Miracle-dz/UniFAR-FTUs huggingface dataset:
ReefCoreSeg: A Clustering-Based Framework for Multi-Source Data Fusion for Segmentation of Reef Drill Cores

Coral reefs are among the most biologically diverse and economically valuable ecosystems on Earth, but they are threatened by climate change. Understanding how reefs developed over geological timescales can provide important information about past environmental changes and their impacts on reef systems. Significant effort and capital have been invested in drilling and analyzing reef cores. Recognizing coral and sediment patterns visually from fossil reefs is a laborious task that demands domain expertise. In this paper, we present a machine learning-based framework that utilizes clustering and classification methods to fuse multiple sources of data for the segmentation and annotation of reef cores. The framework produces an annotated image of a reef core with six lithologies identified; massive corals, encrusted corals, coralline algae, microbialite, sand, and silt. We utilize reef cores recovered from Expedition 325 of the International Ocean Discovery Program (IODP) to the Great Barrier Reef. We use reef core image data and physical properties data to segment reef cores. We evaluate the framework using selected clustering and classification models. The results show that Gaussian mixture models can provide accurate segmentation of reef core image data, with a clear visual distinction between two major classes: massive corals and stromatolitic microbialites. Furthermore, we find that the random forest classifier provides the best annotations for the segmented reef core image data with an accuracy of 96%.
Higher antibody titres against Pseudogymnoascus destructans are associated with less white-nose syndrome skin lesions in Palearctic bats

Introduction Serological tests can be used to test whether an animal has been exposed to an infectious agent, and whether its immune system has recognized and produced antibodies against it. Paired samples taken several weeks apart then document an ongoing infection and/or seroconversion. Methods In the absence of a commercial kit, we developed an indirect enzyme-linked immunosorbent assay (ELISA) to detect the fungus-specific antibodies for Pseudogymnoascus destructans, the agent of white-nose syndrome in bats. Results and Discussion Samples collected from European Myotis myotis (n=35) and Asian Myotis dasycneme (n=11) in their hibernacula at the end of the hibernation period displayed 100% seroprevalence of antibodies against P. destructans, demonstrating a high rate of exposure. Our results showed that the higher the titre of antibodies against P. destructans, the lower the infection intensity, suggesting that a degree of protection is provided by this arm of adaptive immunity in Palearctic bats. Moreover, P. destructans infection appears to be a seasonally self-limiting disease of Palearctic bats showing seroconversion as the WNS skin lesions heal in the early post-hibernation period.
Estimation of geoid and sea surface topography from satellite altimetry by the adjoint method

In the North Atlantic fully reprocessed ERS-1 altimeter data of the year 1993 are analysed in a simultaneous estimation of the geoid undulations and the sea surface topography. The estimation is based on an assimilation of so-called sea surface heights maps into a dynamic model by the adjoint method. The preliminary result for the geoid of the North Atlantic corresponds remarkably well with the geoid of the EGM96 gravity model.
DSM-5 non-suicidal self-injury disorder in a community sample: comparing NSSI engagement, recency and severity among emerging adults

Up to one in five emerging adults engage in non-suicidal self-injury (NSSI). Providing a better understanding of factors that differentiate between who engages in lifetime NSSI and who is more likely to engage in recent and clinically severe NSSI can provide meaningful information for prevention and intervention of NSSI. The present study (n = 669) considered NSSI lifetime engagement (no prior history of NSSI vs. lifetime NSSI), recency [past NSSI (>12 months ago) vs. recent (≤12-month) NSSI], and clinical severity among those with recent NSSI (subthreshold vs. DSM-5 NSSI disorder). The prevalence of NSSI disorder was 8.4% in emerging adults aged 18 to 26 years old. Higher anxiety levels were related to NSSI engagement, but only depressive symptoms and NSSI versatility were consistently associated with more recent NSSI and NSSI disorder. A stepped-care approach may be required in addressing NSSI among emerging adults.
Phyllosphere microbial associations improve plant reproductive success

The above-ground (phyllosphere) plant microbiome is increasingly recognized as an important component of plant health. We hypothesized that phyllosphere bacterial recruitment may be disrupted in a greenhouse setting, and that adding a bacterial amendment would therefore benefit the health and growth of host plants. Using a newly developed synthetic phyllosphere bacterial microbiome for tomato (Solanum lycopersicum), we tested this hypothesis across multiple trials by manipulating microbial inoculation of leaves and measuring subsequent plant growth and reproductive success, comparing results from plants grown in both greenhouse and field settings. We confirmed that greenhouse-grown plants have a relatively depauperate phyllosphere bacterial microbiome, which both makes them an ideal system for testing the impact of phyllosphere communities on plant health and important targets for microbial amendments as we move towards increased agricultural sustainability. We find that the addition of the synthetic microbial community early in greenhouse growth leads to an increase in fruit production in this setting, implicating the phyllosphere microbiome as a key component of plant fitness and emphasizing the role that these bacterial microbiomes likely play in the ecology and evolution of plant communities.
Title: Pseudogenization of Mc1r gene associated with transcriptional 1 changes related to melanogensis explains leucistic phenotypes in 2 Oreonectes cavefish (Cypriniformes , Nemacheilidae)

21 Organisms that have colonized underground caves encounter vastly different selective 22 pressures than their relatives in above-ground habitats. While disruption of certain 23 pigmentation genes has been documented in various cave-dwelling taxa, little is 24 known about wider impacts across pigmentation and other gene pathways. We here 25 study the timeframe and transcriptional landscape of a leucistic and blind cypriniform 26 fish ( Oreonectes daqikongensis , Nemacheilidae) that inhabits karst caves in Guizhou, 27 China. Based on data from the mitochondrial ND4 , ND5 and Cytb genes we show that 28 the divergence between O. daqikongensis and its most closely related pigmented 29 species occurred ca. 6.82 million years ago (95% HPD, 5.12 – 9.01), providing ample 30 time for widespread phenotypic change. Indeed, we found that the DNA sequence of 31 Mc1r (melanocortin-1 receptor), a key gene regulating the biosynthesis of melanin in 32 most vertebrates, is pseudogenized in O. daqikongensis , caused by a 29-bp deletion in 33 the protein-coding region. Furthermore, 99,305 unigenes were annotated based on the 34 transcriptome of skin tissue of Oreonectes fish. Among the differentially expressed 35 unigenes, 7,326 (7.4% of the total unigenes) had decreased expression and 2,530 36 (2.5% of the total unigenes) had increased expression in O. daqikongensis skin. As 37 predicted, the expression of Mc1r and 18 additional genes associated with melanin 38 biosynthesis were significantly down-regulated in the skin tissue of O. daqikongensis , 39 but not in its congener. Our results, integrating with other studies on cavefishes, 40 suggest that loss of pigmentation was caused by coding region loss-of-function 41 mutations along with widespread transcriptional changes, resulting from extended 42 evolutionary time as a cave-dwelling form.
Multiscale Heterogeneous Polymer Composites for High Stiffness 4D Printed Electrically Controllable Multifunctional Structures.

4D printing is an emerging field where 3D printing techniques are used to pattern stimuli-responsive materials to create morphing structures, with time serving as the fourth dimension. However, current materials utilized for 4D printing are typically soft, exhibiting an elastic modulus (E) range of 10-4 to 10 MPa during shape change. This restricts the scalability, actuation stress, and load-bearing capabilities of the resulting structures. To overcome these limitations, multiscale heterogeneous polymer composites are introduced as a novel category of stiff, thermally responsive 4D printed materials. These inks exhibit an E that is four orders of magnitude greater than that of existing 4D printed materials and offer tunable electrical conductivities for simultaneous Joule heating actuation and self-sensing capabilities. Utilizing electrically controllable bilayers as building blocks, a flat geometry that morphs into a 3D self-standing lifting robot is designed and printed, setting new records for weight-normalized load lifted and actuation stress when compared to other 3D printed actuators. Furthermore, this ink palette is employed to create and print planar lattice structures that transform into various self-supporting complex 3D shapes. The contributions are integrated into a 4D printed electrically controlled multigait crawling robotic lattice structure that can carry 144 times its own weight.
A reappraisal of transcriptional regulation by NR5A1 and beta-catenin in adrenocortical carcinoma

Background Overexpression of the transcription factor NR5A1 and constitutive activation of canonical Wnt signalling leading to nuclear translocation of beta-catenin are hallmarks of malignancy in adrenocortical carcinoma (ACC). Based on the analysis of genomic profiles in H295R ACC cells, Mohan et al. (Cancer Res. 2023; 83: 2123-2141) recently suggested that a major determinant driving proliferation and differentiation in malignant ACC is the interaction of NR5A1 and beta-catenin on chromatin to regulate gene expression. Methods I reanalyzed the same set of data generated by Mohan et al. and other published data of knockdown-validated NR5A1 and beta-catenin target genes, Results Beta-catenin is mainly found in association to canonical T cell factor/lymphoid enhancer factor (TCF/LEF) motifs in genomic DNA. NR5A1 and beta-catenin regulate distinct target gene sets in ACC cells. Conclusion Overall, my analysis suggests a model where NR5A1 overexpression and beta-catenin activation principally act independently, rather than functionally interacting, to drive ACC malignancy.
Lipase‐catalyzed production of biodiesel: a critical review on feedstock, enzyme carrier and process factors

Biodiesel is a green and renewable alternative energy source which can be produced through lipase‐catalyzed transesterification process. Enzymatic biodiesel production has generated much interest owing to its environmentally friendly process, low wastewater treatment requirements and easy product separation. In this work, we attempt to review some of the recent patents and state‐of‐the‐art technology in lipase‐catalyzed transesterification for biodiesel production including feedstock, lipases, novel carriers and process factors. This work will provide useful guidance for researchers to develop cost efficient process for production of biodiesels.
Constraining depth range of S wave velocity decrease after large earthquakes near Parkfield, California

We use noise correlation and surface wave inversion to measure the S wave velocity changes at different depths near Parkfield, California, after the 2003 San Simeon and 2004 Parkfield earthquakes. We process continuous seismic recordings from 13 stations to obtain the noise cross‐correlation functions and measure the Rayleigh wave phase velocity changes over six frequency bands. We then invert the Rayleigh wave phase velocity changes using a series of sensitivity kernels to obtain the S wave velocity changes at different depths. Our results indicate that the S wave velocity decreases caused by the San Simeon earthquake are relatively small (~0.02%) and access depths of at least 2.3 km. The S wave velocity decreases caused by the Parkfield earthquake are larger (~0.2%), and access depths of at least 1.2 km. Our observations can be best explained by material damage and healing resulting mainly from the dynamic stress perturbations of the two large earthquakes.
Treatment of Scaphoid Non-Unions with Custom-Made 3D-Printed Titanium Partial and Total Scaphoid Prostheses and Scaphoid Interosseous Ligament Reconstruction

Purpose: Treatment of scaphoid fracture sequelae is still an unsolved problem in hand surgery. Custom-made 3D-printed titanium partial and total scaphoid prosthesis and scaphoid interosseous ligament reconstruction (SLIL) are performed in cases of non-union and isolated aseptic necrosis of the proximal scaphoid pole and when it is impossible to save the scaphoid bone, respectively. This study aims to evaluate the clinical, functional and radiographic results after these two prosthesis implantations. Methods: Between January 2019 and July 2020, nine partial and ten total scaphoid prostheses were implanted using custom-made 3D-printed titanium implants. Evaluation criteria included carpal height ratio (CHR), radioscaphoid angle, wrist extension and flexion, radial deviation and ulnar deviation of the wrist, grip strength and pinch strength, Visual Analogue Scale (VAS), the Disabilities of Arm, Shoulder, and Hand (DASH) score, and the Patient-Rated Wrist Evaluation (PRWE). Results: Clinical, functional, and radiographic improvements were found in all outcomes analyzed for both patient groups. The VAS pain scale obtained the most remarkable improvement at the one-year follow-up. The results of the DASH scores and the PRWE were good, with a great rate of patient satisfaction at the end of the follow-up. SLIL reconstruction also provided excellent stability and prevented a mid-carpal bone collapse in the short- and medium-term follow-up. Conclusions: A custom-made 3D-printed titanium partial or total scaphoid prosthesis is a viable solution for patients with scaphoid non-union and necrosis or complete scaphoid destruction in whom previous conservative or surgical treatment has failed.
Yield Forecasting Model for Maize Using Satellite Multispectral Imagery Driven Vegetation Indices

In recent decades, the cultivation of maize (_Zea mays_ L.) has witnessed remarkable growth in Bangladesh, particularly in the northern regions. Maize, as a high-yielding grain crop with diverse applications, plays a pivotal role in the country's agricultural landscape. Traditional methods of yield prediction involve time-consuming and subjective on-site field visits, resulting in significant errors and delayed information dissemination to government authorities and decision-makers. This study explores the potential of remote sensing technology to predict maize yields before harvest, thereby enhancing agricultural decision-making processes. The research utilizes 16-day (~30 m) Landsat 8 and 10-day (~10 m) Sentinel 2A imagery of two years November 2018 to February 2019 and November 2019 to February 2020 to forecast maize yields in the Kaharole upazila of the Dinajpur district, Bangladesh. Four cloud-free images, representing the maximum normalized difference vegetation index (NDVI) for each maize growing season, are selected from the Landsat 8 and Sentinel 2A data. Regression models are established to relate NDVI values to the maize yields across 20 individual farmers' fields. The results reveal that the prediction models based on mean NDVI values for the combined growing seasons outperform those based on single growing seasons and the finer spatial resolution of Sentinel 2A contributes to its superior performance in comparison to Landsat 8, offering valuable insights for improved agricultural management and food security.
The Record-Breaking Hot Summer in 2015 over Hawaii and Its Physical Causes

AbstractHawaiian surface air temperature (HST) during the summer of 2015 (from July to October) was about 1.5°C higher than the climatological mean, which was the hottest since records began in 1948. In the context of record-breaking seasonal-mean high temperature, 98 exceptional local heatwave days occurred during the summer of 2015. Based on diagnoses and simulations, this paper demonstrates that the record-high HST during the summer of 2015 arose mainly from the combined effects of the interannual and interdecadal variability of sea surface temperature anomalies (SSTAs). The interannual variability of SSTAs, with an El Nino–like pattern in the tropics and cold (warm) anomalies over the western (eastern) North Pacific, was the primary contributor to the abnormally high HST in the summer of 2015. This interannual tropical–extratropical SSTA pattern was accompanied by low-level southwesterly anomalies over the central North Pacific, which weakened the climatological northeasterly trade winds and reduced t.
A New Calibration Algorithm of Interferometric Parameters for Dual-antenna Airborne InSAR

It is significant to calibrate interferometric parameters of dual-antenna airborne InSAR systems for deriving accurate DEM with large areas. A new calibration model considering phase offset,baseline length and baseline angle was proposed in order to calibrate interferometric parameters effectively,which was induced from the basic theory of DEM deriving from InSAR. And its solution scheme was designed. The calibration experiments of interferometric parameters were done with height control points measured by GPS to calibrate the dual-antenna airborne InSAR system researched independently by Institute of Electronics,Chinese Academy of Sciences. The errors of heights derived with calibrated interferometric parameters were calculated,as validated the proposed calibration model and its solution algorithm.
Arbuscular mycorrhizal fungi increased peanut (Arachis hypogaea L.) yield by changing the rhizosphere microbial community structure in saline-alkali soil

Arbuscular mycorrhizal fungi (AMF) have demonstrated the potential to enhance the saline-alkali tolerance in plants. Nevertheless, the extent to which AMF can ameliorate the tolerance of salt-sensitive plants to alkaline conditions necessitates further investigation. The current study is primarily centered on elucidating the impact of AMF on the growth of the Huayu22 (H22) when cultivated in saline-alkaline soil. We leveraged DNA of rhizosphere microorganisms extracted from saline-alkali soil subjected to AMF treatment and conducted high-throughput sequencing encompassing 16S rRNA gene and ITS sequencing. Our findings from high-throughput sequencing unveiled Proteobacteria and Bacillus as the prevailing phylum and genus within the bacterial population, respectively. Likewise, the predominant fungal phylum and genus were identified as Ascomycota and Haematonectria. It is noteworthy that the relative abundance of Proteobacteria, Actinobacteria, Chloroflexi, Bacteroidetes, and Ascomycota exhibited significant increments subsequent to AMF inoculation. Our investigation into soil enzyme activity revealed a remarkable surge post-AMF inoculation. Notably, the amounts of pathogen growth inhibitory enzymes and organic carbon degrading enzymes rise, as predicted by the putative roles of microbial communities. In saline-alkali soil, inoculation of AMF did boost the yield of H22. Notable improvements were observed in the weight of both 100 fruits and 100 grains, which increased by 20.02% and 22.30%, respectively. Conclusively, this study not only provides a theoretical framework but also furnishes empirical evidence supporting the utilization of AMF as a viable strategy for augmenting the yield of salt-sensitive plants grown in alkaline conditions.
TAS2R38 and responsiveness to lifestyle intervention

28 Background: Although vegetable consumption is associated with decreased risk for a variety of 29 chronic diseases, few Americans meet the CDC recommendations for vegetable intake. The 30 TAS2R38 gene encodes a taste receptor that confers bitter taste sensing from chemicals found in 31 some vegetables. Common polymorphisms in TAS2R38 , including rs713598, rs1726866, and 32 rs10246939, lead to coding substitutions that alter receptor function and result in the loss of bitter 33 taste perception. 34 Objective: Our study examines whether bitter taste perception TAS2R38 diplotypes were 35 associated with vegetable consumption in participants enrolled in either an enhanced or a 36 minimal nutrition counseling intervention within a community-based dietary intervention. 37 Methods: DNA was isolated from the peripheral blood cells of study participants (N = 497) and 38 analyzed for polymorphisms using genotyping arrays. The Block Fruit and Vegetable screener 39 was used to determine frequency of vegetable consumption. Mixed effects models were used to 40 test differences in frequency of vegetable consumption between intervention and genotype 41 groups over time. 42 Results: There was no association between baseline vegetable consumption frequency and the 43 bitter taste diplotype ( p = 0.937), however after six months of the intervention, we observed an 44 interaction between bitter taste diplotypes and time ( p = 0.046). Participants in the enhanced 45 intervention increased their vegetable consumption frequency ( p = 0.020) and within this 46 intervention group, the non-bitter and intermediate-bitter tasting participants had the largest 47 increase in vegetable consumption. In contrast, in the minimal intervention group, the bitter 48 tasting participants reported a decrease in vegetable consumption. 49 Conclusions: Non-and intermediate-bitter taste blind participants increased vegetable 50 consumption in either intervention group more than those who perceive bitterness. Future 51 applications of precision medicine could consider genetic variation in bitter taste perception 52 genes when designing dietary interventions. 53