nils-herrmann/clean_scirepeval huggingface dataset:
Rain Streak Removal Using Layer Priors
Venue: 2016 IEEE Conference on Computer Vision and Pattern Recognition (CVPR)

This paper addresses the problem of rain streak removal from a single image. Rain streaks impair visibility of an image and introduce undesirable interference that can severely affect the performance of computer vision algorithms. Rain streak removal can be formulated as a layer decomposition problem, with a rain streak layer superimposed on a background layer containing the true scene content. Existing decomposition methods that address this problem employ either dictionary learning methods or impose a low rank structure on the appearance of the rain streaks. While these methods can improve the overall visibility, they tend to leave too many rain streaks in the background image or over smooth the background image. In this paper, we propose an effective method that uses simple patch based priors for both the background and rain layers. These priors are based on Gaussian mixture models and can accommodate multiple orientations and scales of the rain streaks. This simple approach removes rain streaks better than the existing methods qualitatively and quantitatively. We overview our method and demonstrate its effectiveness over prior work on a number of examples.
Reading Room.
Venue: Biomedical instrumentation technology Association for the Advancement of Medical Instrumentation

Many systems administrators are not aware of the subtle differences between Mac OS X and its Unix operating system brethren (Jepson, Rothman, &amp; Rosen, 2008) Hackers can exploit this ignorance when hiding their presence on compromised systems (Skoudis, 2007) In this paper, I apply the Covering the Tracks techniques described in the SANS SEC 504 course to Mac OS X. Doing so highlights the ways in which Mac OS X and Unix diverge, increasing awareness of how an attacker might conceal himself in Mac OS X. The go.
Targeting cancer metabolism by simultaneously disrupting parallel nutrient access pathways.
Venue: The Journal of clinical investigation

Oncogenic mutations drive anabolic metabolism, creating a dependency on nutrient influx through transporters, receptors, and macropinocytosis. While sphingolipids suppress tumor growth by downregulating nutrient transporters, macropinocytosis and autophagy still provide cancer cells with fuel. Therapeutics that simultaneously disrupt these parallel nutrient access pathways have potential as powerful starvation agents. Here, we describe a water soluble, orally bioavailable synthetic sphingolipid, SH BC 893, that triggers nutrient transporter internalization and also blocks lysosome dependent nutrient generation pathways. SH BC 893 activated protein phosphatase 2A (PP2A) leading to mislocalization of the lipid kinase PIKfyve. The concomitant mislocalization of the PIKfyve product PI(3,5)P2 triggered cytosolic vacuolation and blocked lysosomal fusion reactions essential for LDL, autophagosome, and macropinosome degradation. By simultaneously limiting access to both extracellular and intracellular nutrients, SH BC 893 selectively killed cells expressing an activated form of the anabolic oncogene Ras in vitro and in vivo. However, slower growing, autochthonous PTEN deficient prostate tumors that did not exhibit a classic Warburg phenotype were equally sensitive. Remarkably, normal proliferative tissues were unaffected by doses of SH BC 893 that profoundly inhibited tumor growth. These studies demonstrate that simultaneously blocking parallel nutrient access pathways with sphingolipid based drugs is broadly effective and cancer selective, suggesting a potential strategy for overcoming the resistance conferred by tumor heterogeneity.
Azacyclic FTY720 Analogues That Limit Nutrient Transporter Expression but Lack S1P Receptor Activity and Negative Chronotropic Effects Offer a Novel and Effective Strategy to Kill Cancer Cells in Vivo.
Venue: ACS chemical biology

FTY720 sequesters lymphocytes in secondary lymphoid organs through effects on sphingosine 1 phosphate (S1P) receptors. However, at higher doses than are required for immunosuppression, FTY720 also functions as an anticancer agent in multiple animal models. Our published work indicates that the anticancer effects of FTY720 do not depend on actions at S1P receptors but instead stem from FTY720s ability to restrict access to extracellular nutrients by down regulating nutrient transporter proteins. This result was significant because S1P receptor activation is responsible for FTY720s dose limiting toxicity, bradycardia, that prevents its use in cancer patients. Here, we describe diastereomeric and enantiomeric 3 and 4 C aryl 2 hydroxymethyl pyrrolidines that are more active than the previously known analogues. Of importance is that these compounds fail to activate S1P1 or S1P3 receptors in vivo but retain inhibitory effects on nutrient transporter proteins and anticancer activity in solid tumor xenograft models. Our studies reaffirm that the anticancer activity of FTY720 does not depend upon S1P receptor activation and uphold the promise of using S1P receptor inactive azacyclic FTY720 analogues in human cancer patients.
Effect of annealing temperature on the morphology and optical properties of ZnO tetrapods grown by a thermal evaporation technique

The effect of the thermal annealing temperature was investigated on ZnO tetrapods grown by a thermal evaporation method. The ZnO tetrapods were synthesized by thermal evaporation of Zn powder in air. The annealing was done in an oxygen gas environment at temperatures ranging from 400 to 1000 degC for 1 h. As the annealing temperature increased from 400 degC to 800 degC, the morphology of the tetrapod remained unchanged; however, the size of the tetrapods increased. With a further increase in the annealing temperature from 800 degC to 1000 degC, the ZnO tetrapod changed drastically to nanoneedles. As grown and annealed samples had an identical crystal structure, which was a wurtzite structure. A strong and sharp ultraviolet emission at 380 nm was observed for the 600 degC annealed sample indicating the high crystalline quality. The ultraviolet emission intensity decreased abruptly for the samples annealed at 800 degC and 1000 degC, which exhibits the degradation in crystallinity.
Colonization with the enteric protozoa Blastocystis is associated with increased diversity of human gut bacterial microbiota
Venue: Scientific reports

Alterations in the composition of commensal bacterial populations, a phenomenon known as dysbiosis, are linked to multiple gastrointestinal disorders, such as inflammatory bowel disease and irritable bowel syndrome, or to infections by diverse enteric pathogens. Blastocystis is one of the most common single celled eukaryotes detected in human faecal samples. However, the clinical significance of this widespread colonization remains unclear, and its pathogenic potential is controversial. To address the issue of Blastocystis pathogenicity, we investigated the impact of colonization by this protist on the composition of the human gut microbiota. For that purpose, we conducted a cross sectional study including 48 Blastocystis colonized patients and 48 Blastocystis free subjects and performed an Ion Torrent 16S rDNA gene sequencing to decipher the Blastocystis associated gut microbiota. Here, we report a higher bacterial diversity in faecal microbiota of Blastocystis colonized patients, a higher abundance of Clostridia as well as a lower abundance of Enterobacteriaceae. Our results contribute to suggesting that Blastocystis colonization is usually associated with a healthy gut microbiota, rather than with gut dysbiosis generally observed in metabolic or infectious inflammatory diseases of the lower gastrointestinal tract.
Separation and recovery of vanadium from a sulfuric acid leaching solution of stone coal by solvent extraction using trialkylamine

Trialkylamine N235, diluted with sulfonated kerosene containing tri butyl phosphate, was used to separate vanadium and impurities as Fe, Al, Mg, K, Ca, P, and Si from a leaching solution generated by the sulfuric acid leaching of vanadium containing stone coal. Variations in aqueous pH exhibited good extraction of vanadium at an equilibrium pH of 1.6. Vanadium was successfully extracted by a three stage countercurrent process using 20% N235 and 5% tri butyl phosphate at an organic to aqueous (A/O) phase ratio of 2:1. The loaded organic was then scrubbed with 0.5 mol/L H 2 SO 4 and most impurities were scrubbed by three stage scrubbing. 1.0 mol/L NaOH was used to strip of vanadium from the scrubbed organic solution at an O/A phase ratio of 2:1, where >99% of vanadium was stripped in three stages. After regeneration by 1.0 mol/L H 2 SO 4 the regenerated organic phase showed a good performance on vanadium extraction even after 5 cycles. Finally, a process flow sheet was established to recover of vanadium from a sulfuric acid leaching solution of stone coal.
Separation and recovery of sulfuric acid from acidic vanadium leaching solution of stone coal via solvent extraction

The separation and recovery of sulfuric acid from an acidic leaching solution of stone coal containing 110 g/L of H2SO4 and 1.98 g/L of vanadium and other metal ions with the use of TEHA was investigated. Vanadium valence has a significant effect on the separation of sulfuric acid and vanadium because of the speciation of the anion VO2SO4 of V(V) in the solution. V(IV) almost has no effect on sulfuric acid separation from vanadium because V(IV) exists as VO2+ in the acidic leaching solution, and the influence of vanadium on sulfuric acid recovery can be decreased by reducing V(V) to V(IV) with Na2SO3. Acid extraction rate increases with an increase in TEHA concentration and O/A phase ratio but decreases with an increase in temperature. Under optimized conditions, sulfuric acid extraction capacity is 86.25 g/L of sulfuric acid with 40% TEHA and a phase ratio (O/A) of 2:1 in a 10 min phase contact at 25 degC. The raffinate containing only 12.74 g/L of sulfuric acid can be directly used for vanadium extraction. Approximately 99% of sulfuric acid could be stripped with hot water at 65 degC and an O/A ratio of 1/3 in a three stage extraction process.
Recovery of Vanadium from H2SO4 HF Acidic Leaching Solution of Black Shale by Solvent Extraction and Precipitation

The recovery of vanadium from sulfuric and hydrofluoric mixed acid solutions generated by the direct leaching of black shale was investigated using solvent extraction and precipitation methods. The process consisted of reduction, solvent extraction, and stripping, followed by precipitation and calcination to yield vanadium pentoxide. The influence of various operating parameters on the extraction and recovery of vanadium was studied. Vanadium (IV) was selectively extracted using a mixture of 10% (v/v) di(2 ethylhexyl)phosphoric acid and 5% (v/v) tri n butylphosphate in sulfonated kerosene. Using six extraction and five stripping stages, the extraction efficiency for vanadium was 96.7% and the stripping efficiency was 99.7% V2O5 with a purity of 99.52% was obtained by oxidation of the loaded strip solution and precipitation of ammonium polyvanadate at pH 1.8 to 2.2, followed by calcination of the dried precipitate at 550 degC for 2 h. It was concluded that the combination of solvent extraction and precipitation is an efficient method for the recovery of vanadium from a multi element leach solution generated from black shale.
Ultraviolet (250 550 nm) absorption spectrum of pure water.
Venue: Applied optics

Data for the spectral light absorption of pure water from 250 to 550 nm have been obtained using an integrating cavity made from a newly developed diffuse reflector with a very high UV reflectivity. The data provide the first scattering independent measurements of absorption coefficients in the spectral gap between well established literature values for the absorption coefficients in the visible >400 nm) and UV <200 nm) A minimum in the absorption coefficient has been observed in the UV at 344 nm; the value is 0.000811+ 0.000227 m 1.
Measurement of absorption spectrum of deuterium oxide (D2O) and its application to signal enhancement in multiphoton microscopy at the 1700 nm window

1700 nm window has been demonstrated to be a promising excitation window for deep tissue multiphoton microscopy (MPM) Long working distance water immersion objective lenses are typically used for deep tissue imaging. However, absorption due to immersion water at 1700 nm is still high and leads to dramatic decrease in signals. In this paper, we demonstrate measurement of absorption spectrum of deuterium oxide (D2O) from 1200 nm to 2600 nm, covering the three low water absorption windows potentially applicable for deep tissue imaging (1300 nm, 1700 nm, and 2200 nm) We apply this measured result to signal enhancement in MPM at the 1700 nm window. Compared with water immersion, D2O immersion enhances signal levels in second harmonic generation imaging, 3 photon fluorescence imaging, and third harmonic generation imaging by 8.1, 24.8, and 24.7 times with 1662 nm excitation, in good agreement with theoretical calculation based on our absorption measurement. This suggests D2O a promising immersion medium for d.
Analyses of Impact of Needle Surface Properties on Estimation of Needle Absorption Spectrum: Case Study with Coniferous Needle and Shoot Samples
Venue: Remote. Sens.

Leaf scattering spectrum is the key optical variable that conveys information about leaf absorbing constituents from remote sensing. It cannot be directly measured from space because the radiation scattered from leaves is affected by the 3D canopy structure. In addition, some radiation is specularly reflected at the surface of leaves. This portion of reflected radiation is partly polarized, does not interact with pigments inside the leaf and therefore contains no information about its interior. Very little empirical data are available on the spectral and angular scattering properties of leaf surfaces. Whereas canopy structure effects are well understood, the impact of the leaf surface reflectance on estimation of leaf absorption spectra remains uncertain. This paper presents empirical and theoretical analyses of angular, spectral, and polarimetric measurements of light reflected by needles and shoots of Pinus koraiensis and Picea koraiensis species. Our results suggest that ignoring the leaf surface reflected radiation can result in an inaccurate estimation of the leaf absorption spectrum. Polarization measurements may be useful to account for leaf surface effects because radiation reflected from the leaf surface is partly polarized, whereas that from the leaf interior is not.
Machiavelli's walls: The legacy of realism in international relations theory

In this article we argue that Niccolo Machiavelli has little to do with Realism in International Relations theory. By concentrating, as Machiavelli did, on the walls that define political relations both inside and outside the polity we find his insights deeply rooted in the specific political contexts of sixteenth century Italy. Others may wish to generalize from them, but Machiavelli did not. In fact, as we show, Machiavelli was mindful of the difficulties of generalizing about walls and acknowledged the dangers political actors faced in navigating between the internal and external walls of the polity. We examine the geopolitical contours of Machiavelli's walls and seek to demonstrate how morality is present in these historical spaces. In contrast to Realists, Machiavelli was ready and willing to make ethical judgments. We argue that theorists of international politics should exercise care in reaching for Machiavelli as the iconic thinker for making sense of anarchy in world politics. This article concludes by suggesting that the ideology of Machiavellianism has obscured deeper understanding of the particular contexts of Machiavelli's own world.
Soft Skills for Sustainable Employment: Does It Really Matter?

A tremendous change has occurred in the professional world of learning. In order to develop a knowledge based economy, a growing awareness about the importance of proper higher education has transpired in Bangladesh. Evidence from contemporary literature suggests that Soft Skill Attributes contribute to the sustainable employment of the business graduates significantly. This paper is based on descriptive and inferential research. The study has tried to identify the top ten Soft Skill attributes frequently asked by the employers among the potential candidates to attain and sustain the employments for business graduates in Bangladesh. It is found in this paper, that most of the employers search for the soft skill attributes like Communication Skill (Both Verbal Writing) Interpersonal Skill, Ability to work under pressure, Team Player, Analytical Ability, Self Motivated, Deadline Oriented/Target Oriented, Leadership Skill, Problem Solving Ability, Proactive, etc. The study also opens avenue for further research in this field implementing training program for attaining most desired soft skills among the higher education institutions.
Computer Programming Competencies Required by Computer Education Graduates for Sustainable Employment

This study identified the computer programming competencies required of computer education graduates for sustainable employment in Enugu metropolis, Enugu state, Nigeria. Three research questions and one null hypothesis guided the study. The study adopted descriptive survey research design. The population for the study was 95, which comprised of 74 computing lecturers, 6 IT programming instructors, and 15 programmers. A structured questionnaire was used for data collection. The instrument was face validated by three experts in computer programming. Cronbach Alpha statistic was used to determine the internal consistency of the instrument, yielding reliability co efficient of 0.83. Mean and Standard deviation were used to answer the research questions while ANOVA statistic was used to test the hypothesis. The study found out that 25 hard competencies, 18 business competencies, and 19 soft competencies are required by computer education graduates for sustainable employment in programming jobs. These competencies identified include among others, ability to code, test and debug programs quickly and efficiently; ability to explore and evaluate application design considerations for multiple technologies, ability to analyze users' needs and specifications then design, test, and develop software to meet those needs, ability to recommend software upgrades for clients' existing programs and systems, proficiency in data mining, confidence in personal ideas but open to feedbacks, adapting to changes while remaining focused on project with topmost priority and good sense of judgment. It was therefore recommended that the identified competencies should be incorporated in the curriculum for training Computer Education graduates for sustainability in programming jobs.
Hyperconnected City Logistics and Last Mile Delivery in Casablanca City

City logistics provides the final and last segments of the physical internet logistics and transportation networks. In this paper, we will present a new scheme for big cities where we imagine the use of existing infrastructures and non pollutant means of transportation to deliver encapsulated goods rapidly and safely from origin to destination. In order to clarify the idea, we will use the map of rail network of Casablanca city (the biggest city, chief port, and economic capital of Morocco) to minimize the maximum travel time (or distance) and ensure a better interconnectivity between nodes. We will also propose the use of nearby agencies as a Distribution Centers (DCs) to improve the last Mile Deliveries. Using existing means of transportation and platforms intelligently, encapsulated goods will be delivered more efficiently.
Identification of key player genes in gene regulatory networks
Venue: BMC Systems Biology

BackgroundIdentifying the gene regulatory networks governing the workings and identity of cells is one of the main challenges in understanding processes such as cellular differentiation, reprogramming or cancerogenesis. One particular challenge is to identify the main drivers and master regulatory genes that control such cell fate transitions. In this work, we reformulate this problem as the optimization problems of computing a Minimum Dominating Set and a Minimum Connected Dominating Set for directed graphs.ResultsBoth MDS and MCDS are applied to the well studied gene regulatory networks of the model organisms E. coli and S. cerevisiae and to a pluripotency network for mouse embryonic stem cells. The results show that MCDS can capture most of the known key player genes identified so far in the model organisms. Moreover, this method suggests an additional small set of transcription factors as novel key players for governing the cell specific gene regulatory network which can also be investigated with regard to diseases. To this aim, we investigated the ability of MCDS to define key drivers in breast cancer. The method identified many known drug targets as members of the MDS and MCDS.ConclusionsThis paper proposes a new method to identify key player genes in gene regulatory networks. The Java implementation of the heuristic algorithm explained in this paper is available as a Cytoscape plugin at http:/apps.cytoscape.org/apps/mcds. The SageMath programs for solving integer linear programming formulations used in the paper are available at https:/github.com/maryamNazarieh/KeyRegulatoryGenesand as supplementary material.
Computational Identification of Key Regulators in Two Different Colorectal Cancer Cell Lines
Venue: Front. Genet.

Transcription factors (TFs) are gene regulatory proteins that are essential for an effective regulation of the transcriptional machinery. Today, it is known that their expression plays an important role in several types of cancer. Computational identification of key players in specific cancer cell lines is still an open challenge in cancer research. In this study, we present a systematic approach which combines colorectal cancer (CRC) cell lines, namely 1638N T1 and CMT 93, and well established computational methods in order to compare these cell lines on the level of transcriptional regulation as well as on a pathway level, i.e. the cancer cell intrinsic pathway repertoire. For this purpose, we firstly applied the Trinity platform to detect signature genes, and then applied analyses of the geneXplain platform to these for detection of upstream transcriptional regulators and their regulatory networks. We created a CRC specific position weight matrix (PWM) library based on the TRANSFAC database (release 2014.1) to minimize the rate of false predictions in the promoter analyses. Using our proposed workflow, we specifically focused on revealing the similarities and differences in transcriptional regulation between the two CRC cell lines, and report a number of well known, cancer associated TFs with significantly enriched binding sites in the promoter regions of the signature genes. We show that, although the signature genes of both cell lines show no overlap, they may still be regulated by common TFs in CRC. Based on our findings, we suggest that canonical Wnt signaling is activated in 1638N T1, but inhibited in CMT 93 through cross talks of Wnt signaling with the VDR signaling pathway and/or LXR related pathways. Furthermore, our findings provide indication of several master regulators being present such as MLK3 and Mapk1 (ERK2) which might be important in cell proliferation, migration, and invasion of 1638N T1 and CMT 93, respectively. Taken together, we provide new insights into the invasive potential of these cell lines, which can be used for development of effective cancer therapy.