Miracle-dz/UniFAR-FTUs huggingface dataset:
Rapid 3D isotropic imaging of whole organ with double-ring light-sheet microscopy and self-learning side-lobe elimination

Bessel-like plane illumination forms a new type of light-sheet microscopy with ultra-long optical sectioning distance that enables rapid 3D imaging of fine cellular structures across an entire large tissue. However, the side-lobe excitation of conventional Bessel light sheets severely impairs the quality of the reconstructed 3D image. Here, we propose a self-supervised deep learning (DL) approach that can completely eliminate the residual side lobes for a double-ring-modulated non-diffraction light-sheet microscope, thereby substantially improving the axial resolution of the 3D image. This lightweight DL model utilizes the own point spread function (PSF) of the microscope as prior information without the need for external high-resolution microscopy data. After a quick training process based on a small number of datasets, the grown-up model can restore sidelobe-free 3D images with near isotropic resolution for diverse samples. Using an advanced double-ring light-sheet microscope in conjunction with this efficient restoration approach, we demonstrate 5-minute rapid imaging of an entire mouse brain with a size of ∼12 mm × 8 mm × 6 mm and achieve uniform isotropic resolution of ∼4 µm (1.6-µm voxel) capable of discerning the single neurons and vessels across the whole brain.
Deficiency in NDH-cyclic electron transport retards heat acclimation of photosynthesis in tobacco over day and night shift

In order to cope with the impact of global warming and frequent extreme weather, thermal acclimation ability is particularly important for plant development and growth, but the mechanism behind is still not fully understood. To investigate the role of NADH dehydrogenase-like complex (NDH) mediated cyclic electron flow (CEF) contributing to heat acclimation, wild type (WT) tobacco (Nicotiana tabacum) and its NDH-B or NDH-C, J, K subunits deficient mutants (ΔB or ΔCJK) were grown at 25/20°C before being shifted to a moderate heat stress environment (35/30°C). The photosynthetic performance of WT and ndh mutants could all eventually acclimate to the increased temperature, but the acclimation process of ndh mutants took longer. Transcriptome profiles revealed that ΔB mutant exhibited distinct photosynthetic-response patterns and stress-response genes compared to WT. Metabolite analysis suggested over-accumulated reducing power and production of more reactive oxygen species in ΔB mutant, which were likely associated with the non-parallel recovery of CO2 assimilation and light reactions shown in ΔB mutant during heat acclimation. Notably, in the warm night periods that could happen in the field, NDH pathway may link to the re-balance of excess reducing power accumulated during daytime. Thus, understanding the diurnal cycle contribution of NDH-mediated CEF for thermal acclimation is expected to facilitate efforts toward enhanced crop fitness and survival under future climates.
Urban income and city size: Ecological Inference with Entropy Econometrics for the Spanish municipalities

Most of the regional empirical analyses are limited by the lack of data. Researches have to use information which is structured in administrative or political regions not always economically meaningful. Any aggregation of a territory in regions with economic sense requires data of the main economic variables at basic spatial units, like GDP at a local level. In this paper a methodology to approximate local GDP values is proposed using entropy econometrics which can be defined as an exercise of ecological inference. In addition to the analysis of the main characteristics of the techniques proposed, the paper illustrates how the procedure works taking as empirical application the estimation of income for the Spanish municipalities according to their size. As an example of the possibilities open by this methodology a regional classification based on the relevance of the cities size, which allows us to measure the relevance of agglomeration economics, is empirically applied to the Spanish case obtaining some interesting first results.
Lead isotope analyses of Islamic pottery glazes from Fustat, Egypt

Lead isotope analyses have been undertaken on a group of Islamic lead-glazed pottery artefacts from Fustat, Egypt, spanning the period from the eighth to the 14th century ad, that had previously been the subject of a comprehensive typological, chronological, petrographic and technological study. Comparison of the lead isotope ratios for the glazes with those for lead ores from Egypt, Iran, Tunisia, Anatolia, Greece, Sardinia and Spain provided information on the possible sources of the lead used in the production of the glazes. The results show that the lead used in glaze production by the Islamic potters at Fustat was most probably obtained from distant ore sources in Iran or Tunisia, Sardinia, Spain and the Taurus Mountains. Different ore sources were favoured in different periods and, to a limited extent, for different types of pottery, but at no time did the Fustat potters use the potentially more accessible Egyptian ore sources.
Development of Affibody molecules for radionuclide molecular imaging and therapy of cancer

Honarvar, H. 2016. Development of Affibody molecules for radionuclide molecular imaging and therapy of cancer. Digital Comprehensive Summaries of Uppsala Dissertations from the Faculty of Medicine 1237. 71 pp. Uppsala: Acta Universitatis Upsaliensis. ISBN 978-91-554-9624-1. Affibody molecules are a promising class of scaffold-based targeting proteins for radionuclidebased imaging and therapy of cancer. This thesis work is based on 5 original research articles (papers I-V), which focus on optimization of molecular design of HER2-binding Affibody variants for high contrast imaging of this predictive biomarker as well as development of Affibody molecules suitable for radionuclide-based targeted therapies. Papers I and II were dedicated to evaluation of the influence of the macrocyclic chelator DOTA positioning at N-terminus, in the middle of helix-3 and at C terminus of a synthetic Affibody molecule, ZHER2:S1. These synthetic variants were labelled with different radionuclides i.e. In and Ga to study also the effect of different labels on their biodistribution properties. In paper III a 2-helix variant, Z342min, was developed using native ligation cyclization to crosslink helices one and two resulting in a stable 2-helix scaffold and characterized in vivo. This study was performed with the aim to obtain structure-properties relationship for development of smaller Affibody molecules. Papers IV and V were devoted to development of therapeutic strategies. In paper IV, a series of peptide based chelators was investigated for labelling of Affibody molecules with Re to provide low renal retention. In paper V, a pretargeting approach using peptide nucleic acid was investigated. These studies were performed with the aim to overcome the high renal retention of Affibody molecules when labelled with residualizing therapeutic radionuclides. Otherwise, the particle emitting radiometals could damage the kidneys more than the tumours. The results obtained for anti-HER2 Affibody molecules summarized in this thesis might be of importance for the development of other scaffold protein based targeting agents.
PROPOSTA DE AMOSTRAGEM PADRONIZADA PARA MACRO- VESTÍGIOS BIOARQUEOLÓGICOS: ANTRACOLOGIA, ARQUEOBOTÂNICA, ZOOARQUEOLOGIA

This paper calls the attention of Brazilian archaeologists to the importance of bioarchaeological studies. We offer a sampling protocol that can be a useful tool for fulfilling the needs of the bioarchaeological research in the field, leading to a systematic sampling of charcoal, plant, and faunal remains. We propose a sampling strategy that provides comparable data, from diverse sites, on paleoenvironmental conditions, subsistence systems, and interactions between the social and the environmental domains.
Effect of Stroboscopic Vision Training on Dynamic Visual Acuity Effect of Stroboscopic Vision Training on Dynamic Visual Acuity Scores: Nike Vapor Strobe® Eyewear Scores: Nike Vapor Strobe® Eyewear

The field of sports vision is continuing to grow, with athletes seeing the benefit of incorporating vision drills as part of their training regimen. Dynamic visual acuity (DVA) is a very important aspect of the visual system and is necessary for sport, providing the ability to track a moving object while our head is moving. A recently released product called the Nike Vapor Strobe® Eyewear introduces a stroboscopic effect to vision training. The effect of stroboscopic training on DVA is unexplored territory. Purpose: The main aims of this study were to test the immediate effect of stroboscopic training after one training session, after a two week training program, and two weeks post training. Additionally, we tested the effect of stroboscopic vision training on catching performance. Methods: Sixteen participants were divided evenly into two groups according to baseline DVA scores, recorded using the NeuroCom inVision system. Participants then completed 9 days of vision training with three DVA assessments: immediately after day one of ball training, the day after final ball training, and two weeks after the completion of ball training. Results: The experimental group had statistically significant improvement in test session two from test session one for left DVA, total vertical DVA, downward DVA, and upward DVA, with no change on test sessions three and four. The control group worsened in performance for total DVA, downward DVA, and upward DVA in test two, three, and four. Both groups had statistically significant improvement in ball catching performance. Conclusion: Stroboscopic training increased dynamic visual acuity (after one training session) and ball catching performance (over the course of the training) compared to training without a stroboscopic effect. The Nike Vapor Strobe eyewear is a practical tool for improving catching performance and dynamic visual acuity immediately following training.
marine drugs

: Marine algae represent an important source of novel natural products. While their bioactive potential has been studied to some extent, limited information is available on marine algae from the Red Sea. This study aimed at the broad discovery of new bioactivities from a collection of twelve macroalgal species from the Central Red Sea. We used imaging-based High-Content Screening (HCS) with a diverse spectrum of cellular markers for detailed cytological proﬁling of fractionated algal extracts. The cytological proﬁles for 3 out of 60 algal fractions clustered closely to reference inhibitors and showed strong inhibitory activities on the HIV-1 reverse transcriptase in a single-enzyme biochemical assay, validating the suggested biological target. Subsequent chemical proﬁling of the active fractions of two brown algal species by ultra-high resolution mass spectrometry (FT-ICR-MS) revealed possible candidate molecules. A database query of these molecules led us to groups of compounds with structural similarities, which are suggested to be responsible for the observed activity. Our work demonstrates the versatility and power of cytological proﬁling for the bioprospecting of unknown biological resources and highlights Red Sea algae as a source of bioactives that may serve as a starting point for further studies.
A $(3+\varepsilon)$-Approximate Correlation Clustering Algorithm in Dynamic Streams

Grouping together similar elements in datasets is a common task in data mining and machine learning. In this paper, we study streaming and parallel algorithms for correlation clustering, where each pair of elements is labeled either similar or dissimilar. The task is to partition the elements and the objective is to minimize disagreements, that is, the number of dissimilar elements grouped together and similar elements that get separated. Our main contribution is a semi-streaming algorithm that achieves a $(3 + \varepsilon)$-approximation to the minimum number of disagreements using a single pass over the stream. In addition, the algorithm also works for dynamic streams. Our approach builds on the analysis of the PIVOT algorithm by Ailon, Charikar, and Newman [JACM'08] that obtains a $3$-approximation in the centralized setting. Our design allows us to sparsify the input graph by ignoring a large portion of the nodes and edges without a large extra cost as compared to the analysis of PIVOT. This sparsification makes our technique applicable in several models of massive graph processing, such as semi-streaming and Massively Parallel Computing (MPC), where sparse graphs can typically be handled much more efficiently. Our work improves on the approximation ratio of the recent single-pass $5$-approximation algorithm and on the number of passes of the recent $O(1/\varepsilon)$-pass $(3 + \varepsilon)$-approximation algorithm [Behnezhad, Charikar, Ma, Tan FOCS'22, SODA'23]. Our algorithm is also more robust and can be applied in dynamic streams. Furthermore, it is the first single pass $(3 + \varepsilon)$-approximation algorithm that uses polynomial post-processing time.
(2018). An Initial Investigation into Non-visual Code Structure Overviews: Speech, Non-speech and Spearcons. In CHI 2018: Proceedings of the 2018 CHI Conference on Human Factors in Computing Systems [LBW562] Association for Computing Machinery

We investigate a novel, non-visual approach to overviewing object-oriented source code and evaluate the efﬁciency of different categories of sounds for the purpose of getting an overview of source code structure for a visually-impaired computer programmer. A user-study with ten sighted and three non-sighted participants compared the effectiveness of speech, non-speech and spearcons on measures of accuracy and enjoyment for the task of quickly overviewing a class ﬁle. Results showed positive implications for the use of non-speech sounds in identifying programming constructs and for aesthetic value, although the effectiveness of the other sound categories in these measurements are not ruled out. Additionally, various design choices of the application impacted results, which should be of interest to designers of auditory display, accessibility and education.
1 COMPUTATIONAL AND EXPERIMENTAL STUDY OF A COMPLETE HEAT DISSIPATION SYSTEM USING WATER AS HEAT CARRIER PLACED ON A THERMOELECTRIC GENERATOR

The heat dissipation systems which have liquids as heat carriers outperform conventional dissipation systems at thermoelectric generators (TEGs). However, new elements need to be introduced such as pumps, secondary heat exchangers and piping. A predictive computational model of a dissipation system involving refrigerant liquids has been implemented. The accuracy of the model is 93 % for all its outputs: the total thermal resistance, the hydraulic losses and the auxiliary power consumption. The validation of the model has been done with a prototype mainly composed by a multi-channel heat exchanger, a fan-coil, a pump and several sensors: temperature, pressure and flow meters. A study on the influence of the water and the air mass flow over the total thermal resistance has been conducted. The total resistance dependence on the air mass flow shows the importance of including the secondary heat exchanger into the thermal and hydraulic calculations. The smallest resistance does not always obtain the highest net power generation, the high demanding power of the auxiliary equipment needed to obtain this resistance influences negatively on the net power generation. Among the experimental points, the optimum scenario obtains a 40 % additional power generation with respect to the smallest resistance point.
Clinics in Oncology

Objective: To investigate the clinical and pathological features of thoracic SMARCA4-deficient undifferentiated tumor. Methods: The clinical data, images, histopathological features, treatment regimens, and follow-up results of two cases of SMARCA4-deficient undifferentiated tumor diagnosed by clinicians at the First Affiliated Hospital of Bengbu Medical College were retrospectively analyzed. Results: Both patients were male, aged 65 and 81 years, respectively, and both had a history of smoking. The images showed that both patients had lung masses and mediastinal enlarged lymph nodes. Histopathological analysis revealed that the tumor cells had a solid structure formed by epithelioid/rhabdoid cells
Tansley review Enabling sustainable agriculture through understanding and enhancement of microbiomes

of the structure and function of native microbial communities. Such insights are paving the way towards development of microbial products as well as microbiomes engineered with synthetic microbial communities capable of delivering agronomic solutions. While there is a growing market for microbial-based solutions to improve crop productivity, challenges with commercialization of these products remain. The continued translation of plant-associated microbiome knowledge into real-world scenarios will require concerted transdisciplinary research, cross-training of a next generation of scientists, and targeted educational efforts to prime growers and the general public for successful adoption of these innovative technologies
Upregulation of γ-catenin compensates for the loss of β-catenin in adult cardiomyocytes

Recent progresses in signal transduction have revealed that β-catenin signaling controls embryonic development, tumorigenesis, cell shape, and polarity. The role of this pathway in myocyte shape regulation during cardiac hypertrophy and failure is, however, not clearly defined. Since homozygous knockout of β-catenin is embryonically lethal, we have deleted β-catenin genes specifically in the heart of adult mice by crossing loxP-flanked β-catenin mice with transgenic mice expressing tamoxifen-activated MerCreMer protein (MCM) driven by the α-myosin heavy chain promoter. Administration of tamoxifen to homozygous loxP-flanked β-catenin mice positive for MCM induces the deletion of β-catenin only in cardiomyocytes. Immunolabeling with β-catenin antibody demonstrates that 90% of cardiomyocytes completely lose their β-catenin expression but maintain normal rod-shaped morphology. The intercalated disk of cardiomyocytes lacking β-catenin is morphologically unremarkable with normal distribution of vinculin, N-cadherin, desmoplakin, ZO-1, connexin43, and α-, γ-, and p120 catenins. The expression level of these proteins, except that of γ-catenin, is also similar in tamoxifen-treated and control mice with both homozygous loxP-flanked β-catenin genes and the MCM transgene. Western blot analyses reveal that γ-catenin increases in the heart of β-catenin knockout mice compared with controls. Confocal microscopy also demonstrates that γ-catenin has significantly increased in the intercalated disk of cardiomyocytes lacking β-catenin. Echocardiographic data indicate that the knockout mice maintain normal ventricular geometry and cardiac function. The results suggest that upregulation of γ-catenin can compensate for the loss of β-catenin in cardiomyocytes to maintain normal cardiac structure and function.
A Methodology for Architectural-Level Reliability Risk Analysis

risk analysis, risk modeling, componentdependency graphs, software architecture, dynamic metrics Risk assessment is an essential process of every software risk management plan. Several risk assessment techniques are based on the subjective judgement of domain experts. Subjective risk assessment techniques are human intensive and error-prone. Risk assessment should be based on product attributes that we can quantitatively measure using product metrics.
Spatially Explicit Models of City Population Growth in India

This paper presents state-of-the-art econometric models of city population growth in India. Although forecasts of city growth are urgently needed in poor countries to address the challenges they will face in development, environment, and climate change, city-level population forecasting in these countries is still uncommon. However, the data needed to support forecasting are becoming more readily available across a range of poor countries, and in some countries a solid empirical foundation for modelling now exists. India offers not only longitudinal data at the city level for a great number of cities from 1901 to 2001, but also provides disaggregated time-series of important demographic determinants of this growth, state-level urban total fertility rates, child mortality rates, and rates of migration. In methodological terms, this paper combines panel data spatial econometrics with multi-level modelling. We depart from conventional models of spatial correlation in allowing spatial effects to emerge not only from geographic distance, but also from the political and economic context in which the city is situated, with important influences at the state and regional level in India as well as spill-over effects from neighboring cities. To estimate these effects in India, both classical and Bayesian methods are applied. Our initial analysis shows that urban fertility rates display very strong positive effects on city population growth rates and confirms that city growth is spatially correlated. These results will be extended with more additional data and models in which spatial correlation stems from an explicitly multi-level structure.
Soil organic carbon and biological indicators in an Acrisol under tillage systems and organic management in north-eastern Brazil

No-tillage and organic farming are important strategies to improve soil quality. This study aimed to quantify the effects of the tillage systems and organic management on total organic carbon (TOC), labile C (CL), and biological indicators in an Acrisol in north-eastern Brazil. Five systems were studied: NV, native vegetation; NT/ORG, no-tillage plus organic fertiliser; NT/CHE, no-tillage plus chemical fertiliser; NT/CHE/ORG, no-tillage plus organic and chemical fertiliser; CT/CHE, conventional tillage plus chemical fertiliser. Soil samples were collected in the 0–0.10 and 0.10–0.20 m depths. TOC stocks were higher in NT/CHE/ORG (0–0.10 m, 14.0 Mg/ha; 0.10–0.20 m, 13.0 Mg/ha) and NT/ORG (0–0.10 m, 12.6 Mg/ha; 0.10–0.20 m, 11.6 Mg/ha) than in CT/CHE and NV systems. CL stocks were higher in NT/ORG (3.61 Mg/ha) at 0–0.10 m and in NT/ORG, NT/CHE, and NT/CHE/ORG at 0.10–0.20 m. At 0–0.10 m, microbial biomass C content was higher in the NT/CHE/ORG (190 mg/kg) and NT/ORG (155 mg/kg). Soil microbial respiration rate was similar in all systems. However, qCO2 was higher in the NT/CHE and CT/CHE systems, suggesting a stress in the soil microbial biomass. No-tillage and organic management promoted positive changes in soil organic carbon and soil microbial properties and improved soil quality.
TECHNICAL ASSESSMENT OF A UNIVERSITY-BASED OZONE-TREATED BOTTLED WATER PRODUCTION SYSTEM

The work is a case study of an ozone-disinfected bottled water production system located on a university campus in a developing economy. The package system as installed by the supplier was studied in detail. Physico-chemical and bacteriological quality of the raw water and the treated water was determined. It was found that the laboratory attached to the plant contains no chemicals or equipment to carry out any analysis. Being within an academic community helps because of possibilities for cooperative use of laboratories. This and the fact that the source water contains no harmful chemicals or microbes help this plant to produce bottled water of adequate quality. The concern in the set up is in the form of an absence of ozone decomposer or dosage control and facilities for determination of ozone residual. The tests show that both the raw and the treated water samples contain no fecal coliforms. However, the presence of non-fecal coliforms in the treated water points to the need for a firmer handle on ozone dosage control.