Miracle-dz/UniFAR-FTUs huggingface dataset:
Delayed accumulation of plagioclase in the Bushveld Complex

Abstract The Upper Critical Zone of the Bushveld Complex consists of several cyclic units, each ranging from ultramafic to leucocratic. One view is that they were initiated by addition of, and crystallization from, relatively magnesian magma. Experimental studies on plausible parental magma compositions to this sequence show that plagioclase joins orthopyroxene in the crystallization sequence once the Mg# of the orthopyroxene has decreased below 83. Some norites from the Upper Critical Zone contain orthopyroxene with this Mg#, supporting the validity of the experimental studies. There are no orthopyroxene compositions with higher Mg# than 83 in the entire Upper Critical Zone in either the eastern or western limbs of the Bushveld Complex. This observation suggests that all these rocks formed from plagioclase-saturated magmas. If this interpretation is correct, pyroxenites in this succession are not the result of crystallization from a magnesian magma. Instead, they result from the mechanical separation of plagioclase and orthopyroxene, probably due to crystal sorting during settling, from a magma lying at the cotectic for these two minerals. Rocks exist in the Upper Critical Zone that contain non-cotectic proportions of cumulus plagioclase and orthopyroxene, again supporting models of crystal sorting during settling. In such a model, anorthosites result from the delayed accumulation of plagioclase relative to pyroxene, andnot to formation from a magma saturated only in plagioclase. When traced from northwest to southeast in the western limb, there is a change in the relative proportions of plagioclase to orthopyroxene in the Upper Group 2 chromitite cyclic unit. In the northwest the unit is dominated by ultramafic rocks. In the southeast the plagioclase to pyroxene ratio exceeds that of the cotectic proportion, relations that may result from the lateral transport of suspended plagioclase grains to the southeast.
FAst and Scalable Software Execution on Multicores/ Adam, Morrison

This dissertation addresses three major challenges in designing high-performance concurrent software for modern multicore processors: realizing the potential parallelism of the problem, efficiently dealing with synchronization tasks, and overcoming system-level bottlenecks. Realizing parallelism Obtaining a scalable solution – in which performance improves as close as possible to linearly with the number of threads – can be difficult even for an inherently parallel problem. We demonstrate this using the rendezvous problem, in which threads of two types, consumers and producers, show up and need to be matched each with a unique thread of the other type. The parallel nature of rendezvousing allows each thread to look for a match independently of the other threads. Yet existing algorithms often waste work by attempting to match threads of the same type and by allowing a thread to idly wait until another thread attempts to match with it. We describe an efficient rendezvousing system which avoids these problems, so that every execution cycle goes towards making a successful match, leading to a significant performance improvement. Based on our rendezvousing system, we also construct a highly scalable and competitive concurrent stack implementation (Chapter 4). Efficient synchronization Two notorious synchronization-related performance penalties in concurrent programs are due to accessing a contended memory location (thereby serializing memory operations of threads) and issuing a memory fence (thus stalling the execution of a thread). We show that detailed understanding of the hardware mechanisms causing these penalties reveals opportunities to reduce or eliminate the penalty. First, we find that on modern multicores performing one access to a contended location is relatively fast; contention-related performance meltdowns only occur when an algorithm repeatedly performs contended accesses. Based on this observation, we construct a high performance nonblocking concurrent FIFO queue in which one (contended) fetch-and-add operation is used to spread threads among items in the queue, allowing them to enqueue and de-
Overview of topographic effects based on experimental observations: meaning, causes and possible interpretations

Marco Massa,1 Simone Barani2,3 and Sara Lovati1 1Istituto Nazionale di Geofisica e Vulcanologia, Sezione Milano-Pavia, via Bassini 15, 20133 Milano, Italy. E-mail: marco.massa@mi.ingv. it 2Dipartimento di Scienze della Terra, dell’Ambiente e della Vita, Università di Genova, Viale Benedetto XV, 5, 16132 Genova, Italy 3GEAmb S.r. l. (Academic spin-off company), piazza Martinez 6/4, 16143 Genova, Italy
[WORKSHOP] Radical Alternate Futurescoping: Solarpunk versus Grimdark

While designing social and political futures through an ’eco’ lens is becoming more popular with movements like solarpunk in the media, there are fewer studies of their use and potential in critical games for climate change education, communication and engagement. In this workshop, we plan to bring together people with diverse backgrounds to collaborate and co-create mock-ups of play experiences following solarpunk and grimdark themes. Solarpunk and grimdark are two extreme ends of the spectrum of alternate climate futures. While solarpunk presents a hopeful technological utopia, grimdark uses a more nihilistic setting. The workshop will take its participants through a series of exercises enabling a critical, rebellious and radical approach to their design processes and conclude with a critical reflection session. We believe that it will be a novel opportunity to explore and investigate the potential of playful and rebellious eco-envisioning or ’ecopunk’, artefacts in terms of their aesthetics, rhetoric and emotions as they get created side by side.
Deep-Feature-Based Visual Odometry for Autonomous Emergency Parking

The task of automatic parking is to manoeuvre the vehicle from its current position to an identified goal position. In order to achieve this accurately, the vehicle needs to track its position continuously with respect to the parking spot. Most existing systems rely on wheel odometry, IMU, or structured environments to accomplish the tracking, which may be unreliable or difficult to generalize. In this paper, we propose a tracking method that combines the strengths of a deep learning based feature extractor and classical geometric visual odometry methods. We show that the performance of R2D2, a recently-proposed deep-learning-based feature extractor, is consistently superior to traditional feature extractors (such as SIFT, SURF, and ORB), and the proposed approach provides a viable alternative for autonomous emergency parking.
High performance deep packet inspection

Deep packet inspection (DPI) is a form of network packet filtering that can search the packet’s content and locate the presence of certain patterns. These include headers and data-protocol structures as well as the payload of the message. It enables advanced network management, user service, and security functions as well as Internet data mining, eavesdropping, and censorship. It is currently being used by enterprises, service providers, and governments in a wide range of applications. DPI may be implemented by a wide range of pattern matching algorithms. The general problem of pattern matching is considered fundamental in computer science and has been researched thoroughly over the last decades. Still, when applied to the network domain of recent years, the traditional algorithms fail to face current challenges. The first challenge is the continual increase in Internet traffic rates, which requires a scalable design in terms of speed and memory usage. The second challenge arises from the increase in Web traffic compression due to the increasing popularity of Web surfing over mobile devices. The security device is forced to decompress this traffic prior to inspection, leading in turn to processing and space penalties. The third challenge is due to the requirement for a solution that is resilient to attacks that overload the security device. We address these challenges here. Moreover, we apply several technological advances to boost the performance of the traditional algorithms, including, for example, the presence of Ternary Content Addressable Memory (TCAM) elements in network devices and the availability of multi-core platforms for the DPI task. The work presented in this thesis focuses on DPI algorithms and techniques that relate to network security elements. In Chapter 3, we provide an algorithm for a scalable design of a DPI engine. Our design reduces the problem of pattern matching to the well-studied problem of Longest Prefix Match (LPM), which can be solved either in TCAM, in IP-lookup chips, or in software. Next we deal with the challenge of DPI over compressed traffic. Chapters 4 and 5 focus on reducing the space and time penalties resulting from the compressed traffic. These works show that, by using the meta-data generated during the compression stage, pattern matching over compressed traffic can be accelerated significantly as compared to traditional pattern matching over non-compressed traffic, and that the space penalty can be reduced by a factor of six as compared to current designs. Chapter 6 introduces an algorithm for scanning traffic compressed by SDCH compression, which is the compression scheme used by Google. Our design gains a performance boost of over 40%. Finally, we address the challenge of performing DPI when the system is under denialof-service via algorithmic complexity attacks. We provide a system design that takes advantage of commercial multi-core platforms to efficiently mitigate complexity attacks of varying intensity. The algorithms and techniques presented in this thesis provide a suitable DPI solution that confronts today’s network challenges.
Algorithms for optimization problems on networks and graphs

There is substantial literature dealing with online and approximation algorithms for network problems. In this work we study various optimization problems, focusing on admission control, approximate counting of small subgraphs within large graphs, the minimum dominating set problem, and the prize collecting generalized Steiner forest problem. We first address in Chapter 1 the admission control problem in general networks. Communication requests arrive over time, and the online algorithm accepts or rejects each request while maintaining the capacity limitations of the network. We consider preemptive online algorithms whose goal is to minimize the number of rejected requests. Each request arrives together with the path it should be routed on. We show an O(log(mc))-competitive randomized algorithm for the weighted case, where m is the number of edges in the graph and c is the maximum edge capacity. For the unweighted case, we give an O(log m log c)-competitive randomized algorithm. This settles an open question of Blum, Kalai and Kleinberg raised in [37]. The admission control problem is a generalization of the online set cover with repetitions problem, whose input is a family of m subsets of a ground set of n elements. Elements of the ground set are given to the online algorithm one by one, possibly requesting each element a multiple number of times. The algorithm must cover each element by different subsets, according to the number of times it has been requested. We give an O(log m log n)-competitive randomized algorithm for the online set cover with repetitions problem. This matches an Ω(log m log n) lower bound of Feige and Korman [74] for the competitive ratio of any randomized polynomial time algorithm, under the BPP 6= NP assumption.
Contributions to the complexity analysis of optimization algorithms

The main focus of this work is the introduction of a novel approach for the worst-case analysis of first-order methods. The approach is based on the observation that the worst-case performance of a given algorithm can be expressed as an optimization problem (which attempts to find the “worst-case input” to the algorithm), and that problem can be tackled using tools from the field of optimization. In Chapter 2, we focus on smooth and convex optimization problems, and show how to apply this approach on the gradient method, thereby achieving a new and tight complexity result for this algorithm. In addition, we show how to apply the approach on a wide family of algorithms, which includes the fast gradient method and the heavy ball method, and show that when an analytical solution to the resulting optimization problem is not available, it is possible to efficiently approximate its solution using numerical tools. Furthermore, we show how to numerically find the best algorithm in this class, and that it has an efficiency estimate that it two times better than the known bounds on fast gradient method. In Chapter 3, we further extend the aforementioned approach, and show how it can be used to find a new optimization method in the non-smooth case. We detail the construction of the algorithm and prove that it attains the optimal efficiency estimate on the class of Lipschitzcontinuous functions. Surprisingly, the resulting algorithm turns out to be very similar to Kelley’s cutting-plane method. In Chapter 4, we suggest a new method for solving structured saddle-point problems. The method is simple and possesses some technical advantages over existing methods, such as Nesterov’s smoothing technique. We present the method, establish its efficiency estimate and demonstrate its effectiveness on some practical problems. In addition, we demonstrate how to apply the technique introduced in the previous chapters in order to derive a numerical bound on the efficiency of this method. Finally, in Chapter 5, we consider a class non-convex quadratically constrained quadratic problems. By a refined examination on the problem structure, we derive an improved characterization on the situation where the convex semidefinite relaxation provides an exact solution. We demonstrate the usefulness of the results both in practice and in theory by several examples. Chapter
STANDARD UPLAND REVEGETATION SPECIFICATIONS FOR THE BUTTE PRIORITY SOILS OPERABLE UNIT SILVER BOW CREEK/BUTTE AREA SUPERFUND SITE BUTTE, MONTANA

This paper will describe the development and implementation of standards for the revegetation of lands disturbed by mining activities in Butte, Montana. The Butte area has served as a globally important mining, milling, and smelting district since the time gold was discovered in the area in 1864. Metal-sulfide deposits rich in copper and zinc were discovered a short time later and became the primary ores in Butte. Over a century of mining resulted in the development of more than 500 underground mines with roughly 3,000 miles of underground workings and numerous waste rock dumps. The operation of mines, mills, concentrators, and smelters generated a variety of waste materials containing elevated concentrations of arsenic, lead, and other metals. In the early 1980s, the Butte area was designated as a Superfund site by the U.S. Environmental Protection Agency (EPA). Land reclamation involving vegetated soil caps has been a vital component of cleanup actions taken to address mine-impacted lands within the largely urban area known as the Butte Priority Soils Operable Unit (BPSOU). Several parties, including EPA, the state abandoned mine lands bureau, the local county government, and members of the responsible party group, have implemented reclamation activities that include the use of vegetated soil caps placed over mining-related wastes. The results of early reclamation efforts were mixed, with both successes and failures. Successful reclamation using soil caps is a critical component of the long-term cleanup plan for the BPSOU. In the late 1990s, EPA, in conjunction with the responsible party group and other stakeholders, agreed upon a standard set of site-specific revegetation construction specifications for upland areas in the BPSOU to ensure consistency in the reclamation work. Criteria were established for pH testing of the subgrade, limestone application, cover soil quality and texture, organic amendment application, seed mixtures, fertilizer, mulch, and seed application. The specifications were derived from a variety of sources including existing abandoned mine reclamation specifications, previous reclamation practices established by EPA and by the local county government, and technical standards developed by the Reclamation Research Unit at Montana State University, as well as negotiation with the responsible party group and input from other stakeholders at the site. The specifications have strengths and weaknesses, but have served the site well in establishing the standards, expectations, and quality of revegetation work conducted at the BPSOU. Additional
Rapid activation of IL-2 receptor signaling by CD301b+ DC-derived IL-2 dictates the outcome of helper T cell differentiation

Effector T helper (Th) cell differentiation is fundamental to functional adaptive immunity. Different subsets of dendritic cells (DCs) preferentially induce different types of Th cells, but the fate instruction mechanism for Th type 2 (Th2) differentiation remains enigmatic, as the critical DC-derived cue has not been clearly identified. Here, we show that CD301b+ DCs, a major Th2-inducing DC subset, drive Th2 differentiation through cognate interaction by ‘kick-starting’ IL-2 receptor signaling in CD4T cells. Mechanistically, CD40 engagement induces IL-2 production selectively from CD301b+ DCs to maximize CD25 expression in CD4 T cells, which is required specifically for the Th2 fate decision. On the other hand, CD25 in CD301b+ DCs facilitates directed action of IL-2 toward cognate CD4T cells. Furthermore, CD301b+ DC-derived IL-2 skews CD4T cells away from the T follicular helper fate. These results highlight the critical role of DC-intrinsic CD40–IL-2 axis in bifurcation of Th cell fate.
Colloidal aggregation confounds cell-based Covid-19 antiviral screens

Colloidal aggregation is one of the largest contributors to false-positives in early drug discovery and chemical biology. Much work has focused on its impact on pure-protein screens; here we consider aggregations role in cell-based infectivity assays in Covid-19 drug repurposing. We began by investigating the potential aggregation of 41 drug candidates reported as SARs-CoV-2 entry inhibitors. Of these, 17 formed colloidal-particles by dynamic light scattering and exhibited detergent-dependent enzyme inhibition. To evaluate antiviral efficacy of the drugs in cells we used spike pseudotyped lentivirus and pre-saturation of the colloids with BSA. The antiviral potency of the aggregators was diminished by at least 10-fold and often entirely eliminated in the presence of BSA, suggesting antiviral activity can be attributed to the non-specific nature of the colloids. In confocal microscopy, the aggregates induced fluorescent puncta of labeled spike protein, consistent with sequestration of the protein on the colloidal particles. Addition of either non-ionic detergent or of BSA disrupted these puncta. These observations suggest that colloidal aggregation is common among cell-based anti-viral drug repurposing, and perhaps cell-based assays more broadly, and offers rapid counter-screens to detect and eliminate these artifacts, allowing the community invest resources in compounds with true potential as a Covid-19 therapeutic.
A Perturbation Approach for Refining Boolean Models of Cell Cycle Regulation

Considerable effort is required to build mathematical models of large protein regulatory networks. Utilizing computational algorithms that guide model development can significantly streamline the process and enhance the reliability of the resulting models. In this article we present a perturbation approach for developing data-centric Boolean models of cell cycle regulation. We assign a score to a network based on the steady states of the network-dynamics, and the dynamical trajectories corresponding to the initial conditions. Then, perturbation analysis is used to find new networks with lower scores, in which dynamical trajectories traverse through the correct cell cycle path with high frequency. We apply this method to refine Boolean models of cell cycle regulation in budding yeast and mammalian cells.
Reproductive character displacement explains strengthening of mechanical barriers in damselflies

Reinforcing natural selection against maladaptive hybrids can favor the strengthening of premating reproductive isolation driving a pattern of Reproductive Character Displacement (RCD). In a recent study conducted in North-West (NW) (older) Spanish hybrid zone, was detected an asymmetric reinforcement of the mechanical isolation in the reciprocal cross direction between I. graellsii males and I. elegans females. Furthermore, in the North-Central and Mediterranean (NCM) (younger) hybrid zone was also detected a similar strengthening of the mechanical isolation, consistent with a pattern of asymmetric reinforcement in this hybrid zone as well. In this study, we did geometric morphometrics analyses, shape, and Centroid Size (CS), on male and female secondary sexual traits to investigate whether reinforcement has generated a pattern of RCD of these traits in both hybrid zones. We detected, in the NW hybrid zone, unidirectional RCD (CS) of the male caudal appendages of I. graellsii, and bidirectional RCD (shape) of the female prothorax. Consistently with the prediction that the signal of reinforcement may diminish rapidly once reinforcement ceases to operate, a stronger signal of RCD was detected in the NCM than in the NW hybrid region. In this region, was detected unidirectional RCD (CS) of the male caudal appendages which was consistent with the lock-and-key mechanism of genital coevolution, as well as RCD (shape) of the female prothorax of I. elegans. Interestingly, our study highlights the importance of using geometric morphometrics to deal with the complexity of reproductive structures and controlling for environmental and geographic factors to investigate RCD.
Nuclear eDNA Metabarcoding Primers for Anthozoan Coral Biodiversity Assessment

The distributions of anthozoan corals are under-characterized due to their wide bathymetric range, occurrences in remote locales, and difficulties of identification from morphology alone. Environmental DNA (eDNA) sequencing promises to be a non-invasive strategy to complement conventional approaches for mapping and monitoring coral communities. Primers for eDNA meta-barcoding have been designed to amplify nuclear and mitochondrial DNA barcodes in shallow scleractinians and mitochondrial MutS in deep-sea octocorals. However, a comprehensive method for eDNA meta-barcoding from all anthozoan corals, including black corals, has not been developed. We leveraged a sequence database of global coral collections, from shallow water to the deep sea, to design new PCR primers for coral eDNA sequencing that target the 28S rRNA gene. We tested the performance of these primers by amplifying and sequencing eDNA from water samples collected in the Gulf of Mexico near mesophotic and deep-sea corals that were also imaged, sampled, and sequenced. Sequencing libraries produced using the primers were highly enriched in coral eDNA, with up to 99.8% of the reads originating from corals. Further, the 28S barcode amplified using the primers distinguished coral genera. We recovered amplicon sequencing variants (ASVs) identical to DNA barcodes derived from Sanger sequencing and genome skimming of corals sampled at the same field sites. This new eDNA meta-barcoding strategy permits targeted eDNA sequencing of black corals, octocorals, and scleractinians at sites where they co-occur and expands our current toolkit for mapping and monitoring coral communities in shallow coral reefs and the deep sea.