Miracle-dz/UniFAR-FTUs huggingface dataset:
DETORQUEO, QUIRKY, and ZERZAUST Represent Novel Components Involved in Organ Development Mediated by the Receptor-Like Kinase STRUBBELIG in Arabidopsis thaliana

Intercellular signaling plays an important role in controlling cellular behavior in apical meristems and developing organs in plants. One prominent example in Arabidopsis is the regulation of floral organ shape, ovule integument morphogenesis, the cell division plane, and root hair patterning by the leucine-rich repeat receptor-like kinase STRUBBELIG (SUB). Interestingly, kinase activity of SUB is not essential for its in vivo function, indicating that SUB may be an atypical or inactive receptor-like kinase. Since little is known about signaling by atypical receptor-like kinases, we used forward genetics to identify genes that potentially function in SUB-dependent processes and found recessive mutations in three genes that result in a sub-like phenotype. Plants with a defect in DETORQEO (DOQ), QUIRKY (QKY), and ZERZAUST (ZET) show corresponding defects in outer integument development, floral organ shape, and stem twisting. The mutants also show sub-like cellular defects in the floral meristem and in root hair patterning. Thus, SUB, DOQ, QKY, and ZET define the STRUBBELIG-LIKE MUTANT (SLM) class of genes. Molecular cloning of QKY identified a putative transmembrane protein carrying four C2 domains, suggesting that QKY may function in membrane trafficking in a Ca2+-dependent fashion. Morphological analysis of single and all pair-wise double-mutant combinations indicated that SLM genes have overlapping, but also distinct, functions in plant organogenesis. This notion was supported by a systematic comparison of whole-genome transcript profiles during floral development, which molecularly defined common and distinct sets of affected processes in slm mutants. Further analysis indicated that many SLM-responsive genes have functions in cell wall biology, hormone signaling, and various stress responses. Taken together, our data suggest that DOQ, QKY, and ZET contribute to SUB-dependent organogenesis and shed light on the mechanisms, which are dependent on signaling through the atypical receptor-like kinase SUB.
ESTIMATION OF THYROID RADIATION DOSES FOR THE HANFORD THYROID DISEASE STUDY: RESULTS AND IMPLICATIONS FOR STATISTICAL POWER OF THE EPIDEMIOLOGICAL ANALYSES

Residents of eastern Washington, northeastern Oregon, and western Idaho were exposed to 131I released into the atmosphere from operations at the Hanford Nuclear Site from 1944 through 1972, especially in the late 1940’s and early 1950’s. This paper describes the estimated doses to the thyroid glands of the 3,440 evaluable participants in the Hanford Thyroid Disease Study, which investigated whether thyroid morbidity was increased in people exposed to radioactive iodine from Hanford during 1944–1957. The participants were born during 1940–1946 to mothers living in Benton, Franklin, Walla Walla, Adams, Okanogan, Ferry, or Stevens Counties in Washington State. Whenever possible someone with direct knowledge of the participant’s early life (preferably the participant’s mother) was interviewed about the participant’s individual dose-determining characteristics (residence history, sources and quantities of food, milk, and milk products consumed, production and processing techniques for home-grown food and milk products). Default information was used if no interview respondent was available. Thyroid doses were estimated using the computer program Calculation of Individual Doses from Environmental Radionuclides (CIDER) developed by the Hanford Environmental Dose Reconstruction Project. CIDER provided 100 sets of doses to represent uncertainty of the estimates. These sets were not generated independently for each participant, but reflected the effects of uncertainties in characteristics shared by participants. Estimated doses (medians of each participant’s 100 realizations) ranged from 0.0029 mGy to 2823 mGy, with mean and median of 174 and 97 mGy, respectively. The distribution of estimated doses provided the Hanford Thyroid Disease Study with sufficient statistical power to test for dose-response relationships between thyroid outcomes and exposure to Hanford’s 131I.
Perspectives on Media Effects

The social, cultural, and psychological impacts of mass media communication are explored in this volume by top media effects researchers. These experts review traditional topics (agenda setting, violence, aggression), and offer new insights into questions largely left untapped -- television addiction, pornography, the social effects of new technologies, and the idea that entertainment is itself a media effect.
Synaptic heterogeneity between mouse paracapsular intercalated neurons of the amygdala

GABAergic medial paracapsular intercalated (Imp) neurons of amygdala are thought of as playing a central role in fear learning and extinction. We report here that the synaptic network formed by these neurons exhibits distinct short‐term plastic synaptic responses. The success rate of synaptic events evoked at a frequency range of 0.1–10 Hz varied dramatically between different connected cell pairs. Upon enhancing the frequency of stimulation, the success rate increased, decreased or remained constant, in a similar number of cell pairs. Such synaptic heterogeneity resulted in inhibition of the firing of the postsynaptic neurons with different efficacies. Moreover, we found that the different synaptic weights were mainly determined by diversity in presynaptic release probabilities rather than postsynaptic changes. Sequential paired recording experiments demonstrated that the same presynaptic neuron established the same type of synaptic connections with different postsynaptic neurons, suggesting the absence of target‐cell specificity. Conversely, the same postsynaptic neuron was contacted by different types of synaptic connections formed by different presynaptic neurons. A detailed anatomical analysis of the recorded neurons revealed discrete and unexpected peculiarities in the dendritic and axonal patterns of different cell pairs. In contrast, several intrinsic electrophysiological responses were homogeneous among neurons, and synaptic failure counts were not affected by presynaptic cannabinoid 1 or GABAB receptors. We propose that the heterogeneous functional connectivity of Imp neurons, demonstrated by this study, is required to maintain the stability of firing patterns which is critical for the computational role of the amygdala in fear learning and extinction.
Xkr8 phospholipid scrambling complex in apoptotic phosphatidylserine exposure

Significance In healthy cells, phosphatidylserine (PtdSer) is exclusively localized at inner leaflets of plasma membranes. When cells undergo apoptosis, caspases cleave a membrane protein, XK-related protein (Xkr) 8, at the C terminus, and the cleaved Xkr8 supports scrambling of phospholipids between inner and outer leaflets of plasma membranes. The PtdSer, thus exposed to the cell surface, is recognized by macrophages as an “eat me” signal for engulfment of dead cells. We report that Xkr8 is present as a complex with basigin or neuroplastin that work as a chaperone to localize Xkr8 at plasma membranes. When Xkr8 is cleaved by caspase, the complex undergoes a higher-order structure. These results will contribute to our understanding of how the Xkr8 scrambles phospholipids when cells undergo apoptosis. Xk-related protein (Xkr) 8, a protein carrying 10 transmembrane regions, is essential for scrambling phospholipids during apoptosis. Here, we found Xkr8 as a complex with basigin (BSG) or neuroplastin (NPTN), type I membrane proteins in the Ig superfamily. In BSG−/−NPTN−/− cells, Xkr8 localized intracellularly, and the apoptosis stimuli failed to expose phosphatidylserine, indicating that BSG and NPTN chaperone Xkr8 to the plasma membrane to execute its scrambling activity. Mutational analyses of BSG showed that the atypical glutamic acid in the transmembrane region is required for BSG’s association with Xkr8. In cells exposed to apoptotic signals, Xkr8 was cleaved at the C terminus and the Xkr8/BSG complex formed a higher-order complex, likely to be a heterotetramer consisting of two molecules of Xkr8 and two molecules of BSG or NPTN, suggesting that this cleavage causes the formation of a larger complex of Xkr8-BSG/NPTN for phospholipid scrambling.
Qualitative Methods for Marketplace Research

PART ONE: APPROACHING QUALITATIVE METHODS Why Qualitative Research? Five Models of Qualitative Research Applications of Qualitative Methods for Marketing PART TWO: GETTING READY TO RESEARCH Issues and Concerns Designing a Study and Writing a Proposal PART THREE: CHOOSING A RESEARCH MODEL History, Living Biography and Self-Narrative Using the Case Method Phenomenology and Grounded Theory Using an Ethnographic Approach PART FOUR: DATA COLLECTION TECHNIQUES AND TOOLS Observation and Fieldwork Ways of Knowing Field Interviews Ways of Knowing Structured Interviews Projective Techniques PART FIVE: TEXT ANALYSIS AND REPORTING Analyzing Visual and Material Text Analyzing Verbal Data Writing Field Stories and Narrative Reports
Endotoxemia stimulates skeletal muscle Na+-K+-ATPase and raises blood lactate under aerobic conditions in humans.

We assessed the hypothesis that the epinephrine surge present during sepsis accelerates aerobic glycolysis and lactate production by increasing activity of skeletal muscle Na(+)-K(+)-ATPase. Healthy volunteers received an intravenous bolus of endotoxin or placebo in a randomized order on two different days. Endotoxemia induced a response resembling sepsis. Endotoxemia increased plasma epinephrine to a maximum at t = 2 h of 0.7 +/- 0.1 vs. 0.3 +/- 0.1 nmol/l (P < 0.05, n = 6-7). Endotoxemia reduced plasma K(+) reaching a nadir at t = 5 h of 3.3 +/- 0.1 vs. 3.8 +/- 0.1 mmol/l (P < 0.01, n = 6-7), followed by an increase to placebo level at t = 7-8 h. During the declining plasma K(+), a relative accumulation of K(+) was seen reaching a maximum at t = 6 h of 8.7 +/- 3.8 mmol/leg (P < 0.05). Plasma lactate increased to a maximum at t = 1 h of 2.5 +/- 0.5 vs. 0.9 +/- 0.1 mmol/l (P < 0.05, n = 8) in association with increased release of lactate from the legs. These changes were not associated with hypoperfusion or hypoxia. During the first 24 h after endotoxin infusion, renal K(+) excretion was 27 +/- 7 mmol, i.e., 58% higher than after placebo. Combination of the well-known stimulatory effect of catecholamines on skeletal muscle Na(+)-K(+)-ATPase activity, with the present confirmation of an expected Na(+)-K(+)- ATPase-induced decline in plasma K(+), suggests that the increased lactate release was due to increased Na(+)-K(+)-ATPase activity, supporting our hypothesis. Thus increased lactate levels in acutely and severely ill patients should not be managed only from the point of view that it reflects hypoxia.
Moderate Peep After Tracheal Lipopolysaccharide Instillation Prevents Inflammation and Modifies the Pattern of Brain Neuronal Activation

Background: Ventilatory strategy and specifically positive end-expiratory pressure (PEEP) can modulate the inflammatory response and pulmonary-to-systemic translocation of lipopolysaccharide (LPS). Both inflammation and ventilatory pattern may modify brain activation, possibly worsening the patient's outcome and resulting in cognitive sequelae. Methods: We prospectively studied Sprague–Dawley rats randomly assigned to undergo 3 h mechanical ventilation with 7 mL/kg tidal ventilation and either 2 cmH2O or 7 cmH2O PEEP after intratracheal instillation of LPS or saline. Healthy nonventilated rats served as baseline. We analyzed lung mechanics, gas exchange, lung and plasma cytokine levels, lung apoptotic cells, and lung neutrophil infiltration. To evaluate brain neuronal activation, we counted c-Fos immunopositive cells in the retrosplenial cortex (RS), thalamus, supraoptic nucleus (SON), nucleus of the solitary tract (NTS), paraventricular nucleus (PVN), and central amygdala (CeA). Results: LPS increased lung neutrophilic infiltration, lung and systemic MCP-1 levels, and neuronal activation in the CeA and NTS. LPS-instilled rats receiving 7 cmH2O PEEP had less lung and systemic inflammation and more c-Fos-immunopositive cells in the RS, SON, and thalamus than those receiving 2 cmH2O PEEP. Applying 7 cmH2O PEEP increased neuronal activation in the CeA and NTS in saline-instilled rats, but not in LPS-instilled rats. Conclusions: Moderate PEEP prevented lung and systemic inflammation secondary to intratracheal LPS instillation. PEEP also modified the neuronal activation pattern in the RS, SON, and thalamus. The relevance of these differential brain c-Fos expression patterns in neurocognitive outcomes should be explored.
The Oxford Handbook of Computational and Mathematical Psychology

Preface 1. Introduction Jerome R. Busemeyer, Zheng Wang, James T. Townsend, and Ami Eidels Part I. Elementary Cognitive Mechanisms 2. Multidimensional Signal Detection Theory F. Gregory Ashby and Fabian A. Soto 3. Modeling Simple Decisions and Applications Using a Diffusion Model Roger Ratcliff and Philip Smith 4. Features of Response Times: Identification of Cognitive Mechanisms through Mathematical Modeling Daniel Algom, Ami Eidels, Robert X. D. Hawkins, Brett Jefferson, and James T. Townsend 5. Computational Reinforcement Learning Todd M. Gureckis and Bradley C. Love Part II. Basic Cognitive Skills 6. Why Is Accurately Labeling Simple Magnitudes So Hard? A Past, Present, and Future Look at Simple Perceptual Judgment Chris Donkin, Babette Rae, Andrew Heathcote, and Scott D. Brown 7. An Exemplar-Based Random-Walk Model of Categorization and Recognition Robert M. Nosofsky and Thomas J. Palmeri 8. Models of Episodic Memory Amy H. Criss and Marc W. Howard Part III. Higher Level Cognition 9. Structure and Flexibility in Bayesian Models of Cognition Joseph L. Austerweil, Samuel J. Gershman, and Thomas L. Griffiths 10. Models of Decision Making under Risk and Uncertainty Timothy J. Pleskac, Adele Diederich, and Thomas S. Wallsten 11. Models of Semantic Memory Michael N. Jones, Jon Willits, and Simon Dennis 12. Shape Perception Tadamasa Sawada, Yunfeng Li, and Zygmunt Pizlo Part IV. New Directions 13. Bayesian Estimation in Hierarchical Models John K. Kruschke and Wolf Vanpaemel 14. Model Comparison and the Principle of Parsimony Joachim Vandekerckhove, Dora Matzke, and Eric-Jan Wagenmakers 15. Neurocognitive Modeling of Perceptual Decision Making Thomas J. Palmeri, Jeffrey D. Schall, and Gordon D. Logan 16. Mathematical and Computational Modeling in Clinical Psychology Richard W. J. Neufeld 17. Quantum Models of Cognition and Decision Jerome R. Busemeyer, Zheng Wang, and Emmanuel Pothos Index
Prospective Study of Laparoscopic Nissen Fundoplication in a Community Hospital and Its Effect on Typical, Atypical, and Nonspecific Gastrointestinal Symptoms

Background: Laparoscopic Nissen fundoplication (LNF) provides long-term improvement in the typical symptoms of gastroesophageal reflux disease. Few studies have prospectively addressed LNF in the community hospital or the effect of LNF on specific atypical symptoms, other related gastrointestinal symptoms, and weight change. Methods: Data were collected prospectively on consecutive patients having LNF. Three typical, 6 atypical, and 3 other gastrointestinal symptoms were studied. Results: Short-term data on 91 patients and long-term data on 84 patients were studied. Overall long-term improvement was 98%. Regarding typical symptoms, the greatest improvement occurred in heartburn and regurgitation. Regarding atypical symptoms, the greatest improvement occurred in cough and sore throat, but chest pain, hoarseness, and throat clearing also showed significant durable improvement. Bloating, nausea, and diarrhea showed no significant change from preoperative to postoperative surveys. Mild weight loss was common. Conclusion: LNF can be safely performed in a community hospital with results equal to those of university hospitals. Improvement in typical symptoms was greater than improvement in atypical symptoms, but results for both were significant and durable. Nonspecific gastrointestinal symptoms, such as nausea, bloating, and diarrhea, may be unrelated to Nissen fundoplication.
Circadian oscillation of gibberellin signaling in Arabidopsis

Circadian clocks are endogenous timekeeping mechanisms that allow organisms to anticipate rhythmic, daily environmental changes. Temporal coordination of transcription results in a set of gene expression patterns with peak levels occurring at precise times of the day. An intriguing question is how a single clock can generate different oscillatory rhythms, and it has been proposed that hormone signaling might act in plants as a relay mechanism to modulate the amplitude and the phase of output rhythms. Here we show that the circadian clock gates gibberellin (GA) signaling through transcriptional regulation of the GA receptors, resulting in higher stability of DELLA proteins during daytime and higher GA sensitivity at night. Oscillation of GA signaling appears to be particularly critical for rhythmic growth, given that constitutive expression of the GA receptor expands the daily growth period in seedlings, and complete loss of DELLA function causes continuous, arrhythmic hypocotyl growth. Moreover, transcriptomic analysis of a pentuple della KO mutant indicates that the GA pathway mediates the rhythmic expression of many clock-regulated genes related to biotic and abiotic stress responses and cell wall modification. Thus, gating of GA sensitivity by the circadian clock represents an additional layer of regulation that might provide extra robustness to the diurnal growth rhythm and constitute a regulatory module that coordinates the circadian clock with additional endogenous and environmental signals.
The quest for the function of simple epithelial keratins

Simple epithelial keratins K8 and K18 are components of the intracellular cytoskeleton in the cells of the single‐layered sheet tissues inside the body. As members of the intermediate filament family of proteins, their function has been a matter for debate since they were first discovered. Whilst there is an indisputable case for a structural cell‐reinforcing function for keratins in the mutilayered squamous epithelia of external barrier tissues, some very different stress‐protective features now seem to be emerging for the simple epithelial keratins. Even the emerging evidence of pathological mutations in K8/K18 looks very different from mutations in stratified epithelial keratins. K8/K18‐like keratins were probably the first to evolve and, whilst stratified epithelial (keratinocyte) keratins have diversified into a large group of keratins highly specialised for providing mechanical stability, the simple epithelial keratins have retained early features that may protect the internal epithelia from a broader range of stresses, including osmotic stress and chemical toxicity. BioEssays 25:748–758, 2003. © 2003 Wiley Periodicals, Inc.
Hyperspectral Unmixing: Ground Truth Labeling, Datasets, Benchmark Performances and Survey

Hyperspectral unmixing (HU) is a very useful and increasingly popular preprocessing step for a wide range of hyperspectral applications. However, the HU research has been constrained a lot by three factors: (a) the number of hyperspectral images (especially the ones with ground truths) are very limited; (b) the ground truths of most hyperspectral images are not shared on the web, which may cause lots of unnecessary troubles for researchers to evaluate their algorithms; (c) the codes of most state-of-the-art methods are not shared, which may also delay the testing of new methods. Accordingly, this paper deals with the above issues from the following three perspectives: (1) as a profound contribution, we provide a general labeling method for the HU. With it, we labeled up to 15 hyperspectral images, providing 18 versions of ground truths. To the best of our knowledge, this is the first paper to summarize and share up to 15 hyperspectral images and their 18 versions of ground truths for the HU. Observing that the hyperspectral classification (HyC) has much more standard datasets (whose ground truths are generally publicly shared) than the HU, we propose an interesting method to transform the HyC datasets for the HU research. (2) To further facilitate the evaluation of HU methods under different conditions, we reviewed and implemented the algorithm to generate a complex synthetic hyperspectral image. By tuning the hyper-parameters in the code, we may verify the HU methods from four perspectives. The code would also be shared on the web. (3) To provide a standard comparison, we reviewed up to 10 state-of-the-art HU algorithms, then selected the 5 most benchmark HU algorithms, and compared them on the 15 real hyperspectral datasets. The experiment results are surely reproducible; the implemented codes would be shared on the web.
Genetic studies of bipolar disorder and recurrent major depression in a large Scottish family

s and oral presentations Lorna M Houlihan, David Porteous, Douglas Blackwood, Kathryn Evans (2006) “Investigations into a chromosome 4p bipolar disorder susceptibility gene; Allelic expression assays and an association study in PI4K2B” American Journal of Medical Genetics 2006, 141B (1) P83 Lorna Houlihan, Margaret McLean, Walter Muir, David Porteous, Douglas Blackwood, Kathryn Evans “Analysis of a phosphoinositol kinase as a candidate bipolar disorder susceptibility gene on chromosome 4p” (2006) Bipolar Disorders 8 (S1) 63 Lorna Houlihan, Margaret McLean, Pippa Thompson, Andrea Christoforou, Walter Muir, David Porteous, Douglas Blackwood, Kathryn Evans “Analysis of PI4KIIβ, a Candidate Gene from the Bipolar Disorder Susceptibility Locus on Chromosome 4p15-16”. (2005) American Journal of Medical Genetics 138B (1) 86
The Monarch Initiative: an integrative data and analytic platform connecting phenotypes to genotypes across species

The principles of genetics apply across the whole tree of life: on a cellular level, we share mechanisms with species from which we diverged millions or even billions of years ago. We can exploit this common ancestry at the level of sequences, but also in terms of observable outcomes (phenotypes), to learn more about health and disease for humans and all other species. Applying the range of available knowledge to solve challenging disease problems requires unified data relating genomics, phenotypes, and disease; it also requires computational tools that leverage these multimodal data to inform interpretations by geneticists and to suggest experiments. However, the distribution and heterogeneity of databases is a major impediment: databases tend to focus either on a single data type across species, or on single species across data types. Although each database provides rich, high-quality information, no single one provides unified data that is comprehensive across species, biological scales, and data types. Without a big-picture view of the data, many questions in genetics are difficult or impossible to answer. The Monarch Initiative (https://monarchinitiative.org) is an international consortium dedicated to providing computational tools that leverage a computational representation of phenotypic data for genotype-phenotype analysis, genomic diagnostics, and precision medicine on the basis of a large-scale platform of multimodal data that is deeply integrated across species and covering broad areas of disease.