Miracle-dz/UniFAR-FTUs huggingface dataset:
Estimating distances to tipping points from dryland ecosystem images

Resource-limited environments, such as drylands, can exhibit self-organized spatial patterns. Theory suggests that these patterns could be indicators of approaching tipping points towards ecosystem degradation. However, we still lack ways of estimating a distance to tipping points that is comparable across sites. Here, we present a model-driven approach to do just that in self-organized ecosystems based on images. After validating the approach on simulated data, we applied it to a global dryland dataset, placed sites along a vulnerability gradient and studied the drivers of the estimated distance to tipping points. Crossing this distance with the sites’ aridity projections made it possible to pinpoint the most fragile sites among those studied. Our approach paves the way for a general risk assessment method for spatially self-organized ecosystems.
Studying complex systems in silico A National Coordinated Initiative : ' White Paper '

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the archived peer-reviewed author-version of: Sustainable load of fibre delay line buffers

We discuss the sustainable load of fiber delay line buffers, defined as the load at which a system with infinite buffering capacity becomes unstable. Due to the particularities of fiber delay line buffers, namely their finite delay granularity, this sustainable load is generally less than 100%. We further show that the packet-size distribution has some impact too.
ODU Digital Commons ODU Digital Commons

Blockchain (BC), as an emerging technology, is revolutionizing Business Process Management (BPM) in multiple ways. The main adoption is to serve as a trusted infrastructure to guarantee the trust of collaborations among multiple partners in trustless environments. Especially, BC enables trust of information by using Distributed Ledger Technology (DLT). With the power of smart contracts, BC enforces the obligations of counterparties that transact in a business process (BP) by programming the contracts as transactions. This paper aims to study the state-of-the-art of BC technologies by (1) exploring its applications in BPM with the focus on how BC provides the trust of BPs in their lifecycles; (2) identifying the relations of BPM as the need and BC as the solution with the assessment towards BPM characteristics; (3) discussing the up-to-date progresses of critical BC in BPM; (4) identifying the challenges and research directions for future advancement in the domain. The main conclusions of our comprehensive review are (1) the study of adopting BC in BPM has attracted a great deal of attention that has been evidenced by a rapidly growing number of relevant articles. (2) The paradigms of BPM over Internet of Things (IoT) have been shifted from persistent to transient, from static to dynamic, and from centralized to decentralized, and new enabling technologies are highly demanded to fulﬁll some emerging functional requirements (FRs) at the stages of design, conﬁguration, diagnosis, and evaluation of BPs in their lifecycles. (3) BC has been intensively studied and proven as a promising solution to assure the trustiness for both of business processes and their executions in decentralized BPM. (4) Most of the reported BC applications are at their primary stages, future research efforts are needed to meet the technical challenges involved in interoperation, determination of trusted entities, conﬁrmation of time-sensitive execution, and support of irreversibility.
Effects of El-Niño, Indian Ocean Dipole and Madden-Julian Oscillation on Sea Surface Temperature and Rainfall Anomalies in Southeast Asia. Case Study: Biomass Burning Episode of 2015

Maritime Continent (MC) positions in between Asian and Australian summer monsoons zone. Its complex topography and shallow seas around it is a major challenge for the climate researchers to model and understand it. Monsoon in this area is affected by inter-scale ocean-atmospheric interactions like El-Niño Southern Oscillation (ENSO), Indian Ocean Dipole (IOD) and Madden-Julian Oscillation. Monsoon rainfall in MC (especially in Indonesia and Malaysia) profoundly exhibits its variability dependency on ocean-atmospheric phenomena in this region. This monsoon shift often introduces to dreadful events like biomass burning (BB) in Southeast Asia (SEA) which sometimes leads to severe trans-boundary haze pollution. In this study, the episode of BB in 2015 of SEA is highlighted and discussed. Observational satellite datasets are tested by performing simulations with numerical weather prediction (NWP) model using WRF-ARW (Advanced research WRF). Observed and model datasets are compared to study the sea surface temperature (SST) and precipitation (rainfall) anomalies influenced by ENSO, IOD and MJO. Correlations have been recognised which explains the delayed rainfall of regular monsoon in MC due to the influence of ENSO, IOD and MJO during 2015 BB episode, eventually leading to intensification of fire and severe haze.
GenRGenS: software for generating random genomic sequences and structures

SUMMARY GenRGenS is a software tool dedicated to randomly generating genomic sequences and structures. It handles several classes of models useful for sequence analysis, such as Markov chains, hidden Markov models, weighted context-free grammars, regular expressions and PROSITE expressions. GenRGenS is the only program that can handle weighted context-free grammars, thus allowing the user to model and to generate structured objects (such as RNA secondary structures) of any given desired size. GenRGenS also allows the user to combine several of these different models at the same time.
Fast and accurate short read alignment with hybrid hash-tree data structure

Rapidly increasing amount of short read data generated by NGSs (new-generation sequencers) calls for the development of fast and accurate read alignment programs. The programs based on hash table (BLAST) and Burrows-Wheeler transform (bwa-mem) are used, and the latter is known to give superior performance. We here present a new algorithm, a hybrid of hash table and suffix tree, which we designed to speed up the alignment of short reads against large reference sequences such as human genome. The total turnaround time for processing one human genome sample (read depth of 30) is just 31 minutes with our system while that was more than 25 hours with bwa-mem/gatk. The time for aligner alone is 28 minutes for our system but around 2 hours for bwa-mem. Our new algorithm is 4.4 times faster than bwa-mem while achieving similar accuracy. Variant calling and other downstream analyses after the alignment can be done with open-source tools such as SAMtools and Genome Analysis Toolkit (gatk) packages, as well as our own fast variant caller, which is well parallelized and much faster than gatk.
Monitoring the explosive activity of the July–August 2001 eruption of Mt. Etna (Italy) by ash characterization

During the summer 2001 eruption of Mt. Etna, Italy, we developed a method for monitoring explosive activity through the study of airborne ash. The method is based on two routine and fast techniques for ash characterization: i) component analysis, that quantifies the proportion of juvenile particles, crystals, and non‐juvenile lithics in the ash; ii) Scanning Electron Microscope semi‐quantitative description of the morphology of ash particles. With these techniques we daily analyzed airborne ash from the eruption plume. Temporal evolution of particle shape and vesicularity, and of component proportion in the ash, documented initial crater excavation by hydromagmatic explosions, strong magmatic activity due to volatile exsolution, and final fragmentation of a cooling top of magma column. Favorable conditions of the studied eruption allowed validation of these results by comparison with other monitoring techniques. We also evaluate the applicability of the method to other cases, as well as its limits.
Veriflow: verifying network-wide invariants in real time

Networks are complex and prone to bugs. Existing tools that check configuration files and data-plane state operate offline at timescales of seconds to hours, and cannot detect or prevent bugs as they arise. Is it possible to check network-wide invariants in real time, as the network state evolves? The key challenge here is to achieve extremely low latency during the checks so that network performance is not affected. In this paper, we present a preliminary design, VeriFlow, which suggests that this goal is achievable. VeriFlow is a layer between a software-defined networking controller and network devices that checks for network-wide invariant violations dynamically as each forwarding rule is inserted. Based on an implementation using a Mininet OpenFlow network and Route Views trace data, we find that VeriFlow can perform rigorous checking within hundreds of microseconds per rule insertion.
Mining the Past: Data-Intensive Knowledge Discovery in the Study of Historical Textual Traditions

Text-heavy and unstructured data constitute the primary source materials for many historical reconstructions. In history and the history of religion, text analysis has typically been conducted by systematically selecting a small sample of texts and subjecting it to highly detailed reading and mental synthesis. But two interrelated technological developments have rendered a new data-intensive paradigm—one that can usefully supplement qualitative analysis—possible in the study of historical textual traditions. First, the availability of significant computing power has made it possible to run algorithms for automated text analysis on most personal computers. Second, the rapid increase in full text digital databases relevant to the study of religion has considerably reduced costs related to data acquisition and digitization. However, a limited understanding of the scope, advantages, and limitations of data-intensive methods, combined with an overly enthusiastic praise of big data by policy-makers and data scientists, have created real obstacles to the implementation of this paradigm in historical research. This is unfortunate, because history offers a rich and uncharted field for data-intensive knowledge discovery, and historians already have the much sought after and necessary domain expertise. In this article we seek to remove obstacles to the data intensive paradigm by presenting its methods and models for handling text-heavy data.
Coarse Sediment Transport in the Modern Martian Environment

The occurrence of regional and global dust storms, observations of migrating ripples and dunes, and the recognition of aeolian sandstone outcrops demonstrate that aeolian processes have been and continue to be a significant agent of surface modification on Mars. However, the mechanisms of aeolian transport within Mars' low atmospheric pressure surface environment are still not fully understood. This work presents a synthesis of change detection observations conducted with the Mars Science Laboratory Curiosity rover in Gale crater over three Martian years. Sediment mobility during this period was highly variable, consistent with previous orbiter‐based observations showing strong seasonal variability, with strongest winds expected during southern summer. Wind activity inferred at each change detection site helps test the accuracy of atmospheric models, as well as constrain the intensity of current atmosphere‐surface interactions and the physics of sand transport in the tenuous Martian atmosphere. Results indicate an apparent discrepancy between predicted wind speeds and the wind strengths required by classical incipient‐motion models to explain observed sediment motion. Observed mobilization of perched and/or isolated very coarse sand grains and fine pebbles (i.e., grain sizes 1 mm ≤d≤3 mm) likely requires an alternate explanation, such as very strong but infrequent wind gusts, drag‐induced rolling, or impact‐driven creep caused by smaller saltating particles.
New floristic records in the Balkans

New chorological data are presented for 181 species and subspecies from Bulgaria (72-88, 92, 93, 98-124, 139-144), Macedonia (89-91, 132-138), Greece (12-71, 94-97, 125-131, 145-181), and Turkey-in-Europe (1-11). The taxa belong to the following families: Aceraceae (146), Alismataceae (138), Alliaceae (88, 95), Amaranthaceae (12, 13, 68), Amaryllidaceae (52, 53, 181), Anacardiaceae (147, 148), Apiaceae (14, 15, 98, 115, 125, 126, 132, 133, 149), Apocynaceae (150), Aspleniaceae (145), Asteraceae (16-22, 72, 73, 103-108, 116118, 127, 134, 139-142, 151, 152), Balsaminaceae (109), Berberidaceae (110), Betulaceae (153), Boraginaceae (1, 23-25, 74, 154-156), Brassicaceae (26, 27, 69, 128, 157, 158), Callitrichaceae (75), Campanulaceae (119, 159), Caryophyllaceae (28, 76, 77, 135), Chenopodiaceae (29, 30), Cistaceae (160), Commelinaceae (111), Convolvulaceae (31), Crassulaceae (112), Cuscutaceae (78), Cyperaceae (102), Euphorbiaceae (32-35, 120, 161, 162), Fabaceae (2, 36-38, 79-80, 99, 121, 122, 129, 136, 163), Fagaceae (164), Fumariaceae (165), Gentianaceae (39), Gesneriaceae (100), Hyacinthaceae (54, 55, 130), Hypericaceae (166), Iridaceae (56-59, 96), Juncaceae (89, 124), Lamiaceae (3, 40, 167-170), Liliaceae s.l. (4, 90), Malvaceae (94), Oleaceae (171), Onagraceae (113), Orchidaceae (5-11, 60, 97), Phytolaccaceae (143), Pinaceae (114), Plantaginaceae (41, 137), Poaceae (61-67, 9193), Polygonaceae (42, 43, 81), Primulaceae (172), Ranunculaceae (44, 45, 82, 173, 174), Rhamnaceae (46, 70), Rosaceae (71, 83), Rubiaceae (84), Saxifragaceae (101), Scrophulariaceae s.l. (85, 86, 175, 176), Solanaceae (47, 48, 87, 144), Tamaricaceae (49), Thymelaeaceae (123, 131), Urticaceae (177), Valerianaceae (50), Veronicaceae (51, 178, 179), and Vitaceae (180). A new species for science is: Verbascum corinthiacum (176). New species for the countries are: Bulgaria – Cosmos bipinnatus (105), Oenothera speciosa (113), Physalis philadelphica (144), Sedum sarmentosum (112), Tagetes patula (108); Macedonia – Wulfenia carinthiaca (137). The publication includes contributions by: M. Aybeke (1-11), R.M. Burton & Kit Tan (12-67), C. Cattaneo & M. Grano (68-71), D. Dimitrov & V. Vutov (72-93), K. Giannopoulos, Kit Tan & G. Vold (94-97), Y. Marinov & S. Stoyanov (98-102), A. Petrova (103-113), A. Petrova & S. Dalakchieva (114-124), K. Polymenakos & Kit Tan (125-130), Kit Tan (131), A. Teofilovski (132-138), V. Vladimirov & A. Tashev (139-144), G. Zarkos, V. Christodoulou, Kit Tan & G. Vold (145-181). This is an ongoing report in the series dealing with the new chorological data on vascular plants in the Balkans. For details on the presentation of information see Phytologia Balcanica, vol. 12(1), pp. 107-108 and vol. 12(2), p. 279. *Reports for Bulgaria have been reviewed by V. Vladimirov, for Greece by Kit Tan, for Macedonia by V. Matevski, and for Turkey-inEurope by M. Aybeke. 414 Vladimirov, V. & al. • New floristic records in the Balkans: 34
Clustering Genetic Algorithm

In this paper we present and study a clustering technique based on genetic algorithms Clustering Genetic Algorithm. Performance of the algorithm is demonstrated on experiments. We have shown that it outperforms the k-means algorithm on some tasks. In addition, it is capable of optimising the number of clusters for tasks with well formed and separated clusters.
Voxel-Based Morphometry

The human brain is in a state of constant change and adaptation. This may be driven either by normal developmental or aging processes or by the effects of learning, training, and new occurrences in daily life. In addition to these aforementioned changes, more systematic influences such as gender, disease, and genes affect the brain’s structure. Using magnetic resonance imaging, brain changes and differences can be measured noninvasively and in vivo, making them particularly interesting for both basic research and clinical research. The easiest way to assess brain changes (or group differences) is to measure whole-brain volume. However, assessing the volume of the entire brain is rather unspecific. So-called region-of-interest (ROI) analyses are more sensitive to local changes than are whole-brain assessments but are also subject to several limitations. For example, if one specific region is measured, other brain structures are ignored, and possible effects remain undetected elsewhere in the brain. Moreover, ROIs are usually created based on individual protocols and depend on raterspecific ‘judgment calls,’ thus requiring a clearly definable and unambiguous structure. For large parts of the brain, however, it may be difficult to precisely define (or identify) unambiguous boundaries. Finally, if an ROI is only partially different, this will lower the sensitivity to detect any effects in this region. This is where voxel-based morphometry (VBM) comes into play, as VBM allows for the examination of brain changes and/or group differences across the entire brain with a high regional specificity (i.e., voxel by voxel), without requiring the a priori definition of particular ROIs (Ashburner & Friston, 2000, 2001, 2007).
Unexpected similarity between HIV-1 reverse transcriptase and tumor necrosis factor revealed by binding site image processing

Rationalizing the identification of hidden similarities across the repertoire of druggable protein cavities remains a major hurdle to a true proteome-wide structure-based discovery of novel drug candidates. We recently described a new computational approach (ProCare), inspired by numerical image processing, to identify local similarities in fragment-based subpockets. During the validation of the method, we unexpectedly identified a possible similarity in the binding pockets of two unrelated targets, human tumor necrosis factor alpha (TNF-α) and HIV-1 reverse transcriptase (HIV-1 RT). Microscale thermophoresis experiments confirmed the ProCare prediction as two of the three tested and FDA-approved HIV-1 RT inhibitors indeed bind to soluble human TNF-α trimer. Interestingly, the herein disclosed similarity could be revealed neither by state-of-the-art binding sites comparison methods nor by ligand-based pairwise similarity searches, suggesting that the point cloud registration approach implemented in ProCare, is uniquely suited to identify local and unobvious similarities among totally unrelated targets. AUTHOR SUMMARY Computational comparison of binding sites in proteins can provide insights on potential unrelated proteins that may bind to similar ligands. However, accurate prediction of binding site similarity requires powerful methods, ideally able to detect even local similarities. We herewith applied a recently developed computer vision method to identify an unexpected binding site similarity between two totally unrelated proteins that was confirmed experimentally by in vitro biophysical binding assays. Considering more precisely local similarities can therefore efficiently guide drug discovery, notably to repurpose existing drug candidates.
Hierarchies in classes of program schemesArgimiro

We begin by proving that the class of problems accepted by the program schemes of NPS is exactly the class of problems deened by the sentences of transitive closure logic (program schemes of NPS are obtained by generalizing basic non-deterministic while-programs whose tests within while instructions are quantiier-free rst-order formulae). We then show that our program schemes form a proper innnite hierarchy within NPS whose analogy in transitive closure logic is a proper innnite hierarchy, the union of which is full transitive closure logic but for which every level of the hierarchy has associated with it a rst-order deenable problem not in that level. We then proceed to add a stack to our program schemes, so obtaining the class of program schemes NPSS, and characterize the class of problems accepted by the program schemes of NPSS as the class of problems deened by the sentences of path system logic. We show that there is a proper innnite hierarchy within NPSS, with an analogous hierarchy within path system logic (again, such that every level of the hierarchy has associated with it a rst-order deenable problem not in that level). Like the hierarchies in transitive closure logic and NPS, the hierarchies in path system logic and NPSS are all proper even when we consider only problems involving undirected trees or problems involving out-trees. One aspect of our analysis that we believe to be particularly interesting is that we do not use Ehrenfeucht-Fra ss e games for our inexpressibility results, as is usually the case in nite model theory, but we simply consider computations of program schemes on certain nite structures.
Frontiers in Computational Neuroscience

hand, the temporal convolution models summation of postsynap-tic potentials over time together with axonal propagation delay. Note that even more general versions of neural fi eld equations contain a distribution of propagation velocities ρ(c), instead of a fi xed velocity c. Accordingly, they involve a third integration over dc at the r.h. s. of the neural fi eld equation (Nunez, 1995; Hutt and Atay, 2006). Hutt and Atay (2006) were able to demonstrate that the variance of the velocity distribution affects the frequency of bifur-cating periodic solutions and the phase speed of travelling waves. More interestingly, they discovered that the introduction of velocity distributions lead to the maximization of travelling front speed. Equation 1 can be substantially simplifi ed by assuming spatial homogeneity of time constants, τ(x) = τ, infi nite signal propagation c = ∞ and instantaneous postsynaptic processing, G(t) = δ(t). As a result, one obtains the Amari equation (Amari, 1977) with inhomogeneous kernel in the form ∫ u x t t u x t w x y f u y t dy x D t D () () () (()) 0 (2) where the nonlinear activation function f is given as f z e z η β β η , () () = + − − 1 1 (3) with constants gain β > 0, and threshold η ∈ R. The Amari equation characterizes a simple neural fi eld theory and serves as a basic model to discuss and implement neural fi eld architectures and neural fi eld phenomena. We shall restrict our attention to basic important phenomena here.