Miracle-dz/UniFAR-FTUs huggingface dataset:
Molecular evolution and mutation accumulation lines in the nematode Pristionchus pacificus

Evolutionary reconstruction of the natural history of an organism ultimately requires knowledge about the development, population genetics, ecology, and phylogeny of the species. Such investigations would benefit from studies of mutational processes because mutations are the source of natural variation. The nematode Pristionchus pacificus has been developed as a model organism in evolutionary biology by comparing its development with Caenorhabditis elegans. Pristionchus pacificus and related species are associated with scarab beetles, and their ecology and phylogeny are well known. More than 200 P. pacificus isolates from all over the world are available for this cosmopolitan species. We generated mutation accumulation (MA) lines in P. pacificus to study spontaneous mutation rates in the mitochondrial genome and compared mutation rate estimates with natural variation between nine representative isolates of the species. The P. pacificus mitochondrial genome is 15,955 bp in length and is typical for nematodes. Pristionchus pacificus has all known mitochondrial genes and contains an unusual suppressor transfer RNA (tRNA) for the codon UAA. This has most likely influenced the spectrum of observable mutations because 6 of 12 mutations found in the 82 MA lines analyzed are nonsense mutations that can be suppressed by the suppressor tRNA. The overall mutation rate in P. pacificus is 7.6 10 8 per site per generation and is less than one order of magnitude different from estimates in C. elegans and Drosophila. Using this mutation rate estimate in a comparison of the mitochondrial genome of nine P. pacificus isolates, we calculate the minimum time to the most recent common ancestor at 10–10 generations. The combination of mutation rate analysis with intraspecific divergence provides a powerful tool for the reconstruction of the natural history of P. pacificus, and we discuss the ecological implication of these findings.
A novel adaptive balance-drive mechanism for industrial robots using a series elastic actuator

ABSTRACT To compensate the joint torque of Axis-II caused by end loading and mass of links in industrial robots, static balancing mechanisms are generally used. There are several existing balancing mechanism techniques. However, as these techniques lack autonomy, continuity and dynamics, they cannot completely compensate the joint torque in the presence of dynamic or multiple types of loads. In this paper, a new balancing mechanism technique for industrial robots, based on series elastic actuator (SEA) devices is presented. Simulation and experimental results prove that the devices combine the effects of the balancing mechanism and driving motor of Axis-II, as well as increase load capacity and flexibility. Therefore, this technique can be used to devise a novel dynamic balancing cylinder for heavily loaded industrial robots with active control ability, and simultaneously improve the load-to-weight ratio.
Mycobacteria in water, soil, plants and air: a review.

Amazingly, despite the 24 143 papers on mycobacteria, indexed in the Web of Science database during the last six years, published by 67 008 authors from 13 128 organizations located in 166 countries or territories, interna- tionally accepted legal directives on how to control the public health risk associated with environmental mycobacteria have yet to be developed. Mycobacteria are human and animal pathogens, causing not only tuberculosis and leprosy, but mycobacterioses of skin, soft tissues and lung. Due to their cell wall composition and their adaptability mycobac - teria can survive in different habitats for years. Their immunomodulatory ability has been recognised for more than 50 years and hundreds of papers published during the last two decades have demonstrated that small chemical products derived from mycobacterial cells participate in inflammatory pathways involved the pathogenesis of important human diseases like Crohn's disease, asthma, type 1 diabetes mellitus, psoriasis, arthrosis, Blau syndrom, sarcoidosis, autism etc. Mycobacteria can influence inflammatory pathways not only as live organisms, but also by means of components derived from dead cells. Pasteurisation or cooking does not affect this ability. Hence, how many mycobacterial cells are ingested, what factors play a role concurrently, and how long the harmful effect persists become important questions. This paper presents only a short review based on selected papers about mycobacteria in water, soil, plants and air with the aim of attracting attention to this significant global problem and of making the first steps towards protection of people. Selected bibliographic references of published data from 2007 to 2012 are presented in easy-to-navigate tables. CFU = colony forming units; DGGE = denaturation gradient gel electrophoresis; IMS = immuno-magnetic separation; IS = insertion sequence; ITS = intergenic transcribed spacer; MAC = Mycobacterium avium complex; MAP/Map = Mycobacterium avium subsp. paratuberculosis; MTC = Mycobacterium tuberculosis complex; MWF = metal working fluids; nPCR = nested PCR; NTM = non-tuberculous mycobacteria; PCR = polymerase chain reaction; PPM = poten- tially pathogenic mycobacteria; qPCR = quantitative real time PCR; RFLP = restriction fragment length polymorphism
Species Diversity of Lichens in Balh Valley of Himachal Pradesh, North Western Himalaya

During present investigation a total of sixty specimens of lichens were collected from Balh valley. The lichens were collected during November 2018 to February 2019 from twenty eight localities of Balh Valley in Mandi district of Himachal Pradesh, North Western Himalaya. A total of nineteen species of lichens were identified on the basis of morphological and anatomical characters. Relevant literature was consulted for confirmation of species identification. Out of the identified species, one species viz. Usnea longissima is being reported for the first time from Mandi district. Phaeophyscia hispidula is most common out of the nineteen species and is found in fifteen localities. The species diversity index (α, β, ɤ) of all the localities was calculated. The highest alpha diversity (four) was found in Bagla and Kasarla. The lowest alpha diversity (one) was found at Bhour, Chakker, Kansa, Nagchala and Pairi. Beta diversity of all localities was 47 and gamma diversity was 19. The identified specimens have been deposited in CPUH (The Herbarium, Department of Biosciences, Career Point University Hamirpur) for preservation and future reference.
Using VR-based interventions, wearable technology, and text mining to improve military and Veteran mental health

Introduction: Smartphones have made promising contributions to the field of military mental health by providing novel app-based approaches to enhance training and deployment, data collection, and creating social domains for participants to share information and perform research. Methods: This article reviews four applications designed specifically for military members and Veterans that increase mental health literacy, overcome barriers to care, and enhance well-being and performance. Results: The Road to Mental Readiness (R2MR) app is an on-the-go training tool based on cognitive behavioural theory (CBT). Unit Victor connects Veterans in a secure chat environment and provides information on available supports. UrMMIND is a pre-deployment tool designed to reinforce healthy behaviours and teach coping techniques. iFeel passively collects and analyses individual smartphone data to detect early signs of depression. Discussion: Mobile apps are playing an ever-increasing role within health care and, when designed and integrated correctly, can yield many benefits. While security and privacy need to be carefully weighed and addressed, they hold the potential to empower the end user in a range of novel ways that were not possible before.
Multiplexed Supply of a MISO Wireless Power Transfer System for Battery-Free Wireless Sensors

Multi-input single output wireless power transmission (MISO-WPT) systems have decisive advantages concerning flexible receiver position in comparison to single coil systems. However, the supply of the primary side brings a large uncertainty in case of variable positions of the secondary side. In this paper, a compact multiplexed primary side electronic circuit is proposed, which includes only one signal generator, a passive peak detector, a communication module, and a compensation capacitor. The novel approach has been studied and evaluated for a MISO-WPT system having a 16 coils on primary side and one coil on secondary side having the double diameter. Results show that a standard microcontroller, in this case an STM32, is sufficient for the control of the whole system, so that the costs and the energy consumption are significantly reduced. An activation strategy has been proposed, which allows to determine the optimal transmitting coil for each position of the receiving coil and to switch it on. The time-to-start-charging at different positions of the receiving coil and different number of neighbors has been determined. It remains in all cases under 2.5 s.
Development of a Functional Assessment of Chronic Illness Therapy item library and primary symptom list for the assessment of patient-reported adverse events associated with immune checkpoint modulators

Aim: To develop a comprehensive item library of patient-reported, immunotherapy-related adverse events (irAEs) that draws from and expands on the Functional Assessment of Chronic Illness Therapy (FACIT) Measurement System. Methods: Literature review and iterative expert input. Based on a literature review of irAEs, we developed a framework of immunotherapy classes and their associated symptoms. Clinical experts then reviewed iterations of symptom summaries and item maps linked to the immunotherapy framework. Experts provided content review and feedback was shared across experts until consensus was reached. The iterative process facilitated creation of a Primary Symptom List associated with immune checkpoint modulators (ICMs), drawn from the larger set of symptoms. Existing FACIT items were mapped to the symptom list, and new items were written as needed to create the item library. Results: The full item library of irAEs is comprised of 239 items, covering 142 unique symptoms across 75 inflammatory reactions/immune conditions. A subset of 66 items comprises a Primary Symptom List considered most common/relevant to ICM treatment. This includes gastrointestinal, skin, pulmonary, neurologic, musculoskeletal, and multiple miscellaneous and constitutional symptoms. Conclusion: The FACIT Immunotherapy Item Library is a compilation of 239 self-report items that capture the wide range of AEs experienced by people receiving immune treatments. A subset of 66 items comprises a Primary Symptom List meant for ICM therapy. Use of items selected from this library is encouraged in clinical research and clinical practice evaluation.
The characteristics of the complete chloroplast genome of Enhalus acoroides

Abstract Enhalus acoroides is the largest tropic seagrass, occurring in the shallow coastal areas. In this study, we characterized the complete chloroplast genome sequence of this species. The whole chloroplast genome was 176,211 bp in length with a typical quadripartite structure, including one large single-copy (LSC) region (89,851 bp), one small single-copy (SSC) region (2150 bp), and a pair of inverted repeats (IRs) (42,105 bp). The guanine-cytosine (GC) content of this genome was 38.4%. A total of 142 genes were found in this genome, including 95 protein-coding genes, 39 tRNA genes, and 8 rRNA genes. The phylogenetic analysis indicated that E. acoroides and Thalassia hemprichii formed a distinct clade.
Distinguishing Characteristics of Spring and Summer Onset El Niño Events

El Niño events can be classified into two categories according to the onset time: the spring (SP) El Niño with onset time from April to June and the summer (SU) El Niño with onset time from July to October. The SP El Niño is a basin-scale phenomenon and is closer to the conventional ENSO. It goes through the earlier and stronger heat build-up process, and the earlier occurrence of westerlies in the equatorial Pacific, which can partly explain its earlier onset time. For SU El Niño, in contrast, the anomalous signals, such as SSTAs, zonal wind anomalies, and subsurface variations, are much weaker, which can be attributed to the weaker accumulation of warm water and shorter duration of positive Bjerknes feedback. During its peak phase, anomalous southeasterlies over the eastern Pacific enhance the wind–evaporation–SST (WES) feedback and impede the development of positive SSTAs there, and then lead to a west shift of SSTA center. Recharge/discharge processes exist in both types of events but are weaker in the SU type, which may be caused by the lack of meridional Sverdrup transports as a result of weak zonal wind anomalies. A heat budget analysis demonstrates that the relative importance of thermocline (TH) and zonal advective (ZA) feedbacks in SP and SU El Niño is different. In SP El Niño, the TH feedback is dominant compared to ZA feedback in both the GODAS and SODA datasets. In SU El Niño, however, these two terms are equally important in GODAS, but not in the SODA dataset.
Gas migration for terrestrial gas hydrates in the Juhugeng mining area of Muli basin, Qilian Mountains, Northwest China

The Juhugeng mining area in the Qilian Mountains is the only district of China where terrestrial gas hydrate has been found. This paper aimed at studying the gas migration for gas hydrates based on fluid inclusion and apatite fission track experiments with samples being collected in both the hanging wall (Triassic strata, non-hydrocarbon source rocks) and footwall (Jurassic strata, hydrocarbon source rocks) of drilling cores. Fluid inclusions are found in both the hanging wall and footwall, and are characterized by two generations: the first generation includes gaseous and liquid hydrocarbon fluid inclusions with the homogenization temperature of concomitant saline water inclusions being 83–115°C, and the second generation includes gaseous fluid inclusions with the concomitant homogenization temperature of saline water inclusions being 115–149 °C, suggesting two periods of gas migration. Combining with the reconstruction of the burial and thermal histories, the gas migration history can be elaborated as follows: (1) In the Late Paleogene period (>30 Ma), the gas in the footwall migrated to the hanging wall because of the thrusting of Triassic strata, with the temperature being more than 110 ± 10°C (derived from apatite fission track results), corresponding well with the homogenization temperature of the saline water inclusions of the first generation being 115–149 °C; (2) In the Late Neogene to Quaternary (<8 Ma), the study area were impacted by the intensive faults, leading to the second gas migration with a good match between temperature lower than 110 ± 10°C (derived from apatite fission track results) and the homogenization temperature of saline water inclusions in the second generation (83–115 °C), and the geological age of the second gas migration can be restricted from 8 to 1.8 Ma. The permafrost was formed in Quaternary, so the controversial gas hydrate formation pattern can be determined that the gas should be accumulated before the permafrost was formed.
Recent population expansion in the evolutionary history of the Californian anchovy Engraulis mordax

The Californian anchovy Engraulis mordax, a temperate species, may have undergone a process of population disjunction from experiencing post-glacial water heating processes around the tip of the Baja California Peninsula, Mexico about 10,000 b.p. A genetic analysis was performed to test the null hypothesis of genetic homogeneity between the Gulf of California and Southern California, U. S. A. , and if this is the case, to estimate the time of haplotype emergence in terms of coalescence. A total of 80 sequences of the mtDNA hypervariable control region of E. mordax captured in the central Gulf of California (n = 40) and Southern California (n = 40) were analyzed. In spite of the large number of private haplotypes, no significant genetic differentiation among sites (FST = –0.0025, p = 0.686) was observed. An unimodal distribution of mismatch frequency between haplotypes indicated a model of rapid expansion in population size that, based on a mutation rate of 3.6% per million years in the control region, indicates a relatively recent nucleotide differentiation time of approximately 61,000 years. This time period corresponds to the late Pleistocene, suggesting population expansions at each locality, followed by the last episode of glaciation, which may have contributed to migration of this temperate-affinity species between two locations and the genetic homogenization. However this unique recent event of gene flow in the evolutionary history of species does not explain by itself the mismatch distribution patterns found.
Genetic Diversity of Saccostrea forskali Rock Oyster in the Gulf of Thailand

Located in the tropical region, many oysters are widely distributed near-shore in the shallow water along the Gulf of Thailand. Rock oyster, Saccostrea forskali , is commonly found attached to the rocks along the beach. In order to fully utilize them as bioindicators of aquatic pollution, in this study, the genetic diversity and distribution of S. forskali was assessed by using microsatellite markers. A total of 240 S. forskali oyster samples were collected from eight locations in seven provinces along the Gulf of Thailand including Trat, Chanthaburi, Rayong, Chon Buri, Phetchaburi, Prachuap Khiri Khan (two locations) and Chumphon, and were analyzed based on eleven microsatellite loci developed from oyster species. The average number of amplified DNA bands per locus varied between one to four bands. The observed heterozygosity of oyster populations ranged from 0.365 to 0.523 while the expected heterozygosity ranged from 0.537 and 0.597. The genetic differentiation between populations was high, suggestive of isolated populations with very low gene flow. By regular monitoring of the genetic diversities of these S. forskali populations, emerging environment threats could be efficiently detected before more catastrophic damages would occur.
Nanodiamond-polymer composite gratings as diffractive optical elements for light and neutrons I: their fabrication and light optical diffraction properties

We demonstrate for the first time the use of nanodiamond in constructing holographic nanoparticle-polymer composite transmission gratings with large saturated refractive index modulation amplitudes at both optical and slow-neutron wavelengths, resulting in efficient control of light and slow-neutron beams. This is so because nanodiamond possesses a high refractive index at optical wavelengths and large coherent and small incoherent scattering cross sections with low absorption at slow-neutron wavelengths. In the first part of the work we describe the synthesis of nanodiamond, the preparation of photopolymerizable nanodiamond-polymer composite films, the construction of transmission gratings in nanodiamond-polymer composite films and light optical diffraction experiments. Experiments of slow-neutron diffraction from such gratings will be described in the second part.
Deep3DSCan: Deep residual network and morphological descriptor based framework for lung cancer classification and 3D segmentation

With the increasing incidence rate of lung cancer patients, early diagnosis could help in reducing the mortality rate. However, accurate recognition of cancerous lesions is immensely challenging owing to factors such as low contrast variation, heterogeneity and visual similarity between benign and malignant nodules. Deep learning techniques have been very effective in performing natural image segmentation with robustness to previously unseen situations, reasonable scale invariance and the ability to detect even minute differences. However, they usually fail to learn domain-specific features due to the limited amount of available data and domain agnostic nature of these techniques. This work presents an ensemble framework Deep3DSCan for lung cancer segmentation and classification. The deep 3D segmentation network generates the 3D volume of interest from computed tomography scans of patients. The deep features and handcrafted descriptors are extracted using a fine-tuned residual network and morphological techniques, respectively. Finally, the fused features are used for cancer classification. The experiments were conducted on the publicly available LUNA16 dataset. For the segmentation, the authors achieved an accuracy of 0.927, significant improvement over the template matching technique, which had achieved an accuracy of 0.927. For the detection, previous state-of-the-art is 0.866, while ours is 0.883.
Boundary Control With Corrected Second-Order Switching Surface for Buck Converters Connected to Capacitive Loads

Boundary control (BC) with second-order switching surface is exploited for achieving faster response time and robust operation of switching power converters. However, the system performance of the boundary-controlled converters is significantly affected when it is connected to a second-stage converter with a large input capacitor. This article studies the shortcomings in second-order BC schemes of buck converter with capacitive loads and nonlinear switching loads. Second, this article proposes a BC scheme with corrected second-order switching surface to drive buck converters cascaded to boost converters. The switching criteria of the corrected control law account for the effect of unknown load capacitance as well as the variation in filter parameters. Therefore, an outer voltage ripple feedback loop is introduced to determine the corresponding switching criteria gain factor that adjusts the overall gain, while maintaining the output voltage ripple at a specified voltage band. The proposed method is verified by both simulation and hardware experiments. A 250-W buck converter prototype has been built to validate the control scheme under different load types, including a resistive-capacitive load, a boost converter, and a commercial dc electronic load. A comparison is drawn between conventional BC and the proposed method in both simulation and experimental environment, in order to highlight the advantages of the proposed method. With this approach, the converter operates at designed BC parameters independent of load capacitance and system parameter variations.
Enhancing Integrated Power and Water Distribution Networks Seismic Resilience Leveraging Microgrids

An earthquake, as one of the natural disasters, can damage vital infrastructures including the power distribution network (PDN) and water distribution network (WDN). The dependency of WDN on PDN is the other challenge that can be highlighted after the earthquake. In this paper, the resilience improvement planning of integrated PDN and WDN against earthquakes is solved through stochastic programming. Power lines and substation hardening in PDN and water pipes rehabilitation with better material are the candidate strategies to minimize the expected inaccessibility value of loads to power and water as the resilience index and to minimize the cost of strategies. The proposed model is tested on the modified IEEE 33-bus PDN with a designed WDN and its performance is evaluated under different cases where the impacts of using distributed generations (DG) in PDN, equipping the water pumps to back-up generators, and the value of loads accessibility to water on the system resilience are investigated.