Miracle-dz/UniFAR-FTUs huggingface dataset:
Ekho: Synchronizing cloud gaming media across multiple endpoints

Online cloud gaming platforms stream game media to multiple end-points (e.g., a television display and a controller-connected headset) via possibly different networks with considerably different latencies. This leads to the media being played out of sync with one another, and severely degrades user experience. Typical approaches that rely on network and software timing measurements fail to reach synchronization goals. In this work, we propose Ekho, a robust and efficient end-to-end approach for synchronizing streams transmitted to two devices. Ekho adds faint, human-inaudible pseudo-noise (PN) markers to the game audio, and listens for these markers in the chat audio captured by the player's microphone to measure inter-stream delay (ISD). The game server then compensates for the ISD to synchronize the streams. We evaluate Ekho in depth, with a corpus of audio samples from popular online games, and demonstrate that it calculates ISD with sub-millisecond accuracy, has low computational overhead, and is resilient to background chatter, compression and microphone quality. In end-to-end tests over WiFi and cellular links with frequent packet loss and playback disruption, Ekho maintains human-imperceptible ISD (< 10 ms) 86.8% of the time. Without Ekho, the ISD exceeds 50 ms at all times.
Switchboard: Efficient Resource Management for Conferencing Services

Resource management is important for conferencing services (such as Microsoft Teams, Zoom) to ensure good user experience while keeping the costs low. Key to this is the efficient provisioning and assignment of media processing (MP) servers, which do the heavy lifting of mixing and redistributing the media streams from and to the call participants. We introduce Switchboard - a controller for efficient resource management for conferencing services. Switchboard is peak-aware, recognizing that cost depends on the peak resource usage and that there is a temporal shift in peak demand across time zones. This allows a server in a region to serve calls at peak time, and double up as backup for other regions during non-peak times. Furthermore, it improves efficiency by performing joint network and compute provisioning and application aware provisioning. We evaluate Switchboard using 1+ year of records from Microsoft Teams. Switchboard achieves upto 51% lower provisioning cost while achieving similar or better latency over state-of-the-art baselines.
Taming the transient while reconfiguring BGP

BGP reconfigurations are a daily occurrence for most network operators, especially in large networks. Yet, performing safe and robust BGP reconfiguration changes is still an open problem. Few BGP reconfiguration techniques exist, and they are either (i) unsafe, because they ignore transient states, which can easily lead to invariant violations; or (ii) impractical, as they duplicate the entire routing and forwarding states, and require special hardware. In this paper, we introduce Chameleon, the first BGP reconfiguration framework capable of maintaining correctness throughout a reconfiguration campaign while relying on standard BGP functionalities and minimizing state duplication. Akin to concurrency coordination in distributed systems, Chameleon models the reconfiguration process with happens-before relations. This modeling allows us to capture the safety properties of transient BGP states. We then use this knowledge to precisely control the BGP route propagation and convergence, so that input invariants are provably preserved at any time during the reconfiguration. We fully implement Chameleon and evaluate it in both testbeds and simulations, on real-world topologies and large-scale reconfiguration scenarios. In most experiments, our system computes reconfiguration plans within a minute, and performs them from start to finish in a few minutes, with minimal overhead.
PAINTER: Ingress Traffic Engineering and Routing for Enterprise Cloud Networks

Enterprises increasingly use public cloud services for critical business needs. However, Internet protocols force clouds to contend with a lack of control, reducing the speed at which clouds can respond to network problems, the range of solutions they can provide, and deployment resilience. To overcome this limitation, we present PAINTER, a system that takes control over which ingress routes are available and which are chosen to the cloud by leveraging edge proxies. PAINTER efficiently advertises BGP prefixes, exposing more concurrent routes than existing solutions to improve latency and resilience. Compared to existing solutions, PAINTER reduces path inflation by 75% while using a third of the prefixes of other solutions, avoids 20% more path failures, and chooses ingresses from the edge at finer time (RTT) and traffic (per-flow) granularities, enhancing our agility.
High-accuracy mapping of human and viral direct physical protein-protein interactions using the novel computational system AlphaFold-pairs

Protein-protein interactions are central, highly flexible components of regulatory mechanisms in all living cells. Over the years, diverse methods have been developed to map protein-protein interactions. These methods have revealed the organization of protein complexes and networks in numerous cells and conditions. However, these methods are also time consuming, costly and sensitive to various experimental artifacts. To avoid these caveats, we have taken advantage of the AlphaFold-Multimer software, which succeeded in predicting the structure of many protein complexes. We designed a relatively simple algorithm based on assessing the physical proximity of a test protein with other AlphaFold structures. Using this method, named AlphaFold-pairs, we have successfully defined the probability of a protein-protein interaction forming. AlphaFold-pairs was validated using well-defined protein-protein interactions found in the literature and specialized databases. All pairwise interactions forming within the 12-subunit transcription machinery RNA Polymerase II, according to available structures, have been identified. Out of 66 possible interactions (excluding homodimers), 19 specific interactions have been found, and an additional previously unknown interaction has been unveiled. The SARS-CoV-2 surface glycoprotein Spike (or S) was confirmed to interact with high preference with the human ACE2 receptor when compared to other human receptors. Notably, two additional receptors, INSR and FLT4, were found to interact with S. For the first time, we have successfully identified protein-protein interactions that are likely to form within the reassortant Eurasian avian-like (EA) H1N1 swine G4 genotype Influenza A virus, which poses a potential zoonotic threat. Testing G4 proteins against human transcription factors and molecular chaperones (a total of 100 proteins) revealed strong specific interactions between the G4 HA and HSP90B1, the G4 NS and the PAQosome subunit RPAP3, as well as the G4 PA and the POLR2A subunit. We predict that AlphaFold-pairs will revolutionize the study of protein-protein interactions in a large number of healthy and diseased systems in the years to come.
Global, Passive Detection of Connection Tampering

In-network devices around the world monitor and tamper with connections for many reasons, including intrusion prevention, combating spam or phishing, and country-level censorship. Connection tampering seeks to block access to specific domain names or keywords, and it affects billions of users worldwide with little-to-no transparency. To detect, diagnose, and measure connection-level blocking, "active" measurement techniques originate queries with domains or keywords believed to be blocked and send them from vantage points within networks of interest. Active measurement efforts have been critical to understanding how traffic tampering occurs, but they inherently are unable to capture critical parts of the picture. For instance, knowing the set of domains in a block-list (i.e., what could get blocked) is not the same as knowing what real users are actively experiencing (i.e., what is actively getting blocked). We present the first global study of connection tampering through a passive analysis of traffic received at a global CDN, Cloudflare. We analyze a sample of traffic to all of Cloudflare's servers to construct the first comprehensive list of tampering signatures: sequences of packet headers that are indicative of connection tampering. We then apply these tampering signatures to analyze our global dataset of real user traffic, yielding a more comprehensive view of connection tampering than has been possible with active measurements alone. In particular, our passive analysis allows us to report on how connection tampering is actively affecting users and clients from virtually every network, without active probes, vantage points in difficult-to-reach networks and regions, or test lists (which we analyze for completeness against our results). Our study shows that passive measurement can be a powerful complement to active measurement in understanding connection tampering and improving transparency.
A practical guide for buprenorphine initiation in the primary care setting

Buprenorphine is a safe and effective treatment for opioid use disorder but remains underutilized because a major challenge of conventional buprenorphine initiation (termed induction) is that the patient must already be in opioid withdrawal. Previous legal barriers and clinician lack of familiarity with the unique pharmacology of buprenorphine have also limited its use. In this review, we outline changes regarding buprenorphine prescribing laws and physician perceptions of buprenorphine. We also review buprenorphine pharmacology and novel low-dose buprenorphine induction procedures that can be adopted in primary care settings to improve treatment acceptability, retention, and outcomes. The authors review changes in prescribing laws and outline buprenorphine induction protocols that can be adopted in the primary care setting.
LES Investigation with an Eulerian Stochastic Field Cavitation Model

Due to an ongoing trend of high injection pressures in the realm of internal combustion engines, the role of cavitation that typically happens inside the injector nozzle has become increasingly important. In this work, a large eddy simulation (LES) with cavitation modeled on the basis of an Eulerian Stochastic Field (ESF) method and a homogeneous mixture model is performed to investigate the role of cavitation on academic injector. The ESF cavitation model is coupled to a pressure based solver for the flow, which lowers the computational cost, thereby making the methodology highly applicable to realistic injector geometries. Moreover, the nature of the ESF method makes it more convenient to achieve a high scalability when applied to parallel cases, which gives the method an edge over cavitation models that are based on Lagrangian tracking. The result of the ESF simulation is compared against that from a typical single volume fraction solver for validation. The capability of the ESF model to capture the probability density function (PDF) of vapor bubble radii is also demonstrated.
CellFusion: Multipath Vehicle-to-Cloud Video Streaming with Network Coding in the Wild

This paper presents CellFusion, a system designed for high-quality, real-time video streaming from vehicles to the cloud. It leverages an innovative blend of multipath QUIC transport and network coding. Surpassing the limitations of individual cellular carriers, CellFusion uses a unique last-mile overlay that integrates multiple cellular networks into a single, unified cloud connection. This integration is made possible through the use of in-vehicle Customer Premises Equipment (CPEs) and edge-cloud proxy servers. In order to effectively handle unstable cellular connections prone to intense burst losses and unexpected latency spikes as a vehicle moves, CellFusion introduces XNC. This innovative network coding-based transport solution enables efficient and resilient multipath transport. XNC aims to accomplish low latency, minimal traffic redundancy, and reduced computational complexity all at once. CellFusion is secure and transparent by nature and does not require modifications for vehicular apps connecting to it. We tested CellFusion on 100 self-driving vehicles for over six months with our cloud-native back-end running on 50 CDN PoPs. Through extensive road tests, we show that XNC reduced video packet delay by 71.53% at the 99th percentile versus 5G. At 30Mbps, CellFusion achieved 66.11% ~ 80.62% reduction in video stall ratio versus state-of-the-art multipath transport solutions with less than 10% traffic redundancy.
Population genomic analyses reveal extensive genomic regions within selective sweeps associated with adaptation and demographic history of a wheat fungal pathogen

Plant pathogens can quickly evolve in response to the changing host and environment, resulting in destructive epidemics. The fungus Puccinia striiformis f. sp. tritici (Pst), causing wheat stripe rust disease worldwide, is one such pathogen. In the arms race between pathogens and hosts, changes in host populations exerted continuous selective forces on the dynamics of pathogens. However, the footprints of these selection forces and the demography of Pst remain poorly explored, limited our understanding the evolutionary processes that shape the spread and evolution of pathogens. In this study, we revealed several features of worldwide Pst populations through population genomic analyses. There might be limited gene flow between Pst populations from China and other countries. A slower rate of linkage disequilibrium decay was detected comparing to rust fungi with known sexual reproduction. Furthermore, we detected extensive hard and soft sweeps associated with Pst adaptation. Genes within the selective sweeps were enriched in secreted proteins and effectors and showed functions related to pathogenicity or virulence, temperature tolerance, and fungicide resistance implying that Chinese Pst populations suffered positive selection pressures from host and abiotic factors. Moreover, demographic history indicated Pst populations experienced strong bottlenecks at the beginning of the wheat domestication around 10,000 years ago and during modern agriculture around 100 years ago, suggesting that the crop domestication and breeding programs could continuously contribute to the decline of pathogen effective population sizes. Our results provided insights into the evolution of the Pst genome and highlighted the role of modern agriculture on pathogen demography. Author Summary Wheat stripe rust, as a pathogen of wheat, is capable of inducing significant yield reduction on a global scale. Traditional epidemiological investigations have elucidated the causative agent behind this disease, the wheat stripe rust pathogen, as an organism exhibiting swift adaptive evolution in response to its environment. However, the precise mechanisms underpinning its adaptive strategies and the ensuing alterations in population dynamics remain relatively unexplored. In our research, we have undertaken an analysis encompassing wheat stripe rust samples throughout the world. Employing population genomics methods, we have sought to discern the genomic footprints corresponding to the adaptive process within the pathogen. These genomic footprints have illuminated the operation of positive selection pressures caused by both the host plant and the ecological context. Concurrently, it have provided insights into the population size that the wheat stripe rust pathogen has undergone over millennia. Notably, its change in population size revealed the demographic history associated with wheat domestication.
Poster: Programmable Cycle-Specified Queue for Deterministic Networking

The emerging time-critical applications pose intense demands for enabling large-scale deterministic networks. In this paper, we propose a new Programmable Cycle-Specified Queue (PCSQ) for wide-area deterministic packet scheduling. We implement the first end-to-end high-precision rotation dequeuing, which enables microsecond-level time slot resource reservation (noted as T) and especially jitter control of up to 2T. We prototype the PCSQ scheduler on an FPGA. The PCSQ-enabled switches can guarantee bounded delay and jitter transmission on a realistic testbed.
Improving Network Availability with Protective ReRoute

We present PRR (Protective ReRoute), a transport technique for shortening user-visible outages that complements routing repair. It can be added to any transport to provide benefits in multipath networks. PRR responds to flow connectivity failure signals, e.g., retransmission timeouts, by changing the FlowLabel on packets of the flow, which causes switches and hosts to choose a different network path that may avoid the outage. To enable it, we shifted our IPv6 network architecture to use the FlowLabel, so that hosts can change the paths of their flows without application involvement. PRR is deployed fleetwide at Google for TCP and Pony Express, where it has been protecting all production traffic for several years. It is also available to our Cloud customers. We find it highly effective for real outages. In a measurement study on our network backbones, adding PRR reduced the cumulative region-pair outage time for RPC traffic by 63--84%. This is the equivalent of adding 0.4--0.8 "nines" of availability.
Ribose lowers RpoS translation through RbsD mRNA

The Escherichia coli sigma factor RpoS accumulates during starvation, activates transcription of the general stress response, and then rapidly returns to low levels upon nutrient replenishment. Sugar levels modulate RpoS levels by signaling though central metabolism, ATP and the phosphoenolpyruvate-carbohydrate phosphotransferase system (PTS) transport system, which favors glucose. However, there have been few examples of dedicated control pathways for specific sugars regulating RpoS. We screened an overexpression library with a RpoS’-‘LacZ reporter and found that overexpressing the ribose metabolism rbsD gene reduced RpoS levels. A functional RbsD ribose pyranase protein was not necessary for the effect, suggesting that the RbsD mRNA was responsible for the effect. We used a series of LacZ fusions and RT-qPCR to determine how RbsD mRNA affects RpoS and found that regulation of RpoS occurred at the level of translation. Furthermore, the effect of rbsD overexpression was diminished in strain that did not have the RpoS untranslated hairpin loop or the small RNA chaperone Hfq. RbsD mRNA has previously been shown to bind to the sRNA DsrA. We demonstrated that the effect of RbsD on RpoS was dependent on the sRNAs DsrA and ArcZ and Hfq. Finally, we showed that the sugar ribose lowers RpoS levels in a manner that requires RbsD. In summary, our results demonstrate that RpoS levels respond specifically to ribose though a component of the ribose metabolism pathway and the main player, RbsD, acts as dual function mRNA that has a regulatory role by interacting with the sRNAs that control RpoS.
High-efficiency gene editing in Anopheles sinensis using ReMOT control

CRISPR/Cas9-mediated gene editing provides an effective method for deciphering the molecular mechanisms underlying mosquito development and mosquito-borne disease transmission, as well as for exploring genetic control strategies. However, delivering the Cas9 ribonucleoprotein complex by embryo injection to produce genetic modifications is challenging, is mostly confined to model mosquitoes and specialized laboratories, and has low editing efficiency. Here, we established an effective Receptor-Mediated Ovary Transduction of Cargo (ReMOT) control method, enabling the introduction of heritable mutations into Anopheles sinensis, the major malaria vector in China and Southeast Asia, via the injection of female adult mosquitoes. Injection of a mixture of P2C-DsRed and saponin resulted in red fluorescence in the ovaries, with a 100% success rate. Using this system, we knocked-out the pigment synthesis genes, Aswhite and Asyellow, using injected wild-type (WT) females mated with WT males, resulting in the highest efficiency of gene editing among mosquitoes under the same mating conditions. Furthermore, the gene-editing efficiency was increased by at least 2.1-fold using injected WT females mated with mutant males. This improved ReMOT control method exhibits high editing efficiency, with important benefits in terms of functional genomics research and genetic control strategies in An. sinensis. Moreover, this represents a convenient method for gene manipulation in laboratories that are unable to perform embryo injection or that lack embryo-injection equipment.
UPP affects chloroplast development by interfering with chloroplast proteostasis

Arabidopsis uracil phosphoribosyltransferase (UPP) is an essential enzyme which appears to have a previously unknown, moonlighting activity. Our analysis of UPP amiRNA mutants has confirmed that this vital function is crucial for chloroplast development and growth. Interestingly, this function appears to be unrelated to nucleotide homeostasis since nucleotide levels were not altered in the studied mutants. Transcriptomics and proteomic analysis suggest that UPP plays a role in chloroplast proteostasis, especially under high light (HL). Immunoblots of mature plants and a de-etiolation experiment with young seedlings revealed PetC, the iron-sulfur protein of the cytochrome b6f complex, as a putative UPP target. In addition, UPP and PetC were identified in a high molecular weight complex. Consistently, we show that PetC is massively reduced in UPP knock-down plants. The block observed in photosynthetic electron transport, as evidenced by reduced high light-induced non-photochemical quenching (NPQ) but increased unregulated energy dissipation (NO), might be therefore a consequence of reduced PetC. After HL treatment, UPP amiRNA mutants showed impaired photosynthesis and reduced carbohydrate contents, resulting in an inability to induce flavonoid biosynthesis. In addition, the levels of the osmoprotectants raffinose, proline and fumarate were found to be reduced. Proteases, including thylakoid filamentation temperature-sensitive 1, 5 (FtsH), caseinolytic protease proteolytic subunit 1 (ClpP1), and processing peptidases, as well as components of the chloroplast protein import machinery, were up-regulated. In sum, our work suggests that UPP assists in stabilizing and protection of PetC during the assembly of the Fe-S cluster and targeting to the thylakoid.
ClipperQTL: ultrafast and powerful eGene identification method

A central task in expression quantitative trait locus (eQTL) analysis is to identify cis-eGenes (henceforth “eGenes”), i.e., genes whose expression levels are regulated by at least one local genetic variant. Among the existing eGene identification methods, FastQTL is considered the gold standard but is computationally expensive as it requires thousands of permutations for each gene. Alternative methods such as eigenMT and TreeQTL have lower power than FastQTL. In this work, we propose ClipperQTL, which reduces the number of permutations needed from thousands to 20 for data sets with large sample sizes (> 450) by using the contrastive strategy developed in Clipper; for data sets with smaller sample sizes, it uses the same permutation-based approach as FastQTL. We show that ClipperQTL performs as well as FastQTL and runs about 500 times faster if the contrastive strategy is used and 50 times faster if the conventional permutation-based approach is used. The R package ClipperQTL is available at https://github.com/heatherjzhou/ClipperQTL.