Miracle-dz/UniFAR-FTUs huggingface dataset:
Mixed layer variability and chlorophyll a biomass in the Bay of Bengal

The mixed layer is the most variable and dynamically active part of the marine environment that couples the underlying ocean to the atmosphere and plays an important role in determining the oceanic primary productivity. We examined the basin-scale processes controlling the seasonal variability of mixed layer depth in the Bay of Bengal and its association with chlorophyll using a suite of in situ as well as remote sensing data. A coupling between mixed layer depth and chlorophyll was seen during spring intermonsoon and summer monsoon, but for different reasons. In spring intermonsoon the temperature-dominated stratification and associated shallow mixed layer makes the upper waters of the Bay of Bengal nutrient depleted and oligotrophic. In summer, although the salinity-dominated stratification in the northern Bay of Bengal shallows the mixed layer, the nutrient input from adjoining rivers enhance the surface chlorophyll. This enhancement is confined only to the surface layer and with increase in depth, the chlorophyll biomass decreases rapidly due to reduction in sunlight by suspended sediment. In the south, advection of high salinity waters from the Arabian Sea and westward propagating Rossby waves from the eastern Bay of Bengal led to the formation of deep mixed layer. In contrast, in the Indo–Sri Lanka region, the shallow mixed layer and nutrient enrichment driven by upwelling and Ekman pumping resulted in chlorophyll enhancement. The mismatch between the nitrate and chlorophyll indicated the inadequacy of present data to fully unravel its coupling to mixed layer processes.
Auraptene Enhances AMP-Activated Protein Kinase Phosphorylation and Thereby Inhibits the Proliferation, Migration and Expression of Androgen Receptors and Prostate-Specific Antigens in Prostate Cancer Cells

Citrus hassaku extract reportedly activates AMPK. Because this extract contains an abundance of auraptene, we investigated whether pure auraptene activates AMPK and inhibits proliferation using prostate cancer cell lines. Indeed, auraptene inhibited the proliferation and migration of LNCaP cells and induced phosphorylation of AMPK or its downstream ACC in LNCaP, PC3, and HEK-293 cells, but not in DU145 cells not expressing LKB1. In addition, the mTOR-S6K pathway, located downstream from activated AMPK, was also markedly suppressed by auraptene treatment. Importantly, it was shown that auraptene reduced androgen receptor (AR) and prostate-specific antigen (PSA) expressions at both the protein and the mRNA level. This auraptene-induced downregulation of PSA was partially but significantly reversed by treatment with AMPK siRNA or the AMPK inhibitor compound C, suggesting AMPK activation to, at least partially, be causative. Finally, in DU145 cells lacking the LKB1 gene, exogenously induced LKB1 expression restored AMPK phosphorylation by auraptene, indicating the essential role of LKB1. In summary, auraptene is a potent AMPK activator that acts by elevating the AMP/ATP ratio, thereby potentially suppressing prostate cancer progression, via at least three molecular mechanisms, including suppression of the mTOR-S6K pathway, reduced lipid synthesis, and AR downregulation caused by AMPK activation.
Higher PD-1/Tim-3 expression on IFN-γ+ T cells is associated with poor prognosis in patients with acute myeloid leukemia

ABSTRACT With the success of immune checkpoint inhibitors (ICI), such as anti- programmed death-1 (PD-1) antibody for solid tumors and lymphoma immunotherapy, a number of clinical trials with ICIs have been attempted for acute myeloid leukemia (AML) immunotherapy; however, limited clinical efficacy has been reported. This may be due to the heterogeneity of immune microenvironments and various degrees of T cell exhaustion in patients and may be involved in the IFN-γ pathway. In this study, we first characterized the percentage of PD-1+ and T cell immunoglobulin mucin-domain-containing-3 (Tim-3) +IFN-γ+ T cells in peripheral blood (PB) in AML compared with healthy individuals (HIs) by flow cytometry and further discussed the possibility of the reversal of T cell exhaustion to restore the secretion capacity of cytokines in T cells in AML based on blockade of PD-1 or Tim-3 (anti-PD-1 and anti-Tim-3 antibody) in vitro using a cytokine protein chip. A significantly increased percentage of PD-1+, Tim-3+, and PD-1+Tim-3+ IFN-γ+ T cells was observed in PB from patients with AML in comparison with HIs. Moreover, higher PD-1+IFN-γ+CD3+/CD8+ T cell levels were associated with poor overall survival in AML patients. Regarding leukemia cells, the percentage of Tim-3 in CD117+CD34+ AML cells was positively correlated with PD-1 in IFN-γ+CD4+ T cells. Furthermore, blocking PD-1 and Tim-3 may involve multiple cytokines and helper T cell subsets, mainly Th1 and Treg cells. Blockade of PD-1 or Tim-3 tends to restore cytokine secretion to a certain extent, a synergistic effect shown by the co-blockade of PD-1 and Tim-3. However, we also demonstrated the heterogeneity of secretory cytokines in ICI-treated T cells in AML patients. GRAPHICAL ABSTRACT
Reported Outcome Measures in Mohs Micrographic Surgery in Studies With Defined Techniques for Embedding and Processing of Tissue: A Systematic Review

Supplemental Digital Content is Available in the Text. BACKGROUND Mohs micrographic surgery (MMS) is a technique that combines surgical excision and histologic evaluation to achieve higher cure rates for skin cancer than traditional surgical excision. Competing performance measures have fostered numerous histologic techniques for MMS. OBJECTIVE To analyze differences in primary outcomes in the published literature regarding the technique of tissue processing and embedding during the MMS process. METHODS A systematic review was performed of the published literature in MEDLINE, PubMed, Embase, and Cochrane library that included a description of the manipulation of tissue during the grossing and embedding steps of MMS. RESULTS Inclusion criteria were met by 61 articles. Of these studies, the cure/recurrence rate was assessed in 1 article (1.6%), tissue conservation was assessed in 47 (77%), time-saving was assessed in 35 (57%), cost-saving was assessed in 6 (10%), and decreased artifact were assessed in 20 (33%). CONCLUSION There is a lack of standardization for assessing clinical outcomes in the published literature regarding MMS process techniques. Cure is a critical outcome in studies comparing MMS processing methodologies.
Chocolate unicorns and smiling teddy biscuits: analysis of the use of child-directed marketing on the packages of Australian foods

Abstract Objective: The use of food packaging as a vehicle for marketing to children is under investigated. Our objective was to determine the prevalence and types of child-directed promotional techniques used on food packaging in Australia. Design: Based on existing literature and regulations, we developed a framework to classify on-pack child-directed promotional techniques involving the use of characters and other elements that appeal to children. We analysed the packaging of all products in eight food categories available for sale from supermarkets in 2019 and recorded the use of child-directed promotions on pack. We assessed the number and proportion of products displaying child-directed promotional techniques overall and assessed the healthiness of products using child-directed promotions against four indicators of healthiness to provide summary data overall and for the manufacturers who most frequently employed child-targeted strategies. Setting: Data were collected from the FoodSwitch database in Sydney, Australia. Results: 901/8006 (11·3 %) products displayed one or more child-directed on-pack element. Most frequent was on foods for infants and young children (n 315), confectionery (n 283), snack foods (n 172) and dairy (n 168). Personified characters were the most commonly used element (n 512). Products using child-directed promotional techniques scored poorly on all four indicators of healthiness: mean health star rating 2·34 (out of 5); 81 % ultra-processed and 6·1 % and 4·5 % products eligible to market to children under Western Pacific and Mexican nutrient profiling schemes, respectively. Conclusions: Australian children are targeted by promotional techniques on the packaging of unhealthy food products. Stronger regulation of these techniques is warranted to protect children’s health.
Association between sex hormones and anti-S/RBD antibody responses to COVID-19 vaccines in healthcare workers

ABSTRACT Healthcare workers (HCWs) are the target population for vaccination against coronavirus disease (COVID-19) as they are at a high risk of exposure and transmission of pathogens to patients. Neutralizing antibodies developed after COVID-19 vaccination decline within few months of vaccination. Several factors, including age and sex, can affect the intensity, efficacy, and duration of immune response to vaccines. However, sex-specific analyses of humoral responses to COVID-19 vaccines are lacking. This study aimed to evaluate sex-based differences in anti-S/RBD (Receptor Binding Domain) responses at three different time points after the second dose of mRNA COVID-19 vaccine in HCWs in relation to age, and to investigate the role of sex hormones as potential markers of response. Anti-S/RBD levels after two doses of the mRNA vaccine were collected from 521 HCWs naïve to COVID-19, working at two Italian Clinical Centers. Multiple regression analysis was applied to evaluate the association between anti-S levels and sex, age, and plasma levels of sex hormones. Significantly higher anti-S/RBD response to the COVID-19 vaccination was found in female HCWs, and a significant and more abrupt decline in response with time was observed in women than that in men. A novel, positive association of testosterone plasma levels and higher anti-S levels in male HCWs was found, suggesting its potential role as sex specific marker in males. In conclusion, understanding the sex-based differences in humoral immune responses to vaccines may potentially improve vaccination strategies and optimize surveillance programs for HCWs.
CHEMICAL PROPERTIES EVALUATION OF SOIL AND DRY MATTER PRODUCTIVITY OF MOMBASA GRASS IRRIGATED WITH CHEESE WHEY

Due to the large world production of cheese whey, its high nutritional load, its pollution potential and the current water shortage, this study evaluated the physicochemical characteristics of the soil in the North West region of São Paulo state, and the grass productivity guinea grass (Panicummaximum) when irrigated with whey in different concentration gradients (zero, 25, 50, 75 and 100% dilution in water) as the water requirement of the plant over 154 days. Except pots only irrigated with whey, which there was no germination, all other showed a higher growth rate than the control group (irrigated only with water). A better response as the relative growth rate and the average percentage of dry matter was observed in irrigated pots with cheese whey at a concentration of 25%. Macro and micronutrients were quantified using designs and it was observed that the guinea grass irrigated with cheese whey diluted in water at concentrations between 25 and 41%, besides provide the water requirement of the plant it was shown to be effective in replacing mineral fertilizers.
PathBank 2.0—the pathway database for model organism metabolomics

Abstract PathBank (https://pathbank.org) and its predecessor database, the Small Molecule Pathway Database (SMPDB), have been providing comprehensive metabolite pathway information for the metabolomics community since 2010. Over the past 14 years, these pathway databases have grown and evolved significantly to meet the needs of the metabolomics community and respond to continuing changes in computing technology. This year's update, PathBank 2.0, brings a number of important improvements and upgrades that should make the database more useful and more appealing to a larger cross-section of users. In particular, these improvements include: (i) a significant increase in the number of primary or canonical pathways (from 1720 to 6951); (ii) a massive increase in the total number of pathways (from 110 234 to 605 359); (iii) significant improvements to the quality of pathway diagrams and pathway descriptions; (iv) a strong emphasis on drug metabolism and drug mechanism pathways; (v) making most pathway images more slide-compatible and manuscript-compatible; (vi) adding tools to support better pathway filtering and selecting through a more complete pathway taxonomy; (vii) adding pathway analysis tools for visualizing and calculating pathway enrichment. Many other minor improvements and updates to the content, the interface and general performance of the PathBank website have also been made. Overall, we believe these upgrades and updates should greatly enhance PathBank's ease of use and its potential applications for interpreting metabolomics data.
Combined effect of left ventricular ejection fraction and obesity on sedentary behavior in patients with coronary artery disease

Sedentary behavior has been associated with poor adherence to treatment in patients with coronary artery disease. Low left ventricular ejection fraction and obesity have been separately linked to increased sedentary behavior in patients with coronary artery disease. However, the combined effect of low left ventricular ejection fraction and obesity on sedentary behavior in patients with coronary artery disease has not been thoroughly investigated. Therefore, this study aimed to examine the combined influence of left ventricular ejection fraction and obesity on sedentary behavior in patients with coronary artery disease. This descriptive cross-sectional study enrolled 200 inpatients aged ≥ 20 years who were diagnosed with coronary artery disease at a tertiary hospital in Korea between March and August 2022. Data were collected using structured questionnaires, and multivariate logistic regression analysis was performed to determine the combined effect of left ventricular ejection fraction and obesity on sedentary behavior in patients with coronary artery disease. Among the 111 patients with sedentary behavior, 38 (34.2%) had both low left ventricular ejection fraction and obesity, whereas only 11 (12.4%) of the 89 patients without sedentary behavior had both low left ventricular ejection fraction and obesity. In multivariate logistic regression analysis, patients with coronary artery disease who had both low left ventricular ejection fraction and obesity had the highest risk of sedentary behavior compared to those without either low left ventricular ejection fraction or obesity (odds ratio = 13.98, 95% confidence interval = 5.19–37.69, P < .001). The co-existence of low left ventricular ejection fraction and obesity in patients with coronary artery disease may be associated with sedentary behavior. Therefore, evaluating both left ventricular ejection fraction and obesity when assessing sedentary behavior in patients with coronary artery disease may be valuable in implementing patient-centered approaches for the secondary prevention and management of sedentary behavior in patients with coronary artery disease. However, further prospective cohort studies with larger sample sizes are required to establish causal relationships and explore interventions to mitigate sedentary behavior in this population.
Coupling of deformation and reactions during mid‐crustal shear zone development: an in situ frictional–viscous transition

A well preserved strain and reaction gradient records the progressive transformation of a megacrystic Kfs+Cpx+Opx+Bt1±Qtz syenitic pluton to a strongly sheared Kfs+Act+Bt2+Ab+Qtz tectonite within the exhumed Norumbega Fault System, Maine, USA. Detailed microstructural analysis indicates that fracturing and localized fluid infiltration initiated the deconstruction of the existing K‐feldspar and two‐pyroxene load‐bearing framework, and that feedback among metamorphic reactions, fabric development and enhanced permeability during progressive shearing led to the development of an interconnected, biotite‐ and actinolite‐rich foliation. The activation of dislocation creep in biotite and quartz, and dissolution–precipitation creep in actinolite and feldspar, with increasing strain ultimately resulted in a transition from dominantly frictional to dominantly viscous deformation processes. Petrological data show that various scales of geochemical disequilibrium exist across the strain and reaction gradient, and that reaction progress was limited by slow chemical diffusion during the early stages of deformation. Petrological modelling results indicate that the existing plutonic assemblage was metastable at mid‐crustal conditions, and that fluid infiltration and deformation allowed the product assemblage to advance towards chemical equilibration. Comparison of the observed microstructures and deformation mechanisms with experimental and numerical modelling results suggest that the development of an interconnected biotite‐dominated fabric probably caused a major (up to three fold) reduction in bulk rock strength and localization of strain into the foliated margin.
Classification system for partial distal biceps tendon tears: a descriptive 3-Tesla magnetic resonance imaging study of tear morphology

Background There is minimal literature on the morphology of partial distal biceps tendon (DBT) tears. We sought to investigate tear morphology by retrospectively reviewing 3-Tesla magnetic resonance imaging (3T MRI) scans of elbows with partial DBT tears and to propose a basic classification system. Methods 3T MRI scans of elbows with partial DBT tears were retrospectively reviewed by two experienced observers. Basic demographic data were collected. Tear morphology was recorded including type, presence of retraction (>5 mm), and presence of discrete long-head and short-head tendons at the DBT insertion. Results For analysis, 44 3T MRI scans of 44 elbows with partial DBT tears were included. There were 9 isolated long-head tears (20%), 13 isolated short-head tears (30%), 2 complete long-head tears with a partial short-head tear (5%), 5 complete short-head tears with a partial long-head tear (11%), and 15 peel-off tears (34%). Retraction was seen in 5 or 44 partial tears (11%), and 13 of the 44 DBTs were bifid tendons at the insertion (30%). Conclusions Partial DBT tears can be classified into five sub-types: long-head isolated tears, short-head isolated tears, complete long-head tears with partial short-head involvement, complete short-head tears with partial long-head involvement, and peel-off tears. Classification of tears may have implications for operative and non-operative management. Level of evidence III.
Splicing factor Prp18p promotes genome-wide fidelity of consensus 3′-splice sites

Abstract The fidelity of splice site selection is critical for proper gene expression. In particular, proper recognition of 3′-splice site (3′SS) sequences by the spliceosome is challenging considering the low complexity of the 3′SS consensus sequence YAG. Here, we show that absence of the Prp18p splicing factor results in genome-wide activation of alternative 3′SS in S. cerevisiae, including highly unusual non-YAG sequences. Usage of these non-canonical 3′SS in the absence of Prp18p is enhanced by upstream poly(U) tracts and by their potential to interact with the first intronic nucleoside, allowing them to dock in the spliceosome active site instead of the normal 3′SS. The role of Prp18p in 3′SS fidelity is facilitated by interactions with Slu7p and Prp8p, but cannot be fulfilled by Slu7p, identifying a unique role for Prp18p in 3′SS fidelity. This fidelity function is synergized by the downstream proofreading activity of the Prp22p helicase, but is independent from another late splicing helicase, Prp43p. Our results show that spliceosomes exhibit remarkably relaxed 3′SS sequence usage in the absence of Prp18p and identify a network of spliceosomal interactions centered on Prp18p which are required to promote the fidelity of the recognition of consensus 3′SS sequences.
Automatic Sleep Staging Based on Contextual Scalograms and Attention Convolution Neural Network Using Single-Channel EEG

Single-channel EEG based sleep staging is of interest to researchers due to its broad application prospect in daily sleep monitoring recently. We proposed using contextual scalograms as input and developed a convolutional neural network with attention modules named Co-ScaleNet for sleep staging. The contextual scalograms were obtained by combining the same color channels of three original RGB scalograms from consecutive epochs, and a simple and efficient data augmentation was designed according to their various forms. The Co-ScaleNet consists of two main parts. Firstly, three parallel convolutional branches with attention modules correspondingly extract and fuse features from contextual scalograms at the top layers. The remaining part is a stack of lightweight blocks. We achieved an overall accuracy of 87.0% for healthy individuals, 84.7% for depressed patients. And we obtained comparable performance on the public Sleep-EDFx (82.8%), ISRUC (84.6%) and SHHS datasets (87.7%), including a high recall of N1. The contextual scalograms of R channel as input achieved the best performance, which conform to the features of interest in visual scoring. The attention modules improved the recall of N1 and N3. Overall, the contextual scalograms provided a novel scheme for both contextual information extraction and data augmentation. Our study successfully expanded its application to depression datasets, as well as patients with sleep apnea, demonstrating its wide applicability.
MINERALOGY AND PETROLOGY OF ASSOCIATED Mg-RICH ULTRAPOTASSIC, SHOSHONITIC, AND CALC-ALKALINE ROCKS: THE MIDDLE LATIN VALLEY MONOGENETIC VOLCANOS, ROMAN MAGMATIC PROVINCE, SOUTHERN ITALY

In the Middle Latin Valley, in the Roman Magmatic Province, southern Italy, volcanism developed during the Late Pleistocene, with eruption of high-Mg magmas characterized by a low content of phenocrysts. Small volumes of magma, transported to the surface rapidly, favored by an extensional post-collision regime, led to small monogenetic centers aligned along two main tectonic trends. The absence of a large magmatic reservoir allowed the occurrence of a fairly large amount of mafic, strongly primitive volcanic rocks with a fairly large enrichment in potassium. They range in composition from plagioclase-free ultrapotassic melilite-bearing (kamafugites) to ultrapotassic leucitites and plagioclase leucitites, to trachybasalts (shoshonites), and calc-alkaline basaltic rocks (subalkaline). The composition of minerals from the four different groups of rock is reported. The Fe–Mg distribution between olivine crystals and whole rocks indicates equilibrium crystallization. The clinopyroxene shows the typical trend of alkaline potassic and ultrapotassic rocks, ranging in composition from diopside to hedenbergite. Melilite-bearing ultrapotassic rocks are found beside feldspar-bearing ultrapotassic and potassic primitive rocks. Magnesiochromite is the main spinel; it has been found enclosed in olivine cores. Olivine–spinel pairs indicate that the magmas from which they crystallized were in equilibrium with a strongly depleted mantle source. An origin from a common mantle source, in terms of a peridotitic component, is inferred for the different varieties of ultrapotassic to subalkaline primitive rocks. This source was characterized by different degrees of metasomatic enrichment arranged in a network of veins, possibly within the lithospheric upper mantle.
Isavuconazole use and TDM in real-world pediatric practice

ABSTRACT Isavuconazole (ISA) is approved for treating invasive aspergillosis and mucormycosis in adults, but its use in children remains off-label. We report on the use of ISA in real-world pediatric practice with 15 patients receiving ISA for treatment of invasive fungal infections. Therapeutic drug monitoring (TDM) was performed in all patients, with 52/111 (46.8%) Ctrough determinations out of range, thus supporting the need for TDM in children, especially those receiving extracorporeal membrane oxygenation (ECMO).