Miracle-dz/UniFAR-FTUs huggingface dataset:
STED microscopy in the visible range

Light microscopy is a key scientific instrument in the life sciences. However, the resolution of far-field light microscopy is limited by diffraction. Exploiting a saturated depletion of the molecular excited state by stimulated emission, stimulated emission depletion (STED) breaks the resolution barrier in the important subfield of fluorescence microscopy. To this end, STED microscopy utilizes a doughnut-shaped beam featuring a central zero which is capable of quenching the fluorescence solely in the focal periphery. While STED microscopy was initially restricted to near infrared-emitting fluorophores, in this thesis STED microscopy is shown to be viable with visible (green-yellow-red) fluorophores. In particular, STED is established with the green and yellow fluorescent proteins (GFP, YFP) which are endogenous cellular markers of outstanding biological importance. The spectral conditions for STED with these fluorophores are given. The expansion of STED to the visible range has enabled the first application to biophysics and to addressing unsolved problems of cell biology. For example, STED microscopy revealed that the synaptic vesicle protein synaptotagmin remains an integral patch following fusion with the plasma membrane. Moreover, membrane microdomains were resolved with unprecedented (65 nm) spatial resolution. Furthermore, a novel doughnut-shape of the STED beam utilizing a helical phase ramp and a central singularity was established for STED. Finally, due to the smaller wavelength for stimulated emission, the viability of STED with visible dyes pushes the resolution down to smaller attainable values.
Stereospecific pharmacokinetic characterization of liquiritigenin in the rat

Liquiritigenin is a chiral flavonoid present in licorice and other medicinal plants. The nature of its biological fate with respect to the individual enantiomers has not been examined. In this study, we characterize, for the first time, the stereoselective pharmacokinetics of liquiritigenin. Liquiritigenin was intravenously (20 mg/kg) and orally (50 mg/kg) administered to male Sprague-Dawley rats (n = 4 per route of administration). Concentrations in serum and urine were characterized via stereospecific reversed-phase, isocratic HPLC method with UV detection. Serum concentrations were quantified but rapidly fell to undetectable levels. S-liquiritigenin showed a short half-life (0.25-0.54 h), while a better estimation of half-life (26-77 h) and other pharmacokinetic parameters was observed using urinary data. The flavonoid is predominantly excreted via non-renal routes (fe values of 0.16-3.46 %), and undergoes rapid and extensive phase II metabolism. Chiral differences in the chemical structure of the compound result in some pharmacokinetic differences. Serum concentrations rapidly declined, making modeling difficult. S-liquiritigenin showed an increased urinary half-life.
Long-term water stress leads to acclimation of drought sensitivity of photosynthetic capacity in xeric but not riparian Eucalyptus species.

BACKGROUND AND AIMS Experimental drought is well documented to induce a decline in photosynthetic capacity. However, if given time to acclimate to low water availability, the photosynthetic responses of plants to low soil moisture content may differ from those found in short-term experiments. This study aims to test whether plants acclimate to long-term water stress by modifying the functional relationships between photosynthetic traits and water stress, and whether species of contrasting habitat differ in their degree of acclimation. METHODS Three Eucalyptus taxa from xeric and riparian habitats were compared with regard to their gas exchange responses under short- and long-term drought. Photosynthetic parameters were measured after 2 and 4 months of watering treatments, namely field capacity or partial drought. At 4 months, all plants were watered to field capacity, then watering was stopped. Further measurements were made during the subsequent 'drying-down', continuing until stomata were closed. KEY RESULTS Two months of partial drought consistently reduced assimilation rate, stomatal sensitivity parameters (g1), apparent maximum Rubisco activity (V'(cmax)) and maximum electron transport rate (J'(max)). Eucalyptus occidentalis from the xeric habitat showed the smallest decline in V'(cmax) and J'(max); however, after 4 months, V'(cmax) and J'(max) had recovered. Species differed in their degree of V'(cmax) acclimation. Eucalyptus occidentalis showed significant acclimation of the pre-dawn leaf water potential at which the V'(cmax) and 'true' V(cmax) (accounting for mesophyll conductance) declined most steeply during drying-down. CONCLUSIONS The findings indicate carbon loss under prolonged drought could be over-estimated without accounting for acclimation. In particular, (1) species from contrasting habitats differed in the magnitude of V'(cmax) reduction in short-term drought; (2) long-term drought allowed the possibility of acclimation, such that V'(cmax) reduction was mitigated; (3) xeric species showed a greater degree of V'(cmax) acclimation; and (4) photosynthetic acclimation involves hydraulic adjustments to reduce water loss while maintaining photosynthesis.
Exploiting superword level parallelism with multimedia instruction sets

Increasing focus on multimedia applications has prompted the additionof multimedia extensions to most existing general purpose microprocessors. This added functionality comes primarily with the addition of short SIMD instructions. Unfortunately, access to these instructions is limited to in-line assembly and library calls. Generally, it has been assumed that vector compilers provide the most promising means of exploiting multimedia instructions. Although vectorization technology is well understood, it is inherently complex and fragile. In addition, it is incapable of locating SIMD-style parallelism within a basic block. In this paper we introduce the concept of Superword Level Parallelism (SLP) ,a novel way of viewing parallelism in multimedia and scientific applications. We believe SLPP is fundamentally different from the loop level parallelism exploited by traditional vector processing, and therefore demands a new method of extracting it. We have developed a simple and robust compiler for detecting SLPP that targets basic blocks rather than loop nests. As with techniques designed to extract ILP, ours is able to exploit parallelism both across loop iterations and within basic blocks. The result is an algorithm that provides excellent performance in several application domains. In our experiments, dynamic instruction counts were reduced by 46%. Speedups ranged from 1.24 to 6.70.
Concrete surface roughness testing using nondestructive three-dimensional optical method

In building practice the durability of concrete floors is to a large degree determined by the surface layer’s pull-off adhesion to the structural layer. The strength of the bond between the two layers largely depends on the preparation of the structural layer. Structural layer preparation can be described by surface roughness parameters. This paper presents results of concrete floor structural layer surface roughness tests done using 3D optical surface scanning. Two differently prepared structural layers were examined in this way. The results show that this method can be successfully used for this purpose.
SIFT Features Using Vector Quantization histogram for Image Retrieval

features are identified as being invariant to common image deformations caused by the rotation, scaling, and illumination. In this paper, we apply VQ histogram as an alternate representation for SIFT features. Experimental results demonstrate that SIFT features using VQ-based local descriptors are more robust to image deformations and lead to better image retrieval results than original SIFT algorithm.
Conditional deletion of the human ortholog gene Dicer1 in Pax2-Cre expression domain impairs orofacial development

BACKGROUND: Orofacial clefts are common worldwide and result from insufficient growth and/or fusion during the genesis of the derivatives of the first pharyngeal arch and the frontonasal prominence. Recent studies in mice carrying conditional and tissue-specific deletions of the human ortholog Dicer1, an RNAse III family member, have highlighted its importance in cell survival, differentiation, proliferation, and morphogenesis. Nevertheless, information regarding Dicer1 and its dependent microRNAs (miRNAs) in mammalian palatogenesis and orofacial development is limited. AIMS: To describe the craniofacial phenotype, gain insight into potential mechanisms underlying the orofacial defects in the Pax2-Cre/Dicer1 CKO mouse, and shed light on the role of Dicer1 in mammalian palatogenesis. MATERIALS AND METHODS: Histological and molecular assays of wild type (WT) and Pax2-Cre/Dicer1loxP/loxP (Dicer1 CKO) mice dissected tissues have been performed to characterize and analyze the orofacial dysmorphism in Pax2-Cre/Dicer1loxP/loxP mouse. RESULTS: Dicer1 CKO mice exhibit late embryonic lethality and severe craniofacial dysmorphism, including a secondary palatal cleft. Further analysis suggest that Dicer1 deletion neither impacts primary palatal development nor the initial stages of secondary palatal formation. Instead, Dicer1 is implicated in growth, differentiation, mineralization, and survival of cells in the lateral palatal shelves. Histological and molecular analysis demonstrates that secondary palatal development becomes morphologically arrested prior to mineralization around E13.5 with a significant increase in the expression levels of apoptotic markers (P < 0.01). CONCLUSIONS: Pax2-Cre-mediated Dicer1 deletion disrupts lateral palatal outgrowth and bone mineralization during palatal shelf development, therefore providing a mammalian model for investigating the role of miRNA-mediated signaling pathways during palatogenesis.
Photovoltaic–Pyroelectric Coupled Effect Induced Electricity for Self‐Powered Photodetector System

Ferroelectric materials have demonstrated novel photovoltaic effect to scavenge solar energy. However, most of the ferroelectric materials with wide bandgaps (2.7–4 eV) suffer from low power conversion efficiency of less than 0.5% due to absorbing only 8–20% of solar spectrum. Instead of harvesting solar energy, these ferroelectric materials can be well suited for photodetector applications, especially for sensing near‐UV irradiations. Here, a ferroelectric BaTiO3 film‐based photodetector is demonstrated that can be operated without using any external power source and a fast sensing of 405 nm light illumination is enabled. As compared with photovoltaic effect, both the responsivity and the specific detectivity of the photodetector can be dramatically enhanced by larger than 260% due to the light‐induced photovoltaic–pyroelectric coupled effect. A self‐powered photodetector array system can be utilized to achieve spatially resolved light intensity detection by recording the output voltage signals as a mapping figure.
Cycling of calcite in hard water lakes of different trophic states

Based on oxygen (O2), pH, calcium (Ca2+), and carbonate (CO32‐) sediment pore‐water concentration profiles, we compare the benthic dissolution of autochthonous calcite in oligotrophic Lake Lucerne and eutrophic Lake Sempach. Despite their difference in trophic state, the two lakes have similar benthic O2 regimes because L. Sempach is artificially oxygenated. This peculiarity enabled the study of the direct effect of trophic state on benthic calcite dissolution. Although areal benthic O2 fluxes did not differ, O2 penetrated deeper into the sediment of the oligotrophic L. Lucerne, where most organic matter (OM, 96%) was degraded aerobically, whereas in L. Sempach, aerobic and anaerobic decomposition contributed about equal amounts to the biogenic carbon dioxide production. Release rates of bicarbonate from L. Sempach sediments exceeded those of L. Lucerne nearly twofold. The HCO3− : Ca2+ ratio of benthic fluxes was 3.7 in L. Lucerne compared to 10.3 in L. Sempach, suggesting that in L. Sempach most of the released HCO3− did not originate from calcite dissolution. Furthermore, benthic calcite dissolution in L. Lucerne exceeded that in L. Sempach by two‐fold, despite lower pH values in the pore water of L. Sempach. Differences in benthic microbial decomposition of OM and redissolution of calcite crystals are explained by the longer residence time of OM and calcite in the oxic sediment layer of the oligotrophic lake and the larger weight‐specific surface area of its smaller autochthonous calcite crystals. We suggest that trophic state and O2 supply to the sediment are key parameters controlling the cycling of calcite and organic carbon in lakes.
Accuracy of staging in early oesophageal cancer using high resolution endoscopy and high resolution endosonography: a comparative, prospective, and blinded trial

Background and aims: The increasing use of endoscopic resection for curative treatment of early oesophageal cancers requires accurate staging before therapy. In a prospective blinded trial, we compared staging of early oesophageal carcinoma using high resolution endoscopy (HR-E) with staging using high resolution endosonography (HR-EUS). Patients and methods: A total of 100 patients (89 men, 11 women; mean age 63.9 (10.8) years (range 31–91)) with a suspicion of early oesophageal adenocarcinoma (n = 81) or squamous cell carcinoma (n = 19) were enrolled in the study. After endoscopic staging with high resolution video endoscopy by two experienced endoscopists, HR-EUS was performed by an experienced endosonographer who was blinded to the endoscopic assessment. Results of the staging examinations were correlated with the histology of the resected tumours. Results: Overall rates for accuracy of the endoscopic and endosonographic staging were 83.4% and 79.6%, respectively. Sensitivity for mucosal tumours (n = 68) was more than 90% (EUS 91.2%, endoscopy 94.1%) while sensitivity for submucosal tumours (n = 25) was lower, at 48% for EUS and 56% for endoscopic staging. A combination of the two techniques increased the sensitivity for submucosal tumours to 60%. Submucosal tumours in the tubular oesophagus were significantly better staged with HR-EUS than submucosal tumours close to the oesophagogastric junction (10/11 v 2/14; p<0.001). Tumours infiltrating the second and third submucosal layers were also more correctly diagnosed than tumours with slight infiltration of the first submucosal layer (sm1). Conclusions: The overall diagnostic accuracy of both HR-E and HR-EUS with a 20 MHz miniprobe in early oesophageal cancer was high (approximately 80%), with no significant differences between the two techniques. HR-E and HR-EUS provide a high level of diagnostic accuracy for mucosal tumours and submucosal tumours located in the tubular part of the oesophagus. With submucosal tumours located at the oesophagogastric junction or with infiltration of the first third of the submucosa however, the diagnostic accuracy of both techniques is not yet satisfactory.
Applying Lean Startup: An Experience Report -- Lean &amp; Lean UX by a UX Veteran: Lessons Learned in Creating &amp; Launching a Complex Consumer App

This paper outlines lessons learned from a senior UX, product and software development consultant's experiences in conceiving, designing, developing and launching MiniDates.com, a complex consumer dating application. Key decisions and moments over our 15 month process are highlighted, including what we worked and what didn't, what we should have done that we didn't, and what we encountered that we couldn't have foreseen, in the belief that we can help other UX and product-focused startups and Agile teams be more effective. Key lessons include: 1. Beware fads and advice from others; 2. Optimize your team and the development process as much as possible; 3. Beware of seemingly innocent technological and architecture decisions; 4. Ensure UX planning, design and customer validation are up-front in your process; 5. TEST, TEST and TEST some more- at all levels of the business and at all stages, not just the software itself.
Equivalence Checking Using Cuts And Heaps

This paper presents a verification technique which isspecifically targeted to formally comparing large combinational circuits with some structural similarities. The approach combines the application of BDDs withcircuit graph hashing, automatic insertion of multiple cut frontiers, and a controlled elimination of false negative verification results caused by the cuts. Twoideas fundamentally distinguish the presented technique from previous approaches. First, originating from the cut frontiers, multiple BDDs are computedfor the internal nets of the circuit, and second, theBDD propagation is prioritized by size and discontinued once a given limit is exceeded.
SCAM: Scenario-based Clustering Algorithm for Mobile ad hoc networks

This paper proposes a scenario based, adaptive and distributed clustering algorithm SCAM (Scenario-based Clustering Algorithm for Mobile ad hoc networks). A distributed algorithm based on (k, r) - Dominating Set is used for the selection of clusterheads and gateway nodes, here k is the minimum number of clusterheads per node in the network and r is the maximum number of hops between the node and the clusterhead. From among the k dominating nodes, the non-clusterhead node can select the most qualified dominating node as its clusterhead. The quality of the clusterhead is calculated based on various metrics, which include connectivity, stability and residual battery power. Long-term service as clusterhead depletes their energy, causing them to drop out of the network. Similarly, the clusterhead with relatively high mobility than its neighbours leads to frequent clusterhead election process. This perturbs the stability of the network and adversely affects the performance of the network. Load balancing among clusterheads and correct positioning of clusterhead in a cluster are also vital to increase the life span of the network. The proposed algorithm periodically calculates the quality of all dominating nodes and if it goes below the threshold level it resigns the job as clusterhead and sends this message to all other member nodes. Since these nodes have k dominating nodes within r - hop distance, it can choose the current best-qualified node as its clusterhead. SCAM uses techniques to maintain the cluster structure as stable as possible with less control messages.
Classic Selective Sweeps Revealed by Massive Sequencing in Cattle

Human driven selection during domestication and subsequent breed formation has likely left detectable signatures within the genome of modern cattle. The elucidation of these signatures of selection is of interest from the perspective of evolutionary biology, and for identifying domestication-related genes that ultimately may help to further genetically improve this economically important animal. To this end, we employed a panel of more than 15 million autosomal SNPs identified from re-sequencing of 43 Fleckvieh animals. We mainly applied two somewhat complementary statistics, the integrated Haplotype Homozygosity Score (iHS) reflecting primarily ongoing selection, and the Composite of Likelihood Ratio (CLR) having the most power to detect completed selection after fixation of the advantageous allele. We find 106 candidate selection regions, many of which are harboring genes related to phenotypes relevant in domestication, such as coat coloring pattern, neurobehavioral functioning and sensory perception including KIT, MITF, MC1R, NRG4, Erbb4, TMEM132D and TAS2R16, among others. To further investigate the relationship between genes with signatures of selection and genes identified in QTL mapping studies, we use a sample of 3062 animals to perform four genome-wide association analyses using appearance traits, body size and somatic cell count. We show that regions associated with coat coloring significantly (P<0.0001) overlap with the candidate selection regions, suggesting that the selection signals we identify are associated with traits known to be affected by selection during domestication. Results also provide further evidence regarding the complexity of the genetics underlying coat coloring in cattle. This study illustrates the potential of population genetic approaches for identifying genomic regions affecting domestication-related phenotypes and further helps to identify specific regions targeted by selection during speciation, domestication and breed formation of cattle. We also show that Linkage Disequilibrium (LD) decays in cattle at a much faster rate than previously thought.
Outdoor grilling hazard: Wire bristle esophageal foreign body—a report of six cases

Esophageal foreign bodies are frequently encountered, with coin ingestion the most common in the pediatric population and fish bone ingestion the most common in the adult population worldwide. Many people cook with outdoor grills and use wire brushes to clean them. We present the largest case series with six adult cases involving ingestion of wire brush bristles from food prepared on outdoor grilling surfaces. The occurrence of six cases within a small geographic area over a relatively brief time span raises important safety concerns and warrants attention to prevent serious complications.
Articular Cartilage Repair

The articular cartilage repair can be achieved through different ways that is cell based repair, articular cartilage transplant, the use of micro fracture technique, the use of osteochondral autograft transplant, palliative care and the use of cell and scaffold technology. Articular cartilage repair is ineffective in some cases depending on the method which is used in the repair processes. The replacement does not help most of the patients, and this has dramatically resulted in other adverse effects to the clients. The majority of the patients who have adverse symptoms and considerable tear damage of tissues do not heal faster. The surgeons should take advantage of the rapidly growing technology in the field of medicine. This will help them to adopt those technologically based modes of articular cartilage methods which are more effective than those other method. The processes should be conducted with a lot of care as any defect can lead to further damage to the articular cartilage tissues which are very delicate. ■
Phase retrieval in phase contrast imaging

一种用于获得在贯穿辐射入射到目标上时由目标引入的相位变化图象的方法,它包括:用具有高横向空间相关性的贯穿辐射照射目标;在辐射从目标射出后,在探测器装置处接收至少一部分所述辐射,由此获得并存储至少两个所接收辐射的强度记录,其每一个都包括有预定间隔的强度值。 利用这些值,推导出定义处于贯穿辐射中目标所引入的相位变化图象的数值阵列。 这些强度记录是在辐射从目标射出后于相同有限距离处获得的，而且所探测到的辐射有其各不相同的分布。 此外。 还公开了其装置。