nils-herrmann/clean_scirepeval huggingface dataset:
Numerical analysis of the effects of reformer gas on supercharged n heptane HCCI combustion
Year: 2017

Main purpose of this paper is investigating on the effect of reformer gas addition on combustion, performance and emission characteristics of a n heptane fueled HCCI supercharged engine. A validated multi zone model, which is accurate for modeling of HCCI engine, is used. Heat and mass transfer between zones and convective heat transfer between in cylinder charge and combustion chamber walls are considered in the multi zone model. A semi detailed chemical kinetics mechanism, containing 57 species and 290 reactions, is used for simulating the combustion process of n heptane. Four different values of reformer gas are added to the main fuel and its effects on engine performance and chemical reactions are studied. The results show that addition of reformer gas retards the start of combustion and causes to lower in cylinder peak pressure and temperature. Chemical, dilution and thermodynamic effects of RG are studied and the results show that the chemical effect of reformer gas is more significant than its dilution and thermal effects. Hydrogen in comparison to carbon monoxide has more chemical effects. Chemical analyses show that RG affects the chemical reactions and intermediate species concentration.
Efficient Combinations of Rejection Strategies for Dense Point Clouds Registration
Year: 2017

The Iterative Closest Point (ICP) algorithm has been viewed as a standard approach to registering two point clouds. In the process of point clouds registration, the eliminating incorrect point pairs has important effect on the accuracy and stability of registration. In the past two decades, numerous strategies of excluding point pairs have been developed and various combinations of them have been applied to the variants of ICP algorithm. In this paper, an efficient combination of rejection strategies is proposed. It also is compared with other heuristic combinations. As shown in our case studies, the proposed combination can realize more accurate registration without sacrificing computational efficiency.
The Merits of Passive Compliant Joints in Legged Locomotion: Fast Learning, Superior Energy Efficiency and Versatile Sensing in a Quadruped Robot
Year: 2017

A quadruped robot with four actuated hip joints and four passive highly compliant knee joints is used to demonstrate the potential of underactuation from two standpoints: learning locomotion and perception. First, we show that: (i) forward locomotion on flat ground can be learned rapidly (minutes of optimization time) (ii) a simulation study reveals that a passive knee configuration leads to faster, more stable, and more efficient locomotion than a variant of the robot with active knees; (iii) the robot is capable of learning turning gaits as well. The merits of underactuation (reduced controller complexity, weight, and energy consumption) are thus preserved without compromising the versatility of behavior. Direct optimization on the reduced space of active joints leads to effective learning of model free controllers. Second, we find passive compliant joints with potentiometers to effectively complement inertial sensors in a velocity estimation task and to outperform inertial and pressure sensors in a terrain detection task. Encoders on passive compliant joints thus constitute a cheap and compact but powerful sensing device that gauges joint position and force/torque, and if mounted more distally than the last actuated joints in a legged robot it delivers valuable information about the interaction of the robot with the ground.
Retention Correlated Read Disturb Errors in 3 D Charge Trap NAND Flash Memory: Observations, Analysis, and Solutions
Venue: IEEE Transactions on Computer Aided Design of Integrated Circuits and Systems
Year: 2020

3 D NAND flash memory has been attracting much attention owing to its ultrahigh storage density and low bit cost, and it has been widely applied in data centers and mobiles. 3 D triple level cell (TLC) NAND flash memory can achieve much larger storage capacity by storing 3 bits in each cell. However, the data reliability issues induced by data retention (DR) and read disturb (RD) greatly limit 3 D TLC NAND applications in hot data storage where the stored data are frequently accessed and RD is more serious. In this article, we first systematically study the retention correlated RD (RCRD) errors in 3 D charge trap (CT) TLC NAND flash memory under various conditions. Error characteristics and underlying mechanisms much different from 2 D NAND flash memory are observed: 1) for RCRD with short retention after data program, error bits increase due to the negative shift of program states and 2) for RCRD with long retention after retention 12 h, error bits can be partially recovered on the contrary due to the charge compensation. We propose schemes of precharge the storage layer (PCSL) and thermally stabilize the storage layer (TSSL) to improve the reliability of 3 D NAND flash memory. By using these two methods, experimental results show that raw bit error rates (RBERs) can be significantly reduced by 30% and 20% respectively.
Generating Property Matched Decoy Molecules Using Deep Learning
Year: 2020

An essential step in the development of virtual screening methods is the use of established sets of actives and decoys for benchmarking and training. However, the decoy molecules in commonly used sets are biased meaning that methods often exploit these biases to separate actives and decoys, rather than learning how to perform molecular recognition. This fundamental issue prevents generalisation and hinders virtual screening method development. We have developed a deep learning method (DeepCoy) that generates decoys to a user's preferred specification in order to remove such biases or construct sets with a defined bias. We validated DeepCoy using two established benchmarks, DUD E and DEKOIS 2.0. For all DUD E targets and 80 of the 81 DEKOIS 2.0 targets, our generated decoy molecules more closely matched the active molecules' physicochemical properties while introducing no discernible additional risk of false negatives. The DeepCoy decoys improved the Deviation from Optimal Embedding (DOE) score by an average of 81% and 66% respectively, decreasing from 0.163 to 0.032 for DUD E and from 0.109 to 0.038 for DEKOIS 2.0. Further, the generated decoys are harder to distinguish than the original decoy molecules via docking with Autodock Vina, with virtual screening performance falling from an AUC ROC of 0.71 to 0.63. The code is available at https:/github.com/oxpig/DeepCoy. Generated molecules can be downloaded from http:/opig.stats.ox.ac.uk/resources.
Anatomy of the Persian Cat's Skull and its Clinical Value During Regional Anesthesia
Year: 2013

The head of Persian cats is characterized by a short face and open orbits. Also, the phenotypic appearance of the cat head depends on the shape of the skull and is strongly related to breed specific skeletal properties. Since, there is a lack of information on anatomical measurements of the skulls of Persian cats and its clinical value during regional anesthesia; the present work was taken. The investigation was carried out on sixteen mandibles and upper jaws from cats older than one year without any apparent skeletal disorders. Then, a total of seventeen skull measurements and indices were recorded. The skull length, cranial length, nasal length and cranial width of the adult cats were 10.58 cm, 7.38 cm, 3.32 cm and 4.1 cm respectively. Also, the cranial index was 55.55. In addition, the distances from the root of premolar tooth to infra orbital canal and from the latter to the root of the canine tooth were 0.94 cm and 2.3 cm, respectively. The length and height of the mandibles of the adult cats were 8.3 cm and 3.7 cm, respectively. Furthermore, the distances from the lateral alveolar root to mental foramen and from the mental foramen to caudal mandibular border were 1.4 cm and 6.9 cm, respectively. In the current work, the distances from mandibular foramen to the base of mandible as well as from caudal border of mandible to below of the mandibular foramen were 0.8 cm and 1.04 cm, respectively. Also, the distances from the base of mandible to condyloid fossa and from the latter to the maximum height of mandible were 3.07 cm and 0.76 cm, respectively. Finally, the distance from caudal border of mandible to mandibular foramen and from the latter to mandibular angle were 0.65 cm and 0.83 cm, respectively. These data as important landmarks are discussed with regard to their application to clinical maneuvers around the head of the Persian cats such as regional anesthesia during treating head injury and dental extraction.
Cramer Rao Lower Bound for Prior Subspace Estimation
Venue: Fourth IEEE Workshop on Sensor Array and Multichannel Processing, 2006.
Year: 2006

In the context of the localization of digital multi source, we can sometimes assume that we have some a priori knowledge of the location/direction of several sources. In that situation, some works have proposed to tacking into account of this knowledge to improve the localization of the unknown sources. These solutions are based on an orthogonal deflation of the signal subspace. In this paper, we derive the Cramer Rao lower bound for orthogonally deflated MIMO model and we show that the estimation schemes based on this model can help the estimation of the unknown DOA in some limit situations as for coherent or highly correlated sources but cannot totally cancel the influence of the known directions, in particular for uncorrelated sources with closely spaced DOA with finite number of sensors
Solution structure and assembly of b amylase 2 from Arabidopsis thaliana
Year: 2019

Starch is a key energy storage molecule in plants that requires controlled synthesis and breakdown for effective plant growth. b amylases (BAMs) hydrolyze starch into maltose to help meet the metabolic needs of the plant. In the model plant, Arabidopsis thaliana, there are nine BAMs which have apparently distinct functional and domain structures, although the functions of only a few of the BAMs are known and there are no 3 D structures of BAMs from this organism. Recently, AtBAM2 was proposed to form a tetramer based on chromatography and activity assays of mutants, however there was no direct observation of this tetramer. We collected small angle X ray scattering data on AtBAM2 and N terminal mutants to describe the structure and assembly of the tetramer. Comparison of the scattering of the AtBAM2 tetramer to data collected using the sweet potato (Ipomoea batatas) BAM5, which is also reported to form a tetramer, showed there were differences in the overall assembly. Analysis of N terminal truncations of AtBAM2 identified a loop sequence found only in BAM2 orthologs that appears to be critical for AtBAM2 tetramer assembly as well as activity.
Synthesis and biochemical evaluation of a range of (4 substituted phenyl)sulfonate derivatives of 4 hydroxybenzyl imidazole based compounds as potent inhibitors of 17alpha hydroxylase/17,20 lyase (P45017alpha) derived from rat testicular microsomes.
Venue: Bioorganic medicinal chemistry letters
Year: 2010

We report the synthesis, biochemical evaluation and rationalisation of the inhibitory activity of a range of (4 substituted phenyl)sulfonate derivatives of 4 hydroxybenzyl imidazole against the two components of 17alpha hydroxylase/17,20 lyase (P450(17alpha) namely, 17alpha hydroxylase (17alpha OHase) and 17,20 lyase (lyase) The results show the compounds to be highly potent inhibitors with limited selectivity towards the lyase component [e.g. toluene 4 sulfonic acid 4 imidazol 1 ylmethyl phenyl ester (4) possessed an IC(50) value of 40 nM against 17alpha OHase and 30 nM against lyase]
Doping control in sport: An investigation of how elite athletes perceive and trust the functioning of the doping testing system in their sport
Year: 2016

Doping testing is a key component enforced by anti doping authorities to detect and deter doping in sport. Policy is developed to protect athletes' right to participate in doping free sport; and testing is a key tool to secure this right. Accordingly, athletes' responses to anti doping efforts are important. This article explores how the International Standards for Testing, which face different interpretations and challenges when policy is implemented, are perceived by elite athletes. Particularly, this article aims to investigate how elite athletes perceive the functioning of the testing system (i.e. the efforts of stakeholders involved in testing) in their own sport both nationally and worldwide. Moreover, it seeks to identify whether specific factors such as previous experience of testing and perceived proximity of doping have an impact on athletes' perceptions of the testing system. The study comprises a web based questionnaire (N=645; response rate 43% and uses qualitative findings to elaborate on and explain quantitative results. Results showed that two thirds of the athletes reported the national testing programme in their sport to be appropriate. A majority of the athletes who had an opinion on the subject regarded testing programmes in some countries as not extensive enough or believed that in certain countries doping control was downgraded to win medals. Past experience of testing seemed to have a positive influence on trust in the concrete measures; however, if athletes experienced flaws during the control procedures, this could increase distrust and cause worry. The proximity of doping in an athlete's sport influenced the athlete's perception of the testing system. Particularly, athletes who need the testing system to be effective and to function well across the world show greater distrust of or dissatisfaction with the current testing system. The athletes' diverging views indicate that contemporary anti doping policy is simultaneously met with support, (dis)trust and frustration. By integrating the views and experiences of Danish elite athletes, this study confirms that the current testing system is confronted with obstacles, and it contributes knowledge about some of the challenges WADA faces when policy is implemented. Implications of results and recommendations for anti doping authorities are outlined in the paper.
Neuropilin 1 facilitates SARS CoV 2 cell entry and provides a possible pathway into the central nervous system
Year: 2020

The causative agent of the current pandemic and coronavirus disease 2019 (COVID 19) is the severe acute respiratory syndrome coronavirus 2 (SARS CoV 2)1. Understanding how SARS CoV 2 enters and spreads within human organs is crucial for developing strategies to prevent viral dissemination. For many viruses, tissue tropism is determined by the availability of virus receptors on the surface of host cells2. Both SARS CoV and SARS CoV 2 use angiotensin converting enzyme 2 (ACE2) as a host receptor, yet, their tropisms differ3 5. Here, we found that the cellular receptor neuropilin 1 (NRP1) known to bind furin cleaved substrates, significantly potentiates SARS CoV 2 infectivity, which was inhibited by a monoclonal blocking antibody against the extracellular b1b2 domain of NRP1. NRP1 is abundantly expressed in the respiratory and olfactory epithelium, with highest expression in endothelial cells and in the epithelial cells facing the nasal cavity. Neuropathological analysis of human COVID 19 autopsies revealed SARS CoV 2 infected NRP1 positive cells in the olfactory epithelium and bulb. In the olfactory bulb infection was detected particularly within NRP1 positive endothelial cells of small capillaries and medium sized vessels. Studies in mice demonstrated, after intranasal application, NRP1 mediated transport of virus sized particles into the central nervous system. Thus, NRP1 could explain the enhanced tropism and spreading of SARS CoV 2.
Enforced Planar FOX 7 like Molecules: A Strategy for Thermally Stable and Insensitive p Conjugated Energetic Materials.
Venue: Journal of the American Chemical Society
Year: 2020

Exploring new energetic derivatives of 1,1 diamino 2,2 dinitroethylene (FOX 7) is still a key aspect in the field of energetic materials. However, so far most of the attention has been focused on modification of FOX 7 via different reaction strategies. Now we report the design of three new FOX 7 like compounds (3 5) where one nitro group in FOX 7 is replaced by a nitrogen rich heterocyclic ring. Each of them is characterized by single crystal X ray crystallography. Electronic structures are studied through computational methods in comparison with FOX 7. In addition, the chemical reactivity of 3 was also investigated. Its hydroxylammonium (7) hydrazinium (8) and ammonium (9) salts were prepared and the nitrate product (10) was also isolated. Compound 10 has a C N bond length of 1.577 A that is one of the longest values found for the C NO2 bond. It was found that the incorporation of a tetrazole or triazole ring into the backbone of a conjugated nitroenamine does lead to a planar structure, which not only enhances the thermal stability but also improves the sensitivity of the product.
ANALYSIS, DESIGN AND DEVELOPMENT OF POINT OF SALES AND ACCOUNTING APPLICATION FOR RESTAURANT SMES
Year: 2014

The purpose of this study was to analyze all the information required to support the operations of two restaurants in Depok, West Java (Soto Ngawi and Nasi Pecel mba Ira) especially in the sales system, inventory records and accounting records. The results of the analysis then used to build Point of Sales (POS) and accounting applications for operational support and reduce the level of error that often occurs because of the manual transaction records. The research methodology used in designing this application begins with the collection and analysis of requirements (interviews, document examination) conceptual database design, logical database design, physical database design, DBMS selection, application development and implementation. Application development is funded by the government through a program of Science and Technology for Society/Ipteks bagi Masyarakat (IbM) by the DP2M Directorate General of Higher Education (Dikti) The result of this research is a Point of Sales (POS) and accounting application specifically for restaurants. The results of the application development have been evaluated with regard to integrity, security, concurrency and recovery.Conclusions from this research is by using this Point of Sales (POS) and accounting system, which is specifically developed for restaurant, the transaction at Nasi Soto Ngawi and Nasi Pecel mba Ira run easier, more effective and more efficient in recording in terms of time.  systems analysis, applications design, Point of Sales (POS) accounting
Kantian fractionalization predicts the conflict propensity of the international system
Venue: Proceedings of the National Academy of Sciences
Year: 2015

Many studies in international relations have investigated relationships between pairs of countries and the likelihood of conflict, yet none have connected the overall structure of the network of relationships between countries with the total level of international conflict. Here, we blaze a new path in the study of international conflict by introducing a measure of the overall fractionalization in the network of international relationships which we call Kantian fractionalization and demonstrating that this measure has been closely correlated with the number of new international conflicts in the following year. Moreover, we show that jointly democratic pairs of countries contribute negligibly to Kantian fractionalization, casting doubt on one of the most prominent concepts in international relations and policy prescriptions in Washington. Network science has spurred a reexamination of relational phenomena in political science, including the study of international conflict. We introduce a new direction to the study of conflict by showing that the multiplex fractionalization of the international system along three key dimensions is a powerful predictor of the propensity for violent interstate conflict. Even after controlling for well established conflict indicators, our new measure contributes more to model fit for interstate conflict than all of the previously established measures combined. Moreover, joint democracy plays little, if any, role in predicting system stability, thus challenging perhaps the major empirical finding of the international relations literature. Lastly, the temporal variability of our measure with conflict is consistent with a causal relationship. Our results have real world policy implications as changes in our fractionalization measure substantially aid the prediction of conflict up to 10 years into the future, allowing it to serve as an early warning sign of international instability.
Expression of FGFR3 during human testis development and in germ cell derived tumours of young adults.
Venue: The International journal of developmental biology
Year: 2013

Observations in patients with an activating mutation of fibroblast growth factor receptor 3 (FGFR3) suggest a role for FGFR3 signalling in promoting proliferation or survival of germ cells. In this study, we aimed to identify the FGFR3 subtype and the ontogeny of expression during human testis development and to ascertain whether FGFR3 signalling is linked to germ cell proliferation and the pathogenesis of testicular germ cell tumours (TGCTs) of young adult men. Using RT PCR, immunohistochemistry and Western blotting, we examined 58 specimens of human testes throughout development for FGFR3 expression, and then compared expression of FGFR3 with proliferation markers (PCNA or Ki67) We also analysed for FGFR3 expression 30 TGCTs and 28 testes containing the tumour precursor cell, carcinoma in situ (CIS) Fetal and adult testes expressed exclusively the FGFR3IIIc isoform. FGFR3 protein expression was restricted to the cytoplasm/plasma membrane of spermatogonia and was most prevalent at mid gestation, infancy and from puberty onwards. Phosphorylated (p)FGFR was detected in pre spermatogonia at mid gestation and in spermatogonia during puberty and in the adult testis. Throughout normal human testis development, expression of FGFR3 did not directly correlate with proliferation markers. In preinvasive CIS cells and in TGCTs, including classical seminoma and embryonal carcinoma, FGFR3IIIc was detected only in a small number of cells, with a heterogeneous expression pattern. FGFR3 is an excellent marker for human pre /spermatogonia throughout development. Signalling through this receptor is likely associated with spermatogonial survival rather than proliferation. FGFR3 is not expressed in gonocytes and may not be essential to the aetiology of TGCTs stemming from CIS.
Experimental Research on Hysteretic Behaviors of Square Tubular T joint
Year: 2015

In order to study the failure modes and hysteretic behaviors of square tubular T joints, three specimens were made to conduct the cyclic loading test. The test stimulated the constrain condition with hinge connection of both ends of chord member, and the brace was subjected to axial cyclic loading. Based on the experiment, the specimen consisting of small geometry brace showed a good ductility compared with the big one, and the obvious plastic deformation occurred at the intersection between chord and brace member, finally the welding was failure. However, the specimen consisting large size brace appeared a large deformation on the side wall of chord member. In addition, due to the poor ductility of welding on the plates contained in chord member, the welding fracture on the intersection between upper flange and web plates leaded to test end for all the specimens.  Steel tube structure can be used in variety architectural appearance with large span  So, various references can be found related to steel tube structure.