Miracle-dz/UniFAR-FTUs huggingface dataset:
P4LRU: Towards An LRU Cache Entirely in Programmable Data Plane

The data plane cache, a critical functionality found in numerous network devices, such as programmable switches, intelligent NICs, and DPUs, is often subject to limitations in its programmability and memory access capacity. As a result, the majority of existing data plane caches rely on simple and inefficient replacement policies. This paper is set to introduce LRU, a near-optimal replacement policy, into the programmable data plane. We first explore the reasons why the traditional implementation of LRU is not suitable for deployment on the data plane. Consequently, we propose P4LRU, a pipeline-optimized version of the LRU implementation. Building on P4LRU, we conceive three distinct in-network systems - LruTable, LruIndex, and LruMon, and successfully bring them to life on Tofino switches. Our thorough experimental trials establish that P4LRU provides a significant performance boost over existing data plane caches in these three systems. We have open-sourced the source codes for the three systems on GitHub [1].
Microevolutionary Hypothesis of the Obesity Epidemic

The obesity epidemic represents potentially the largest phenotypic change in Homo sapiens since the origin of the species. Despite obesity’s high heritability, a change in the gene pool has not generally been presumed as a potential cause of the obesity epidemic. Here we advance the hypothesis that a rapid change in the obesogenic gene pool has occurred second to the introduction of modern obstetrics dramatically altering evolutionary pressures on obesity - the microevolutionary hypothesis of the obesity epidemic. Obesity is known to increase childbirth related mortality several fold. Prior to modern obstetrics, childbirth related mortality occurred in over 10% of women. After modern obstetrics, this mortality reduced to a fraction of a percent, thereby lifting a strong negative selection pressure. Regression analysis of data for ∼ 190 countries was carried out to examine associations between 1990 maternal death rates (MDR) and current obesity rates. Multivariate regression showed MDR correlated more strongly with national obesity rates than GDP, calorie intake and physical inactivity. Analyses controlling for confounders via partial correlation show that MDR explains approximately 11% of the variability of obesity rate between nations. For nations with MDR above the median (>0.45%), MDR explains over 20% of obesity variance, while calorie intake, and physical inactivity show no association with obesity in these nations. The microevolutionary hypothesis offers a parsimonious explanation of the global nature of the obesity epidemic. Significance Statement Humans underwent a rapid increase in obesity in the 20th century, and existing explanations for this trend are unsatisfactory. Here we present evidence that increases in obesity may be in large part attributable to microevolutionary changes brought about by dramatic reduction of childbirth mortality with the introduction of modern obstetrics. Given the higher relative risk of childbirth in women with obesity, obstetrics removed a strong negative selection pressure against obesity. This alteration would result in a rapid population-wide rise in obesity-promoting alleles. A cross-country analysis of earlier maternal death rates and obesity rate today found strong evidence supporting this hypothesis. These findings suggest recent medical intervention influenced the course of human evolution more profoundly than previously realized.
XRON: A Hybrid Elastic Cloud Overlay Network for Video Conferencing at Planetary Scale

Quality and cost are two key considerations for video conferencing services. Service providers face a dilemma when selecting network tiers to build their infrastructure---relying on Internet links has poor quality, while using premium links brings excessive cost. We present XRON, a hybrid elastic cloud overlay network for our planetary-scale video conferencing service. XRON differs from prior overlays with two distinct features. First, XRON is hybrid, i.e., it leverages both Internet and premium links to simultaneously achieve high quality and low cost. Second, XRON is elastic, i.e., it exploits elastic cloud resources to adaptively scale its capacity based on realtime demand. The data plane of XRON combines active probing and passive tracking for scalable link state monitoring, uses asymmetric forwarding based on heterogeneous bidirectional link qualities, and quickly reacts to sudden link degradations without the control plane involvement. The control plane of XRON predicts video traffic based on application knowledge, and computes global forwarding paths and reaction plans with scalable algorithms. Large-scale deployment in DingTalk shows that XRON reduces video stall ratio and bad audio fluency by 77% and 65.2%, respectively, compared to using Internet links only, and reduces cost by 79%, compared to using premium links only.
Poster: Q-Scanner: A Fast Scanning Tool for Large-Scale SSL/TLS Configurations Measurement

Secure Sockets Layer (SSL) and Transport Layer Security (TLS) protocols are used to encrypt data, protect privacy, and authenticate. However, the security of SSL/TLS itself depends on its configurations. While some scanning tools are used to measure SSL/TLS configurations, their performance is far from meeting the requirement of large-scale measurements. In this paper, we propose a fast SSL/TLS configuration scanning tool, Q-Scanner, which can generate a lightweight scanning solution based on the characteristics of the configurations to be scanned. The experiment shows Q-Scanner achieves a speedup of over 30,000 times compared to SSL Pulse without loss of accuracy.
The geometry of photopolymerized topography influences neurite pathfinding by directing growth cone morphology and migration

Cochlear implants (CIs) provide auditory perception to those with profound sensorineural hearing loss: however, the quality of sound perceived by a CI user does not approximate natural hearing. This limitation is due in part to the large physical gap between the stimulating electrodes and their target neurons. Therefore, directing the controlled outgrowth of processes from spiral ganglion neurons (SGNs) into close proximity to the electrode array could provide significantly increased hearing function. For this objective to be properly designed and implemented, the ability and limits of SGN neurites to be guided must first be determined. In this work, we engineered precise topographical microfeatures with angle turn challenges of various geometries to study SGN pathfinding. Additionally, we analyze sensory neurite growth in response to topographically patterned substrates and use live imaging to better understand how neurite growth is guided by these cues. In assessing the ability of neurites to sense and turn in response to topographical cues, we find that the geometry of the angled microfeatures determines the ability of neurites to navigate the angled microfeature turns. SGN neurite pathfinding fidelity can be increased by 20-70% through minor increases in microfeature amplitude (depth) and by 25% if the angle of the patterned turn is made more obtuse. Further, by using engineered topographies and live imaging of dorsal root ganglion neurons (DRGNs), we see that DRGN growth cones change their morphology and migration to become more elongated within microfeatures. However, our observations also indicate complexities in studying neurite turning. First, as the growth cone pathfinds in response to the various cues, the associated neurite often reorients across the angle topographical microfeatures. This reorientation is likely related to the tension the neurite shaft experiences when the growth cone elongates in the microfeature around a turn. Additionally, neurite branching is observed in response to topographical guidance cues, most frequently when turning decisions are most uncertain. Overall, the multi-angle channel micropatterned substrate is a versatile and efficient system to assess SGN neurite turning and pathfinding in response to topographical cues. These findings represent fundamental principles of neurite pathfinding that will be essential to consider for the design of 3D systems aiming to guide neurite growth in vivo.
Size-Correlated Polymorphisms in Phyllotaxis-Like Periodic and Symmetric Tentacle Arrangements in Hydrozoan Polyps

Introduction Periodic organ arrangements occur during growth and development and are widespread in animals and plants. In bilaterian animals, the organs can be interpreted as being periodically arranged along the two-dimensional space and defined by two body axes; on the other hand, in radially symmetrical animals and plants, organs are arranged in the three-dimensional space around the body axis and around plant stems, respectively. The principles of periodic organ arrangement have primarily been investigated in bilaterians; however, studies on this phenomenon in radially symmetrical animals are scarce. Methods In the present study, we combined live imaging, quantitative analysis, and mathematical modeling to elucidate periodic organ arrangement in a radially symmetrical animal, Coryne uchidai (Cnidaria, Hydrozoa). Results The polyps of C. uchidai simultaneously formed multiple tentacles to establish a regularly angled, ring-like arrangement with radial symmetry. Multiple rings periodically appeared throughout the body and mostly maintained symmetry. Furthermore, we observed polymorphisms in symmetry type, including tri-, tetra-, and pentaradial symmetries, as individual variations. Notably, the types of radial symmetry were positively correlated with polyp diameter, with a larger diameter in pentaradial polyps than in tetra- and triradial ones. Our mathematical model suggested the selection of size-correlated radial symmetry based on the activation-inhibition and positional information from the mouth of tentacle initiation. Discussion Our established quantification methods and mathematical model for tentacle arrangements are applicable to other radially symmetrical animals, and will reveal the widespread association between size-correlated symmetry and periodic arrangement principles.
The Chaotic Motion of the Solar System

In a previous paper (Laskar, Nature, 338,237-238), the chaotic nature of the solar system excluding Pluto was e s t a b lished by the numerical computation of the maximum Lyapunov exponent of i t s secular system over 200 Myr. In the present an explanation i s given for the exponential divergence of the o rb i t s : i t i s due to the t r a n s i t i o n from l i b r a t i o n to c i r c u l ation of the c r i t i c a l argument of the secular resonance 2(g4~g3 ) ( s 4 s „ ) r e l a t e d to the motions of pe r ihe l i ons and nodes of the Earth and Mars. An other important secular r e s o nance i s i d e n t i f i e d : (g1~g5 ) ( s . s 2 ) . I t s c r i t i c a l argument stays in l i b r a t i o n over 200 Myr with a period of about 10 Myr and amplitude from 85° to 135°. The main f ea tu re s of the solu t ions of the inner p l a n e t s a re now iden t i f i ed when taking these resonances in to account . Estimates of the s ize of the chaotic reg ions a r e determined by a new numerical method using the evolut ion with time of the fundamental f requencies . The size of the chaot ic reg ions in the inner solar system are large and correspond to v a r i a t i o n s of about 0.2 arcsec/year in the fundamental f requencies . The chaot ic nature of the in ner solar system can thus be considered as robust agains t snail v a r i a t i o n s of the i n i t i a l condi t ions or of the model. The chaot ic reg ions r e l a t e d to the outer p l ane t s frequencies are very t h i n except for gg which present v a r i a t i o n s s u f f i c i ently l a rge to be s ign i f i can t over the age of the solar;, sys tem .
HIV-1 binds dynein directly to hijack microtubule transport machinery

Viruses exploit host cytoskeletal elements and motor proteins for trafficking through the dense cytoplasm. Yet the molecular mechanism that describes how viruses connect to the motor machinery is unknown. Here, we demonstrate the first example of viral microtubule trafficking from purified components: HIV-1 hijacking microtubule transport machinery. We discover that HIV-1 directly binds to the retrograde microtubule-associated motor, dynein, and not via a cargo adaptor, as previously suggested. Moreover, we show that HIV-1 motility is supported by multiple, diverse dynein cargo adaptors as HIV-1 binds to dynein light and intermediate chains on dynein’s tail. Further, we demonstrate that multiple dynein motors tethered to rigid cargoes, like HIV-1 capsids, display reduced motility, distinct from the behavior of multiple motors on membranous cargoes. Our results introduce a new model of viral trafficking wherein a pathogen opportunistically ‘hijacks’ the microtubule transport machinery for motility, enabling multiple transport pathways through the host cytoplasm.
Preliminary cross-sectional investigations into the human glymphatic system using multiple novel non-contrast MRI methods

We discuss two potential non-invasive MRI methods to cross-sectionally study two distinct facets of the glymphatic system and its association with sleep and aging. We apply diffusion-based intravoxel incoherent motion (IVIM) imaging to evaluate pseudodiffusion coefficient, D*, or cerebrospinal fluid (CSF) movement across large spaces like the subarachnoid space (SAS). We also performed perfusion-based multi-echo, Hadamard encoded multi-delay arterial spin labeling (ASL) to evaluate whole brain cortical cerebral blood flow (CBF) and transendothelial exchange (Tex) of water from the vasculature into the perivascular space and parenchyma. Both methods were used in young adults (N=9, 6F, 23±3 years old) in the setting of sleep and sleep deprivation. To study aging, 10 older adults, (6F, 67±3 years old) were imaged after a night of normal sleep only and compared with the young adults. D* in SAS was significantly (p<0.05) lesser after sleep deprivation (0.014±0.001 mm2/s) than after normal sleep (0.016±0.001 mm2/s), but was unchanged with aging. Cortical CBF and Tex on the other hand, were unchanged after sleep deprivation but were significantly lower in older adults (37±3 ml/100g/min, 476±66 ms) than young adults (42±2 ml/100g/min, 624±66 ms). IVIM was thus, sensitive to sleep physiology and multi-echo, multi-delay ASL was sensitive to aging.
Post-glacial recolonization and multiple scales of secondary contact contribute to contemporary Atlantic salmon (Salmo salar) genomic variation in North America

Aim In northern environments, periods of isolation during Pleistocene glaciations and subsequent recolonization and secondary contact have had a significant influence on contemporary diversity of many species. The recent advent of high-resolution genomic analyses allows unprecedented power to resolve genomic signatures of such events in northern species. Here, we provide the highest resolution genomic characterization of Atlantic salmon in North America to infer glacial refugia and the geographic scales of postglacial secondary contact. Location North America. Taxon Atlantic salmon, Salmo salar. Methods Samples were collected for 5455 individuals from 148 populations encompassing the majority of Atlantic salmon’s native range in North America, from Labrador to Maine. Individuals were genotyped using a 220K SNP array aligned to the Atlantic salmon (Salmo salar) genome. Spatial genetic structure (PCA, k-means clustering, admixture) was evaluated in conjunction with genomic comparisons of identified lineages to infer the refugia during the last glacial maximum and regions of secondary contact following recolonization. Results Spatial genomic analyses identified three phylogeographic groups, consistent with the northward recolonization from two southern glacial refugia in North America (a western Maritime lineage and an eastern Newfoundland and Labrador lineage), with subsequent differentiation of the eastern lineage into two separate groups. Secondary contact among these North American groups was present within the northern Gulf of St. Lawrence and evidence of trans-Atlantic secondary contact was detected within the eastern Newfoundland and Labrador lineage. Comparison of groups from insular Newfoundland with those from mainland Labrador suggests genomic regions displaying high differentiation were characterized by elevated European admixture, suggesting a possible role of European secondary contact in population divergence. Main Conclusions These findings present the first evidence suggesting that genomic diversity in extant North American Atlantic salmon populations has resulted from allopatric isolation in two glacial refugia followed by both regional and trans-Atlantic recolonization and secondary contact and demonstrate the power of genomic tools to resolve historical drivers of diversity in wild populations.
BitSense: Universal and Nearly Zero-Error Optimization for Sketch Counters with Compressive Sensing

Sketch algorithms have been widely deployed for network measurement as they achieve high accuracy with restricted resource usage. They store measurement results compactly in fixed-size counters. However, as sketch counters are skewed towards low values, higher bits in most counters remain zero. Such massive unused bits impair the space efficiency valued by sketch algorithms. Unfortunately, efforts to mitigate the issue either apply to specific algorithms or compromise accuracy. In this paper, we design BitSense, a novel optimization framework that integrates with existing sketch algorithms. The key idea is to regard higher bits in sketch counters as a sparse vector and leverage compressive sensing techniques to compress and restore counters. Further, BitSense provides a programming model to help developers easily realize sketch algorithms without dealing with the details of compression and recovery. Bit-Sense proposes an automatic approach for parameter configuration. It theoretically guarantees nearly zero error under the configuration. We have built a BitSense prototype in P4 and a software platform and integrated it with fourteen sketch solutions. Extensive experiments show that BitSense significantly reduces the memory usage of existing sketch solutions by 25%-80% while incurring little overhead and almost zero accuracy drop, outperforming five state-of-the-art optimization frameworks.
Population dynamic population delineation in North American birds

Andrewartha and Birch (1954) envisioned that natural populations are surrounded by ecological barriers, yet statistical estimates of population structure are almost completely driven by genetic analyses void of ecological information. I develop an ecological clustering routine that delineates natural populations from the synchronisation and desynchronisation in the population dynamics of continuously distributed species. The method is applied to the North American Breeding Bird Survey (Sauer et al. 2017), where it identifies two to five populations per species for 160 species, and leaves the population differentiation unresolved for 139 species. This provides one of the first statistical methods for population dynamics delineated population structure.
High quality genome assembly of the brown hare (Lepus europaeus) with chromosome-level scaffolding

We present here a high-quality genome assembly of the brown hare (Lepus europaeus Pallas), based on a fibroblast cell line of a male specimen from Liperi, Eastern Finland. This brown hare genome represents the first Finnish contribution to the European Reference Genome Atlas pilot effort to generate reference genomes for European biodiversity. The genome was assembled using 25X PacBio HiFi sequencing data and scaffolded utilizing a Hi-C chromosome structure capture approach. After manual curation, the assembled genome length was 2,930,972,003 bp with N50 scaffold of 125.8 Mb. 93.16% of the assembly could be assigned to 25 identified chromosomes (23 autosomes plus X and Y), matching the published karyotype. The chromosomes were numbered according to size. The genome has a high degree of completeness based on the BUSCO score (mammalia_odb10 database), Complete: 96.1% [Single copy: 93.1%, Duplicated: 3.0%], Fragmented 0.8%, and Missing 2.9%. The mitochondrial genome of the cell line was sequenced and assembled separately. The final annotated genome has 30,833 genes of which 21,467 code for a polypeptide. The brown hare genome is particularly interesting as this species readily hybridizes with the mountain hare (Lepus timidus L.) at the species contact zone in northern Eurasia, producing fertile offspring and resulting in gene flow between the two species. In addition to providing a useful comparison for population studies, the genome can offer insight into the chromosomal evolution among Glires in general and Lagomorpha in particular. The chromosomal assembly of the genome also demonstrates that the cell line has not acquired karyotypic changes during culture.
A Parallel Implementation of a 3D Reconstruction Algorithm for Real-Time Vision

Artificial vision requires of large amount of computing power, especially when operating on the fly on digital video streams. For these applications, real-time processing is needed to allow the system to interact with its environment, like in robotic applications or man/machine interfaces. Two braod classes of solutions have been used to solve the problem of balancing application needs and the constraints of the real-time processing: degrading algorithms or using dedicated hardware architecture like FPGA or GPU. These strategies were effective because of the specific properties of the images and the structure of the associated algorithms. However, the constant and fast progression of general purpose computers performance makes these specific solutions less and less interesting. Development time and cost now plead in favor of architectures based on standard components. During the last ten years, the use of these solutions increased with the generalization of clusters made up of off-the-shelf personal computers. But this type of solution has been rarely used in the context of complex vision applications operating on the fly. This paper evaluates this opportunity by proposing a cluster architecture dedicated to real-time vision applications. We describe the hardware architecture of such a solution – by justifying the technological choices carried out on the application requirements and the current state of the art – then the associated software architecture. The validity of the approach is shown with the description and performance evaluation of a real-time 3D reconstruction application.
Statistical Machine Translation

Statistical Machine Translation (SMT) systems are based on bilingual sentence aligned data. The quality of translation depends on the data provided for translation learning. A huge parallel corpus is required for performing the statistical machine translation. The aim of this paper is to explore SMT using the Moses toolkit for creating a German-English translator. To perform the German to English translation, a parallel corpus of this language pair has been provided. Larger the size of the data provided for the training of the Moses decoder, more accurate is the translated output.