Miracle-dz/UniFAR-FTUs huggingface dataset:
LDBC Graphalytics: A Benchmark for Large-Scale Graph Analysis on Parallel and Distributed Platforms

In this paper we introduce LDBC Graphalytics, a new industrial-grade benchmark for graph analysis platforms. It consists of six deterministic algorithms, standard datasets, synthetic dataset generators, and reference output, that enable the objective comparison of graph analysis platforms. Its test harness produces deep metrics that quantify multiple kinds of system scalability, such as horizontal/vertical and weak/strong, and of robustness, such as failures and performance variability. The benchmark comes with open-source software for generating data and monitoring performance. We describe and analyze six implementations of the benchmark (three from the community, three from the industry), providing insights into the strengths and weaknesses of the platforms. Key to our contribution, vendors perform the tuning and benchmarking of their platforms.
Synthesizing benchmarks for predictive modeling

Predictive modeling using machine learning is an effective method for building compiler heuristics, but there is a shortage of benchmarks. Typical machine learning experiments outside of the compilation field train over thousands or millions of examples. In machine learning for compilers, however, there are typically only a few dozen common benchmarks available. This limits the quality of learned models, as they have very sparse training data for what are often high-dimensional feature spaces. What is needed is a way to generate an unbounded number of training programs that finely cover the feature space. At the same time the generated programs must be similar to the types of programs that human developers actually write, otherwise the learning will target the wrong parts of the feature space. We mine open source repositories for program fragments and apply deep learning techniques to automatically construct models for how humans write programs. We sample these models to generate an unbounded number of runnable training programs. The quality of the programs is such that even human developers struggle to distinguish our generated programs from hand-written code. We use our generator for OpenCL programs, CLgen, to automatically synthesize thousands of programs and show that learning over these improves the performance of a state of the art predictive model by 1.27� . In addition, the fine covering of the feature space automatically exposes weaknesses in the feature design which are invisible with the sparse training examples from existing benchmark suites. Correcting these weaknesses further increases performance by 4.30� .
SMS spam ltering: Methods and Data

Mobile or SMS spam is a real and growing problem primarily due to the availability of very cheap bulk pre-pay SMS packages and the fact that SMS engenders higher response rates as it is a trusted and personal service. SMS spam ltering is a relatively new task which inherits many issues and solutions from email spam ltering. However it poses its own specic challenges.
Diversité génétique de l’allèle O dans des populations berbères

Nous avons analyse le polymorphisme de l’allele O chez 33 individus non apparentes de phenotype O d’une population berbere de l’oasis de Siwa en Egypte. Malgre le faible nombre d’individus etudies, les resultats montrent un polymorphisme important de l’allele O. Cette population a probablement eu des contacts avec d’autres populations malgre son isolement geographique. Siwa fut une etape importante pour les caravanes parcourant le desert ; elle fut soumise a de nombreux raids et conflits. Les frequences des alleles O01 et O02 sont similaires a celles retrouvees dans une population berbere de l’Atlas marocain (Amizmiz). Trois nouveaux alleles ont ete mis en evidence dans la population de Siwa. Ces resultats confirment tout l’interet d’etudier le polymorphisme moleculaire de l’allele O pour mieux comprendre l’histoire genetique des populations.
SHI/STY-family members redundantly regulate auxin homeostasis in basal and higher plants

The hormone auxin plays fundamental roles in plant development by stimulating growth and differentiation of cells and tissues. Auxin action appears to rely on the formation of auxin gradients and/or concentration maxima, in large created by polar auxin transport. However, recent studies suggest that auxin synthesis also commence at sites of high auxin signaling and that spatiotemporal control of auxin biosynthesis may be required in the formation or maintenance of certain auxin maxima. The SHI/STY-family member STYLISH1 (STY1) has previously been shown to induce the activity of the auxin biosynthesis gene YUCCA4 in lateral organs of Arabidopsis thaliana. This thesis describe the functional characterization of members of the embryophyte specific SHI/STY-family in the model species A. thaliana and Physcomitrella patens. Phenotypic analysis of A. thaliana plants carrying mutations in SHI/STY-family genes revealed that the gene products act highly redundant and in a dose-dependent manner in flower and leaf development. Protein studies showed that SHI/STY proteins regulate auxin biosynthesis by acting as transcriptional activators interacting with the YUC4 promoter. Additionally, promoters of other auxin biosynthesis-related genes were activated by STY1. The sequence targeted by STY1 was identified by comparing target gene promoters. Mutations in the identified element abolished STY1-YUC4 interaction in yeast. A conserved promoter element was also discovered in most SHI/STY members, including STY1. This element was shown to be essential for gene expression in most aerial organs and could be the target of AP2/ERF-family members. Identical expression patterns and knock-out mutant phenotypes of the moss P. patens SHI/STY-family members indicated that they act redundantly, as in A. thaliana. The knock-out and overexpressor lines showed phenotypes related to reduced and increased auxin levels, respectively, and the overexpressor lines indeed displayed elevated auxin levels. The SHI/STY genes of moss and higher plants are very similar and we suggest that they perform conserved functions.
The Role of BDNF on Neural Plasticity in Depression

Using behavioral, pharmacological, and molecular methods, lots of studies reveal that depression is closely related to the abnormal neural plasticity processes occurring in the prefrontal cortex and limbic system such as the hippocampus and amygdala. Meanwhile, functions of the brain-derived neurotrophic factor (BDNF) and the other neurotrophins in the pathogenesis of depression are well known. The maladaptive neuroplastic in depression may be related to alterations in the levels of neurotrophic factors, which play a central role in plasticity. Enhancement of neurotrophic factors signaling has great potential in therapy for depression. This review highlights the relevance of neurotrophic factors mediated neural plasticity and pathophysiology of depression. These studies reviewed here may suggest new possible targets for antidepressant drugs such as neurotrophins, their receptors, and relevant signaling pathways, and agents facilitating the activation of gene expression and increasing the transcription of neurotrophic factors in the brain.
Dietary Patterns in Black Abalone Haliotis cracherodii Leach, 1814 as Indicated by Observation of Drift Algal and Seagrass Capture at San Nicolas Island, California, USA, 1982 to 2019

ABSTRACT Black abalone Haliotis cracherodii Leach, 1814 are known to feed on drift plant macrodetritus moved about in the intertidal zone by waves and currents. Drift capture is a trait shared by at least several other abalone species. Drift materials are entrapped beneath the anterior foot and held for ingestion. The quantitative significance of feeding on entrapped drift macrodetritus for black abalone is unknown. Furthermore, there are no published data on the extent to which local and mesoscale spatial distributions of source plant populations influence the composition of drift plant material in black abalone diet as acquired by entrapment. From February 1982 through March 2019, occurrences of macrodetrital entrapment by black abalone were observed in nine rocky intertidal study plots, with a summed surface area of 2,054 m2, on the periphery of San Nicolas Island (SNI), California (Island centroid at ∼33.25°, –119.50°). A small preliminary survey and 27 complete surveys were performed during the study period (mean of ∼1.4 y between complete surveys). During the study, more than 1.5 × 105 black abalone were examined. The total likely included repeated observations of many individuals as a result of the known longevity and limited mobility of the species. Of those observed, ∼1.65 × 103 black abalone were recorded as apparently ingesting entrapped items. Frequency data were dominated (∼95% of all records) by three species of kelp Macrocystis pyrifera (Linnaeus) C. Agardh; commonly known as “giant kelp”, Egregia menziesii (Turner), and Eisenia arborea Areschoug. Of those, giant kelp was the most frequently observed entrapped category (∼76%). Living, attached giant kelp is rarely observed in intertidal habitats at SNI, and it follows that utilization of giant kelp by black abalone requires physical importation of the kelp from other locations. Frequencies of occurrence of giant kelp entrapment by individual study site were clearly associated with the relative surface canopy sizes and persistence patterns of offshore kelp forests adjacent (≤2 km) to the respective study sites. The pattern suggests that subsidies of drift giant kelp to black abalone diet involve mesoscale physical processes largely proximate to SNI but probably not subsidies from more distant locations such as other islands or the California mainland. Utilization of other frequently recorded kelps as food by black abalone likely involves spatial subsidies as well, but on smaller scales of distance (∼10–100 m for E. arborea; ∼0–100 m for E. menziesii). In the context of the imperiled status of black abalone, recovery actions may include outplants of captive-reared animals or transplantation of wild animals from other populations. For such actions, data from SNI suggest a need for consideration of scales of separation among release locations and nearby populations of the three apparently predominant kelp species in black abalone diet.
A New Series of Carlactonoic Acid Based Strigolactone Analogs for Fundamental and Applied Research

Strigolactones (SLs) are a group of carotenoid derived plant hormones that play a key role in establishing plant architecture and adapting it to environmental changes, and are involved in plants response to biotic and abiotic stress. SLs are also released into the soil to serve as a chemical signal attracting beneficial mycorrhizal fungi. However, this signal also induces seed germination in root parasitic weeds that represent a major global threat for agriculture. This wide spectrum of biological functions has made SL research one of the most important current topics in fundamental and applied plant science. The availability of SLs is crucial for investigating SL biology as well as for agricultural application. However, natural SLs are produced in very low amounts, and their organic synthesis is quite difficult, which creates a need for efficient and easy-to-synthesize analogs and mimics. Recently, we have generated a set of SL analogs, Methyl Phenlactonoates (MPs), which resemble the non-canonical SL carlactonoic acid. In this paper, we describe the development and characterization of a new series of easy-to-synthesize MPs. The new analogs were assessed with respect to regulation of shoot branching, impact on leaf senescence, and induction of seed germination in different root parasitic plants species. Some of the new analogs showed higher efficiency in inhibiting shoot branching as well as in triggering parasitic seed germination, compared to the commonly used GR24. MP16 was the most outstanding analog showing high activity in different SL biological functions. In summary, our new analogs series contains very promising candidates for different applications, which include the usage in studies for understanding different aspects of SL biology as well as large scale field application for combating root parasitic weeds, such as Striga hermonthica that devastates cereal yields in sub-Saharan Africa.
Immunomodulatory Roles of Polysaccharide Capsules in the Intestine

The interplay between the immune system and the microbiota in the human intestine dictates states of health vs. disease. Polysaccharide capsules are critical elements of bacteria that protect bacteria against environmental and host factors, including the host immune system. This review summarizes the mechanisms by which polysaccharide capsules from commensal and pathogenic bacteria in the gut microbiota modulate the innate and adaptive immune systems in the intestine. A deeper understanding of the roles of polysaccharide capsules in microbiota-immune interactions will provide a basis to harness their therapeutic potential to advance human health.
The secretome of a parasite alters its host's behaviour but does not recapitulate the behavioural response to infection

Parasites with complex life cycles have been proposed to manipulate the behaviour of their intermediate hosts to increase the probability of reaching their final host. The cause of these drastic behavioural changes could be manipulation factors released by the parasite in its environment (the secretome), but this has rarely been assessed. We studied a non-cerebral parasite, the cestode Schistocephalus solidus, and its intermediate host, the threespine stickleback (Gasterosteus aculeatus), whose response to danger becomes significantly diminished when infected. These altered behaviours appear only during late infection, when the worm is ready to reproduce in its final avian host. Sympatric host–parasite pairs show higher infection success for parasites, suggesting that the secretome effects could differ for allopatric host–parasite pairs with independent evolutionary histories. We tested the effects of secretome exposure on behaviour by using secretions from the early and late infection of S. solidus and by injecting them in healthy sticklebacks from a sympatric and allopatric population. Contrary to our prediction, secretome from late infection worms did not result in more risky behaviours, but secretome from early infection resulted in more cautious hosts, only in fish from the allopatric population. Our results suggest that the secretome of S. solidus contains molecules that can affect host behaviour, that the causes underlying the behavioural changes in infected sticklebacks are multifactorial and that local adaptation between host–parasite pairs may extend to the response to the parasite's secretome content.
Intertidal Zonation of the Suminoe Oyster Crassostrea ariakensis and the Kumamoto Oyster Crassostrea sikamea on the Coast of the Northern East China Sea

ABSTRACT The Suminoe oyster Crassostrea ariakensis and the Kumamoto oyster Crassostrea sikamea coexist and are habitat-forming ecosystem engineers in the Yangtze River estuary and its adjacent coasts. To date, little quantitative information is available on the intertidal zonation patterns of these two oysters within their native range or on the related mechanisms generating these spatial patterns. This study first carried out field surveys and laboratory experiments to explore the vertical zonation patterns of the two oysters in the intertidal habitats of northern Hangzhou Bay, assess the roles of abiotic (aerial exposure stress) and biotic (larval distribution, recruitment, and competition) factors in regulating vertical zonation and understand their driving mechanisms. At the study site, C. sikamea dominated the higher intertidal zone (approximately 6.7 h and 56% emersion/12 h tidal cycle), whereas C. ariakensis occupied the three deeper intertidal zones (mid, mid-low, and low intertidal). Mean aerial exposures of 56% and 42% represented the optimal growth zones and the lower limits of C. sikamea, respectively. The growth boundary of the two oysters was located in the intertidal zone that was exposed 42% of the time. The area with the highest C. ariakensis densities (the optimal growth zone) was the mid-low intertidal (mean: 3.0 h and 25% emersion/tidal cycle). In a laboratory 72-h aerial exposure experiment, the percentage of water loss was significantly greater for C. ariakensis than for C. sikamea after 24 h (P < 0.01), which was also supported by the result that C. ariakensis had a relatively greater dry tissue weight and lower water weight of soft tissue than C. sikamea (P < 0.001). The results from the real-time quantitative PCR examining the oyster larvae abundances found that C. sikamea and C. ariakensis larvae dominated the surface and bottom layers of water, respectively. Oyster recruits were significantly more abundant in the low intertidal zone (380.2 ± 48.6 spats/400 cm2) than in the high intertidal zone (153.2 ± 45.9 spats/400 cm2) (P < 0.05), whereas the mortality of the oyster spats recruited to the experimental plates did not differ between the high and low intertidal zones (P > 0.05). Twenty-two individuals among the 30 oyster recruits (73%) in the high intertidal region were identified as C. sikamea, and six recruits (20%) were identified as C. ariakensis. All 36 recruits (100%) in the low intertidal region were identified as C. ariakensis. It was concluded that the differential larval distribution, settlement, and post-settlement mortality along the intertidal elevation gradients served as a mechanism for vertical zonation of these two oyster species.
Book Review: Modern Psychometrics With R

The book “Modern Psychometrics with R” by Patrick Mair provides extensive information about recent R (R Core Team, 2020) implementations of psychometric models. The book follows a broad definition of psychometrics in order to meet “the statistical needs of modern measurement” and exceeds the standard definition of psychological measurement (Mair, 2018, p. v). The author admits that several uncommon topics are included in the book, and the strength of the book is in its discussion of a broad range of R packages. The author has extensive expertise in the R community of psychometrics and is the maintainer of the CRAN task view “Psychometrics” (Mair, 2019). The book covers 14 chapters, and in the following review, I classify the chapters into core, broadened, and uncommon psychometrics and provide a discussion of the contents. In Table 1, the titles and the R packages used in the chapters are displayed.
Simulation of the Effects of Extracellular Calcium Changes Leads to a Novel Computational Model of Human Ventricular Action Potential With a Revised Calcium Handling

The importance of electrolyte concentrations for cardiac function is well established. Electrolyte variations can lead to arrhythmias onset, due to their important role in the action potential (AP) genesis and in maintaining cell homeostasis. However, most of the human AP computer models available in literature were developed with constant electrolyte concentrations, and fail to simulate physiological changes induced by electrolyte variations. This is especially true for Ca2+, even in the O’Hara-Rudy model (ORd), one of the most widely used models in cardiac electrophysiology. Therefore, the present work develops a new human ventricular model (BPS2020), based on ORd, able to simulate the inverse dependence of AP duration (APD) on extracellular Ca2+ concentration ([Ca2+]o), and APD rate dependence at 4 mM extracellular K+. The main changes needed with respect to ORd are: (i) an increased sensitivity of L-type Ca2+ current inactivation to [Ca2+]o; (ii) a single compartment description of the sarcoplasmic reticulum; iii) the replacement of Ca2+ release. BPS2020 is able to simulate the physiological APD-[Ca2+]o relationship, while also retaining the well-reproduced properties of ORd (APD rate dependence, restitution, accommodation and current block effects). We also used BPS2020 to generate an experimentally-calibrated population of models to investigate: (i) the occurrence of repolarization abnormalities in response to hERG current block; (ii) the rate adaptation variability; (iii) the occurrence of alternans and delayed after-depolarizations at fast pacing. Our results indicate that we successfully developed an improved version of ORd, which can be used to investigate electrophysiological changes and pro-arrhythmic abnormalities induced by electrolyte variations and current block at multiple rates and at the population level.
Exogenous Melatonin Application Enhances Rhizophagus irregularis Symbiosis and Induces the Antioxidant Response of Medicago truncatula Under Lead Stress

Melatonin is a new kind of plant growth regulator. The aim of this study was to figure out the effect of melatonin on arbuscular mycorrhizal (AM) symbiosis and heavy metal tolerance. A three-factor experiment was conducted to determine the effect of melatonin application on the growth, AM symbiosis, and stress tolerance of Medicago truncatula. A two-factor (AM inoculation and Pb stress) experiment was conducted to determine the effect of AM fungus on melatonin accumulation under Pb stress. AM plants under Pb stress had a higher melatonin accumulation than non-mycorrhizal (NM) plants under Pb stress. Acetylserotonin methyltransferase (ASMT) is the enzymatic reaction of the last step in melatonin synthesis. The accumulation of melatonin may be related to the expression of MtASMT. Melatonin application increased the relative expression of MtPT4 and AM colonization in AM plants. Melatonin application decreased Pb uptake with and without AM inoculation. Both melatonin application and AM inoculation improved M. truncatula growth and increased antioxidant response with Pb stress. These results indicated that melatonin application has positive effects on AM symbiosis and Pb stress tolerance under Pb stress. AM inoculation improve melatonin synthesis capacity under Pb stress. Melatonin application may improve AM plant growth by enhancing AM symbiosis, stimulating antioxidant response, and inhibiting Pb uptake.