Miracle-dz/UniFAR-FTUs huggingface dataset:
A Dataflow System for Unreliable Computing Environments

This paper presents the design, implementation and evaluation of a dataflow system, including a dataflow programming model and a dataflow engine, for coarse-grained distributed data intensive applications. The dataflow programming model provides users with a transparent interface for application programming and execution management in a parallel and distributed computing environment. The dataflow engine dispatches the tasks onto candidate distributed computing resources in the system, and manages failures and load balancing problems in a transparent manner. The system has been implemented over . NET platform and deployed in a Windows Desktop Grid. This paper uses two benchmarks to demonstrate the scalability and fault tolerance properties of our system.
Testing the impact of environmental change on hunter‐gatherer settlement organization during the Upper Paleolithic in western Iberia

Recent cross‐disciplinary research in the Iberian Peninsula has revealed a synchronous pattern between rapid climate change and widespread cultural modifications during the Late Paleolithic. The beginning and development of each traditionally defined techno‐complex is thought to be associated with different environmental conditions. A main contrast is put on the impact of cold and arid conditions at the onset of the Last Glacial Maximum (LGM) and its coincidence with the development of blade/flake‐size projectiles and bifacial technologies, against the dominance of bladelet‐size backed points across more temperate and forested environments. Based on the long‐recognized assumption that lithic technology operates within the broader context of Pleistocene human ecodynamics, here we test the hypothesis that climate‐related lithic techno‐typological changes across the Upper Paleolithic are linked to modifications in land‐use patterns and settlement organization. We present statistical analysis comparing the Shannon–Weaver diversity index for retouched stone tool assemblages (used as proxy for site function) and locational parameters of a series of contexts from Central Portugal. The results show a trend of continuity and change between periods, with some of the most important deviations starting at the onset of the LGM, with the Heinrich Event 2 associated with patterns of technological diversification and biocultural expansion.
Proofreading of Peptide—MHC Complexes through Dynamic Multivalent Interactions

The adaptive immune system is able to detect and destroy cells that are malignantly transformed or infected by intracellular pathogens. Specific immune responses against these cells are elicited by antigenic peptides that are presented on major histocompatibility complex class I (MHC I) molecules and recognized by cytotoxic T lymphocytes at the cell surface. Since these MHC I-presented peptides are generated in the cytosol by proteasomal protein degradation, they can be metaphorically described as a window providing immune cells with insights into the state of the cellular proteome. A crucial element of MHC I antigen presentation is the peptide-loading complex (PLC), a multisubunit machinery, which contains as key constituents the transporter associated with antigen processing (TAP) and the MHC I-specific chaperone tapasin (Tsn). While TAP recognizes and shuttles the cytosolic antigenic peptides into the endoplasmic reticulum (ER), Tsn samples peptides in the ER for their ability to form stable complexes with MHC I, a process called peptide proofreading or peptide editing. Through its selection of peptides that improve MHC I stability, Tsn contributes to the hierarchy of immunodominant peptide epitopes. Despite the fact that it concerns a key event in adaptive immunity, insights into the catalytic mechanism of peptide proofreading carried out by Tsn have only lately been gained via biochemical, biophysical, and structural studies. Furthermore, a Tsn homolog called TAP-binding protein-related (TAPBPR) has only recently been demonstrated to function as a second MHC I-specific chaperone and peptide proofreader. Although TAPBPR is PLC-independent and has a distinct allomorph specificity, it is likely to share a common catalytic mechanism with Tsn. This review focuses on the current knowledge of the multivalent protein–protein interactions and the concomitant dynamic molecular processes underlying peptide-proofreading catalysis. We do not only derive a model that highlights the common mechanistic principles shared by the MHC I editors Tsn and TAPBPR, and the MHC II editor HLA-DM, but also illustrate the distinct quality control strategies employed by these chaperones to sample epitopes. Unraveling the mechanistic underpinnings of catalyzed peptide proofreading will be crucial for a thorough understanding of many aspects of immune recognition, from infection control and tumor immunity to autoimmune diseases and transplant rejection.
Performance and correctness of the ATM ABR rate control scheme

We study both the correctness and performance of the source/destination protocol of the available bit rate (ABR) service in asynchronous transfer mode (ATM) networks. Although the basic source/destination protocol for congestion management is relatively simple, the protocol specification has to cope with several "real-world" cases such as failures and delayed/lost feedback which may introduce complexity. Rigorous proofs of the correct functioning of the protocol based on a formal specification is necessary. We use a formal extended finite state machine (EFSM) model to show that the ABR source/destination protocol is free of live-locks, so that under all conditions both resource management (RM) and data cells will be transmitted. We also show that the network options of explicit forward congestion indication (EFCI) and explicit rate (ER) interoperate correctly. We use the understanding of the informal English description of the source/destination behavior and of our EFSM model to derive conditions that ensure that the source transmission rate is stable in the presence of delayed or lost feedback RM cells, especially under the operation of a source rule that requires the reduction of the source rate under these conditions. We arrive at bounds on the number of consecutive RM cell losses tolerated while the rate remains stable. We also provide a worst-case analysis of the delay in turning around RM cells at the destination station and the worst-case inter-departure time of forward RM cells from the source.
A pilot study of rapid benchtop sequencing of Staphylococcus aureus and Clostridium difficile for outbreak detection and surveillance

Objectives To investigate the prospects of newly available benchtop sequencers to provide rapid whole-genome data in routine clinical practice. Next-generation sequencing has the potential to resolve uncertainties surrounding the route and timing of person-to-person transmission of healthcare-associated infection, which has been a major impediment to optimal management. Design The authors used Illumina MiSeq benchtop sequencing to undertake case studies investigating potential outbreaks of methicillin-resistant Staphylococcus aureus (MRSA) and Clostridium difficile. Setting Isolates were obtained from potential outbreaks associated with three UK hospitals. Participants Isolates were sequenced from a cluster of eight MRSA carriers and an associated bacteraemia case in an intensive care unit, another MRSA cluster of six cases and two clusters of C difficile. Additionally, all C difficile isolates from cases over 6 weeks in a single hospital were rapidly sequenced and compared with local strain sequences obtained in the preceding 3 years. Main outcome measure Whole-genome genetic relatedness of the isolates within each epidemiological cluster. Results Twenty-six MRSA and 15 C difficile isolates were successfully sequenced and analysed within 5 days of culture. Both MRSA clusters were identified as outbreaks, with most sequences in each cluster indistinguishable and all within three single nucleotide variants (SNVs). Epidemiologically unrelated isolates of the same spa-type were genetically distinct (≥21 SNVs). In both C difficile clusters, closely epidemiologically linked cases (in one case sharing the same strain type) were shown to be genetically distinct (≥144 SNVs). A reconstruction applying rapid sequencing in C difficile surveillance provided early outbreak detection and identified previously undetected probable community transmission. Conclusions This benchtop sequencing technology is widely generalisable to human bacterial pathogens. The findings provide several good examples of how rapid and precise sequencing could transform identification of transmission of healthcare-associated infection and therefore improve hospital infection control and patient outcomes in routine clinical practice.
Temperature‐dependent gene silencing by an expressed inverted repeat in Drosophila

Summary: Posttranscriptional gene silencing (PTGS) induced by double‐stranded RNA (dsRNA) is an intriguing phenomenon that has been observed in a variety of organisms, including Drosophila melanogaster. Although PTGS in Drosophila is typically observed following direct injection of the dsRNA into embryos, it is theoretically possible that the in vivo transcription of an inverted repeat transgene might also produce a dsRNA “hairpin” that is capable of triggering PTGS. Here we test this idea, and show that an expressed inverted repeat of a portion of the sex differentiation gene, transformer‐2, (tra‐2), driven by a GAL4‐dependent promoter, does genetically repress the endogenous wild‐type tra‐2 function, producing a dominant loss‐of‐function mutant phenotype. Remarkably, this effect is temperature‐sensitive, with phenotypic consequences seen at 29°, but not at 22°. Moreover, by altering the dosage of either the transgenes or the endogenous tra2+ loci, one can vary the effect over a wide range of mutant phenotypes. genesis 26:240–244, 2000. © 2000 Wiley‐Liss, Inc.
Backpropagation without Multiplication

The back propagation algorithm has been modified to work without any multiplications and to tolerate computations with a low resolution, which makes it. more attractive for a hardware implementation. Numbers are represented in floating point format with 1 bit mantissa and 3 bits in the exponent for the states, and 1 bit mantissa and 5 bit exponent. for the gradients, while the weights are 16 bit fixed-point numbers. In this way, all the computations can be executed with shift and add operations. Large networks with over 100,000 weights were trained and demonstrated the same performance as networks computed with full precision. An estimate of a circuit implementation shows that a large network can be placed on a single chip, reaching more than 1 billion weight updates per second. A speedup is also obtained on any machine where a multiplication is slower than a shift operation.
A comparative study of PID, ANFIS and hybrid PID-ANFIS controllers for speed control of Brushless DC Motor drive

This paper presents a comparative study of various controllers for the speed control of Brushless Direct Current Motor (BLDCM) to improve a performance of control. The most commonly used controller for the speed control of BLDCM is Proportional Integral Derivative (PID) controller. However, the PID controller has advantages such as: a good response, the simple structure and robustness of method, but it has disadvantages such as: optimally tuning gains of PID have been quit difficult and it cannot adapt a non-linier state of plant. Further, ANFIS controller has the ability to automatically learn and adapt with a state of plant. A novel hybrid controller that combines the advantages of PID controller and ANFIS controller is desired to improve the response of plant. To model of BLDCM is used an identification system method. Simulation results are presented and analyzed for all the controllers. It is observed that hybrid PID-ANFIS based controllers give better responses than PID or ANFIS for the speed control of BLDCM drive.
Polarization-maintaining photonic-crystal-fiber-based all-optical polarimetric torsion sensor

An application of a polarization-maintaining photonic crystal fiber (PM-PCF) for torsion sensing is proposed and experimentally demonstrated. The response of the sensor is theoretically validated using the Jones matrix. High normalized sensitivity of ∼0.014/° was measured within a linear twist angle range from 30° to 70°. The sensor response was observed to be highly repeatable over a 90° twist in both the clockwise and counterclockwise directions. The proposed sensor exhibits reduced temperature sensitivity due to the low thermal coefficient of PM-PCF, making it an ideal candidate for torsion sensing.
Statistical mechanics of DNA-mediated colloidal aggregation.

We present a statistical mechanical model of aggregation in colloidal systems with DNA-mediated interactions. We obtain a general result for the two-particle binding energy in terms of the hybridization free energy DeltaG of DNA and two model-dependent properties: the average number of available DNA bridges and the effective DNA concentration c(eff). We calculate these parameters for a particular DNA bridging scheme. The fraction of all the n-mers, including the infinite aggregate, are shown to be universal functions of a single parameter directly related to the two-particle binding energy. We explicitly take into account the partial ergodicity of the problem resulting from the slow DNA binding-unbinding dynamics, and introduce the concept of angular localization of DNA linkers. In this way, we obtain a direct link between DNA thermodynamics and the global aggregation and melting properties in DNA-colloidal systems. The results of the theory are shown to be in quantitative agreement with two recent experiments with particles of micron and nanometer size.
Study of resolution for harmonic drives controller with friction in precision robotic system

The friction model with the effects of friction and transmission flexibility of harmonic drives system is used for resolution study in precision control system. First, the resolution of a linear controller and an impulse controller in robotic manipulator system are studied respectively, then friction effect on resolution of impulse control system is investigated. Simulation and experiments show that the resolution of impulse control is much better than that of linear control, the friction in harmonic drive degrades the performance of impulse control, this will benefit the use of harmonic drive in precision control system.
Simultaneous concentration and separation of proteins in a nanochannel.

Molecular separation technologies such as gel electrophoresis and liquid chromatography coupled with mass spectrometry detection have been the foundations of biomarker discovery. This is because medically significant biomarkers, for example in blood, can be as much as 10 fold less common than the most abundant protein, albumin and detecting these low abundance molecules requires high sensitivity and selective depletion of the dominant species. Conventional approaches including antibody depletion remove selected molecules by less than 3 orders of magnitude only. This prevents the isolation, characterization and discovery of millions of new proteins where key disease markers could be identified. Overcoming this barrier requires new approaches to analytical detection that minimize sample pre-processing steps while achieving high throughput with very high levels of sensitivity. Here we describe a new device that demonstrates simultaneous concentration and separation of proteins by conductivity gradient focusing without membranes, external pumps, temperature gradients or ampholytes. Concentration and separation take place in an electric field driven, 120-nm deep nanochannel, supporting a stable salt and conductivity gradient. Conductivity gradient focusing is one of many techniques that use opposing convective flow and electrophoretic forces to focus molecules to an equilibrium position. These methods include a step change in chromatographic packings, electrochromatorgraphy, varying the molecular charge (as in isoelectric focusing), temperature gradient focusing, varying the cross section through which the electric current flows, and varying the buffer conductivity. In contrast to all of these approaches, the device presented here does not require ampholytes, matrices or gels, membranes, temperature gradients, or an external pump. Electrokinetic phenomena at the nanoscale have recently been shown to produce rapid and high preconcentration of proteins and peptides in physiological buffers. In these reports nanochannels in microfluidic devices create gradients in the electric field by their charge selective transport characteristics. By combining this with a transport mechanism, often electro-osmosis, charged molecules can be trapped and accumulated owing to a balance in the viscous drag force and the electrophoretic force. The interaction of surface charges, mobile charges, and water molecules with each other and the electric field is complex but our understanding has been advanced by a number of excellent fundamental studies. Concentration polarization, as it is sometimes known, at the entrance to a nanochannel, gives rise to a gradient in the concentration of salt ions, which, in turn, perturbs the electric field creating a trap. Typically these traps cause sample stacking on the microchannel side of the microto nanochannel junction. In such cases the electric field gradient is very abrupt, causing all molecules to accumulate in a tightly confined region with limited scope for separation.
Sounding‐derived parameters associated with tornadic storms in Catalonia

Catalonia, a southern Europe coastal region in the western Mediterranean basin, is regularly affected by severe local storms which every year produce an average of 5 tornadoes and 12 waterspouts, based on data recorded from 2000 to 2016. Despite these tornadoes mostly being weak – not exceeding EF1 on the enhanced Fujita (EF) damage intensity scale – they occasionally reach stronger intensities, posing an evident threat to population and socio‐economic activity, particularly in densely populated coastal conurbations such as Tarragona or Barcelona. This study provides analysis of upper air conditions that favour the formation of tornadic storms in the region, considering five different stations in Spain and France to build a database of 333 soundings which included 49 tornadic soundings, 104 waterspout soundings (WAT) as well as non‐tornadic thunderstorms and dry period soundings. For each one, 12 different parameters were calculated and analysed to test their potential capacity to discriminate non‐tornadic from tornadic environments and also to assess the feasibility of stratifying tornado intensity (EF0, and EF1 or stronger, on the EF scale). The results indicate that storm‐relative helicity for the layer 0–3 km, with a threshold value of 150 m2 s−2, wind shear for the same layer, with a threshold of 15 m s−1, and composite parameters such as the supercell composite parameter with a threshold of 1.2 and universal tornadic index with a threshold of 0.3 are all useful to distinguish between non‐tornadic thunderstorms and EF1 or stronger tornadic events. These results contribute to a better description of the climatology of upper air conditions that favour tornadic storms in the region and can also help operational weather forecasting and surveillance tasks, thus increasing situational awareness in severe convective weather events.
1 EarlyWork on Similarity Search and k-Nearest Neighbors

In [1], Aha et al. introduced a framework and methodology for machine learning, which is instances-based learning. They defined a set of rules for nearest neighbor algorithms and extended them. These algorithms are still in use for knearest neighbor classifier, which is very much related with my topic “similarity search”. In [2], Galper et al. described the similarity search and proposed a dynamic programming approach to solve it. The importance for that paper is that it is the first parallel approach for solving similarity search problem in parallel setting. Callahan, in his early paper, presented an optimal parallel algorithm for pair decomposition of a point set in high dimensional spaces [3]. He showed a deterministic optimal algorithm which leads to finding k-nearest neighbors of each point in the dataset. Papadoupulos, proposed a parallel algorithm for processing nearest neighbor quesries using R-tress [4]. The settings are for multiprocessing approach with no data sharing, but activation of relevant windows in parallel using an R-tree. Berchtold [5] offered a new solution to k-nearest neighbor problem and proposed to pre-calculate the nearest neighbors instead of finding them on the fly. This solution can be seen as the approximating the solution space of kNN queries by pre-calculating. It is a sequential solution but some of the ideas in this paper was used by some other parallel kNN applications.
Jointly They Edit: Examining the Impact of Community Identification on Political Interaction in Wikipedia

Background In their 2005 study, Adamic and Glance coined the memorable phrase ‘divided they blog’, referring to a trend of cyberbalkanization in the political blogosphere, with liberal and conservative blogs tending to link to other blogs with a similar political slant, and not to one another. As political discussion and activity increasingly moves online, the power of framing political discourses is shifting from mass media to social media. Methodology/Principal Findings Continued examination of political interactions online is critical, and we extend this line of research by examining the activities of political users within the Wikipedia community. First, we examined how users in Wikipedia choose to display their political affiliation. Next, we analyzed the patterns of cross-party interaction and community participation among those users proclaiming a political affiliation. In contrast to previous analyses of other social media, we did not find strong trends indicating a preference to interact with members of the same political party within the Wikipedia community. Conclusions/Significance Our results indicate that users who proclaim their political affiliation within the community tend to proclaim their identity as a ‘Wikipedian’ even more loudly. It seems that the shared identity of ‘being Wikipedian’ may be strong enough to triumph over other potentially divisive facets of personal identity, such as political affiliation.