Miracle-dz/UniFAR-FTUs huggingface dataset:
Quantitative single cell analysis of cell population dynamics during submandibular salivary gland development and differentiation

Summary Epithelial organ morphogenesis involves reciprocal interactions between epithelial and mesenchymal cell types to balance progenitor cell retention and expansion with cell differentiation for evolution of tissue architecture. Underlying submandibular salivary gland branching morphogenesis is the regulated proliferation and differentiation of perhaps several progenitor cell populations, which have not been characterized throughout development, and yet are critical for understanding organ development, regeneration, and disease. Here we applied a serial multiplexed fluorescent immunohistochemistry technology to map the progressive refinement of the epithelial and mesenchymal cell populations throughout development from embryonic day 14 through postnatal day 20. Using computational single cell analysis methods, we simultaneously mapped the evolving temporal and spatial location of epithelial cells expressing subsets of differentiation and progenitor markers throughout salivary gland development. We mapped epithelial cell differentiation markers, including aquaporin 5, PSP, SABPA, and mucin 10 (acinar cells); cytokeratin 7 (ductal cells); and smooth muscle &agr;-actin (myoepithelial cells) and epithelial progenitor cell markers, cytokeratin 5 and c-kit. We used pairwise correlation and visual mapping of the cells in multiplexed images to quantify the number of single- and double-positive cells expressing these differentiation and progenitor markers at each developmental stage. We identified smooth muscle &agr;-actin as a putative early myoepithelial progenitor marker that is expressed in cytokeratin 5-negative cells. Additionally, our results reveal dynamic expansion and redistributions of c-kit- and K5-positive progenitor cell populations throughout development and in postnatal glands. The data suggest that there are temporally and spatially discreet progenitor populations that contribute to salivary gland development and homeostasis.
Towards Stability and Optimality in Stochastic Gradient Descent

Iterative procedures for parameter estimation based on stochastic gradient descent allow the estimation to scale to massive data sets. However, in both theory and practice, they suffer from numerical instability. Moreover, they are statistically inefficient as estimators of the true parameter value. To address these two issues, we propose a new iterative procedure termed averaged implicit SGD (AI-SGD). For statistical efficiency, AI-SGD employs averaging of the iterates, which achieves the optimal Cramer-Rao bound under strong convexity, i.e., it is an optimal unbiased estimator of the true parameter value. For numerical stability, AI-SGD employs an implicit update at each iteration, which is related to proximal operators in optimization. In practice, AI-SGD achieves competitive performance with other state-of-the-art procedures. Furthermore, it is more stable than averaging procedures that do not employ proximal updates, and is simple to implement as it requires fewer tunable hyperparameters than procedures that do employ proximal updates.
Landslide shape, ellipticity and length‐to‐width ratios

This paper presents a new methodology to systematically quantify the shape of landslides by their ellipticity (eL) and length‐to‐width ratio (ΛL), along with variability in these measures over different geomorphic settings. Two large substantially complete triggered‐event landslide inventories (source area and runout) are used: (i) 11 111 earthquake‐triggered landslides (1994 Northridge, USA); and (ii) 9594 rainfall‐triggered landslides (1998, Guatemala). Three methods are trialled to abstract landslide shapes to ellipses. The best method fits a convex hull to each landslide shape, approximates an ellipse with the equivalent convex hull area and perimeter, and scales this ellipse to match the original landslide area. An ellipticity index (eL) is used based on the intersection of the original landslide shape and the elliptical approximation. We consider an ellipse a reasonable approximation of landslide shape if eL ≥ 0.5 (>80% of landslides in each of the two landslide inventories). Landslides with eL < 0.5 reflect processes such as coalescence. We calculate for each landslide an ellipse length‐to‐width ratio (ΛE), finding 1.2 ≤ ΛE ≤ 15.1. The statistical distributions of ΛE are examined for ten categories of landslide area (AL). An inverse‐Gamma probability density function is found to be a good statistical model for landslide ΛE, with model parameters dependent on landslide area category. As landslide area AL increases, ΛE tends to decrease for the Northridge (earthquake‐triggered) inventory and increase for Guatemala (rainfall‐triggered). In three additional (rainfall‐triggered) landslide inventories, ΛE trends are similar to Guatemala. Our findings show that (i) an ellipse is a reasonable model for >80% of landslide shapes across different geomorphic settings, (ii) those landslides significantly deviating from an ellipse can be related to landscape processes, (iii) the length‐to‐width ratios of ellipses are non‐normally distributed, with implications for modelling landslide hazard and risk. Supporting information includes code so that the new methodology may be applied more widely. © 2018 John Wiley & Sons, Ltd.
HIV Disclosure: Parental dilemma in informing HIV infected Children about their HIV Status in Malawi.

BACKGROUND Increasingly many perinatally HIV-infected children are surviving through adolescence and adulthood as a result of improvements in the management of paediatric HIV infection, particularly the increased use of combination therapy. It is usually the parents or guardians of these children who are faced with the task of informing the child living with HIV about his or her positive status. However, many parents-particularly biological parents -find this disclosure process difficult to initiate, and this study explored some of the difficulties that these parents encounter. OBJECTIVE This study set out to explore potential factors that challenge parents and guardians when informing their perinatally HIV-infected child about the child's HIV status. DESIGN This was a qualitative narrative study that employed in-depth interviews with parents or guardians of children perinatally infected with HIV. A total of 20 parents and guardians of children who attend the outpatient HIV clinic at the Baylor College of Medicine-Abbott Fund Children's Clinical Centre of Excellence (COE) in Lilongwe, Malawi were interviewed. Of these, 14 were biological parents and six were guardians. RESULTS Guardians and parents expressed uneasiness and apprehension with the disclosure conversation, whether or not they had already told their child that he or she had HIV. Participants who had not told their children recounted that they had contemplated starting the conversation but could not gather enough courage to follow through with those thoughts. They cited the fear of robbing their child of the happiness of living without the knowledge of being positive, fear of making their own status known to more people, and fear of confrontation or creating enmity with their child as impediments to disclosing their child's positive HIV status to him or her. CONCLUSIONS It is apparent that guardians-more particularly biological parents-of children perinatally infected by HIV find it difficult to inform their children about their children's HIV status. From this disempowered position, parents dread the disclosure of a positive HIV status to a child as a psychosocial process that has the potential to disturb a family's previously established equilibrium with threats of stigmatization, marginalization, and parent-child conflict. This calls for strategies that could support parents to make disclosure to the child less challenging.
Recovery of Mitral Isthmus Conduction Leads to the Development of Macro-Reentrant Tachycardia After Left Atrial Linear Ablation for Atrial Fibrillation

Background— Left atrial linear ablation for atrial fibrillation (AF) may be proarrhythmic, leading to left atrial macro-reentrant tachycardia (LAT). Whether due to failure to achieve block initially or to recovery of conduction after ablation is unknown. This study was designed to evaluate the frequency of recovery of mitral isthmus (MI) conduction compared with cavo-tricuspid isthmus (CTI) conduction, and the relationship between recovery of MI conduction and postablation LAT. Methods and Results— Of 163 patients with AF who underwent circumferential pulmonary vein ablation plus left atrial linear ablation, in whom MI and CTI ablation produced bidirectional conduction block, 52 underwent repeat ablation for recurrent atrial arrhythmias (AF or LAT). Of these 52 patients, coronary sinus ablation was required in 48 to achieve bidirectional MI block at the index ablation. During repeat ablation, MI and CTI conduction was assessed in sinus rhythm. At repeat ablation, MI conduction had recovered in 38 of 52 patients, as compared with CTI conduction which recovered in only 12 of 52 patients (P=0.001). At repeat ablation, the recurrent clinical arrhythmia in 12 patients was MI-dependent LAT. Recovery of MI conduction was associated with development of MI-dependent LAT (P=0.01). Conclusions— Despite using bidirectional conduction block as a procedural end point, recovery of MI conduction is common and may lead to LAT after left atrial linear ablation for AF. The reason for greater recovery of MI versus CTI conduction is unknown but could be due to differences in isthmus anatomy or lower power used for ablation in the left versus right atrium.
Accounting for boundary effects in nearest-neighbor searching

Givenn data points ind-dimensional space, nearest-neighbor searching involves determining the nearest of these data points to a given query point. Most averagecase analyses of nearest-neighbor searching algorithms are made under the simplifying assumption thatd is fixed and thatn is so large relative tod thatboundary effects can be ignored. This means that for any query point the statistical distribution of the data points surrounding it is independent of the location of the query point. However, in many applications of nearest-neighbor searching (such as data compression by vector quantization) this assumption is not met, since the number of data pointsn grows roughly as 2d.Largely for this reason, the actual performances of many nearest-neighbor algorithms tend to be much better than their theoretical analyses would suggest. We present evidence of why this is the case. We provide an accurate analysis of the number of cells visited in nearest-neighbor searching by the bucketing andk-d tree algorithms. We assumemdpoints uniformly distributed in dimensiond, wherem is a fixed integer ≥2. Further, we assume that distances are measured in theL∞ metric. Our analysis is tight in the limit asd approaches infinity. Empirical evidence is presented showing that the analysis applies even in low dimensions.
Early Expression of Hypocretin/Orexin in the Chick Embryo Brain

Hypocretin/Orexin (H/O) neuropeptides are released by a discrete group of neurons in the vertebrate hypothalamus which play a pivotal role in the maintenance of waking behavior and brain state control. Previous studies have indicated that the H/O neuronal development differs between mammals and fish; H/O peptide-expressing cells are detectable during the earliest stages of brain morphogenesis in fish, but only towards the end of brain morphogenesis (by ∼85% of embryonic development) in rats. The developmental emergence of H/O neurons has never been previously described in birds. With the goal of determining whether the chick developmental pattern was more similar to that of mammals or of fish, we investigated the emergence of H/O-expressing cells in the brain of chick embryos of different ages using immunohistochemistry. Post-natal chick brains were included in order to compare the spatial distribution of H/O cells with that of other vertebrates. We found that H/O-expressing cells appear to originate from two separate places in the region of the diencephalic proliferative zone. These developing cells express the H/O neuropeptide at a comparatively early age relative to rodents (already visible at 14% of the way through fetal development), thus bearing a closer resemblance to fish. The H/O-expressing cell population proliferates to a large number of cells by a relatively early embryonic age. As previously suggested, the distribution of H/O neurons is intermediate between that of mammalian and non-mammalian vertebrates. This work suggests that, in addition to its roles in developed brains, the H/O peptide may play an important role in the early embryonic development of non-mammalian vertebrates.
Molecular Requirements for Bi-directional Movement of Phagosomes Along Microtubules

Microtubules facilitate the maturation of phagosomes by favoring their interactions with endocytic compartments. Here, we show that phagosomes move within cells along tracks of several microns centrifugally and centripetally in a pH- and microtubuledependent manner. Phagosome movement was reconstituted in vitro and required energy, cytosol and membrane proteins of this organelle. The activity or presence of these phagosome proteins was regulated as the organelle matured, with “late” phagosomes moving threefold more frequently than “early” ones. The majority of moving phagosomes were minus-end directed; the remainder moved towards microtubule plus-ends and a small subset moved bi-directionally. Minus-end movement showed pharmacological characteristics expected for dyneins, was inhibited by immunodepletion of cytoplasmic dynein and could be restored by addition of cytoplasmic dynein. Plus-end movement displayed pharmacological properties of kinesin, was inhibited partially by immunodepletion of kinesin and fully by addition of an anti-kinesin IgG. Immunodepletion of dynactin, a dynein-activating complex, inhibited only minus-end directed motility. Evidence is provided for a dynactin-associated kinase required for dyneinmediated vesicle transport. Movement in both directions was inhibited by peptide fragments from kinectin (a putative kinesin membrane receptor), derived from the region to which a motility-blocking antibody binds. Polypeptide subunits from these microtubule-based motility factors were detected on phagosomes by immunoblotting or immunoelectron microscopy. This is the first study using a single in vitro system that describes the roles played by kinesin, kinectin, cytoplasmic dynein, and dynactin in the microtubule-mediated movement of a purified membrane organelle.
Conditional Plausibility Measures and Bayesian Networks

A general notion of algebraic conditional plausibility measures is defined. Probability measures, ranking functions, possibility measures, and (under the appropriate definitions) sets of probability measures can all be viewed as defining algebraic conditional plausibility measures. It is shown that algebraic conditional plausibility measures can be represented using Bayesian networks.
The Nuclear Reddening Curve for Active Galactic Nuclei and the Shape of the Infrared to X-Ray Spectral Energy Distribution

We present extinction curves derived from the broad emission lines and continua of samples of 72 radio-loud and 1018 radio-quiet active galactic nuclei (AGNs). The curves are significantly flatter in the UV than curves for the local interstellar medium. The reddening curves for the radio-quiet Large Bright Quasar Survey quasars are slightly steeper than those of the radio-loud quasars in the UV, probably because of additional reddening by dust farther out in the host galaxies of the former. The UV extinction curves for the radio-loud AGNs are very flat. This is explicable with slight modifications to standard Mathis-Rumpl-Nordsieck dust models: there is a relative lack of small grains in the nuclear dust. Our continuum and broad emission line reddening curves agree in both shape and amplitude, confirming that the continuum shape is indeed profoundly affected by reddening for all but the bluest AGNs. With correction by our generic extinction curve, all of the radio-loud AGNs have optical-UV continuous spectra consistent with a single shape. We show that radio-quiet AGNs have very similar intrinsic UV to optical shape over orders of magnitude in luminosity. We also argue that radio-loud and radio-quiet AGNs probably share the same underlying continuum shape and that most of the systematic differences between their observed continuum shapes are due to higher nuclear reddening in radio-selected AGNs and additional reddening from dust farther out in the host galaxies in radio-quiet AGNs. Our conclusions have important implications for the modeling of quasar continua and the analysis of quasar demographics.
A Survey on how Description Logic Ontologies Benefit from Formal Concept Analysis

Although the notion of a concept as a collection of objects sharing certain properties, and the notion of a conceptual hierarchy are fundamental to both Formal Concept Analysis and Description Logics, the ways concepts are described and obtained differ significantly between these two research areas. Despite these differences, there have been several attempts to bridge the gap between these two formalisms, and attempts to apply methods from one field in the other. The present work aims to give an overview on the research done in combining Description Logics and Formal Concept Analysis.
2d resistivity characterization of alluvial deposits near Azuero Fault, Panama

Recent alluvial deposits adjacent to the Azuero-Sona fault zone, at Azuero peninsula, Panama, are inspected with resistivity measurements in order to find narrow vertical ruptures parallel to the main strike of the fault, which could indicate neotectonic activity. Five 2D resistivity sections at three locations, Malena, Sapotal and Quebro, were obtained with semiDemo version of RES2DINV software through six lines of data acquisition: two lines taken at the same location were merged into one. Profiles at Sapotal and Quebro show low resistivity elongated zones (1.40 ? m at Sapotal and 45.7 – 57.3 ? m at Quebro) which indicate percolation of fluids in vertical structures. These structures are interpreted in this study as a product of neotectonic activity of Azuero fault. Inferred ruptures reach depths of 3.13 m at Sapotal and 1 and 5 m at Quebro. At Quebro, a previous GPR survey shows the same vertical structure found with resistivity. Using orientations of both resistivity and GPR profiles, a rupture direction of ~98° is obtained, nearly parallel to the main strike of Azuero fault (120°). The orientation of this structure corresponds to a counterclockwise synthetic structure in the Riedel shear zone of the Azuero Sona fault zone. Also, a model of generation of the terraces is proposed: at Sapotal an erosional-depositional event of a tributary created two terraces while at Quebro one tectonic response and a climatic event, which changed the river course, created three terraces.
Effect of split and foliar application of urea on growth and nutrient balance sheet of rainfed soybean

To find out the optimum N/P ratio (applied as basal or as basal and foliar application) for maximum yield of soybean crop under rainfed situations a field experiment was conducted during kharif 2015. The experiment consists of 13 N/P fertilizer ratios and levels. Foliar application of nitrogen (N) was taken in the form of urea @ 2.00 % at initiation of flowering (i.e., in the treatment T4) or at initiation of flowering and 15 days after first spray (i.e., in the treatments from T5 to T13). At 30 and 60 DAS, the treatment receiving N/P fertilizer ratio of 0.70 produced taller plants (24.55 and 64.67 cm) as compared to control (20.01 and 55.93 cm) and potassium level alone (21.59 and 58.63 cm) respectively. At 60 DAS, the treatment receiving N/P fertilizer ratio of 0.70 recorded higher leaf area plant-1 (12.62 dm2 plant-1) as compared to control (6.82 dm2 plant-1) and potassium level alone (6.96 dm2 plant-1). The balance after the harvest of soybean was the highest (164.23 kg ha-1) in treatment T4 receiving, while the lowest (88.07 kg ha-1) balance was observed in treatment T5 i.e.N/P ratio of 0.70. However, the apparent gain or loss in the available nitrogen was to extent of 188.26 kg ha-1 in treatment T5 receiving N/P ratio of 0.70. The maximum uptake of phosphorus (27.93 kg ha5) was observed in treatment T6 receiving N/P ratio of 0.70. The expected phosphorus balance after the harvest of soybean was highest (91.33 kg ha-1) in treatment T3.
Adverse Listening Conditions and Memory Load Drive a Common Alpha Oscillatory Network

How does acoustic degradation affect the neural mechanisms of working memory? Enhanced alpha oscillations (8–13 Hz) during retention of items in working memory are often interpreted to reflect increased demands on storage and inhibition. We hypothesized that auditory signal degradation poses an additional challenge to human listeners partly because it draws on the same neural mechanisms. In an adapted Sternberg paradigm, auditory memory load and acoustic degradation were parametrically varied and the magnetoencephalographic response was analyzed in the time–frequency domain. Notably, during the stimulus-free delay interval, alpha power monotonically increased at central–parietal sensors as functions of memory load (higher alpha power with more memory load) and of acoustic degradation (also higher alpha power with more severe acoustic degradation). This alpha effect was superadditive when highest load was combined with most severe degradation. Moreover, alpha oscillatory dynamics during stimulus-free delay were predictive of response times to the probe item. Source localization of alpha power during stimulus-free delay indicated that alpha generators in right parietal, cingulate, supramarginal, and superior temporal cortex were sensitive to combined memory load and acoustic degradation. In summary, both challenges of memory load and acoustic degradation increase activity in a common alpha-frequency network. The results set the stage for future studies on how chronic or acute degradations of sensory input affect mechanisms of executive control.
Increased total and mite-specific immunoglobulin E in patients with aspirin-induced urticaria and angioedema.

BACKGROUND An increased prevalence of atopy has been observed in patients with intolerance of aspirin and nonsteroidal anti-inflammatory drugs (NSAIDs). OBJECTIVE To investigate total and mite-specific immunoglobulin (Ig) E in serum from patients with hypersensitivity to NSAIDs and healthy controls. METHODS Patients who reacted to 2 or more chemically unrelated NSAIDs with urticaria and angioedema, confirmed by a double-blinded provocation test with aspirin, were skin tested with inhalant allergens. Total and specific IgE to Dermatophagoides pteronyssinus (Dp) and Blomia tropicalis (Bt) in the serum was quantified by enzyme-linked immunosorbent assay (ELISA) in patients and a control group of healthy blood donors. RESULTS One-hundred-and-fourteen patients and 74 controls were studied. Skin tests were positive in 95 patients (83.3%). Total mean IgE levels were 107.1 (91.3) IU/mL in controls and 161.0 (150.8) IU/mL in patients (P = .006). Mean (SD) levels of IgE to Dp were 0.210 (0.17) optical density (OD) units in controls and 0.473 (0.65) OD units in patients (P = .001). Levels of specific IgE to Bt were 0.230 (0.20) OD units in controls and 0.522 (0.8) OD units in patients (P =.0001). Positive ELISA results for IgE to Dp were found for 29.6% of controls and 70.4% of patients (P =.0001); the corresponding percentages for Bt were 32.4% of controls and 67.6 % of patients (P = .0001). CONCLUSIONS Cross-reactive patients with NSAID-induced urticaria and angioedema exhibit an increased prevalence of sensitization to Dp and Bt and increased total serum IgE. Further research is necessary to determine the reasons for this association.