Miracle-dz/UniFAR-FTUs huggingface dataset:
Rotavirus-associated acute diarrhea outbreak in West Shewa Zone of Oromia Regional State, Ethiopia, 2017

Introduction Rotavirus causes severe-diarrheal diseases in infants. An estimation of 138 million rotavirus-associated diarrheal cases and 215,000 deaths occur every year globally. In December 2016, West-Shewa zone in Ethiopia reported unidentified gastrointestinal diarrhea outbreak. We investigated to identify the causative agent of the outbreak to support response operations. Methods Medical records were reviewed, and the daily line list was collected from health facilities. Descriptive data analysis was done by time, person and place. Stool specimens were first tested by antigen capture enzyme immunoassay (EIA) technique and further confirmed by reverse-transcription polymerase chain reaction (RT-PCR) as a gold standard. The product of RT-PCR was genotyped for each gene using G1-G4, G8-G9 and G12 primers for VP7 gene and P(4), P(6), P(8) and P(14) primers for VP4 gene. Results A total of 1,987 diarrheal cases (5.7 per 1000) and five deaths (case-fatality rate 0.25%) were identified and epidemiologically-linked to confirmed rotavirus from December 2016 to February 2017. Among the cases, 1,946 (98%) were < 5 children. Fourteen (74%) of the 19 tested stool specimens were positive for rotavirus by EIA and RT-PCR. Majority of strains detected were G12P(6) (25%) and G-negative P(8) (25%) followed by G9P(8) (19%), G1P(8) (13%) and G3/G2 P(8), G12P(8), and G-negative P(6) (6% each). Conclusion Diarrheal outbreak which occurred in West-Shewa zone of Ethiopia was associated with rotavirus and relatively more affected districts with low vaccination coverage. Routine rotavirus vaccination quality and coverage should be evaluated and the surveillance system needs to be strengthened to detect, prevent and control a similar outbreak.
Description of a new species of Music frogs (Anura, Ranidae, Nidirana) from Mt Dayao, southern China

Abstract A new species of Music frogs, Nidiranayaoicasp. nov. is described based on a series of adult male specimens collected from Mt Dayao, Guangxi, southern China, providing valuable new information on the phylogeny, bioacoustics, and biogeography of related species within the genus Nidirana. The new species forms the sister taxon to N.daunchina from western China and together the sister taxon to N.chapaensis from northern Vietnam. Nidiranayaoicasp. nov. can be distinguished from all known congeners by a significant genetic divergence in the mitochondrial 16S and CO1 genes, the advertisement call containing 1–3 rapidly repeated regular notes, and the combination of morphological characteristics including a medium-sized body with SVL 40.4–45.9 mm in adult males; lateroventral grooves on every digit, not meeting at the tip of disk; tibio-tarsal articulation reaching the nostril; the presence of a pair of subgular vocal sacs in males; and one single developed nuptial pad on dorsal surface of first finger in males.
Strong Bond Cleavage Promoted by Silyl Group Migration in a Coordination Sphere

C-CN bond cleavage in organonitriles was attained in the photoreaction with HSiEt3 in the presence of a catalytic amount of ( 5 -C5H5)Fe(CO)2Me. The reaction sequence was proposed, where silyl migration from Fe to N in the coordinating nitrile is a key step. DFT calculations proposed a silyl migration with small activation energy of 4.0 kcal/mol and subsequent C-CN bond cleavage on the Fe coordination sphere. N-CN bond cleavage in cyanamide (R2NCN) was also attained by a transition metal catalyst. A catalytic cycle was proposed where a silyl migration from a transition metal to the nitrile nitrogen is involved. An N-silylated  2 -amidino complex was isolated, which was shown to
Link and system performance aspects of proportional fair scheduling in WCDMA/HSDPA

In this paper, the capability of proportional fair (P-FR) packet scheduling for WCDMA/HSDPA is studied considering inherent limitations and system conditions. Specifically, issues of link adaptation dynamic range, power and code resources, convergence settings, signaling overhead, and code multiplexing are studied. Although the P-FR method may ideally offer around 100% capacity gain compared to blind scheduling, this gain largely depends on the operating conditions.
Ammonia Oxidation by the Arctic Terrestrial Thaumarchaeote Candidatus Nitrosocosmicus arcticus Is Stimulated by Increasing Temperatures

Climate change is causing arctic regions to warm disproportionally faster than those at lower latitudes, leading to alterations in carbon and nitrogen cycling, and potentially higher greenhouse gas emissions. It is thus increasingly important to better characterize the microorganisms driving arctic biogeochemical processes and their potential responses to changing conditions. Here, we describe a novel thaumarchaeon enriched from an arctic soil, Candidatus Nitrosocosmicus arcticus strain Kfb, which has been maintained for seven years in stable laboratory enrichment cultures as an aerobic ammonia oxidizer, with ammonium or urea as substrates. Genomic analyses show that this organism harbors all genes involved in ammonia oxidation and in carbon fixation via the 3-hydroxypropionate/4-hydroxybutyrate cycle, characteristic of all AOA, as well as the capability for urea utilization and potentially also for heterotrophic metabolism, similar to other AOA. Ca. N. arcticus oxidizes ammonia optimally between 20 and 28°C, well above average temperatures in its native high arctic environment (−13–4°C). Ammonia oxidation rates were nevertheless much lower than those of most cultivated mesophilic AOA (20–45°C). Intriguingly, we repeatedly observed apparent faster growth rates (based on marker gene counts) at lower temperatures (4–8°C) but without detectable nitrite production. Together with potential metabolisms predicted from its genome content, these observations indicate that Ca. N. arcticus is not a strict chemolithotrophic ammonia oxidizer and add to cumulating evidence for a greater metabolic and physiological versatility of AOA. The physiology of Ca. N. arcticus suggests that increasing temperatures might drastically affect nitrification in arctic soils by stimulating archaeal ammonia oxidation.
Epigenetic Priming in Childhood Acute Lymphoblastic Leukemia

Leukemogenesis is considered to be a process by which a normal cell acquires new but aberrant identity in order to disseminate a malignant clonal population. Under this setting, the phenotype of the leukemic cells is identical to the leukemia-initiating cell in which the genetic insult is taking place. Thus, with some exceptions, B-cell and T-cell childhood leukemias are supposed to arise from B- or T-committed cells. In contrast, several recent studies have revealed that genetic alterations may act in a “hit-and-run” way in the cell-of-origin by imposing the tumor cell identity giving rise to either B-cell or T-cell leukemias. This novel mechanism of cell transformation is mediated by an epigenetic priming mechanism that is established by the initial genetic lesion. This initial hit might be unnecessary for the subsequent tumor evolution and conservation, being the epigenetic priming the engine for the tumor evolution.
Tangram: Bridging Immutable and Mutable Abstractions for Distributed Data Analytics

Data analytics frameworks that adopt immutable data abstraction usually provide better support for failure recovery and straggler mitigation, while those that adopt mutable data abstraction are more efficient for iterative workloads thanks to their support for in-place state updates and asynchronous execution. Most existing frameworks adopt either one of the two data abstractions and do not enjoy the benefits of the other. In this paper, we propose a novel programming model named MapUpdate, which can determine whether a distributed dataset is mutable or immutable in an application. We show that MapUpdate not only offers good expressiveness, but also allows us to enjoy the benefits of both mutable and immutable abstractions. MapUpdate naturally supports iterative and asynchronous execution, and can use different recovery strategies adaptively according to failure scenarios. We implemented MapUpdate in a system, called Tangram, with novel system designs such as lightweight local task management, partition-based progress control, and context-aware failure recovery. Extensive experiments verified the benefits of Tangram on a variety of workloads including bulk processing, graph analytics, and iterative machine learning.
Discussion forum coordination support in distance courses

This work presents a piece of action research which investigates tools that provide coordination support to mediators and learners in discussion forums in a distance course. In an asynchronous environment such as the forums, participants must check the Learning Management System (LMS) regularly to follow the unfolding of the discussion and the activities of other participants. Without such information, learners and mediators do not coordinate their activities according to the group’s progress and miss chances to communicate synchronously. The tools investigated aim at keeping learners and mediators informed of what happens in the forum without the need to connect to the learning environment’s desktop web interface.
Providing absolute QoS in an OBS/WR architecture

By employing optical burst switching (OBS) in its metropolitan portion and wavelength routing (WR) in the backbone portion, the hybrid OBS/WR architecture provides end-to-end all-optical connections to end users while inheriting the fine granularity of OBS and the low loss probability of WR. However, the original OBS/WR architecture can provide only relative quality of service (QoS). That is, the burst loss possibilities of high-priority traffic flows are guaranteed to be lower than those of low-priority traffic flows, but the upper burst loss bound cannot be guaranteed with this model. We propose a call admission control (CAC) scheme to provide absolute QoS in an OBS/WR architecture and a dynamical priority allocation algorithm (DPAA) to enhance the blocking probability performance of the proposed CAC scheme. We first analyze the burst loss performance of traffic flows in the OBS/WR architecture. Based on the analytical results, a CAC scheme is proposed to provide absolute burst loss guarantee. Besides the CAC scheme, we also design a DPAA that assigns priorities to incoming traffic flows according to their QoS requirements to further improve the performance. The analysis and simulation results show that the proposed CAC scheme guarantees upper burst loss bound to different traffic flows while achieving significantly higher bandwidth utilization than other existing absolute QoS schemes in conventional OBS networks, and the proposed DPAA can achieve lower blocking probability than the original CAC scheme while maintaining the absolute QoS.
Which morphological characters are influential in a Bayesian phylogenetic analysis? Examples from the earliest osteichthyans

There has been much recent debate about which method is best for reconstructing the tree of life from morphological datasets. However, little attention has been paid to which characters, if any, are responsible for topological differences between trees recovered from competing methods on empirical datasets. Indeed, a simple procedure for finding characters supporting conflicting tree topologies is available in a parsimony framework, but an equivalent procedure in a model-based framework is lacking. Here, I introduce such a procedure and apply it to the problem of the ‘psarolepid’ osteichthyans. The ‘psarolepids’, which include the earliest known osteichthyans, are weakly supported as stem osteichthyans under parsimony but strongly supported as sarcopterygians in Bayesian analysis. The Bayesian result is driven by just two characters, both of which relate to the intracranial joint of sarcopterygians. Important characters that support a stem osteichthyan affinity for ‘psarolepids’, such as the absence of tooth enamel, have virtually no effect in a Bayesian framework. This is because of a bias towards characters with relatively complete sampling, a bias that has previously been reported for molecular data. This has important implications for Bayesian analysis of morphological datasets in general, as characters from different body parts commonly have different levels of coding completeness. Methods to critically appraise character support for conflicting phylogenetic hypotheses, such as that used here, should form an important part of phylogenetic analyses.
The Association Between Wait Times and Patient Satisfaction: Findings From Primary Health Centers in the Kingdom of Saudi Arabia

Background: It is no doubt that longer wait times can affect patient care and patients’ willingness to seek health-care services. Not only does this disrupt the continuity of treatment and care, but it also negatively impacts patient outcomes. During the past few years, the concept of patient satisfaction has become a vital component in assessing the delivery and efficiency of care. Patient satisfaction is a performance indicator that measures the extent to which patient is content and satisfied with the level of care provided by health-care institutions and providers. Therefore, this research examined association between the wait times and patient satisfaction in selected primary health-care centers in Al Qassim region in the Kingdom of Saudi Arabia. Methodology: A patient satisfaction questionnaire was administered to 850 patients, which collected patient perceptions on the delivery of care at health-care centers in Al Qassim City. Outcome measures included wait times for: registration and payment, seeing the physician, performing radiation and assays, and dispensing the medications. Results: The response rate was 72.94% (n = 620). The study found that 27.90% of the participants stated that the wait time to see the physician ranged between 21 and 30 minutes. Overall patients were mainly dissatisfied for wait times in relation to medication dispensation, vital signs measurement, dental consultations, and radiological investigation. The study found a positive association between the patient satisfaction and their education, marital status, and job. A significant regression equation was established between the patient satisfaction and age-group and literacy. Conclusion: The study advocated the need for recent technology, sufficient staffing, and patient-centered friendly methods to reduce wait times.
Cognitive SSD: A Deep Learning Engine for In-Storage Data Retrieval

Data analysis and retrieval is a widely-used component in existing artificial intelligence systems. However, each request has to go through each layer across the I/O stack, which moves tremendous irrelevant data between secondary storage, DRAM, and the on-chip cache. This leads to high response latency and rising energy consumption. To address this issue, we propose Cognitive SSD, an energy-efficient engine for deep learning based unstructured data retrieval. In Cognitive SSD, a flash-accessing accelerator named DLG-x is placed by the side of flash memory to achieve near-data deep learning and graph search. Such functions of in-SSD deep learning and graph search are exposed to the users as library APIs via NVMe command extension. Experimental results on the FPGA-based prototype reveal that the proposed Cognitive SSD reduces latency by 69.9% on average in comparison with CPU based solutions on conventional SSDs, and it reduces the overall system power consumption by up to 34.4% and 63.0% respectively when compared to CPU and GPU based solutions that deliver comparable performance.
PostMan: Rapidly Mitigating Bursty Traffic by Offloading Packet Processing

Unexpected bursty traffic due to certain sudden events, such as news in the spotlight on a social network or discounted items on sale, can cause severe load imbalance in backend services. Migrating hot data—the standard approach to achieve load balance—meets a challenge when handling such unexpected load imbalance, because migrating data will slow down the server that is already under heavy pressure. This paper proposes PostMan, an alternative approach to rapidly mitigate load imbalance for services processing small requests. Motivated by the observation that processing large packets incurs far less CPU overhead than processing small ones, PostMan deploys a number of middleboxes called helpers to assemble small packets into large ones for the heavily-loaded server. This approach essentially offloads the overhead of packet processing from the heavily-loaded server to others. To minimize the overhead, PostMan activates helpers on demand, only when bursty traffic is detected. To tolerate helper failures, PostMan can migrate connections across helpers and can ensure packet ordering despite such migration. Our evaluation shows that, with the help of PostMan, a Memcached server can mitigate bursty traffic within hundreds of milliseconds, while migrating data takes tens of seconds and increases the latency during migration.
SILK: Preventing Latency Spikes in Log-Structured Merge Key-Value Stores

LSM-based KV stores are designed to offer good write performance, by capturing client writes in memory, and only later flushing them to storage. Writes are later compacted into a tree-like data structure on disk to improve read performance and to reduce storage space use. It has been widely documented that compactions severely hamper throughput. Various optimizations have successfully dealt with this problem. These techniques include, among others, rate-limiting flushes and compactions, selecting among compactions for maximum effect, and limiting compactions to the highest level by so-called fragmented LSMs. In this paper we focus on latencies rather than throughput. We first document the fact that LSM KVs exhibit high tail latencies. The techniques that have been proposed for optimizing throughput do not address this issue, and in fact in some cases exacerbate it. The root cause of these high tail latencies is interference between client writes, flushes and compactions. We then introduce the notion of an I/O scheduler for an LSM-based KV store to reduce this interference. We explore three techniques as part of this I/O scheduler: 1) opportunistically allocating more bandwidth to internal operations during periods of low load, 2) prioritizing flushes and compactions at the lower levels of the tree, and 3) preempting compactions. SILK is a new open-source KV store that incorporates this notion of an I/O scheduler. SILK is derived from RocksDB, but the concepts can be applied to other LSM-based KV stores. We use both a production workload at Nutanix and synthetic benchmarks to demonstrate that SILK achieves up to two orders of magnitude lower 99th percentile latencies than RocksDB and TRIAD, without any significant negative effects on other performance metrics.
Khalkha Mongolian speakers' vowel bias: L1 influences on the acquisition of non-adjacent vocalic dependencies

Native language (L1) phonology has been shown to play an important role in influencing humans' perception and production of novel speech. Yet research examining the conditions which trigger humans to calculate transitional probability between non-adjacent linguistic elements has not considered the potential influence of L1 phonology. For example, previous artificial grammar learning (AGL) literature has shown that participants acquire certain non-adjacent phonological dependencies only with difficulty. However, this previous research used only speakers of English or French, languages which do not exhibit such dependencies. This paper investigates how L1 phonology influences participants' acquisition of non-adjacent phonological dependencies in an AGL task. Five experiments were conducted with speakers of Khalkha Mongolian, a language which exhibits a non-adjacent dependency, vowel harmony and with speakers of American English, a language which exhibits no such dependencies. Khalkha Mongolian speakers successfully acquired non-adjacent vocalic dependencies while American English speakers failed to do so under identical statistical conditions. Besides providing further evidence that statistical learning is not limited to the acquisition of adjacent dependencies, these findings suggest that L1 phonology plays an important role in biasing speakers' attention towards certain aspects of language.
Expected Response Times in a Non-Symmetric Time Sharing Queue with a Limited Number of Service Positions

A single processor time sharing system with a limited number, say r, of service positions and unlimited waiting line is studied under a FIFO waiting line dis­ cipline. The explicit form of the equilibrium expected response time, condition­ al upon the processing requirement length, was derived for the M/M/l case with r = 2. For r . > 2 a spectral method is applied for obtaining numerical values. The behavior of the expected conditional response time, expressed in multiples of the required processing, is then investigated. The second part of the paper presents a closed form approximation of the expected response time in the M/G/l case.
Track-based Translation Layers for Interlaced Magnetic Recording

Interlaced magnetic recording (IMR) is a state-of-the-art recording technology for hard drives that makes use of heat-assisted magnetic recording (HAMR) and track overlap to offer higher capacity than conventional and shingled magnetic recording (CMR and SMR). It carries a set of write constraints that differ from those in SMR: “bottom” (e.g. even-numbered) tracks cannot be written without data loss on the adjoining “top” (e.g. odd-numbered) ones. Previously described algorithms for writing arbitrary (i.e. bottom) sectors on IMR are in some cases poorly characterized, and are either slow or require more memory than is available within the constrained disk controller environment. We provide the ﬁrst accurate performance analysis of the simple read-modify-write (RMW) approach to IMR bottom track writes, noting several inaccuracies in earlier descriptions of its performance, and evaluate it for latency, throughput and I/O ampliﬁcation on real-world traces. In addition we propose three novel memory-efﬁcient, track-based translation layers for IMR— track ﬂipping , selective track caching and dynamic track mapping , which reduce bottom track writes by moving hot data to top tracks and cold data to bottom ones in different ways. We again provide a detailed performance analysis using simulations based on real-world traces. We ﬁnd that RMW performance is poor on most traces and worse on others. The proposed approaches perform much better, especially dynamic track mapping, with low write ampliﬁcation and latency comparable to CMR for many traces.
GAIA: An OS Page Cache for Heterogeneous Systems

We propose a principled approach to integrating GPU memory with an OS page cache. We design GAIA, a weakly-consistent page cache that spans CPU and GPU memories. GAIA enables the standard mmap system call to map files into the GPU address space, thereby enabling data-dependent GPU accesses to large files and efficient write-sharing between the CPU and GPUs. Under the hood, GAIA (1) integrates lazy release consistency protocol into the OS page cache while maintaining backward compatibility with CPU processes and unmodified GPU kernels; (2) improves CPU I/O performance by using data cached in GPU memory, and (3) optimizes the readahead prefetcher to support accesses to files cached in GPUs. We prototype GAIA in Linux and evaluate it on NVIDIA Pascal GPUs. We show up to 3× speedup in CPU file I/O and up to 8× in unmodified realistic workloads such as Gunrock GPU-accelerated graph processing, image collage, and microscopy image stitching.