Individual coactivation patterns improve the subject identification and their behavior association

Brain states can be characterized by recurring coactivation patterns (CAPs). Traditional CAP analysis is performed at the group-level, while the human brain is individualized and the functional connectome has shown the uniqueness as fingerprint. Whether stable individual CAPs could be obtained from a single fMRI scan and could individual CAPs improve the identification is unclear. An open dataset, the midnight scan club was used in this study to answer these questions. Four CAP states were identified at three distinct levels (group-, subject- and scan-level) separately, and the CAPs were then reconstructed for each scan. Identification rate and differential identifiability were used to evaluate the identification performance. Our results demonstrated that the individual CAPs were unstable when using a single scan. By maintaining high intra-subject similarity and inter-subject differences, subject-level CAPs achieved the best identification performance. Brain regions that contributed to the identifiability were mainly located in higher-order networks (e.g., frontal-parietal network). Besides, head motion reduced the intra-subject similarity, while its impact on identification rate was non-significant. Finally, a pipeline was developed to depict brain-behavior associations in dataset with few samples but dense sampling, and individualized CAP dynamics showed an above-chance level correlation with IQ.

Online Phylogenetics using Parsimony Produces Slightly Better Trees and is Dramatically More Efficient for Large SARS-CoV-2 Phylogenies than de novo and Maximum-Likelihood Approaches

Phylogenetics has been foundational to SARS-CoV-2 research and public health policy, assisting in genomic surveillance, contact tracing, and assessing emergence and spread of new variants. However, phylogenetic analyses of SARS-CoV-2 have often relied on tools designed for de novo phylogenetic inference, in which all data are collected before any analysis is performed and the phylogeny is inferred once from scratch. SARS-CoV-2 datasets do not fit this mould. There are currently over 5 million sequenced SARS-CoV-2 genomes in public databases, with tens of thousands of new genomes added every day. Continuous data collection, combined with the public health relevance of SARS-CoV-2, invites an “online” approach to phylogenetics, in which new samples are added to existing phylogenetic trees every day. The extremely dense sampling of SARS-CoV-2 genomes also invites a comparison between Likelihood and Parsimony approaches to phylogenetic inference. Maximum Likelihood (ML) methods are more accurate when there are multiple changes at a single site on a single branch, but this accuracy comes at a large computational cost, and the dense sampling of SARS-CoV-2 genomes means that these instances will be extremely rare. Therefore, it may be that approaches based on Maximum Parsimony (MP) are sufficiently accurate for reconstructing phylogenies of SARS-CoV-2, and their simplicity means that they can be applied to much larger datasets. Here, we evaluate the performance of de novo and online phylogenetic approaches, and ML and MP frameworks, for inferring large and dense SARS-CoV-2 phylogenies. Overall, we find that online phylogenetics produces similar phylogenetic trees to de novo analyses for SARS-CoV-2, and that MP optimizations produce more accurate SARS-CoV-2 phylogenies than do ML optimizations. Since MP is thousands of times faster than presently available implementations of ML and online phylogenetics is faster than de novo, we therefore propose that, in the context of comprehensive genomic epidemiology of SARS-CoV-2, MP online phylogenetics approaches should be favored.

Optimized Classification of Suspended Particles in Seawater by Dense Sampling of Polarized Light Pulses

Suspended particles affect the state and vitality of the marine ecosystem. In situ probing and accurately classifying the suspended particles in seawater have an important impact on ecological research and environmental monitoring. Individual measurement of the optical polarization parameters scattered by the suspended particles has been proven to be a powerful tool to classify the particulate compositions in seawater. In previous works, the temporal polarized light pulses are sampled and averaged to evaluate the polarization parameters. In this paper, a method based on dense sampling of polarized light pulses is proposed and the experimental setup is built. The experimental results show that the dense sampling method optimizes the classification and increases the average accuracy by at least 16% than the average method. We demonstrate the feasibility of dense sampling method by classifying the multiple types of particles in mixed suspensions and show its excellent generalization ability by multi-classification of the particles. Additional analysis indicates that the dense sampling method basically takes advantage of the high-quality polarization parameters to optimize the classification performance. The above results suggest that the proposed dense sampling method has the potential to probe the suspended particles in seawater in red-tide early warning, as well as sediment and microplastics monitoring.

Theta-Rhythmic Oscillation of Working Memory Performance

Representations held in working memory are crucial in guiding human attention in a goal-directed fashion. Currently, it is debated whether only a single representation or several of these representations can be active and bias behavior at any given moment. In the present study, 25 university students performed a behavioral dense-sampling experiment to produce an estimate of the temporal-activation patterns of two simultaneously held visual templates. We report two key novel results. First, performance related to both representations was not continuous but fluctuated rhythmically at 6 Hz. This corresponds to neural oscillations in the theta band, the functional importance of which in working memory is well established. Second, our findings suggest that two concurrently held representations may be prioritized in alternation, not simultaneously. Our data extend recent research on rhythmic sampling of external information by demonstrating an analogous mechanism in the cyclic activation of internal working memory representations.

Collision-Free Path Planning for Efficient Inspection of Free-Form Surface by Using a Trigger Probe

Measurement path planning plays an essential role in on-machine measurement, which is often required to be time-saving and collision-free. This paper proposes a novel path planning methodology and develops an automatic collision avoidance strategy for measurement. Measurement points are generated by Contour section sampling (CSS), Grid mesh sampling (GMS), and Locally dense sampling (LDS) on the free-form surface. Afterwards, a shortest path algorithm (SPA) and a non-interference path algorithm (NIPA) are developed respectively. The simulations show that the proposed method can reduce the total inspection distance to nearly 7.82% than the original one. The presented path planning method can measure the surface of large aerospace parts directly by using a trigger probe.

Craniodental morphology and phylogeny of marsupials

The current literature on marsupial phylogenetics includes numerous studies based on analyses of morphological data with relatively limited sampling of Recent and fossil taxa, and many studies based on analyses of molecular data that include a dense sampling of Recent taxa, but relatively few that combine both data types. Another dichotomy in the marsupial phylogenetic literature is between studies that focus on New World taxa, others that focus on Sahulian taxa. To date, there has been no attempt to assess the phylogenetic relationships of the global marsupial fauna, based on combined analyses of morphology and molecular sequences, for a dense sampling of Recent and fossil taxa. For this report, we compiled morphological and molecular data from an unprecedented number of Recent and fossil marsupials. Our morphological data consist of 180 craniodental characters that we scored for 97 species representing every currently recognized Recent genus, 42 additional ingroup (crown-clade marsupial) taxa represented by well-preserved fossils, and 5 outgroups (non-marsupial metatherians). Our molecular data comprise 24.5 kb of DNA sequences from whole-mitochondrial genomes and six nuclear loci (APOB, BRCA1, GHR, RAG1, RBP3 and VWF) for 97 marsupial terminals (the same Recent taxa scored for craniodental morphology) and several placental and monotreme outgroups. The results of separate and combined analyses of these data using a wide range of phylogenetic methods support many currently accepted hypotheses of ingroup (marsupial) relationships, but they also underscore the difficulty of placing fossils with key missing data (e.g., †Evolestes), and the unique difficulty of placing others that exhibit mosaics of plesiomorphic and autapomorphic traits (e.g., †Yalkaparidon). Unique contributions of our study are (1) critical discussions and illustrations of marsupial craniodental morphology, including descriptions and illustrations of some features never previously coded for phylogenetic analysis; (2) critical assessments of relative support for many suprageneric clades; (3) estimates of divergence times derived from tip-and-node dating based on uniquely taxon-dense analyses; and (4) a revised, higher-order classification of marsupials accompanied by lists of supporting craniodental synapomorphies. Far from the last word on these topics, this report lays the foundation for future research that may be enabled by the discovery of new fossil taxa, better-preserved material of previously described taxa, novel morphological characters, and improved methods of phylogenetic analysis.

Revision of the spider genus Stygopholcus (Araneae, Pholcidae), endemic to the Balkan Peninsula

The genus Stygopholcus Kratochvíl, 1932 is endemic to the Balkan Peninsula and includes only four nominal species: the epigean S. photophilus Senglet, 1971 in the south (Greece to Albania) and the ‘northern clade’ consisting of three troglophile species ranging from Croatia to Albania: S. absoloni (Kulczyński, 1914); S. skotophilus Kratochvíl, 1940; and S. montenegrinus Kratochvíl, 1940 (original rank re-established). We present redescriptions of all species, including extensive data on ultrastructure, linear morphometrics of large samples, and numerous new localities. We georeference previously published localities as far as possible, correct several published misidentifications, and clarify nomenclatorial problems regarding the authority of Stygopholcus and the identity of the type species S. absoloni. We suggest that the ‘northern clade’ has a relict distribution, resulting from past and present geologic and climatic factors. Future work on Stygopholcus should focus on the southern Dinarides, combining dense sampling with massive use of molecular data.

Comparison of moss bag and native moss technique in monitoring airborne particulate and toxic elements

Introduction: In Vietnam, the government has invested in monitoring stations in a few big cities like Hanoi and Ho Chi Minh City, which have transportation centers and industrial zones, to assess and predict levels of air pollution. However, the main disadvantage of installing monitoring stations is the cost of investment for operations, maintenance, and equipment. It is also time-consuming to collect and analyze the results. Therefore, it is generally not suitable for the country as a whole. Methods: Using mosses to monitor air quality brings qualitative and quantitative data with simple, environmentally-friendly economic methods. Mosses have particular biological characteristics that make them very suitable adsorbents for a wide variety of chemical elements. When used as transplants like moss bags, allow them to monitor a highly dense sampling network of any site easily. Mosses are bioindicators, plants with artificial roots. Results: In this study, moss bag and native moss were the two methods used to evaluate the accumulation of trace elements in air through Barbula Indica. Observations showed that both methods could detect the same elements: Al, Si, P, S, Ca, Ti, V, Cr, Mn, Fe, Co, Ni, Cu, Zn, Br, Rb, Y, Sb, Ba, Pb, and U. However, the accumulation of the elements in native moss is higher than in moss bag. The main reason is that the absorption efficiency of native moss in air-deposited elements is higher than in moss bags. Conclusion: Moss bags have been used most extensively and successfully in urban areas, where vegetation samples are either unobtainable or are poorly located to the source. These areas can lack moss, or the native moss simply does not grow during the dry season.