Miracle-dz/UniFAR-FTUs huggingface dataset:
Protein Constellations

In this project, I applied several well-known ideas developed in the computer vision field to problems in protein structure matching. Shape indexing and generalized Hough transforms are classical ideas and have been applied to protein structure matching before (eg, [1, 11, 14]). However, I am using a different representation of protein shape and different matching criteria, which yield results that seem promising. In the shape indexing (or geometric hashing) paradigm, a database of proteins is split into small, overlapping segments (“snippets”), and the local geometry of each snippet is described as a vector of real values. In the generalized Hough transform phase, we take a query protein, apply the same transformation to it, and search for snippets with similar local geometry descriptors. Each descriptor that is within a given tolerance is a vote for a match between a snippet from the query protein and a snippet from the database. By accumulating votes, we arrive at a ranking of matching database proteins. In this work, I extend these ideas by adding relevance-weighted matching and by building global alignments from chains of local matches. I also make the observation that the database of snippets is a valuable source of statistical information about protein structures. By searching for snippets that have a large number of neighbours, I produce a library of structural motifs that is nearly as good as other published libraries which are produced by more complex processes.
Do Gene Variants Influencing Adult Adiposity Affect Birth Weight? A Population-Based Study of 24 Loci in 4,744 Danish Individuals

Background Several obesity risk alleles affecting adult adiposity have been identified by the recent wave of genome wide association studies. We aimed to examine the potential effect of these variants on fetal body composition by investigating the variants in relation to birth weight and ponderal index of the newborn. Methodology/Principal Findings Midwife records from the Danish State Archives provided information on mother's age, parity, as well as birth weight, birth length and prematurity of the newborn in 4,744 individuals of the population-based Inter99 study. Twenty-four risk alleles showing genome-wide associations with adult BMI and/or waist circumference were genotyped. None of the 24 risk variants tested showed an association with birth weight or ponderal index after correction for multiple testing. Birth weight was divided into three categories low (≤10th percentile), normal (10th–90th percentile) and high birth weight (≥90th percentile) to allow for non-linear associations. There was no difference in the number of risk alleles between the groups (p = 0.57). No interactions between each risk allele and birth weight in the prediction of adult BMI were observed. An obesity risk score was created by summing up risk alleles. The risk score did not associate with fetal body composition. Moreover there was no interaction between the risk score and birth weight/ponderal index in the prediction of adult BMI. Conclusion 24 common variants associated with adult adiposity did not affect or interact with birth weight among Danes suggesting that the effects of these variants predominantly arise in the post-natal life.
Recent advances in electron optics and electron microscopy

Electron optics was born in 1927, when Hans Busch showed that the elementary lens equation is applicable to electron image formation. Interest was soon awakened in France and a book on the subject by Louis de Broglie appeared in 1950. We draw attention to the highlights of electron optics and microscopy over the decades, with particular reference to aberra- tion correction, and to some little known French contributions to the story of the scanning electron microscope and to Fourier optics.
MODELING AND MEASUREMENT OF MACROSCOPIC FLOW FIELDS IN STRUCTURED PACKINGS

Corrugated structured packings feature strong preferential flow directions due to their structure of crossing triangular channels. This leads to good radial spreading but makes modelling a challenge. Detailed CFD calculations reflecting the exact packing structure are only feasible for small sections of packing. However, effects like large scale maldistribution and instabilities in the flow field can only be modelled, if the hydrodynamics of the entire column are taken into account. In the present study, the macroscopic flow field of an entire column is modelled and numerically calculated. The model is based on the elementary cell model by Mewes et al. (1999). It is extended to be used on anisotropic porous structures like corrugated structured packings in counter-current operation. For the elementary cell model, flow field variables (velocity, phase volume fraction, pressure, etc.) and packing properties (void fraction, pressure drop, momentum exerted on fluids, etc.) are averaged over the volume of a representative elementary cell. For the gas phase, measurements of the directional pressure drop are conducted and used to model the anisotropic gas flow resistance tensor. To model the liquid flow field, two liquid phases are modelled each representing laminar film flow along one preferential flow direction. The elementary cell model allows to determine the macroscopic flow field in columns of technical dimensions. In the present study, it is used to calculate the two-phase flow field under stationary, counter-current operating conditions below the loading point. The results are tested against X-ray radiographic measurements on a quasi two-dimensional segment of structured packing.
All International Politics is Local: The Diffusion of Conflict, Integration, and Democratization

How does regional interdependence influence the prospects for conflict, integration, and democratization? Some researchers look at the international system at large and disregard the enormous regional variations. Others take the concept of sovereignty literally and treat each nation-state as fully independent. Kristian Skrede Gleditsch looks at disparate zones in the international system to see how conflict, integration, and democracy have clustered over time and space. He argues that the most interesting aspects of international politics are regional rather than fully global or exclusively national. Differences in the local context of interaction influence states' international behavior as well as their domestic attributes. In All International Politics Is Local, Gleditsch clarifies that isolating the domestic processes within countries cannot account for the observed variation in distribution of political democracy over time and space, and that the likelihood of transitions is strongly related to changes in neighboring countries and the prior history of the regional context. Finally, he demonstrates how spatial and statistical techniques can be used to address regional interdependence among actors and its implications.
The Soluble N-Ethylmaleimide-Sensitive Factor Attached Protein Receptor Complex in Growth Cones: Molecular Aspects of the Axon Terminal Development

Soluble N-ethylmaleimide-sensitive factor attached protein (SNAP) receptor (SNARE) mechanisms are thought to be involved in two important processes in axonal growth cones: (1) membrane expansion for axonal growth and (2) vesicular membrane fusion for mature synaptic transmission. We investigated the localization and interactions among the proteins involved in SNARE complex formation in isolated growth cone particles (GCP) from forebrain. We demonstrated that the SNARE complex is present in GCPs morphologically without synaptic vesicles (SVs) and associated with growth cone vesicles. However, the apparently SV-free GCP was lacking in the regulatory mechanisms inhibiting SNARE complex formation proposed in SV fusion, i.e., the association of synaptotagmin with the SNARE complex, and vesicle-associated membrane protein (VAMP)-synaptophysin complex formation. The core components of the SNARE complex (syntaxin, SNAP-25, and VAMP) accumulated for several days before postnatal day 7, when SVs first appeared, and preceded the accumulation of marker proteins such as synaptophysin, SV2, and V-ATPase. Our present results suggest that the SNARE mechanism for vesicular transmitter release is not fully functional in growth cones before the appearance of SVs, but the SNARE mechanism is working for membrane expansion in growth cones, which supports our recent report. We concluded that the regulation of the SNARE complex in growth cones is different from that in mature presynaptic terminals and that this switching may be one of the key steps in development from the growth cone to the presynaptic terminal.
Identification of Early Zygotic Genes in the Yellow Fever Mosquito Aedes aegypti and Discovery of a Motif Involved in Early Zygotic Genome Activation

During early embryogenesis the zygotic genome is transcriptionally silent and all mRNAs present are of maternal origin. The maternal-zygotic transition marks the time over which embryogenesis changes its dependence from maternal RNAs to zygotically transcribed RNAs. Here we present the first systematic investigation of early zygotic genes (EZGs) in a mosquito species and focus on genes involved in the onset of transcription during 2–4 hr. We used transcriptome sequencing to identify the “pure” (without maternal expression) EZGs by analyzing transcripts from four embryonic time ranges of 0–2, 2–4, 4–8, and 8–12 hr, which includes the time of cellular blastoderm formation and up to the start of gastrulation. Blast of 16,789 annotated transcripts vs. the transcriptome reads revealed evidence for 63 (P<0.001) and 143 (P<0.05) nonmaternally derived transcripts having a significant increase in expression at 2–4 hr. One third of the 63 EZG transcripts do not have predicted introns compared to 10% of all Ae. aegypti genes. We have confirmed by RT-PCR that zygotic transcription starts as early as 2–3 hours. A degenerate motif VBRGGTA was found to be overrepresented in the upstream sequences of the identified EZGs using a motif identification software called SCOPE. We find evidence for homology between this motif and the TAGteam motif found in Drosophila that has been implicated in EZG activation. A 38 bp sequence in the proximal upstream sequence of a kinesin light chain EZG (KLC2.1) contains two copies of the mosquito motif. This sequence was shown to support EZG transcription by luciferase reporter assays performed on injected early embryos, and confers early zygotic activity to a heterologous promoter from a divergent mosquito species. The results of these studies are consistent with the model of early zygotic genome activation via transcriptional activators, similar to what has been found recently in Drosophila.
On Many-Task Big Data Processing : from GPUs to Clouds

Big data processing relies today on complex middleware stacks, comprised of high-level languages, programming models, execution engines, and storage engines. Among these, the execution engine is often built in-house, is tightly integrated or even monolithic, and makes coarse assumptions about the hardware. This limits how the future big data processing systems will be able to respond to technological advances and changes in user workloads. To advance the state-of-the-art, we propose a vision for an open big data execution engine. We identify four key requirements and design a modular, task-based architecture to address them. First, to address performance requirements, we envision the use of multi-layer parallelism, which enables the efficient use of heterogeneous platforms (from GPUs to clouds). Second, to address elasticity, we propose the use of online provisioning and allocation of cloud-based resources, which enables economically feasible processing of many big data tasks. Third, to address predictability, we define a performance envelope, which enables early decisions for selecting and sizing execution platforms. Fourth, we characterize the interaction between our execution engine architecture and the other layers, to enable the efficient operation of the entire big data processing stack. We further identify and analyze eleven challenges in realizing our vision. Ultimately, these challenges will inspire and motivate a new generation of execution engines for big data processing.
Alert Correlation through Results Tracing back to Reasons

IDS may result in many intrusion alerts. A general approach for solving this problem is to do some correlation analysis with these alerts and build attack scenario. Author presents a method for alert correlation through results tracing back to reasons. According to hacker attacks linked to a certain sequence characteristics, we correlate the alerts through results tracing back to reasons and gain the correlated alerts. This method can found internal relations of invasion, to accurately identify intrusion targets. Through succeed attacks to match the previous attacks, we can greatly reduce the volume of data, and improve speed and efficiency for correlation analysis.
Stochastic Packet Inspection for TCP Traffic

In this paper, we extend the concept of Stochastic Packet Inspection (SPI) to support TCP traffic classification. SPI is a method based on the statistical fingerprint of the application-layer headers: by characterizing the frequencies of observed symbols, SPI can identify application protocol formats by automatically recognizing group of bits that take e.g., constant values, or random values, or are part of a counter. To correctly characterize symbol frequencies, SPI needs volumes of traffic to obtain statistically significant signatures. Earlier proposed for UDP traffic, SPI has to be modified to cope with the connection oriented service offered by TCP, in which application-layer headers are only found at the beginning of a TCP connection. In this paper, we extend SPI to support TCP traffic, and analyze its performance on real network data. The key idea is to move the classification target from single flows to endpoints, which aggregates all traffic sent/received by the same IP address and TCP port pair. The first few packets of flows sent from (or destined to) the same endpoint are then aggregated to yield a single SPI signature. Results show that SPI is able to achieve remarkably good results, with an average true positive rate of about 98%.
A discrete artificial bee colony algorithm for resource-constrained project scheduling problem

In this paper, we present a new meta-heuristic based on the performance of the artificial bee colony (ABC) for solving the resource-constrained project scheduling problem (RCPSP). The proposed algorithm iteratively solves the RCPSP by utilizing different types of honey bees on three main steps: initialization, update, and termination. The initial population is obtained through randomization and with respect to precedence constraints. Serial schedule generation scheme is applied to generate a feasible solution. Adaptive mechanism and local search approach, based on discrete insert and swap operators, are used for neighborhood search. The performance of the newly method is compared against a set of state-of-art algorithms. Simulation results demonstrate that the algorithm provides an efficient approach for solving RCPSP.
Multiple Target Localisation Using Time of Arrival Information From Multistatic Radar

Time-of-arrival localisation is a technique common to a variety of sensors and scenarios, including multistatic radar. In this paper a single target localisation algorithm is presented that meets the Cramer-Rao lower bound. The issues that arise when there are multiple targets are discussed and an algorithm is introduced that successfully performs multiple target localisation. This algorithm uses only one set of measurements but is shown to be robust to significant levels of noise.
Test Slice Difference Technique for Low-Transition Test Data Compression

This paper presents a low power strategy for test data compression and a new decompression scheme for test vectors. In our method, we propose an efficient algorithm for scan chain reordering to deal with the power dissipation problem. Further, we also propose a test slice difference (TSD) technique to improve test data compression. It is an efficient method and only needs one extra scan cell. In experimental results, the scheme that we presented achieve high compression ratio. The power consumption is also better compared with other well-known compression techniques.
Implementation of a simple 8-bit microprocessor with reversible energy recovery logic

We describe a simple 8-bit adiabatic microprocessor implemented with nMOS reversible energy recovery logic (nRERL) [1]. The implemented adiabatic microprocessor supports only a subset of the DLX instruction set architecture [15] in order to be fitted into a limited silicon area, and is integrated with an energy-efficient 6-phase clocked power generator (CPG). Phase scheduling was employed to reduce the number of the buffers required in the adiabatic microprocessor. Furthermore, reversibility breaking with self-energy recovery circuits (SERCs) was also employed to reduce energy consumption as well as circuit complexity by. The 8-bit microprocessor core and its on-chip 6-phase CPG were implemented in 0.18-mm CMOS technology. The former and the latter occupied 2.62 x 2.03 mm2 and 1.0 x 0.6 mm2, respectively. From the measurements, we have found that its minimum power consumption is 7. 5μW at Vdd =1.8V and f=880kHz
Adaptive mechanisms and genomic plasticity for drought tolerance identified in European black poplar (Populus nigra L.)

Summer droughts are likely to increase in frequency and intensity across Europe, yet long-lived trees may have a limited ability to tolerate drought. It is therefore critical that we improve our understanding of phenotypic plasticity to drought in natural populations for ecologically and economically important trees such as Populus nigra L. A common garden experiment was conducted using ∼500 wild P. nigra trees, collected from 11 river populations across Europe. Phenotypic variation was found across the collection, with southern genotypes from Spain and France characterized by small leaves and limited biomass production. To examine the relationship between phenotypic variation and drought tolerance, six genotypes with contrasting leaf morphologies were subjected to a water deficit experiment. ‘North eastern’ genotypes were collected at wet sites and responded to water deficit with reduced biomass growth, slow stomatal closure and reduced water use efficiency (WUE) assessed by Δ13C. In contrast, ‘southern’ genotypes originating from arid sites showed rapid stomatal closure, improved WUE and limited leaf loss. Transcriptome analyses of a genotype from Spain (Sp2, originating from an arid site) and another from northern Italy (Ita, originating from a wet site) revealed dramatic differences in gene expression response to water deficit. Transcripts controlling leaf development and stomatal patterning, including SPCH, ANT, ER, AS1, AS2, PHB, CLV1, ERL1–3 and TMM, were down-regulated in Ita but not in Sp2 in response to drought.
A Note on Singular Value Decomposition ∗

This note is intended to summarize the definition, properties, interpretation and applications of Singular Value Decomposition (SVD) described by Strang [? ], Shilov [? ], Johnson and Wichern [? ] and Will [? ]. 1 Definition Singular Value Decomposition (SVD) technique decomposes a m × n matrix A into the following factored form :
An EMG-driven musculoskeletal model for robot assisted stroke rehabilitation system using sliding mode control

Numerous researches have been carried out to use robot in the area of stroke rehabilitations. The conventional approach is to assist patient to perform Activities of Daily Living (ADL) through a set of pre-programmed trajectories. The main drawback lies in the lack of voluntary movement by the patient. Many of these works have been carried out by using positional feedback control. In this kind of system, it is difficult to assess patient's muscle condition, which may results in inconveniences due to torques or forces asserted by the rehabilitation robot. The main aim of the project is to build a stroke rehabilitation system using socially inspired robot technique. The system monitors patient's muscle activity and uses this information to drive an exoskeleton robot that will assist patient to his/her arm. Movement is generated based on voluntary muscle activity by patient and therefore will improve their learning curve. Another main advantage is the system minimizes patient's inconveniences due to movement by robot. The system is based on torque feedback control. A sliding mode control was implemented in replace of conventional control. The main advantage of sliding mode control over conventional control is its robustness. Sliding mode control does not require precise mathematical model of the system and it is insensitive to parametric changes and uncertainties within the system.
Errors in estimation of cost of capital in investment appraisal and their significance

In order to check out the significance of errors in the estimation of capital cost in investment appraisal, the simulation experiment has been presented in the paper. On the basis of the simulated development of the comparable firms, we have compared the end values of two simulated companies. Both companies encountered the same investment projects but they assess them differently – one firm with the proper cost of capital and the other with the cost of capital two times higher than it should use. The difference between the end value of such companies were not significant for firms which encounter many profitable investment projects (difference of only 3.3% in the company value after 25 years) and slightly higher for the companies which encounter more projects whose value is positive but is only slightly higher than zero (difference of 39.3% in the company value). Therefore, the significance of proper cost of capital estimation is more important for bigger firms in older economy segments which encounter lack of many highly profitable projects. This outcome is consistent with the pattern of use of advanced investment appraisal methods observed in the practice.
Social loafing and group evaluation.

Recent work (e.g., Harkins, 1987; Szymanski & Harkins, 1987) has suggested that social loafing occurs because participants' outputs cannot be evaluated by the experimenter, by the coactors, or by the participants themselves. This analysis has focused on the output of the individual, but in loafing research, participants work together to produce a group product. However, in this prior work participants have been unable to make anything of this group product, because no standard of comparison has been made available. Several recent formulations (e.g., Goethals & Darley, 1987) have suggested that the potential for group evaluation could motivate performance. Testing this hypothesis in 2 experiments, 1 using an optimizing task and the other a maximizing task, we found that providing a standard that allowed the "group" to evaluate its performance eliminated the loafing effect. The implications of these findings for current theories of group evaluation are discussed.
The Common Core Approach to the European Private Law

This paper discusses the aim, method, and organization of ‘The Common Core of European Private Law’ project, a scholarly initiative launched by the authors in 1994, and that at the moment this paper was written involved one hundred (and now more than two hundred) scholars, mostly from Europe and the United States. Part I describes both the immediate and the long-term goals of the Project. Part II discusses the methodological evolution that has taken place from Schlesinger's Cornell Project to the Common Core work, and tackles the main differences between the Common Core approach and other "integrative" projects taking place in Europe. Part III deals with the Project's framework, structure, and organization.