Miracle-dz/UniFAR-FTUs huggingface dataset:
Effects of Coastal Upwelling and Downwelling on Hydrographic Variability and Dissolved Oxygen in Mobile Bay

Upwellling and downwelling events are important coastal processes that strongly influence shelf ecosystem dynamics. Though changes on the shelf have been well studied, the impact of these events on estuarine systems has received less focus. In summer 2016 a downwelling and upwelling event were observed near the mouth of Mobile Bay. The impact of these events were examined throughout the bay with high spatial resolution observations. Five boat surveys were conducted to capture the spatial response of offshore forcing and its changes in the estuary. In addition to the surveys, 16 CTDs were deployed and measured temporal changes. A 7◦C temperature change was observed in the channel as a result of the offshore changes. In the shipping channel and offshore, advection was a major source of changes in heat content and often exceeded the surface heat flux. Advection of low dissolved oxygen water into the estuary was also observed in the shipping channel and at the Dauphin Island station nearest to the estuary mouth. The extent of these changes highlights the importance of estuary-shelf connectivity in riverdominated systems where offshore forcing can drive large changes in estuaries during low flow summer conditions. Keypoints: • Heat Flux observations highlight large differences in heat content associated with advection from offshore upwelling and downwelling events. • Small thermal eddy diffusivity values are associated with stratification in the estuary. c ©2018 American Geophysical Union. All Rights Reserved. • Advection of low dissolved oxygen water from the shelf into the estuary was observed in the shipping channel and near the estuary mouth. c ©2018 American Geophysical Union. All Rights Reserved.
Health-related quality of life, needs, and concerns among cancer survivors referred to rehabilitation in primary healthcare setting.

BACKGROUND AND PURPOSE There is a growing need for rehabilitation services beyond hospitals. This study aims to describe challenges faced by cancer survivors (CSs) referred for rehabilitation in primary healthcare, employing standardized scales measuring health-related quality of life (HRQOL) and open-ended questions. Furthermore, the study explores the applicability of patient-reported outcomes (PROs) in comprehensively understanding challenges encountered by CSs. MATERIAL AND METHODS This cross-sectional study involves CSs referred for cancer rehabilitation in a primary healthcare setting, including those participating in PROs as a part of routine practice. HRQOL was assessed using the Functional Assessment of Cancer Therapy-General (FACT-G). The International Classification of Functioning, Disability and Health (ICF) framed the analysis of responses to open-ended questions 'what concerns you the most? ' and 'what matters to you? ' Results: FACT-G showed the lowest scores for functional well-being (14.4) and emotional well-being (16.6), with higher scores for physical well-being (18.9) and social/family well-being (21.1). Responses to open-ended questions unveiled worries about everyday life and how cancer will impact family well-being presently and in the future. Furthermore, CSs reported a need to maintain normality and proactively address the challenges posed by the disease. INTERPRETATION CSs referred for rehabilitation in primary healthcare experience comprehensive challenges necessitating a holistic rehabilitation approach. This includes interventions supporting CSs in dealing with uncertainty, regaining a sense of control, and addressing family well-being concerns. When using PROs for need assessment, the combination of validated HRQOL scales and open-ended questions is crucial for an in-depth understanding of CSs' challenges.
Parallel Streams of Direct Corticogeniculate Feedback from Mid-level Extrastriate Cortex in the Macaque Monkey

First-order thalamic nuclei receive feedforward signals from peripheral receptors and relay these signals to primary sensory cortex. Primary sensory cortex, in turn, provides reciprocal feedback to first-order thalamus. Because the vast majority of sensory thalamocortical inputs target primary sensory cortex, their complementary corticothalamic neurons are assumed to be similarly restricted to primary sensory cortex. We upend this assumption by characterizing morphologically diverse neurons in multiple mid-level visual cortical areas of the primate (Macaca mulatta) brain that provide direct feedback to the primary visual thalamus, the dorsal lateral geniculate nucleus (LGN). Although the majority of geniculocortical neurons project to primary visual cortex (V1), a minority, located mainly in the koniocellular LGN layers, provide direct input to extrastriate visual cortex. These “V1-bypassing” projections may be implicated in blindsight. We hypothesized that geniculocortical inputs directly targeting extrastriate cortex should be complemented by reciprocal corticogeniculate circuits. Using virus-mediated circuit tracing, we discovered corticogeniculate neurons throughout three mid-level extrastriate areas: MT, MST, and V4. Quantitative morphological analyses revealed nonuniform distributions of unique cell types across areas. Many extrastriate corticogeniculate neurons had spiny stellate morphology, suggesting possible targeting of koniocellular LGN layers. Importantly though, multiple morphological types were observed across areas. Such morphological diversity could suggest parallel streams of V1-bypassing corticogeniculate feedback at multiple stages of the visual processing hierarchy. Furthermore, the presence of corticogeniculate neurons across visual cortex necessitates a reevaluation of the LGN as a hub for visual information rather than a simple relay.
Semi-supervised training for infrastructure mediated sensing: disaggregated hot and cold water sensing with minimal calibration

This thesis formalizes and evaluates the use a central sensor for detecting and classifying water usage in a home or apartment building. While the discussion largely explores the theory and implementation of the sensing, the main impact of this thesis is to address a single assertion: we are running out of water. With this sensing technology, my aim is to support initiatives in increasing awareness of water consumption and understanding of the diversity in ways that vast populations consume water. Through my sensing, I classify (1) what type of valve was activated in a home (i.e., faucet, dishwasher, toilet), (2) the temperature of water that the valve uses (i.e., hot, cold, or mixed), and (3) where in the home or apartment the valve resides (i.e., kitchen, master bathroom). This is typically known as disaggregated water sensing or end-use water sensing. In my approach, I use a central sensing point based on two pressure sensors. The sensors monitor pressure fluctuations in the home, providing a time series upon which to classify events. I formalize the feature extraction process using template matching, expertly chosen features, and sparse codebooks. Ultimately I show that few features can be created that generalize across residences, necessitating that each residence go through a calibration process. I formalize this calibration process using semi-supervised techniques such as expert knowledge through a rule-based classifier, co-training, and virtual evidence. I evaluate the system in several studies, including a longitudinal deployment of 15,000 water usages across a 1 month period in five homes. The results show that, with about 30-40 labeled examples, the system is 93% accurate at detecting the type of fixture used, 89% accurate at detecting which fixture in the home is activated, and 81% accurate at also detecting the temperature state of the valve. These accuracies are reported on a test set of 2,5004,000 water usage events per residence. This thesis, then, has implications in the water sustainability community, activity detection community, and the machine learning and signal processing communities.
Deep learning in spatially resolved transcriptfomics: a comprehensive technical view

Abstract Spatially resolved transcriptomics (SRT) is a pioneering method for simultaneously studying morphological contexts and gene expression at single-cell precision. Data emerging from SRT are multifaceted, presenting researchers with intricate gene expression matrices, precise spatial details and comprehensive histology visuals. Such rich and intricate datasets, unfortunately, render many conventional methods like traditional machine learning and statistical models ineffective. The unique challenges posed by the specialized nature of SRT data have led the scientific community to explore more sophisticated analytical avenues. Recent trends indicate an increasing reliance on deep learning algorithms, especially in areas such as spatial clustering, identification of spatially variable genes and data alignment tasks. In this manuscript, we provide a rigorous critique of these advanced deep learning methodologies, probing into their merits, limitations and avenues for further refinement. Our in-depth analysis underscores that while the recent innovations in deep learning tailored for SRT have been promising, there remains a substantial potential for enhancement. A crucial area that demands attention is the development of models that can incorporate intricate biological nuances, such as phylogeny-aware processing or in-depth analysis of minuscule histology image segments. Furthermore, addressing challenges like the elimination of batch effects, perfecting data normalization techniques and countering the overdispersion and zero inflation patterns seen in gene expression is pivotal. To support the broader scientific community in their SRT endeavors, we have meticulously assembled a comprehensive directory of readily accessible SRT databases, hoping to serve as a foundation for future research initiatives.
Crustal Magmatic System Beneath the East Pacific Rise (8°20′ to 10°10′N): Implications for Tectonomagmatic Segmentation and Crustal Melt Transport at Fast‐Spreading Ridges

Detailed images of the midcrustal magmatic system beneath the East Pacific Rise (8°20′–10°10′N) are obtained from 2‐D and 3‐D‐swath processing of along axis seismic data and are used to characterize properties of the axial crust, cross‐axis variations, and relationships with structural segmentation of the axial zone. Axial magma lens (AML) reflections are imaged beneath much of the ridge axis (mean depth 1,640 ± 185 m), as are deeper sub‐AML (SAML) reflections (brightest events ~100–800 m below AML). Local shallow regions in the AML underlie two regions of shallow seafloor depth from 9°40′–55′N and 8°26′–33′N. Enhanced magma replenishment at present beneath both sites is inferred and may be linked to nearby off‐axis volcanic chains. SAML reflections, which are observed primarily from 9°20′ to 10°05′N, indicate a finely segmented magma reservoir similar to the AML above, composed of subhorizontal, 2‐ to 7 km‐long AML segments, often with stepwise changes in reflector depth from one segment to the next. We infer that these melt bodies are related to short‐lived melt instability zones. In many locations including where seismic constraints are strongest the intermediate scale (~15–40 km) structural segmentation of the ridge axis identified in this region coincides with (1) changes in average thickness of layer 2A (by 10%–15%), (2) changes in average depth of AML (<100 m), and (3) with the spacing of punctuated low velocity zones mapped in the uppermost mantle. The ~6 km dominant length of multiple AML segments within each of the larger structural segments may reflect the spacing of local sites of ascending magma from discrete melt reservoirs pooled beneath the crust.
Modeling of water flow in multi-channel river system in the Narew National Park

Abstract Modeling of water flow in multi-channel river system in the Narew National Park. Anastomosing rivers constitute a rare example of multi-channel systems, which used to be very common before the agricultural and industrial development. Presently few of them remain worldwide and the only example in Poland is the Upper River Narew within Narew National Park. Although hydraulic modeling using one-dimensional models is commonly used to describe water flow in rivers, for multi-channel rivers problem is more complicated. For this type of rivers it is expected that the feedback between process of plants growth (expressed by Manning’s coefficient) and distribution of flow in anabranches is high. However, assignment procedure on roughness coefficients in splitting and rejoining channels is laborious and difficult. Therefore, for efficient water flow modeling in multi-channel systems a stand-alone hydraulic model equipped with automatic optimization procedure was developed. Optimization and validation stages, based on field measurements data of discharge and water levels, indicated that the model accurately simulates water flow in multi-channel system.
Triggers for transition from active surveillance to radical treatment of prostate cancer 2008-2020 - a case-control study.

OBJECTIVE To examine associations between objective signs of progression (triggers) and transition from active surveillance (AS) to radical treatment for prostate cancer (PC). PATIENTS AND METHODS This case-control study included men with low- or favourable intermediate-risk PC in the region of Halland, with data from The National Prostate Cancer Register (NPCR), Sweden, starting AS between 2008 and 2020. Cases were men who transitioned to radical treatment. For each case, 10 controls who remained in AS were selected without further matching. Triggers for transition to treatment were histopathological progression, magnetic resonance imaging (MRI) progression and increases in prostate-specific antigen (PSA) levels. We compared the probabilities for triggers between cases and controls, in 2008-2014 and 2015-2020, using logistic regression. RESULTS Amongst 846 men, we identified 98 cases in 2008-2014 and 172 cases in 2015-2020. Histopathological progression was associated with transition, most strongly in the later period (2008-2014: odds ratios [OR] 6.88, 95% confidence interval [CI] 3.69-12.80; and 2015-2020: OR 75.29, 95% CI 39.60-143.17). MRI progression was associated with transition in 2015-2020 (OR 6.38, 95% CI 2.70-15.06), whereas an increase in PSA was weakly associated with transition in the early period. The absence of triggers was associated with no transition (2008-2014: OR 0.24, 95% CI 0.15-0.40, and 2015-2020: OR 0.09, 95% CI 0.06-0.14). The probability of no trigger was 27% in cases 2015-2020. CONCLUSION The increase in association between histopathological trigger and transition to treatment indicates increased quality of AS. Still, amongst men treated from 2015 to 2020, 27% transitioned without any trigger.
A CFD-DEM simulation of food grain drying process in a fluidised bed

Drying is the most important step for post-harvest processing of food grains. This project developed a food grain drying model by combining computational fluid dynamics and discrete element method in a fluidised bed. The model incorporated heat transfer sub-models, a water evaporation sub-model in resemblance to a chemical reaction and a shrinkage sub-model. The model is first tested against experimental data from literature in terms of drying and volume shrinkage curves. Then the effects of operating parameters, grain properties and bed geometries on drying and shrinkage rates and dried product quality are quantified and discussed with the grain scale information.
Nautilid nurseries: hatchlings and juveniles of Eutrephoceras dekayi from the lower Maastrichtian (Upper Cretaceous) Pierre Shale of east-central Montana

The nautilid Eutrephoceras dekayi (Morton 1834) is relatively abundant in the lower Maastrichtian (Upper Cretaceous) Pierre Shale of east-central Montana. We analysed the morphology, size frequency distribution, and isotope composition of a large collection of 220 well-preserved specimens including hatchlings, juveniles and adults. The newly hatched shell is approximately 14 mm in diameter with a body chamber one-third whorl in angular length terminating in the nepionic constriction. Internally, the embryonic shell contains five septa. Juveniles are abundant and comprise two-thirds of the sample whereas sub-adults, defined by the incipient flattening of the venter, are rare. Adults comprise approximately one-third of the sample and average 100 mm in diameter. The co-occurrence of newly hatched shells, small juveniles and adults suggests that the eggs were laid in the same area in which the hatchlings developed. Based on the excellent preservation of the juveniles, we conclude that they did not float into the area after death, but lived in the region, implying that this area served as a nursery for young animals. The calculated temperatures of the embryonic shells are similar to those of the post-embryonic shells and generally range from 16 to 18 °C. Upon hatching, the nautilids probably followed a demersal mode of life and lived in well-oxygenated water ≤50 m deep. An examination of lethal injuries (puncture holes) suggests that all ontogenetic stages were equally vulnerable to predation. The proximity of the site to the Sheridan Delta suggests that the specimens were smothered by sudden pulses of sediment transported into the area by major storms.
Fosaprepitant and aprepitant: an update of the evidence for their place in the prevention of chemotherapy-induced nausea and vomiting

Introduction: The selective neurokinin-1 receptor antagonist aprepitant is effective in the treatment of acute and delayed chemotherapy-induced nausea and vomiting (CINV) associated with both moderately and highly emetogenic chemotherapy. Fosaprepitant has been developed as an intravenous prodrug of aprepitant. Aims: To update the evidence underlying the use of fosaprepitant to prevent CINV. Evidence review: Aprepitant in combination with a serotonin antagonist and a corticosteroid controls acute and delayed symptoms of CINV in patients receiving moderately to highly emetogenic chemotherapy. Bioequivalence of fosaprepitant with aprepitant has recently been demonstrated, which has led to its inclusion in clinical guidelines for treatment of acute CINV with highly, and some regimens of moderately, emetogenic chemotherapy. Early studies of the clinical efficacy of fosaprepitant have shown improvement over treatment with ondansetron. Both aprepitant and fosaprepitant are well tolerated with most adverse events observed of mild or moderate intensity. Conflicting economic evidence has shown that whilst aprepitant provides an increased quality of life in patients treated for CINV, there are differing views over its absolute cost in relation to standard therapy. The incremental cost-effectiveness ratio of aprepitant, however, appears to lie within acceptable bounds. Place in therapy: Fosaprepitant and aprepitant are recommended in guidelines for preventing CINV due to moderately and highly emetogenic chemotherapy. Fosaprepitant is bioequivalent to aprepitant, and could offer potential benefits for patients who may be unable to tolerate oral administration of antiemetics during an episode of nausea or vomiting.
Fine Water: A Blind Taste Test

Abstract To test whether consumers can distinguish among different bottled waters and, if so, whether they prefer some to others, we recruited more than 100 subjects to participate in a blind taste test that consisted of four brands of bottled water featured in a restaurant's water menu and a guidebook to fine waters. The tasting involved three successive experiments. First, our subjects tried to distinguish bottled waters in a sensory discrimination test. They were only slightly better than random chance at doing so. Next, they rated bottled waters and tap water on a 14-point scale used at an international water competition. Some subjects preferred the inexpensive tap water to any of the bottled waters, and there was no association or a weak negative association between a bottled water's price and its rating. Finally, our subjects tried to distinguish tap from bottled water while matching the bottled waters to expert descriptions. They were no better than random chance at doing either of those things. Similar results have been found in previous taste tests of beer and wine. Overall, our results suggest consumers do not have strong preferences over different bottled waters to the extent they can even tell a difference. (JEL Classifications: D12, Q25)
Effect of Expeller Press Parameters on Fish Oil Extraction

An investigation was carried out on the effect of expeller press parameters such as choke clearances (1, 2 and 3 mm), screw clearances (1, 2 and 3 mm) and screw (worm) shaft speeds (50, 60 and 70 rpm) on fish oil extraction. The oil extraction rate and extraction efficiency had a negative relationship with choke clearances and screw clearances but had a positive relationship with screw (worm) shaft speeds. The oil extraction rate and extraction efficiency were found to decrease with increase in choke clearances and also decreased with increase in screw clearances. Increase in screw (worm) shaft speeds from 50 to 70 rpm was observed to increase oil extraction rate and extraction efficiency. The extraction loss had a positive relationship with choke clearances and screw clearances but had a negative relationship with screw (worm) shaft speeds. The extraction loss was found to increase with increase in choke clearances and also increased with increase in screw clearances. Increase in screw (worm) shaft speeds from 50 to 70 rpm was observed to decrease extraction loss. The results obtained from the study of the effects of expeller press parameters on fish oil extraction showed that choke clearance, screw clearance and screw speed influenced oil extraction significantly at 95 % confidence level. The best extraction condition was 1 mm choke clearance, 1mm screw clearance and 70 rpm screw speed, which gave oil extraction rate of 18.91 kg/hr, extraction efficiency of 83.96 % and extraction loss of 5.76 % . The results of this study are useful in optimising the design of presses for fish oil extraction.
Divergent Pathogenesis and Transmission of Highly Pathogenic Avian Influenza A(H5N1) in Swine

Highly pathogenic avian influenza (HPAI) viruses have potential to cross species barriers and cause pandemics. Since 2022, HPAI A(H5N1) belonging to the goose/Guangdong 2.3. 4.4b hemagglutinin phylogenetic clade have infected poultry, wild birds, and mammals across North America. Continued circulation in birds and infection of multiple mammalian species with strains possessing adaptation mutations increase the risk for infection and subsequent reassortment with influenza A viruses endemic in swine. We assessed the susceptibility of swine to avian and mammalian HPAI H5N1 clade 2.3. 4.4b strains using a pathogenesis and transmission model. All strains replicated in the lung of pigs and caused lesions consistent with influenza A infection. However, viral replication in the nasal cavity and transmission was only observed with mammalian isolates. Mammalian adaptation and reassortment may increase the risk for incursion and transmission of HPAI viruses in feral, backyard, or commercial swine.