nils-herrmann/clean_scirepeval huggingface dataset:
Type I callus as a bombardment target for generating fertile transgenic maize (Zea mays L.)

To develop a less genotype-dependent maize-transformation procedure, we used 10-month-old Type I callus as target tissue for microprojectile bombardment. Twelve transgenic callus lines were obtained from two of the three anther-culture-derived callus cultures representing different gentic backgrounds. Multiple fertile transgenic plants (T0) were regenerated from each transgenic callus line. Transgenic leaves treated with the herbicide Basta showed no symptoms, indicating that one of the two introduced genes, bar, was functionally expressing. Data from DNA hybridization analysis confirmed that the introduced genes (bar and uidA) were integrated into the plant genome and that all lines derived from independent transformation events. Transmission of the introduced genes and the functional expression of bar in T1 progeny was also confirmed. Germination of T1 immature embryos in the presence of bialaphos was used as a screen for functional expression of bar; however, leaf painting of T1 plants proved a more accurate predictor of bar expression in plants. This study suggests that maize Type I callus can be transformed efficiently through microprojectile bombardment and that fertile transgenic plants can be recovered. This system should facilitate the direct introduction of agronomically important genes in to commercial genotypes.
Wavelet based signal analysis of pulsed eddy current signals

This paper deals with response signals processing in eddy current non-destructive testing. Non-sinusoidal excitation is utilized to drive eddy currents in a conductive specimen. The response signals due to a notch with variable depth are calculated by numerical means. The signals are processed in order to evaluate the depth of the notch. Wavelet transformation is used for this purpose. Obtained results are presented and discussed in this paper. Streszczenie. Praca dotyczy sygnałów wzbudzanych przy nieniszczącym testowaniu za pomocą prądów wirowych. Przy pomocy symulacji numerycznych wyznaczono sygnały odpowiedzi dla niesinusoidalnych sygnałów wzbudzających i defektów o różnej głębokości. Celem symulacji jest wyznaczenie zależności pozwalającej wyznaczyć głębokość defektu w zależności od odbieranego sygnału. W artykule omówiono wykorzystanie do tego celu transformaty falkowej. (Analiza falkowa impulsowych prądów wirowych)
The post that wasn't: exploring self-censorship on facebook

Social networking site users must decide what content to share and with whom. Many social networks, including Facebook, provide tools that allow users to selectively share content or block people from viewing content. However, sometimes instead of targeting a particular audience, users will self-censor, or choose not to share. We report the results from an 18-participant user study designed to explore self-censorship behavior as well as the subset of unshared content participants would have potentially shared if they could have specifically targeted desired audiences. We asked participants to report all content they thought about sharing but decided not to share on Facebook and interviewed participants about why they made sharing decisions and with whom they would have liked to have shared or not shared. Participants reported that they would have shared approximately half the unshared content if they had been able to exactly target their desired audiences.
Nature, Nurture, or Chance: Stochastic Gene Expression and Its Consequences

Gene expression is a fundamentally stochastic process, with randomness in transcription and translation leading to cell-to-cell variations in mRNA and protein levels. This variation appears in organisms ranging from microbes to metazoans, and its characteristics depend both on the biophysical parameters governing gene expression and on gene network structure. Stochastic gene expression has important consequences for cellular function, being beneficial in some contexts and harmful in others. These situations include the stress response, metabolism, development, the cell cycle, circadian rhythms, and aging.
A terrain-based path planning method for mobile robots

This paper presents a technique for incorporating terrain traversability data into a global path planning method for field mobile robots operating on rough natural terrain. The focus of this approach is on assessing the traversability characteristics of the global terrain using a multi-valued map representation of traversal dificulty, and using this information to compute a traversal cost function to ensure robot survivability. The traversal cost is then utilized by a global path planner to find an optimally safe path through the terrain. A graphical simulator for the terrain-basedpath planning is presented. The path planner is applied to a commercial Pioneer 2-AT robot andfield test results are provided.
Resting-State and Task-Based Functional Brain Connectivity in Developmental Dyslexia

Reading requires the interaction between multiple cognitive processes situated in distant brain areas. This makes the study of functional brain connectivity highly relevant for understanding developmental dyslexia. We used seed-voxel correlation mapping to analyse connectivity in a left-hemispheric network for task-based and resting-state fMRI data. Our main finding was reduced connectivity in dyslexic readers between left posterior temporal areas (fusiform, inferior temporal, middle temporal, superior temporal) and the left inferior frontal gyrus. Reduced connectivity in these networks was consistently present for 2 reading-related tasks and for the resting state, showing a permanent disruption which is also present in the absence of explicit task demands and potential group differences in performance. Furthermore, we found that connectivity between multiple reading-related areas and areas of the default mode network, in particular the precuneus, was stronger in dyslexic compared with nonimpaired readers.
Intradialytic aerobic cycling exercise alleviates inflammation and improves endothelial progenitor cell count and bone density in hemodialysis patients

Inflammation, endothelial dysfunction, and mineral bone disease are critical factors contributing to morbidity and mortality in hemodialysis (HD) patients. Physical exercise alleviates inflammation and increases bone density. Here, we investigated the effects of intradialytic aerobic cycling exercise on HD patients. Forty end-stage renal disease patients undergoing HD were randomly assigned to either an exercise or control group. The patients in the exercise group performed a cycling program consisting of a 5-minute warm-up, 20 minutes of cycling at the desired workload, and a 5-minute cool down during 3 HD sessions per week for 3 months. Biochemical markers, inflammatory cytokines, nutritional status, the serum endothelial progenitor cell (EPC) count, bone mineral density, and functional capacity were analyzed. After 3 months of exercise, the patients in the exercise group showed significant improvements in serum albumin levels, the body mass index, inflammatory cytokine levels, and the number of cells positive for CD133, CD34, and kinase insert domain-conjugating receptor. Compared with the exercise group, the patients in the control group showed a loss of bone density at the femoral neck and no increases in EPCs. The patients in the exercise group also had a significantly greater 6-minute walk distance after completing the exercise program. Furthermore, the number of EPCs significantly correlated with the 6-minute walk distance both before and after the 3-month program. Intradialytic aerobic cycling exercise programs can effectively alleviate inflammation and improve nutrition, bone mineral density, and exercise tolerance in HD patients.
An in vivo microanalytical technique for measuring the local biochemical milieu of human skeletal muscle.

Myofascial pain associated with myofascial trigger points (MTrPs) is a common cause of nonarticular musculoskeletal pain. Although the presence of MTrPs can be determined by soft tissue palpation, little is known about the mechanisms and biochemical milieu associated with persistent muscle pain. A microanalytical system was developed to measure the in vivo biochemical milieu of muscle in near real time at the subnanogram level of concentration. The system includes a microdialysis needle capable of continuously collecting extremely small samples (approximately 0.5 microl) of physiological saline after exposure to the internal tissue milieu across a 105-microm-thick semi-permeable membrane. This membrane is positioned 200 microm from the tip of the needle and permits solutes of <75 kDa to diffuse across it. Three subjects were selected from each of three groups (total 9 subjects): normal (no neck pain, no MTrP); latent (no neck pain, MTrP present); active (neck pain, MTrP present). The microdialysis needle was inserted in a standardized location in the upper trapezius muscle. Due to the extremely small sample size collected by the microdialysis system, an established microanalytical laboratory, employing immunoaffinity capillary electrophoresis and capillary electrochromatography, performed analysis of selected analytes. Concentrations of protons, bradykinin, calcitonin gene-related peptide, substance P, tumor necrosis factor-alpha, interleukin-1beta, serotonin, and norepinephrine were found to be significantly higher in the active group than either of the other two groups (P < 0.01). pH was significantly lower in the active group than the other two groups (P < 0.03). In conclusion, the described microanalytical technique enables continuous sampling of extremely small quantities of substances directly from soft tissue, with minimal system perturbation and without harmful effects on subjects. The measured levels of analytes can be used to distinguish clinically distinct groups.
A state of the art review on microbial fuel cells: A promising technology for wastewater treatment and bioenergy.

A microbial fuel cell (MFC) is a bioreactor that converts chemical energy in the chemical bonds in organic compounds to electrical energy through catalytic reactions of microorganisms under anaerobic conditions. It has been known for many years that it is possible to generate electricity directly by using bacteria to break down organic substrates. The recent energy crisis has reinvigorated interests in MFCs among academic researchers as a way to generate electric power or hydrogen from biomass without a net carbon emission into the ecosystem. MFCs can also be used in wastewater treatment facilities to break down organic matters. They have also been studied for applications as biosensors such as sensors for biological oxygen demand monitoring. Power output and Coulombic efficiency are significantly affected by the types of microbe in the anodic chamber of an MFC, configuration of the MFC and operating conditions. Currently, real-world applications of MFCs are limited because of their low power density level of several thousand mW/m2. Efforts are being made to improve the performance and reduce the construction and operating costs of MFCs. This article presents a critical review on the recent advances in MFC research with emphases on MFC configurations and performances.
A Low Power Comparator Design for 6-BitFlash ADC in 90-Nm CMOS

The main focus of this paper is to design a “Low power Flash ADC” for ultra-wide band applications using CMOS 90nm technology. Flash ADC consists of a reference generator, array of comparators, 1-out-of N code generator, Fat tree encoder and output D latches. The demanding issues in the design of a low power flash ADC is the design of low power latched comparator. The proposed comparator in this paper is designed using 90nm technology at 0.8V DC voltage source using H SPICE tool. The Simulation results of a 6-bit flash ADC is shown for a sampling frequency up to 1.2GHz showing an average power dissipation of 7.67mW.
Reprint of: Nutrition in the Management of Cirrhosis and its Neurological Complications.

Malnutrition is a common feature of chronic liver diseases that is often associated with a poor prognosis including worsening of clinical outcome, neuropsychiatric complications as well as outcome following liver transplantation. Nutritional assessment in patients with cirrhosis is challenging owing to confounding factors related to liver failure. The objectives of nutritional intervention in cirrhotic patients are the support of liver regeneration, the prevention or correction of specific nutritional deficiencies and the prevention and/or treatment of the complications of liver disease per se and of liver transplantation. Nutritional recommendations target the optimal supply of adequate substrates related to requirements linked to energy, protein, carbohydrates, lipids, vitamins and minerals. Some issues relating to malnutrition in chronic liver disease remain to be addressed including the development of an appropriate well-validated nutritional assessment tool, the identification of mechanistic targets or therapy for sarcopenia, the development of nutritional recommendations for obese cirrhotic patients and liver-transplant recipients and the elucidation of the roles of vitamin A hepatotoxicity, as well as the impact of deficiencies in riboflavin and zinc on clinical outcomes. Early identification and treatment of malnutrition in chronic liver disease has the potential to lead to better disease outcome as well as prevention of the complications of chronic liver disease and improved transplant outcomes.
Passenger Deletions Generate Therapeutic Vulnerabilities in Cancer

Inactivation of tumour-suppressor genes by homozygous deletion is a prototypic event in the cancer genome, yet such deletions often encompass neighbouring genes. We propose that homozygous deletions in such passenger genes can expose cancer-specific therapeutic vulnerabilities when the collaterally deleted gene is a member of a functionally redundant family of genes carrying out an essential function. The glycolytic gene enolase 1 (ENO1) in the 1p36 locus is deleted in glioblastoma (GBM), which is tolerated by the expression of ENO2. Here we show that short-hairpin-RNA-mediated silencing of ENO2 selectively inhibits growth, survival and the tumorigenic potential of ENO1-deleted GBM cells, and that the enolase inhibitor phosphonoacetohydroxamate is selectively toxic to ENO1-deleted GBM cells relative to ENO1-intact GBM cells or normal astrocytes. The principle of collateral vulnerability should be applicable to other passenger-deleted genes encoding functionally redundant essential activities and provide an effective treatment strategy for cancers containing such genomic events.
Introducing Design Patterns to Knowledge Processing Systems in the Context of Big Data and Cloud Platforms

Knowledge processing systems recently regained attention in the context of big "knowledge" processing and cloud platforms. Therefore, the development of such systems with a high software quality has to be ensured. In this paper an approach to contribute to an architectural guideline for developing such systems using the concept of design patterns is shown. The need, as well as current research in this domain is presented. Further, possible design pattern candidates are introduced that have been extracted from literature.
Improved Semantic-Aware Network Embedding with Fine-Grained Word Alignment

Network embeddings, which learn lowdimensional representations for each vertex in a large-scale network, have received considerable attention in recent years. For a wide range of applications, vertices in a network are typically accompanied by rich textual information such as user profiles, paper abstracts, etc. We propose to incorporate semantic features into network embeddings by matching important words between text sequences for all pairs of vertices. We introduce a word-by-word alignment framework that measures the compatibility of embeddings between word pairs, and then adaptively accumulates these alignment features with a simple yet effective aggregation function. In experiments, we evaluate the proposed framework on three real-world benchmarks for downstream tasks, including link prediction and multi-label vertex classification. Results demonstrate that our model outperforms state-of-the-art network embedding methods by a large margin.
Hiding Data in Video Sequences using LSB with Elliptic Curve Cryptography

Multimedia data security is becoming important with the continuous increase of digital communication on the internet. Without having privacy of data there is no meaning of doing communication using extremely high end technologies. Data encryption is suitable method to protect data, where as steganography is the process of hiding secret information inside some carrier. This paper focus on utilization of digital video/images as a cover to hide data and for insisting more security encryption is done with steganography. In the proposed method encrypting message image with ECC and hiding encrypted image using LSB within cover video. It gives a high level of authentication, security and resistance against extraction by attacker. As ECC offer better security with smaller key sizes, results in faster computation , lower power consumption as well as memory and bandwidth saving.
Association between hemodynamics, morphology, and rupture risk of intracranial aneurysms: a computational fluid modeling study

The objective of the study was to examine the correlations between intracranial aneurysm morphology and wall shear stress (WSS) to identify reliable predictors of rupture risk. Seventy-two intracranial aneurysms (41 ruptured and 31 unruptured) from 63 patients were studied retrospectively. All aneurysms were divided into two categories: narrow (aspect ratio ≥1.4) and wide-necked (aspect ratio <1.4 or neck width ≥4 mm). Computational fluid dynamics was used to determine the distribution of WSS, which was analyzed between different morphological groups and between ruptured and unruptured aneurysms. Sections of the walls of clipped aneurysms were stained with hematoxylin–eosin, observed under a microscope, and photographed. Ruptured aneurysms were statistically more likely to have a greater low WSS area ratio (LSAR) (P = 0.001) and higher aneurysms parent WSS ratio (P = 0.026) than unruptured aneurysms. Narrow-necked aneurysms were statistically more likely to have a larger LSAR (P < 0.001) and lower values of MWSS (P < 0.001), mean aneurysm-parent WSS ratio (P < 0.001), HWSS (P = 0.012), and the highest aneurysm-parent WSS ratio (P < 0.001) than wide-necked aneurysms. The aneurysm wall showed two different pathological changes associated with high or low WSS in wide-necked aneurysms. Aneurysm morphology could affect the distribution and magnitude of WSS on the basis of differences in blood flow. Both high and low WSS could contribute to focal wall damage and rupture through different mechanisms associated with each morphological type.
Epididymitis: revelations at the convergence of clinical and basic sciences

Acute epididymitis represents a common medical condition in the urological outpatient clinic. Mostly, epididymitis is caused by bacterial ascent through the urogenital tract, with pathogens originating either from sexually transmitted diseases or urinary tract infections. Although conservative antimicrobial therapy is possible in the majority of patients and is usually sufficient to eradicate the pathogen, studies have shown persistent oligozoospermia and azoospermia in up to 40% of these patients. Animal models of epididymitis are created to delineate the underlying reasons for this observation and the additional impairment of sperm function that is often associated with the disease. Accumulated data provide evidence of a differential expression of immune cells, immunoregulatory genes and pathogen-sensing molecules along the length of the epididymal duct. The evidence suggests that a tolerogenic environment exists in the caput epididymidis, but that inflammatory responses are most intense toward the cauda epididymidis. This is consistent with the need to provide protection for the neo-antigens of spermatozoa emerging from the testis, without compromising the ability to respond to ascending infections. However, severe inflammatory responses, particularly in the cauda, may lead to collateral damage to the structure and function of the epididymis. Convergence of the clinical observations with appropriate animal studies should lead to better understanding of the immunological environment throughout the epididymis, the parameters underlying susceptibility to epididymitis, and to therapeutic approaches that can mitigate epididymal damage and subsequent fertility problems.
Nasal prosthesis rehabilitation using CAD-CAM technology after total rhinectomy: a pilot study

This study describes a nose prosthetic rehabilitation using computer-aided design and manufacturing (CAD-CAM) technology after facial disfigurement because of a total rhinectomy. A patient with a total rhinectomy was scheduled for a nasal prosthesis. Based on the 3-D model of the patient’s face reconstructed with the CT data, a four-piece mould for the nasal prosthesis was prototyped using a CAD-CAM procedure. Conventional silicone was processed with this physical mould to fabricate the definitive nasal prosthesis. A silicone nasal prosthesis was manufactured. The size, shape, and cosmetic look of the prosthesis were satisfactory and matched the nasal defect area well. The protocol presented herein illustrates favorable clinical treatment outcomes in the prosthetic rehabilitation after a total rhinectomy by means of CAD-CAM technology.
Chemoembolization Combined with Synchronous Carm Cone-Beam CT Guided Radiofrequency Ablation in treatment of Large Hepatocellular Carcinoma

Hepatocellular carcinoma (HCC) is the sixth major malignant tumor in the world and the third tumor leading to deaths. Only 10-54% of patients with HCC are suitable to surgery (Marín-Hargreaves et al., 2003; Takaki et al., 2009; Forner et al., 2012). Transcatheter arterial chemoembolization (TACE) is one of the main measures for treatment of unresectable HCC. However, the low necrosis rate of local tumor after TACE is an important factor leading to tumor recurrence and metastasis and affecting the long-term postoperative efficacy (Georgiades et al., 2008; Takaki et al., 2009; Miyayama et al., 2010; Forner et al., 2012). In addition, tumor size is also one of important factors affecting TACE efficacy and prognosis. The inactivation ability and efficacy of TACE are significantly reduced for large HCC with diameter more than 5 cm (Yamakado et al., 2002; Fan et al., 2011). Compared with simple TACE, combination of TACE and radiofrenquency ablation (RFA) can improve the treatment