Miracle-dz/UniFAR-FTUs huggingface dataset:
Identification of γ-Endorphin-Generating Enzyme as Insulin-Degrading Enzyme†

The EL-4 thymoma cell line contains a peptidase which converts β-endorphin to β-endorphin 1−17 (γ-endorphin), β-endorphin 1−18, and their corresponding C-terminal fragments. This enzyme was purified approximately 700-fold to a single band on an SDS−polyacrylamide gel (106 kDa) in 16% yield. Estimation of the native molecular weight by molecular sieve chromatography gave a value of ∼220 kDa, indicating that this enzyme is a dimer. Peptide sequencing demonstrated this activity can be attributed to insulin degrading enzyme, a previously described member of the inverzincin family (Hooper, 1994). Kinetic studies with a number of peptide substrates indicate that the enzyme preferentially cleaves on the amino side of hydrophobic or basic residues. However, the substrate specificity is more complex since not all basic and hydrophobic residues in a peptide are cleaved. The enzyme exhibits a requirement for a P2‘ residue. On the basis of kcat/Km values, insulin, growth hormone releasing factor, and β-endorphin are .
KOMB: Graph-Based Characterization of Genome Dynamics in Microbial Communities

Characterizing metagenomic samples via kmer-based, database-dependent taxonomic classification methods has provided crucial insight into underlying host-associated microbiome dynamics. However, novel approaches are needed that are able to track microbial community dynamics within metagenomes to elucidate genome flux in response to perturbations and disease states. Here we describe KOMB, a novel approach for tracking homologous regions within microbiomes. KOMB utilizes K-core graph decomposition on metagenome assembly graphs to identify repetitive and homologous regions to varying degrees of resolution. K-core performs a hierarchical decomposition which partitions the graph into shells containing nodes having degree at least K, called K-shells, yielding O(V + E) complexity compared to exact betweenness centrality complexity of O(V E) found in prior related approaches. We show through rigorous validation on simulated, synthetic, and real metagenomic datasets that KOMB accurately recovers and profiles repetitive and homologous genomic regions across organisms in the sample. KOMB can also identify functionally-rich regions in Human Microbiome Project (HMP) datasets, and can be used to analyze longitudinal data and identify pivotal taxa in fecal microbiota transplantation (FMT) samples. In summary, KOMB represents a novel approach to microbiome characterization that can efficiently identify sequences of interest in metagenomes.
Development of a diagnostic technique for civil structures based on the model update of dynamic parameters

Monitoring and diagnosis of civil structures has become a popular topic in the last years, especially through the use of non-invasive tests and techniques. Moreover, the spread of operational modal analysis, that exploit ambient excitations of structures to estimate their modal parameters, allowed to reduce the costs associated to the dynamic identification. In this paper, a technique for the diagnosis of common civil structures, such as residential buildings or warehouses, is presented in order to identify local stiffness decreases that can potentially be associated to structural failures. The technique has been tested on a real warehouse built in 1960 and the results have been analyzed demonstrating the effectiveness of the methodology.
Phylogenetic evidence for a diversification of Pseudomonas syringae pv. pisi race 4 strains into two distinct lineages.

The emergence of race variants among Pseudomonas syringae pv. pisi was investigated. P syringae pv. pisi hrpL, intergenic sequences between hrpKL and hrpJL, and partial hrpK DNA sequences were used to establish the origin of a race 4-like derivative (PT10) obtained as an IncP1 plasmid transconjugant from a race 6 strain (1704B). DNA sequence comparisons of the hrpJKL region from these two strains show 10 substitutions, including silent and nonsilent substitutions in hrpL, and others in intergenic regions. Phylogenetic analysis of these sequences (DNA and deduced amino acids), including homologs from other P. syringae pathovars, group the lineages corresponding to the P. syringae pv. pisi sequences and cluster them with the P. syringae pv. syringae sequence outside a cluster corresponding to the P. syringae pv. phaseolicola/P. syringae pv. morsprunorum sequences. The race 4 derivative (PT10) is part of a lineage different from the race 6 strain. A hrpJKL polymerase chain reaction/restriction fragment length polymorphism method was used to identify environmental strains that correspond to the PT10 race 4- like population. Phylogenetic analysis including partial hrpL sequences from the race 4-type strain (895A), the race 4-like seed strains, and all the other P. syringae homologous sequences available show a divergence of the race 4 strains into two distinct lineages: a type-strain lineage and a PT10-like lineage.
Mechanism of Fatigue Induced by Different Cycling Paradigms With Equivalent Dosage

Leg cycling is one of the most common modes of exercise used in athletics and rehabilitation. This study used a novel cycling setting to elucidate the mechanisms, central vs. peripheral fatigue induced by different resistance with equivalent works (watt∗min). Twelve male adults received low and relatively high resistance cycling fatigue tests until exhausted (RPE > 18) in 2 weeks. The maximal voluntary contraction, voluntary activation level, and twitch forces were measured immediately before and after cycling to calculate General (GFI), central (CFI), and peripheral (PFI) fatigue indices of knee extensors, respectively. The results showed that the CFI (high: 92.26 ± 8.67%, low: 78.32 ± 11.77%, p = 0.004) and PFI (high: 73.76 ± 17.32%, low: 89.63 ± 11.01%, p < 0.017) were specific to the resistance of fatigue protocol. The GFI is influenced by the resistance of cycling to support the equivalent dosage. This study concluded that the mechanism of fatigue would be influenced by the resistance of fatigue protocol although the total works had been controlled.
Beyond Analytics: The Evolution of Stream Processing Systems

Stream processing has been an active research field for more than 20 years, but it is now witnessing its prime time due to recent successful efforts by the research community and numerous worldwide open-source communities. The goal of this tutorial is threefold. First, we aim to review and highlight noteworthy past research findings, which were largely ignored until very recently. Second, we intend to underline the differences between early ('00-'10) and modern ('11-'18) streaming systems, and how those systems have evolved through the years. Most importantly, we wish to turn the attention of the database community to recent trends: streaming systems are no longer used only for classic stream processing workloads, namely window aggregates and joins. Instead, modern streaming systems are being increasingly used to deploy general event-driven applications in a scalable fashion, challenging the design decisions, architecture and intended use of existing stream processing systems.
Defining the MIS-TLIF: A Systematic Review of Techniques and Technologies Used by Surgeons Worldwide

Study Design: Systematic review. Objective: To date there is no consensus among surgeons as to what defines an MIS-TLIF (transforaminal lumbar interbody fusion using minimally invasive spine surgery) compared to an open or mini-open TLIF. This systematic review aimed to examine the MIS-TLIF techniques reported in the recent body of literature to help provide a definition of what constitutes the MIS-TLIF, based on the consensus of the majority of surgeons. Methods: We created a database of articles published about MIS-TLIF between 2010 and 2018. We evaluated the technical components of the MIS-TLIF including instruments and incisions used as well the order in which key steps are performed. Results: We could identify several patterns for MIS-TLIF performance that seemed agreed upon by the majority of MIS surgeons: use of paramedian incisions; use of a tubular retractor to perform a total facetectomy, decompression, and interbody cage implantation; and percutaneous insertion of the pedicle-screw rod constructs with intraoperative imaging. Conclusion: Based on this review of the literature, the key features used by surgeons performing MIS TLIF include the use of nonexpandable or expandable tubular retractors, a paramedian or lateral incision, and the use of a microscope or endoscope for visualization. Approaches using expandable nontubular retractors, those that require extensive subperiosteal dissection from the midline laterally, or specular-based retractors with wide pedicle to pedicle exposure are far less likely to be promoted as an MIS-based approach. A definition is necessary to improve the communication among spine surgeons in research as well as patient education.
Energetic Cost and Kinematics of Pushing a Stroller on Flat and Uphill Terrain

During early parenthood, walking and/or running while pushing a stroller is a common form of endurance exercise among both recreationally active individuals and athletes. Here, we investigate how pushing a stroller influences the energetic cost, gross efficiency (GE), and kinematic behavior of well-trained men and women while walking or running on flat and uphill incline. Eight men and nine women, all recreationally active, performed three 5-min submaximal tests of walking or running during four different testing sessions, in randomized order: with and without pushing a 24.3-kg stroller on a flat (1%; 6, 8/9, and 11/12 km/h for women/men) and uphill (10%; 5, 6.5/7.5, and 7.5/8.5 km/h for women/men) incline. Respiratory parameters, heart rate (HR), blood lactate concentration, and rating of perceived exertion (RPE) were determined and video-based kinematic analysis was performed in connection with all these tests. Except while walking on the flat incline, pushing a stroller increased the energetic cost of walking/running under all conditions (all p < 0.05). This was associated with shorter and more rapid strides on both inclines (all p < 0.05); however, GE was higher when pushing the stroller (p < 0.05). The increase in energetic cost of pushing the stroller was approximately threefold higher uphill than on the flat incline, and women were influenced more than men when running uphill at the highest speed (all p < 0.05). Here, we provide novel insights on the energetic cost and kinematic behavior of pushing a stroller while walking or running on flat and uphill inclines. The energetic cost of pushing a stroller was clearly higher than for unloaded exercise, coincided by shorter and more rapid strides, and especially pronounced on uphill terrain where also women were more influenced than men.
Lack of genetic differentiation in the fat snook Centropomus parallelus (Teleostei: Centropomidae) along the Brazilian coast

The patterns of genetic variation in a fragment of the cytochrome b mtDNA gene in 130 individuals of the fat snook (Centropomus parallelus) did not show evidence of genetic differentiation along the Brazilian coast as shown in F-statistics and AMOVA analyses, indicating the existence of high gene flow among the studied populations. In addition, the study of the evolutionary demography of the species using mismatch distribution analysis and statistical tests such as Tajima’s D and Fu’s F indicate that it experienced a pattern of population expansion during its recent evolutionary history.
Derivational Morphology in Agrammatic Aphasia: A Comparison Between Prefixed and Suffixed Words

Although a relatively large number of studies on acquired language impairments have tested the case of derivational morphology, none of these have specifically investigated whether there are differences in how prefixed and suffixed derived words are impaired. Based on linguistic and psycholinguistic considerations on prefixed and suffixed derived words, differences in how these two types of derivations are processed, and consequently impaired, are predicted. In the present study, we investigated the errors produced in reading aloud simple, prefixed, and suffixed words by three German individuals with agrammatic aphasia (NN, LG, SA). We found that, while NN and LG produced similar numbers of errors with prefixed and suffixed words, SA showed a selective impairment for prefixed words. Furthermore, NN and SA produced more errors specifically involving the affix with prefixed words than with suffixed words. We discuss our findings in terms of relative position of stem and affix in prefixed and suffixed words, as well as in terms of specific properties of prefixes and suffixes.
Timely Reporting of Heavy Hitters Using External Memory

Given an input stream S of size N, a ɸ-heavy hitter is an item that occurs at least ɸN times in S. The problem of finding heavy-hitters is extensively studied in the database literature. We study a real-time heavy-hitters variant in which an element must be reported shortly after we see its T = ɸ N-th occurrence (and hence it becomes a heavy hitter). We call this the Timely Event Detection (TED) Problem. The TED problem models the needs of many real-world monitoring systems, which demand accurate (i.e., no false negatives) and timely reporting of all events from large, high-speed streams with a low reporting threshold (high sensitivity). Like the classic heavy-hitters problem, solving the TED problem without false-positives requires large space (Ω (N) words). Thus in-RAM heavy-hitters algorithms typically sacrifice accuracy (i.e., allow false positives), sensitivity, or timeliness (i.e., use multiple passes). We show how to adapt heavy-hitters algorithms to external memory to solve the TED problem on large high-speed streams while guaranteeing accuracy, sensitivity, and timeliness. Our data structures are limited only by I/O-bandwidth (not latency) and support a tunable tradeoff between reporting delay and I/O overhead. With a small bounded reporting delay, our algorithms incur only a logarithmic I/O overhead. We implement and validate our data structures empirically using the Firehose streaming benchmark. Multi-threaded versions of our structures can scale to process 11M observations per second before becoming CPU bound. In comparison, a naive adaptation of the standard heavy-hitters algorithm to external memory would be limited by the storage device’s random I/O throughput, i.e., ≈100K observations per second.
Beyond Base-2 Logarithmic Number Systems (WiP Paper)

Logarithmic number systems (LNS) reduce hardware complexity for multiplication and division in embedded systems, at the cost of more complicated addition and subtraction. Existing LNS typically use base-2, meaning that representable numbers are some (often fractional) power of two. We argue that other bases should be considered. The base of the LNS determines the distribution of values and may reduce representation errors when converting inputs to LNS in domain-specific embedded hardware accelerators. Further, LNS addition and subtraction are normally implemented with lookup tables whose properties may be a function of the base. We show that other bases can lower both representation and addition and subtraction error. We consider the case of 8-bit LNS, when converting from 8-bit floating point (FP). We find that base-1.984 significantly reduces the conversion error. Where we can scale values, base-1.851 reduces the error to just 0.011 units of least precision (ULP). A suitable base can also reduce average arithmetic errors. For example, base-1.802 LNS has an average error of 0.242 ULP and 0.212 ULP as compared to 0.243 ULP and 0.226 ULP for addition and subtraction, respectively, for base-2.
Comparative kayomorphology of edible Musa cultivars of West Bengal

Seedless cultivars of banana are generally triploids, and diploids or tetraploids are rarer. In the present study, the karyomorphology of eight edible Musa cultivars of West Bengal was investigated for the first time to contribute to a better understanding of chromosome features and chromosome changes in the way of variation. Among the eight cultivars, seven were triploid and only the eighth seeded cultivar was diploid, all with basic chromosome number of x = 11. Karyotypic differences were observed between the cultivars but not enough to serve as a marker for each cultivar. Karyotype analysis has shown predominance of chromosomes with centromeres in median position with a few submedian centromeres. This report is the first of its kind for Musa cultivars where comparative karyotyping indicate that minor structural alterations of the chromosomes may have resulted in the genetic variability within the cultivated bananas, giving rise to numerous varieties or cultivars.
Network structure of interactions between phytophagous mites and their host-plants in natural ecosystems in Brazil

Abstract Phytophagous mites represent a diverse group of Arachnida, however, the patterns of their interactions with their host plants remain little explored. Herein we compare structural patterns of plant-phytophagous mite networks of forest and open habitats in Brazil. We adopted network size, network connectance and network modularity to characterize plant-mite network structure. We analyzed 11 plant-mite networks composed by 106 mite species, 96 host-plant species, and 342 distinct interactions. Tetranychidae and Eriophyidae were the most speciose mite families while Euphorbiaceae and Fabaceae were the most relevant host-plant families, hosting 67 and 16 mite species, respectively. We did not find any differences in network size and modularity between biomes and habitat types. However, network connectance was lower for open vegetation habitats than for forest habitat networks. Open areas can constrain the selection of defensive traits by plant species, leading phytophagous mites to consume plant species more selectively, which generates low connectivity in networks of these environments. The small number of plant-mite networks described here highlights the need for more efforts to increase knowledge about plant mites in Brazilian natural vegetation.
Secondary Invasions: Implications of Riparian Restoration for In‐Stream Invasion by an Aquatic Grass

The complex nature of ecosystems with multiple invaders requires whole‐system approaches to ecosystem management. Undesirable, unintended secondary effects may occur if interspecific interactions are ignored. Although degraded riparian zones urgently need effective restoration, broad‐scale removal of introduced tree species (e.g., willows [Salix spp.]) and fencing of riparian zones to exclude livestock may facilitate spread of the invasive aquatic grass Glyceria maxima in southeastern Australia. We recorded occurrence of the grass at riparian sites with different amounts of woody vegetation, including willows, and monitored spread for 2 years in locations with and without livestock. Glyceria maxima occurred more frequently at sites with little or no woody riparian vegetation. Larger, older patches fenced from livestock spread fastest. Analyses of costs of controlling G. maxima with herbicide showed that it is more cost‐effective to eradicate small patches than large patches if locations are known. However, the cost per m2 reduction in patch size is cheaper for larger patches. We recommend that small, young patches should be eradicated as soon as detected and show that spread of large source patches can be controlled effectively with continued spraying over several years. If restoration of waterways is to succeed, riparian management strategies must recognize connectivity between riparian and freshwater habitats.
Database Workload Capacity Planning using Time Series Analysis and Machine Learning

When procuring or administering any I.T. system or a component of an I.T. system, it is crucial to understand the computational resources required to run the critical business functions that are governed by any Service Level Agreements. Predicting the resources needed for future consumption is like looking into the proverbial crystal ball. In this paper we look at the forecasting techniques in use today and evaluate if those techniques are applicable to the deeper layers of the technological stack such as clustered database instances, applications and groups of transactions that make up the database workload. The approach has been implemented to use supervised machine learning to identify traits such as reoccurring patterns, shocks and trends that the workloads exhibit and account for those traits in the forecast. An experimental evaluation shows that the approach we propose reduces the complexity of performing a forecast, and accurate predictions have been produced for complex workloads.
How many marmoset (Primates: Cebidae: Callitrichinae) genera are there? A phylogenetic analysis based on multiple morphological systems

The marmosets, tribe Callitrichini, are the most speciose clade in the subfamily Callitrichinae, containing 21 species. However, there is no consensus among molecular and morphological systematists as to how many genera should be recognized for the group. To test the morphological support for the alternative generic classifications, this study presents a comprehensive phylogenetic analysis. It is the first such analysis to include all 21 species and employ continuous and discrete osteological, pelage and tegument, karyological and vocal characters. This dataset was combined with nucleotide sequences from two mitochondrial and four nuclear regions. Separate analyses showed that, among morphological datasets, osteological characters were best at solving relationships at more inclusive levels, whilst pelage characters were most informative at the interspecific level. This suggests the presence of different transformation rates for the two character sets. When a single most parsimonious tree was obtained using the 83‐character matrix, three main clades were identified, supporting the division of the marmosets into three genera: Callithrix, Cebuella and Mico. The total evidence analysis that included an additional 3481 molecular characters corroborated most of the morphology‐based clades and also supported a three‐genus classification of the marmosets. This is the first morphological study to support an Amazonian marmoset clade (Cebuella + Mico), which is also strongly supported in exclusively molecular phylogenies, and to synonimize Callibella under Mico.
Rethinking Logging, Checkpoints, and Recovery for High-Performance Storage Engines

For decades, ARIES has been the standard for logging and recovery in database systems. ARIES offers important features like support for arbitrary workloads, fuzzy checkpoints, and transparent index recovery. Nevertheless, many modern in-memory database systems use more lightweight approaches that have less overhead and better multi-core scalability but only work well for the in-memory setting. Recently, a new class of high-performance storage engines has emerged, which exploit fast SSDs to achieve performance close to pure in-memory systems but also allow out-of-memory workloads. For these systems, ARIES is too slow whereas in-memory logging proposals are not applicable. In this work, we propose a new logging and recovery design that supports incremental and fuzzy checkpointing, index recovery, out-of-memory workloads, and low-latency transaction commits. Our continuous checkpointing algorithm guarantees bounded recovery time. Using per-thread logging with minimal synchronization, our implementation achieves near-linear scalability on multi-core CPUs. We implemented and evaluated these techniques in our LeanStore storage engine. For working sets that fit in main memory, we achieve performance close to that of an in-memory approach, even with logging, checkpointing, and dirty page writing enabled. For the out-of-memory scenario, we outperform a state-of-the-art ARIES implementation by a factor of two.