Miracle-dz/UniFAR-FTUs huggingface dataset:
Model-assisted physiological analysis of Phyllo, a rice architectural mutant.

Studies of phenotype of knockout mutants can provide new insights into physiological, phenological and architectural feedbacks in the plant system. Phyllo, a mutant of Nippon Bare rice (Oryza sativa L.) producing small leaves in rapid succession, was isolated during multiplication of a T-DNA insertion library. Phyllo phenotype was compared with the wild type (WT) during vegetative development in hydroponics culture using a wide range of physiological and biometric measurements. These were integrated with the help of the functional-structural model EcoMeristem, explicitly designed to study interactions between morphogenesis and carbon assimilation. Although the phenotype of the mutant was caused by a single recessive gene, it differed in many ways from the WT, suggesting a pleiotropic effect of this mutation. Phyllochron was 25 (1-4 leaf stage) to 38% (>>4 leaf stage) shorter but showed normal transition from juvenile to adult phase after leaf 4. Leaf size also increased steadily with leaf position as in WT. The mutant had reduced leaf blade length : width and blade : sheath length ratios, particularly during the transition from heterotrophic to autotrophic growth. During the same period, root : shoot dry weight ratio was significantly diminished. Specific leaf area (SLA) was strongly increased in the mutant but showed normal descending patterns with leaf position. Probably related to high SLA, the mutant had much lower light-saturated leaf photosynthetic rates and lower radiation use efficiency (RUE) than the WT. Leaf extension rates were strongly reduced in absolute terms but were high in relative terms (normalised by final leaf length). The application of the EcoMeristem model to these data indicated that the mutant was severely deficient in assimilate, resulting from low RUE and high organ initiation rate causing high assimilate demand. This was particularly pronounced during the heterotrophic-autotrophic transition, probably causing shorter leaf blades relative to sheaths, as well as a temporary reduction of assimilate partitioning to roots. The model accurately simulated the mutant's high leaf mortality and absence of tillering. The simulated assimilate shortage was supported by observed reductions in starch storage in sheaths. Soluble sugar concentrations differed between mutant and WT in roots but not in shoots. Specifically, the hexose : sucrose ratio was 50% lower in the roots of the mutant, possibly indicating low invertase activity. Furthermore, two OsCIN genes coding for cell wall invertases were not expressed in roots, and others were expressed weakly. This was interpreted as natural silencing via sugar signalling. In summary, the authors attributed the majority of observed allometric and metabolic modifications in the mutant to an extreme assimilate shortage caused by hastened shoot organogenesis and inefficient leaf morphology.
sRDMA - Efficient NIC-based Authentication and Encryption for Remote Direct Memory Access

State-of-the-art remote direct memory access (RDMA) technologies have shown to be vulnerable against attacks by in-network adversaries, as they provide only a weak form of protection by including access tokens in each message. A network eavesdropper can easily obtain sensitive information and modify bypassing packets, affecting not only secrecy but also integrity. Tampering with packets can have drastic consequences. For example, when memory pages with code are changed remotely, altering packet contents enables remote code injection. We propose sRDMA, a protocol that provides efﬁcient authentication and encryption for RDMA to prevent information leakage and message tampering. sRDMA uses symmetric cryptography and employs network interface cards to perform cryptographic operations. Additionally, we provide an implementation for sRDMA using programmable network adapters.
A Comprehensive Analysis of Superpage Management Mechanisms and Policies

Superpages (2MB pages) can reduce the address translation overhead for large-memory workloads in modern computer systems. This paper clearly outlines the sequence of events in the life of a superpage and explores the design space of when and how to trigger and respond to those events. This provides a framework that enables better understanding of su-perpage management and the trade-offs involved in different design decisions. Under this framework, this paper discusses why state-of-the-art designs exhibit different performance characteristics in terms of runtime, latency and memory consumption. This paper illuminates the root causes of latency spikes and memory bloat and introduces Quicksilver, a novel superpage management design that addresses these issues while maintaining address translation performance.
Composition Changes in a Subandean Avifauna after Long‐Term Forest Fragmentation

Abstract: Current understanding of the effects of forest fragmentation is based largely on studies in temperate regions, Australia, and Neotropical lowlands. In contrast, the consequences of anthropogenic forest fragmentation for Andean avifaunas are poorly understood, despite large‐scale habitat loss and fragmentation. I assessed the effects of long‐term fragmentation on a subandean avifauna in Colombia by comparing the occurrence of bird species in forest fragments isolated over 50–90 years with the original avifauna. Prefragmentation bird composition was based on historical records and current species composition in continuous forest. The original avifauna had approximately 139 forest species and 45 species of open habitats. Among forest species, 30% were currently extinct in fragmented forest and 4% were regionally extinct. At least 23 nonforest species colonized the region from the lowlands following deforestation. Species with small geographic ranges and those that were locally scarce or rare throughout their ranges were likely to be locally extinct. Forest raptors, terrestrial insectivores, and large frugivores were highly extinction prone, whereas nectarivores, small frugivores, and aerial insectivores were highly resilient; other guilds were intermediate. Antbirds (Formicariidae, Thamnophilidae), Cotingas, and, especially, Icterids were highly extinction prone. Large body size was not a determinant of vulnerability except among frugivores. Sixty‐two percent of the species of special conservation concern were extinct in fragments. These results suggest that only large forest tracts will ensure the survival of a large proportion of subandean avifaunas. Fragments of mature forest, however, may support a diverse avifauna, including small populations of globally endangered species several decades after isolation. These fragments could play an important role in the restoration of local avifaunas. A good understanding of the mechanisms that allow persistence in such fragments may prove essential for the conservation of those species for which no large tracts of suitable habitat remain.
Evidence That Reduced Early Marine Growth is Associated with Lower Marine Survival of Coho Salmon

Abstract Coho salmon Oncorhynchus kisutch from the Strait of Georgia were used to test the hypothesis that slower growing fish in their first ocean year had lower survival over the late fall and winter than faster growing fish. The Strait of Georgia provided a suitable area for this study because it is a semi-enclosed rearing area for juvenile Pacific salmon that is distinct from the open marine rearing areas off the west coast. Coho salmon that survived the winter had significantly larger spacing between circuli on scales, indicating that brood year strength is related to growth in the first marine year. Other studies have shown that smaller fish of a cohort are less able to survive periods of energy deficit than larger fish. Thus, size-related mortality in the first marine fall and winter may be an important determinant of brood year strength of some coho salmon stocks and stocks of other species of Pacific salmon.
induces apoptosis in MGC-803 cells through a mitochondrial/caspase pathway

Anti-proliferative and apoptosis-inducing effects of 2,4,3′,4′-tetramethoxy-biphenyl (TMBP) on human gastric cancer MGC-803 cells were investigated. The molecular mechanisms of TMBP-mediated tumor cell death were detected by clonogenic assay, staining with Hoechst 33258, DNA fragmentation assay, Western blot analysis and flow cytometry assay. Studies on MGC-803 cells treated with TMBP showed that TMBP inhibited the proliferation of MGC-803 cells in a time- and dose-dependent manner. The induction of apoptosis by TMBP was accompanied by the loss of mitochondrial membrane potential (ΔΨm), cytochrome C release and activation of caspase cascade, resulting in the cleavage of some specific substrates for caspase-3 such as poly (ADP-ribose) polymerase (PARP). In conclusion, these findings showed that TMBP may induce the apoptosis of MGC-803 through a mitochondrial/caspase pathway, suggesting its possible use for treating human cancers.
IL-12 synergizes with IL-18 or IL-1β for IFN-γ production from human T cells

IL-18 is a proinflammatory cytokine that plays an important role in NK cell activation and T(h)1 response. IL-18 has a structural homology to IL-1, particularly IL-1beta. IL-18R, composed of IL-1R-related protein (IL-18Ralpha) and IL-1R accessory protein-like (IL-18Rbeta), belongs to the IL-1R family. Furthermore, IL-18R at least partly shares the signal transducing system with IL-1R. Thus, the IL-18-IL-18R system has a striking similarity to the IL-1-IL-1R system. For this reason, we regarded it important to investigate whether, like IL-18, IL-1beta synergizes with IL-12 in inducing IFN-gamma production from human T cells and plays an important role in the T(h)1 response. Here we show that IL-12 and IL-1beta synergistically induce T cells to proliferate and produce IFN-gamma without their TCR engagement. IL-12 stimulation induced an increase in the proportion of T cells positive for IL-18R. Then, IL-12-stimulated T cells responded to IL-18 or IL-1beta by their proliferation and IFN-gamma production, although levels of IL-1beta-induced responses were lower. CD4(+)CD45RA(+) T cells, although they constitutively expressed IL-18Rbeta mRNA, did not express IL-18Ralpha mRNA. Phytohemagglutinin (PHA) stimulation alone induced IL-18Ralpha mRNA without affecting the expression of IL-18Rbeta mRNA. T(h)1-inducing conditions (PHA, IL-12 and anti-IL-4) further increased this expression. We also show that T(h)1 cells but not T(h)2 cells have increased expression of IL-18R and IL-1R, and produce IFN-gamma in response to IL-18 and/or IL-1beta.
Offload Annotations: Bringing Heterogeneous Computing to Existing Libraries and Workloads

As specialized hardware accelerators such as GPUs become increasingly popular, developers are looking for ways to target these platforms with high-level APIs. One promising approach is kernel libraries such as PyTorch or cuML, which provide interfaces that mirror CPU-only counterparts such as NumPy or Scikit-Learn. Unfortunately, these libraries are hard to develop and to adopt incrementally: they only support a subset of their CPU equivalents, only work with datasets that ﬁt in device memory, and require developers to reason about data placement and transfers manually. To address these shortcomings, we present a new approach called ofﬂoad annotations (OAs) that enables heterogeneous GPU computing in existing workloads with few or no code modiﬁ-cations. An annotator annotates the types and functions in a CPU library with equivalent kernel library functions and provides an ofﬂoading API to specify how the inputs and outputs of the function can be partitioned into chunks that ﬁt in device memory and transferred between devices. A runtime then maps existing CPU functions to equivalent GPU kernels and schedules execution, data transfers and paging. In data science workloads using CPU libraries such as NumPy and Pandas, OAs enable speedups of up to 1200 ⇥ and a median speedup of 6 . 3 ⇥ by transparently ofﬂoading functions to a GPU us-ing existing kernel libraries. In many cases, OAs match the performance of handwritten heterogeneous implementations. Finally, OAs can automatically page data in these workloads to scale to datasets larger than GPU memory, which would need to be done manually with most current GPU libraries.
OSCA: An Online-Model Based Cache Allocation Scheme in Cloud Block Storage Systems

We propose an Online-Model based Scheme for Cache Allocation for shared cache servers among cloud block storage devices. OSCA can ﬁnd a near-optimal conﬁguration scheme at very low complexity improving the overall efﬁ-ciency of the cache server. OSCA employs three techniques. First, it deploys a novel cache model to obtain a miss ratio curve (MRC) for each storage node in the cloud infrastructure block storage system. Our model uses a low overhead method to obtain data reuse distances from the ratio of re-access traf-ﬁc to the total trafﬁc within a time window. It then translates the obtained reuse distance distribution into miss ratio curves. Second, knowing the cache requirements of storage nodes, it deﬁnes the total hit trafﬁc metric as the optimization target. Third, it searches for a near optimal conﬁguration using a dynamic programming method and performs cache reas-signment based on the solution. Experimental results with real-world workloads show that our model achieves a Mean Absolute Error (MAE) comparable to existing state-of-the-art techniques, but we can do without the overheads of trace collection and processing. Due to the improvement of hit ratio, OSCA reduces IO trafﬁc to the back-end storage server by 13.2% relative to an equal-allocation-to-all-instances policy with the same amount of cache memory.
Application of Image Segmentation in Surface Water Extraction of Freshwater Lakes using Radar Data

Freshwater lakes supply a large amount of inland water resources to sustain local and regional developments. However, some lake systems depend upon great fluctuation in water surface area. Poyang lake, the largest freshwater lake in China, undergoes dramatic seasonal and interannual variations. Timely monitoring of Poyang lake surface provides essential information on variation of water occurrence for its ecosystem conservation. Application of histogram-based image segmentation in radar imagery has been widely used to detect water surface of lakes. Still, it is challenging to select the optimal threshold. Here, we analyze the advantages and disadvantages of a segmentation algorithm, the Otsu Method, from both mathematical and application perspectives. We implement the Otsu Method and provide reusable scripts to automatically select a threshold for surface water extraction using Sentinel-1 synthetic aperture radar (SAR) imagery on Google Earth Engine, a cloud-based platform that accelerates processing of Sentinel-1 data and auto-threshold computation. The optimal thresholds for each January from 2017 to 2020 are − 14.88 , − 16.93 , − 16.96 and − 16.87 respectively, and the overall accuracy achieves 92 % after rectification. Furthermore, our study contributes to the update of temporal and spatial variation of Poyang lake, confirming that its surface water area fluctuated annually and tended to shrink both in the center and boundary of the lake on each January from 2017 to 2020.
New puerulus collector design suitable for fishery-dependent settlement monitoring

Fishery-independent diver-based puerulus settlement monitoring has been conducted for over two decades in sheltered inshore shallow sites on the Tasmanian coast and has been utilized in the development of a predictive capacity for the Tasmanian lobster fishery. However, the majority of catches in this fishery are sourced from deep (>50 m), remote, and highly exposed areas where it is impractical and expensive to conduct fishery independent routine settlement monitoring. To determine if pueruli settle in deeper waters,we adapted a crevice puerulus collector to fit within a lobster trap frame specifically designed to be deployed and serviced by vessels typical of the Tasmanian lobster fleet. A 5-month trial yielded puerulus catches similar to those from inshore shallow sites including recording puerulus from waters more than 100 m depth. The collector design was reported by fishers to be safe and convenient to service in regions exposed to strong westerly winds and swell more than 7 m. This collector will allow a cost-effective fishery-dependent approach to puerulus settlement monitoring utilizing commercial fishers for field operations and researchers for administration, sorting, and analysis.
Towards Plan-aware Resource Allocation in Serverless Query Processing

Resource allocation for serverless query processing is a challenge. Unfortunately, prior approaches have treated queries as black boxes, thereby missing significant resource optimization opportunities. In this paper, we propose a plan-aware resource allocation approach where the resources are adaptively allocated based on the runtime characteristics of the query plan. We show the savings opportunity from such an allocation scheme over production SCOPE workloads at Microsoft. We present our current implementation of a greedy version that periodically estimates the peak resource for the remaining of the query as the query execution progresses. Our experimental evaluation shows that such an implementation could already save more than 8% resource usage over one of our production virtual clusters. We conclude by opening the discussion on various strategies for plan-aware resource allocation and their implications on the cloud computing stack.
Spotnik: Designing Distributed Machine Learning for Transient Cloud Resources

To achieve higher utilisation, cloud providers offer VMs with GPUs as lower-cost transient cloud resources. Transient VMs can be revoked at short notice and vary in their availability. This poses challenges to distributed machine learning (ML) jobs, which perform long-running stateful computation in which many workers maintain and synchronise model replicas. With transient VMs, existing systems either require a ﬁxed number of reserved VMs or degrade performance when recovering from revoked transient VMs. We believe that future distributed ML systems must be designed from the ground up for transient cloud resources. This paper describes S POTNIK , a system for training ML models that features a more adaptive design to accommodate transient VMs: (i) S POTNIK uses an adaptive implementation of the all-reduce collective communication operation. As workers on transient VMs are revoked, S POTNIK updates its membership and uses the all-reduce ring to recover; and (ii) S POTNIK supports the adaptation of the synchronisation strategy between workers. This allows a training job to switch between different strategies in response to the revocation of transient VMs. Our experiments show that, after VM revocation, S POTNIK recovers training within 300 ms for ResNet/ImageNet.
Auto-sizing for Stream Processing Applications at LinkedIn

Stream processing as a platform-as-a-service (PaaS) offering is used at LinkedIn to host thousands of business-critical applications. This requires service owners to manage applications’ resource sizing and tuning. Unfortunately, applications have diverged from their conventional model of a directed acyclic graph (DAG) of operators and incorporate multiple other functionalities, which presents numerous challenges for sizing. We present a controller that dynamically controls applications’ resource sizing while accounting for diverse functionalities, load variations, and service dependencies, to maximize cluster utilization and minimize cost. We discuss the challenges and opportunities in designing such a controller.
Quality Verification of Volunteered Geographic Information Using OSM Notes Data in a Global Context

Although the data obtained from volunteered geographic information (VGI) are inherently different from public surveys, the quantity of the data are vast and the quality of the data are often poor. To improve the quality of VGI data, the positional accuracy and diversity and interaction of the number of users involved in the regional generation of the data are important. This research proposes a new approach for the accumulation of OpenStreetMap (OSM) data by using OSM Notes and attempts to analyze the geographical distribution and the characteristics of the contents of the contributions, quantitatively and qualitatively. Subsequently, the results demonstrated regional differences in OSM Notes, but it provided users with an understanding of the new features of quality management in OSM, even in regions where OSM activities are not necessarily active. In addition, it was also possible to discover new factors such as the time transition required for the correction and contribution of anonymous users. These results are expected to serve as a tool for users to communicate with each other to resolve data bugs that exist in OSM and provide future researchers with examples of user interaction in global OSM activities.
Spectroscopic Evaluation of Red Blood Cells of Thalassemia Patients with Confocal Microscopy: A Pilot Study

Hemoglobinopathies represent the most common single-gene defects in the world and pose a major public health problem, particularly in tropical countries, where they occur with high frequency. Diagnosing hemoglobinopathies can sometimes be difficult due to the coexistence of different causes of anemia, such as thalassemia and iron deficiency, and blood transfusions, among other factors, and requires expensive and complex molecular tests. This work explores the possibility of using spectral confocal microscopy as a diagnostic tool for thalassemia in pediatric patients, a disease caused by mutations in the globin genes that result in changes of the globin chains that form hemoglobin—in pediatric patients. Red blood cells (RBCs) from patients with different syndromes of alpha-thalassemia and iron deficiency (including anemia) as well as healthy (control) subjects were analyzed under a Leica TCS SP8 confocal microscope following different image acquisition protocols. We found that diseased RBCs exhibited autofluorescence when excited at 405 nm and their emission was collected in the spectral range from 425 nm to 790 nm. Three experimental descriptors calculated from the mean emission intensities at 502 nm, 579 nm, 628 nm, and 649 nm allowed us to discriminate between diseased and healthy cells. According to the results obtained, spectral confocal microscopy could serve as a tool in the diagnosis of thalassemia.