to detect number plate and to extract individual characters from it. Recognition system then uses Support Vector Machine (SVM) based learning and prediction on calculated Histograms of Oriented Gradients (HOG) features from each character. The system is evaluated on self-created Nepali number plate dataset. Evaluation accuracy of number plate character dataset is obtained as; 6.79% of average system error rate, 87.59% of average precision, 98.66% of average recall and 92.79% of average f-score. The accuracy of the complete number plate labeling experiment is obtained as 75.0%. Accuracy of the automatic number plate recognition is greatly influenced by the segmentation accuracy of the individual characters along with the size, resolution, pose, and illumination of the given image. Keywords—Nepali License Plate Recognition, Number Plate Detection, Feature Extraction, Histograms of Oriented Gradients, Optical Character Recognition, Support Vector Machines, Computer Vision, Machine Learning
Peripheral Blood Stem Cell Transplantation Improves Liver Functional Reserve

BACKGROUND
Currently available treatment options for decompensated hepatitis B-induced liver cirrhosis are limited and largely ineffective. Recently, stem cell transplantation has emerged as a promising treatment for cirrhosis. The aim of this study was to determine whether autologous peripheral blood stem cell transplantation can improve liver functional reserve in patients with hepatitis B-induced cirrhosis.


MATERIAL/METHODS
In this study, 51 patients with hepatitis B-induced liver cirrhosis were assigned to the treatment group (n=23) or the control group (n=28). The treatment group underwent autologous peripheral blood stem cell transplantation in addition to comprehensive medical treatment, and the control group received comprehensive medical treatment alone. Liver functional reserve was monitored for 48 weeks after autologous peripheral blood stem cell transplantation.


RESULTS
After transplantation, most patients showed improvements in symptoms such as fatigue, anorexia, and abdominal distension. The retention rate of indocyanine green at 15 minutes, a common indicator of liver functional reserve, declined from 41.99±4.68 at baseline to 37.79±3.75 by 48 weeks after transplantation, showing significant improvement.


CONCLUSIONS
Autologous peripheral blood stem cell transplantation can improve several markers of liver health and liver functional reserve and is a promising prospect for clinical application.
Menas' conjecture and generic ultrapowers

Abstract We apply the technique of generic ultrapowers to study the splitting problem of stationary subsets of P K λ . We present some conditions which guarantee the splitting of stationary subsets of P K λ .
Recovery from disturbance of coral and reef fish communities on the Great Barrier Reef, Australia

Coral reefs are consistently and increasingly subject to acute disturbance events that often lead to a reduction in live coral cover with concomitant effects on the diversity and abundance of coral reef fishes. Here we examine changes in both hard coral and reef-fish assemblages over 15 yr following major losses of coral from exposed reefs in 2 widely separated sectors of the Great Barrier Reef (GBR), Australia. While the rate and extent of increase in coral cover (from <15 to >60%) was similar in the 2 sectors, differences in the rugosity of the underlying reef framework influenced the structure of fish communities. Soon after disturbance, when coral cover was very low and the limestone reef framework constituted most of the surface relief, the relatively featureless substrate on reefs of the southern sector supported fewer fish species than reefs of the northern sector, which had a more rugose substrate. At first, northern reefs also had a higher proportion of herbivorous fish species, presumably because the more complex reef surface provided shelter and allowed them to exploit the abundant algal turf. With increasing coral cover, coral colonies came to provide most of the surface relief in both sectors, and species richness and the trophic structure of the fish communities converged. Variation in the cover of branching corals explained significant variation in the fish communities in both sectors over time, reflecting the importance of this growth form to small coralassociated fishes. These results show that the recovery of the coral community and the complexity of underlying reef framework interact to determine the functional structure of associated fish communities despite differences in regional settings.
Enhanced inotropic state of the failing left ventricle by cardiac contractility modulation electrical signals is not associated with increased myocardial oxygen consumption.

BACKGROUND
Previous studies in patients and in dogs with experimentally induced heart failure (HF) showed that electrical signals applied to the failing myocardium during the absolute refractory period improved left ventricular (LV) function. We examined the effects these same cardiac contractility modulating (CCM) electrical signals on myocardial oxygen consumption (MVO(2)) in both patients and dogs with chronic HF.


METHODS AND RESULTS
Six dogs with microembolizations-induced HF and 9 HF patients underwent CCM leads and generator (OPTIMIZER II) implantation. After baseline measurements, CCM signals were delivered continuously for 2 hours in dogs and for 30 minutes in patients. MVO(2) was measured before and after CCM therapy. In dogs, CCM therapy increased LV ejection fraction at 2 hours (26 +/- 1 versus 31 +/- 2 %, P = .001) without increasing MVO(2) (257 +/- 41 versus 180 +/- 34 micromol/min). In patients, CCM therapy increased LV peak +dP/dt by 10.1 +/- 1.5 %. As with dogs, the increase in LV function after 30 minutes of CCM therapy was not associated with increased MVO(2) (13.6 +/- 9.7 versus 12.5 +/- 7.2 mL O(2)/min).


CONCLUSIONS
The study results suggest that unlike cAMP-dependent positive inotropic drugs, the increase in LV function during CCM therapy is elicited without increasing MVO(2).
Multi-Modal Sensor Calibration Using a Gradient Orientation Measure

This paper presents a new metric for automated registration of multi-modal sensor data. The metric is based on the alignment of the orientation of gradients formed from the two candidate sensors. Data registration is performed by estimating the sensors’ extrinsic parameters that minimises the misalignment of the gradients. The metric can operate in a large range of applications working on both 2D and 3D sensor outputs and is suitable for both (i) single scan data registration and (ii) multi-sensor platform calibration using multiple scans. Unlike traditional calibration methods, it does not require markers or other registration aids to be placed in the scene. The effectiveness of the new method is demonstrated with experimental results on a variety of camera-lidar and camera-camera calibration problems. The novel metric is validated through comparisons with state of the art methods. Our approach is shown to give high quality registrations under all tested conditions. C © 2014 Wiley Periodicals, Inc.
A method for improving the robustness of PID control

In this paper, an effective method is proposed for robust proportional-integral-derivative (PID) control that is easily implementable on commonly used equipment such as programmable logic controller (PLC) and programmable automation controller (PAC). The method is based on a two-loop model following control (MFC) system containing a nominal model of the controlled plant and two PID controllers. Basic features exhibited by the MFC structure are presented, and a technique to tune both component controllers is given. The proposed structures have been implemented in a programmable logic controller and tested on control plants with perturbed parameters. Also, the proposed control system has been checked for its performance in cases when the operation of PID controllers is based on fuzzy logic. Tuning rules for the fuzzy controllers in the presented MFC system have been proposed. Results of tests lend support to the view that the proposed control structures may find wide application to robust control of plants with time-varying parameters.
Core stability exercises on and off a Swiss ball.

OBJECTIVES
To assess lumbopelvic muscle activity during different core stability exercises on and off a Swiss ball.


DESIGN
Prospective comparison study.


SETTING
Research laboratory.


PARTICIPANTS
Eight healthy volunteers from a university population.


INTERVENTION
Subjects performed 4 exercises on and off a Swiss ball: inclined press-up, upper body roll-out, single-leg hold, and quadruped exercise.


MAIN OUTCOME MEASURES
Surface electromyography from selected lumbopelvic muscles, normalized to maximum voluntary isometric contraction, and median frequency analysis of electromyography power spectrum. Visual analog scale for perception of task difficulty.


RESULTS
There was a significant increase in the activation of the rectus abdominus with performance of the single-leg hold and at the top of the press-up on the Swiss ball. This led to changes in the relation between the activation levels of the lumbopelvic muscles measured.


CONCLUSIONS
Although there was evidence to suggest that the Swiss ball provides a training stimulus for the rectus abdominus, the relevance of this change to core stability training requires further research because the focus of stabilization training is on minimizing rectus abdominus activity. Further support has also been provided about the quality of the quadruped exercise for core stability.
The social sharing of emotion (SSE) in online social networks: A case study in Live Journal

Social Sharing of Emotion (SSE) occurs when one person shares an emotional experience with another and is considered potentially beneficial. Though social sharing has been shown prevalent in interpersonal communication, research on its occurrence and communication structure in online social networks is lacking. Based on a content analysis of blog posts (n = 540) in a blog social network site (Live Journal), we assess the occurrence of social sharing in blog posts, characterize different types of online SSE, and present a theoretical model of online SSE. A large proportion of initiation expressions were found to conform to full SSE, with negative emotion posts outnumbering bivalent and positive posts. Full emotional SSE posts were found to prevail, compared to partial feelings or situation posts. Furthermore, affective feedback predominated to cognitive and provided emotional support, empathy and admiration. The study found evidence that the process of social sharing occurs in Live Journal, replicating some features of face to face SSE. Instead of a superficial view of online social sharing, our results support a prosocial and beneficial character to online SSE. 2015 Elsevier Ltd. All rights reserved.
Detailed statistical analysis plan for the Danish Palliative Care Trial (DanPaCT)

BACKGROUND
Advanced cancer patients experience considerable symptoms, problems, and needs. Early referral of these patients to specialized palliative care (SPC) could offer improvements. The Danish Palliative Care Trial (DanPaCT) investigates whether patients with metastatic cancer will benefit from being referred to 'early SPC'. DanPaCT is a multicenter, parallel-group, superiority clinical trial with 1:1 randomization. The planned sample size was 300 patients. The primary data collection for DanPaCT is finished. To prevent outcome reporting bias, selective reporting, and data-driven results, we present a detailed statistical analysis plan (SAP) for DanPaCT here.


RESULTS
This SAP provides detailed descriptions of the statistical analyses of the primary and secondary outcomes in DanPaCT. The primary outcome is the change in the patient's 'primary need'. The 'primary need' is a patient-individualised outcome representing the score of the symptom or problem that had the highest intensity out of seven at baseline assessed with the European Organisation for Research and Treatment of Cancer Quality of Life Questionnaire (EORTC QLQ-C30). Secondary outcomes are the seven scales that are represented in the primary outcome, but each scale evaluated individually for all patients, and survival. The detailed description includes chosen significance levels, models for multiple imputations, sensitivity analyses and blinding. In addition, we discuss the patient-individualized primary outcome, blinding, missing data, multiplicity and the risk of bias.


CONCLUSIONS
Only few trials have investigated the effects of SPC. To our knowledge DanPaCT is the first trial to investigate screening based 'early SPC' for patients with metastatic cancer from a broad spectrum of cancer diagnosis.


TRIAL REGISTRATION
Clinicaltrials.gov identifier: NCT01348048 (May 2011).
Abciximab attenuates coronary microvascular endothelial dysfunction after coronary stenting.

BACKGROUND
Platelet glycoprotein IIb/IIIa receptor blockade with abciximab decreases ischemic events after percutaneous coronary intervention (PCI); however, the mechanism of this benefit has not been fully elucidated. The present study was designed to assess endothelium-dependent vasomotion after coronary stenting and to determine if abciximab alters this response.


METHODS AND RESULTS
The study group consisted of 48 patients (59+/-10 years of age) with discrete coronary stenoses who underwent stenting alone (n=28) or stenting plus abciximab (n=20). A control group consisted of 31 additional patients who had vasomotor testing on a non-PCI vessel. Coronary blood flow (CBF) was measured (0.014-inch Doppler wire) 30 minutes after uncomplicated PCI and in response to the intracoronary infusion of acetylcholine (Ach) (10(-7), 10(-6) mol/L Ach) and adenosine (24 microg). Ach-mediated increase in CBF was impaired after stent insertion when compared with the control group (41+/-52% versus 70+/-48%; P<0.05). The stenting plus abciximab group demonstrated a superior CBF response to Ach compared with the stenting alone group (83+/-93% versus 41+/-52%; P<0.05), with no difference between groups in the peak flow or percent change in flow to adenosine. By multivariate analysis, concomitant administration of abciximab was strongly predictive of the change in CBF to Ach (P<0.005).


CONCLUSIONS
Abciximab preserves the CBF response to Ach after coronary stenting. The preservation of microvascular endothelial function may help explain the beneficial clinical effect of this agent in patients undergoing PCI.
Mechanism of Hydrolysis of Inorganic Esters

By the use of water containing an excess over the normal of the heavy oxygen isotope (18O), it has been definitely and very directly shown that during the hydrolysis of the esters of weak carboxylic acids the break occurs at the C—O bond of the ester, thus:
Preserving Privacy in Context-Aware Systems

Recent years have seen a confluence of two major trends -- the increase of mobile devices such as smart phones as the primary access point to networked information and the rise of social media platforms that connect people. Their convergence supports the emergence of a new class of context-aware geosocial networking applications. While existing systems focus mostly on location, our work centers on models for representing and reasoning about a more inclusive and higher-level notion of context, including the user's location and surroundings, the presence of other people and devices, and the inferred activities in which they are engaged. A key element of our work is the use of collaborative information sharing where devices share and integrate knowledge about their context. This introduces the need for privacy and security mechanisms. We present a framework to provide users with appropriate levels of privacy to protect the personal information their mobile devices are collecting, including the inferences that can be drawn from the information. We use Semantic Web technologies to specify high-level, declarative policies that describe user information sharing preferences. We have built a prototype system that aggregates information from a variety of sensors on the phone, online sources, and sources internal to the campus intranet, and infers the dynamic user context. We show how our policy framework can be effectively used to devise better privacy control mechanisms to control information flow between users in such dynamic mobile systems.