nils-herrmann/clean_scirepeval huggingface dataset:
The rolling circle amplification and next generation sequencing approaches reveal genome wide diversity of Kenyan cassava mosaic geminivirus

Rolling circle amplification is a simple approach of enriching populations of single stranded DNA plant begomovirus genomes (genus, Begomovirus; family, Geminiviridae) This is an innovative approach that utilizes the robustness of the bacteriophage phi29 DNA polymerase used in circle amplification, together with deep sequencing using Illumina Miseq and bioinformatics to assess population diversity of begomoviruses in naturally infected cassava. The approach is suitable for detecting rare members in a population in begomoviral populations in situation where mixtures of isolates, strains, and multiple species occur. The main objectives were to increase the sensitivity of detection of next generation sequencing by enriching it using rolling circle amplification then determination of the diversity of the cassava mosaic geminivirus. This was done by total nucleic acids isolated from symptomatic, field cassava infected plants, then using rolling circle amplification to multiply the less abundant viral sequences. Enriched and non enriched virus libraries were subjected to deep sequencing using Illumina Miseq. Using bioinformatic CLC Genomics 5.5.1 software programs the quality assessment of reads and contig assembly of viral sequences. This was done through de novo and reference guided assembly. The identity and diversities of the begomoviral sequences were compared with sequences in Sanger sequencing of viral components deposited in the NCBI Gene Bank. In this study we have demonstrated that RCA increases the chances of detecting the virus by approximately 10 to 1000 fold and wide genome diversity of cassava mosaic geminivirus in various cassava growing zones in Kenya were detected. In conclusion, this approach described herein is simple and will enhance the exploration of begomovirus diversities from cassava infected plants, irrespective of their viral abundance. This will make it possible for routine screening of field samples as the cost of deep sequencing NGS is decreasing and the advances of bioinformatic software development become enhanced. This is the first report of the RCA Illumina NGS approach to explore cassava infected with begomoviruses under field conditions and their diversities.  Illumina Miseq sequencing, geminivirus, ssDNA viruses, viral sequence enrichment, de novo genome assembly, rolling cycle amplification (RCA)
EMT and stemness: flexible processes tuned by alternative splicing in development and cancer progression
Venue: Molecular Cancer

Epithelial to mesenchymal transition (EMT) is associated with metastasis formation as well as with generation and maintenance of cancer stem cells. In this way, EMT contributes to tumor invasion, heterogeneity and chemoresistance. Morphological and functional changes involved in these processes require robust reprogramming of gene expression, which is only partially accomplished at the transcriptional level. Alternative splicing is another essential layer of gene expression regulation that expands the cell proteome. This step in post transcriptional regulation of gene expression tightly controls cell identity between epithelial and mesenchymal states and during stem cell differentiation. Importantly, dysregulation of splicing factor function and cancer specific splicing isoform expression frequently occurs in human tumors, suggesting the importance of alternative splicing regulation for cancer biology.In this review, we briefly discuss the role of EMT programs in development, stem cell differentiation and cancer progression. Next, we focus on selected examples of key factors involved in EMT and stem cell differentiation that are regulated post transcriptionally through alternative splicing mechanisms. Lastly, we describe relevant oncogenic splice variants that directly orchestrate cancer stem cell biology and tumor EMT, which may be envisioned as novel targets for therapeutic intervention.
A Study On Axis Bank Employees Job Satisfaction Levels In Andhra Pradesh

After the liberalization, privatisation and globalization, banking industry has expanded its wings across the globe. Axis bank is one such bank which is providing multi varied services to its customers. In the process of satisfying their customeraEUR(tm)s employees are undergoing lot of stress. This stress is leading to dissatisfaction among employees. The researcher is making an attempt to find out the job satisfaction levels of employees associated with Axis bank. The major objectives of the study are 1. To find out the impact of demographic variables like age, gender, designation and work experience on the satisfaction levels of Axis bank employees and 2. The factors influencingA the job satisfaction. 250 employees from 12 branches in five major citiesA of Andhra Pradesh were surveyed. Convenience sampling method was used to collect the data. A structured questionnaire was administered to collect the data. ANOVA, Chi square, standard deviation and regression analysis were used to analyse the data. From the analysis it was found that, demographic variables are having a greater impact on the employee satisfaction levels. Factors like pay, Pay, Promotion, Supervision etc. are having significant roles in deciding the satisfaction levels.
Kandungan Logam Berat (Cu, Pb, Zn, Cd, dan Cr) dalam Air dan Sedimen di Perairan Teluk Jakarta

Penelitian Lingkungan dan Kebencanaan Geologi Kelautan Perairan Teluk Jakarta (Tanjung Kait aEUR" Muara Gembong) dilakukan pada bulan Oktober November 2010. Uji logam berat (Cu, Pb, Zn, Cd, dan Cr) dilakukan terhadap 28 contoh air laut dan 28 contoh sedimen dasar laut menggunakan metoda Atomic Absorption Spectrophotometry (AAS) Tujuan penelitian ini adalah untuk mendapatkan data dan informasi kondisi lingkungan terkini dari kandungan logam berat dalam air laut dan sedimen dasar laut. Kandungan logam berat (air laut dalam mg/l sedimen dasar laut dalam ppm) terukur sebagai berikut Cu <0.005 15.000 169.500 Pb (0.005 0.011 14.000 58.100) Zn (0.005 0.007 95.800 333.000) Cd (0.006 0.015 0.012 0.750) Cr <0.001 45.320 139.180) Berdasarkan Metode Storet dapat dilihat nilai status mutu air laut perairan ini adalah 12, berarti bahwa kualitas air laut di perairan termasuk kelas C (tercemar sedang) Sedangkan status mutu sedimen di perairan menunjukkan skor nilai status mutu sedimen adalah 0, yang berarti bahwa kualitas sedimen termasuk kelas A (tidak tercemar/memenuhi baku mutu) Jelas terlihat bahwa nilai ambang batas (NAB) logam berat dalam sedimen jauh lebih tinggi dari NAB logam berat dalam air. Kata kunci: logam berat, sedimen dasar laut, air laut, nilai status mutu Marine Environmental and Geological Hazard Survey In Jakarta Bay Waters (Tanjung Kait Muara Gembong) conducted in October November 2010. Testing of heavy metals (Cu, Pb, Zn, Cd, and Cr) performed on 28 samples of sea water and 28 subsurface sediment samples using the method of Atomic Absorption Spectrophotometry (AAS) The purpose of this study was to obtain data and information on current environmental conditions of heavy metal content in seawater and subsurface sediment. Heavy metal content (sea water in mg/l: subsurface sediment in ppm) measured as follows: Cu <0.005 15.000 169.500 Pb (0.005 0.011 14.000 58.100) Zn (0.005 0.007 95.800 333.000) Cd (0.006 0.015 0.012 0.750) Cr <0.001 45.320 139.180) Based on the Storet method shows the value of water quality status of sea waters is 12, which means that the seawater quality in these waters belong to a class C (medium contaminated) While the status of sediment quality in these waters indicate subsurface sediment quality score status value is 0, which means that subsurface sediment quality belongs to the class A (not polluted/correspond to the quality standards) It is clearly seen that the threshold value (NAV) of heavy metals in sediments is much higher than the NAV of heavy metals in water.  heavy metal, subsurface sediment, seawater, quality score status
Mindfulness as a Coping Strategy for Bias Based School Victimization among Latina/o Sexual Minority Youth.
Venue: Psychology of sexual orientation and gender diversity

This study examined whether mindfulness strategies (e.g. acting non judgmentally with awareness and attention to present events) were effective in mitigating the associations among school based victimization related to ethnicity and sexual orientation, well being (i.e. depressive symptoms and self esteem) and grade point average (GPA) The U.S. based sample included 236 Latina/o sexual minority students, ranging in age from 14 to 24 years (47% were enrolled in secondary schools, 53% in postsecondary schools) Results from structural equation modeling revealed that ethnicity based school victimization was negatively associated with GPA but not well being. However, sexual orientation based victimization was not associated with well being or GPA. Mindfulness was positively associated with well being but not GPA. High levels of mindfulness coping were protective when the stressor was sexual orientation based victimization but not ethnicity based school victimization. These findings contribute to a growing literature documenting the unique school barriers experienced by Latina/o sexual minority youth and highlight the promising utility of mindfulness based intervention strategies for coping with minority stress.
Orthorexic eating behaviour as a coping strategy in patients with anorexia nervosa
Venue: Eating and Weight Disorders Studies on Anorexia, Bulimia and Obesity

PurposeOrthorexia nervosa is defined as the fixation on health conscious eating behaviour and has recently been discussed as a new variant of disordered eating. The aim of the present study was to analyse orthorexic eating behaviour in an inpatient treatment sample of female anorexics to investigate the relation between anorexic and orthorexic eating behaviour.MethodFemale anorexic patients with low (n 29) and pronounced (n 13) orthorexic eating behaviour as well as a matched control group composed of healthy females (n 30) were compared with regard to several aspects of disordered eating, hypochondriacal traits, food consumption frequency and fulfilment of basic psychological needs in terms of eating. Orthorexic eating behaviour was assessed using the Dusseldorfer Orthorexie Skala.ResultsFulfilment of basic psychological needs with respect to autonomy and competence is higher in anorexic individuals with pronounced orthorexic eating behaviour compared to patients with low orthorexic eating behaviour. Furthermore, patients with pronounced orthorexic eating behaviour state eating healthy food regardless of calorie content more often. No difference was found for hypochondriacal traits and eating disordered symptoms in general.ConclusionsOrthorexic eating behaviour enhances self perception of eating behaviour as autonomous and competent, indicating that it might serve as a coping strategy in anorexic individuals. Further research is needed to investigate if this tendency in food selection strategy leads to positive effects in the long term.
Image Based Building Regularization Using Structural Linear Features
Venue: IEEE Transactions on Visualization and Computer Graphics

Reconstructed building models using stereo based methods inevitably suffer from noise, leading to the lack of regularity which is characterized by straightness of structural linear features and smoothness of homogeneous regions. We leverage the structural linear features embedded in the mesh to construct a novel surface scaffold structure for model regularization. The regularization comprises two iterative stages: (1) the linear features are semi automatically proposed from images by exploiting photometric and geometric clues jointly; (2) the scaffold topology represented by spatial relations among the linear features is optimized according to data fidelity and topological rules, then the mesh is refined by adjusting itself to the consolidated scaffold. Our method has two advantages. First, the proposed scaffold representation is able to concisely describe semantic building structures. Second, the scaffold structure is embedded in the mesh, which can preserve the mesh connectivity and avoid stitching or intersecting surfaces in challenging cases. We demonstrate that our method can enhance structural characteristics and suppress irregularities in the building models robustly in some challenging datasets. Moreover, the regularization can significantly improve the results of general applications such as simplification and non photorealistic rendering.
Facial Psoriasis Log based Area and Severity Index: A valid and reliable severity measurement method detecting improvement of facial psoriasis in clinical practice settings
Venue: The Journal of dermatology

Facial psoriasis is often observed in moderate to severe degrees of psoriasis. While we previously demonstrated construct validity of the facial Psoriasis Log based Area and Severity Index (fPLASI) system for the cross sectional evaluation of facial psoriasis, its reliability and accuracy to detect clinical improvement has not been confirmed yet. The aim of this study is to analyze whether the fPLASI properly represents the range of improvement for facial psoriasis compared with the existing facial Psoriasis Area and Severity Index (fPASI) after receiving systemic treatments in clinical practice settings. The changing severity of facial psoriasis for 118 patients was calculated by the scales of fPASI and fPLASI between two time points after systemic treatments. Then, percentage changes (DfPASI and DfPLASI) were analyzed from the perspective of both the Physician's Global Assessment of effectiveness (PGA) and patients' Subjective Global Assessment (SGA) As a result, the distribution of the fPASI was more heavily clustered around the low score range compared with the fPLASI at both first and second visits. Linear regression analysis between DfPASI and DfPLASI shows that the correlation coefficient was 0.94, and DfPLASI represented greater percentage changes than DfPASI. Remarkably, degrees of clinical improvement measured by the PGA matched better with DfPLASI, while DfPASI underestimated clinical improvements compared with DfPLASI from treatment responding groups by the PGA and SGA. In conclusion, the fPLASI represented clinical improvement of facial psoriasis with more sensitivity and reliability compared with the fPASI. Therefore, the PLASI system would be a viable severity measurement method for facial psoriasis in clinical practice.
Complete heart block in a Caucasian woman with Behcet's disease: a case report
Venue: Journal of Medical Case Reports

BackgroundBehcet's disease is a progressive diffuse inflammatory vasculitis characterized by recurrent oral and genital ulceration and ocular inflammation. Cardiac involvement is a rare but well documented manifestation of Behcet's disease. Complete heart block in non Caucasian populations has been reported previously; however, in this report, we describe a unique case of complete heart block in a Caucasian woman with Behcet's disease.Case presentationA 48 year old Caucasian woman presented to our hospital with symptomatic complete heart block requiring a pacemaker implant on a background of recurrent oral and genital ulcers and oligoarthritis of 10 months' duration. She also had a history of recurrent diarrhea with a single episode of ocular inflammation in the recent past. She had no evidence of cardiac ischemia, and her autoimmune antibodies were within normal ranges. She was diagnosed with Behcet's disease according to international study group criteria and was commenced on prednisolone and sulfasalazine, to which she responded very well.ConclusionsCardiac complications should be considered when making a diagnosis of Behcet's disease, even in Caucasian patients. While mucocutaneous ulceration is indeed the most common manifestation of Behcet's disease, cardiovascular involvement tends to cause the most morbidity and mortality.
Development Of Titanium Dioxide Nanotube based Arrays For The Electrocatalytic Degradation And Electrochemical Detection Of Emerging Pharmaceuticals In Water

The electrocatalytic degradation and electrochemical detection of ibuprofen (IBU) in water was performed using titanium dioxide nanotube (TiO2 NT) arrays. IBU solutions with starting concentrations of 30 ppm were degraded by 50% in 15 min using a TiO2 NT array annealed in a reducing atmosphere.  25922 was used to determine the radical species generated during degradation in both flow and batch reactors. Semi quantitative radical concentrations were obtained by using a UV Vis spectrophotometer to monitor the color change of an oxidation sensitive DPD dye. Electrochemical detection limits of 4 ppb IBU in 50 ppm NaCl were obtained using a gold coated TiO2 NT array annealed in oxygen. These results demonstrated the feasibility of a combined system that could be deployed for inline effluent treatment as these types of systems are robust, chemical free and could be automated for remote control.
Unconditional quantum teleportation between distant solid state qubits

Realizing robust quantum information transfer between long lived qubit registers is a key challenge for quantum information science and technology. Here we demonstrate unconditional teleportation of arbitrary quantum states between diamond spin qubits separated by 3 meters. We prepare the teleporter through photon mediated heralded entanglement between two distant electron spins and subsequently encode the source qubit in a single nuclear spin. By realizing a fully deterministic Bell state measurement combined with real time feed forward we achieve teleportation in each attempt while obtaining an average state fidelity exceeding the classical limit. These results establish diamond spin qubits as a prime candidate for the realization of quantum networks for quantum communication and network based quantum computing.
Perturbations to the Spatial and Temporal Characteristics of the Diurnally Varying Atmospheric Boundary Layer Due to an Extensive Wind Farm
Venue: Boundary Layer Meteorology

The effect of extensive terrestrial wind farms on the spatio temporal structure of the diurnally evolving atmospheric boundary layer is explored. High resolution large eddy simulations of a realistic diurnal cycle with an embedded wind farm are performed. Simulations are forced by a constant geostrophic velocity with time varying surface boundary conditions derived from a selected period of the CASES 99 field campaign. Through analysis of the bulk statistics of the flow as a function of height and time, it is shown that extensive wind farms shift the inertial oscillations and the associated nocturnal low level jet vertically upwards by approximately 200 m; cause a three times stronger stratification between the surface and the rotor disk region, and as a consequence, delay the formation and growth of the convective boundary layer (CBL) by approximately 2 h. These perturbations are shown to have a direct impact on the potential power output of an extensive wind farm with the displacement of the low level jet causing lower power output during the night as compared to the day. The low power regime at night is shown to persist for almost 2 h beyond the morning transition due to the reduced growth of the CBL. It is shown that the wind farm induces a deeper entrainment region with greater entrainment fluxes. Finally, it is found that the diurnally averaged effective roughness length for wind farms is much lower than the reference value computed theoretically for neutral conditions.
Identifying Problem Statements in Scientific Text

In this work, we focus on the automatic identification of fine grained problem solution structure in scientific argumentation. We operationalise the task of finding problem formulations within scientific text in a supervised setting, using a newly created hand curated corpus from the domain of computational linguistics. In terms of linguistic features for their detection, we distinguish features from within the statement, and features representing the surrounding context. Results from a classification task on our corpus show that the task of identifying problem statements is tractable using a mixture of features, whereby features modelling the rhetorical context are particularly successful. Overall, our experiment shows promise for future work in identifying scientific problem solution structure in a more global way.
Trademarks and Patents

The development and application of science and technology need an enabling regulatory environment that protects intellectual property rights (IPR) to encourage research and inventions. Patents and trademarks are examples of approaches to protecting inventions. Sub Saharan African countries operate under both international, regional, and domestic IPR regimes. For example, the International Treaty on Genetic Resources for Food and Agriculture "Plant Treaty" approved in 2001 announced an important principle under the Plant Treaty, the Farmers' Rights under which farmers are recognized as the guardians and holders of traditional knowledge and stewards of agricultural biodiversity. The Plant Treaty allows farmers to share benefits arising from the utilization of plant genetic resources for food and agriculture. There are only a few court cases involving IPR violation. Most of the cases deal with the situation where an importer attempts to register a product in the domestic market as their own trademark.
Examination of Status and Challenges of Pharmaceutical Trademarks Registration in European :union:

The registration of trademarks related to pharmaceutical trademarks in the European Union in comparison with other trademarks requires more complicated and longer procedure. Respecting health hazards posed by medicine errors, determination of an appropriate legal framework is of particular importance. This article addresses such difficulties and complicity, and reviews and analyses the case law approach to those challenges.  The method used in this Article is descriptive analytical. Data have been compiled by bibliotheca methods through taking notes from relevant sources. The collected data have been analyzed in light of regulations and courts decisions.  On the one hand, in addition to normal application based procedure required at trademark offices, pharmaceutical trademarks must be examined and approved prior to utilization by health related authorities because of their impact on public health. On the other hand, the length of this approval process could put the validity of many registered pharmaceutical trademarks at risk in light of genuine use requirement, because such trademarks cannot be used in the market before obtaining the public health related authorization. Moreover, the particular criteria governing the assessment of the likelihood of confusion add more complicity to the difficulties with the registration of pharmaceutical trademarks. When deciding on a proposed trademark and a prior mark, the difference between the consumers' knowledge that includes not only medicine and medical staff, 1 MA, Medical Ethics and Law Research Center, Shahid Beheshti University of Medical Sciences and Health Services, Tehran, Iran. 2 PhD, Faculty of Law and Political Science, Allameh Tabataba'i University, Tehran, Iran.  When assessing a likelihood of confusion, healthcare professionals and end users should be considered. Also, in assessing the similarity of the goods or services concerned, factors such as their nature, their end users intended purpose and their method of use and whether they are in competition with each other or are complementary should be taken into account.