Miracle-dz/UniFAR-FTUs huggingface dataset:
Comparison of growth hormone-producing and non-growth hormone-producing pituitary adenomas: imaging characteristics and pathologic correlation.

PURPOSE To identify characteristic features of growth hormone (GH)-producing pituitary adenomas. MATERIALS AND METHODS A total of 174 pathologically proven pituitary adenomas were evaluated retrospectively on magnetic resonance (MR) images to determine the signal intensity (on T2-weighted images), maximum diameter, and amount of suprasellar and infrasellar extension. For microadenomas, sellar depth was also measured. GH-producing adenomas were classified at histologic evaluation as densely or sparsely granulated. Specimens from 38 adenomas were stained to assess the amounts of fibrous tissue, iron, and amyloid they contained. Results were correlated with the size and hormonal activity of adenomas by using the chi2, unpaired t, and Mann-Whitney U tests. RESULTS Among 174 pituitary adenomas, 42 were GH-producing adenomas. Of these, 16 were densely granulated, and 24 were sparsely granulated (two histologic specimens were lost). Signal intensity was evaluated among 153 adenomas. On T2-weighted MR images, hypointensity was seen more commonly in adenomas that produced GH (16 of 40 cases [40%]; P <.001) than in those that did not; hypointensity was nearly exclusive to densely granulated GH-producing adenomas. The amounts of amyloid, fibrous tissue, and iron contained in adenomas demonstrated little relationship with signal intensity. Average suprasellar extension was significantly smaller in adenomas that produced GH (-0.8 mm) than in those that did not (5.3 mm) (P <.001). GH-producing adenomas tended to demonstrate infrasellar extension rather than suprasellar extension. Average sellar depth associated with GH-producing microadenomas (13.3 mm) was significantly greater than for non-GH-producing microadenomas (9.7 mm; P <.001). CONCLUSION Characteristic features regarding growth direction and T2 signal intensity can be identified for GH-producing adenomas.
Conformational analysis and molecular dynamics simulation of cellobiose and larger cellooligomers

The conformational behavior of cellobiose (D‐glc‐ß(1→4)‐D‐glc), cellotetraose, and cellooctaose was studied by a combination of energy minimization and molecular dynamics simulations in vacuo at 400 K. These diand oligosaccharide models have considerable flexibility and exhibit a variety of different motions in glycosidic and exocyclic torsions. The glycosidic ϕ, ψ torsions moved frequently between two local minima on the cellobiose energy surface in the region of known crystal structures. Transitions of the hydroxymethyl side chain were observed between gt,gg, and tg conformations accompanied by changes in intramolecular hydrogen bonding patterns. A reasonable fit to the experimental optical rotation and nuclear magnetic resonance vicinal coupling data of cellobiose in solution required a distribution of its conformations. The oligomers, although generally extended, assumed a more coiled or twisted shape than is observed in the crystalline state of cellulose and exhibited considerable backbone motion due to local ring rotations about the glycosidic bonds. Long‐lived transitions to structures having torsion angles 180° from the major minima (ring flips) introduced kinks and bends into the tetramer and octamer. While the glucose rings of the structures remained primarily in the 4C1 conformation, twist and boat structures were also observed in the tetramer and octamer structures. Reducing the simulation temperature to 300 K eliminated some of the transitions seen at 400 K. © 1993 John Wiley & Sons, Inc.
Microbiota and Mucosal Immunity in Amphibians

We know that animals live in a world dominated by bacteria. In the last 20 years, we have learned that microbes are essential regulators of mucosal immunity. Bacteria, archeas, and viruses influence different aspects of mucosal development and function. Yet, the literature mainly covers findings obtained in mammals. In this review, we focus on two major themes that emerge from the comparative analysis of mammals and amphibians. These themes concern: (i) the structure and functions of lymphoid organs and immune cells in amphibians, with a focus on the gut mucosal immune system; and (ii) the characteristics of the amphibian microbiota and its influence on mucosal immunity. Lastly, we propose to use Xenopus tadpoles as an alternative small-animal model to improve the fundamental knowledge on immunological functions of gut microbiota.
Depolarization and Neurotransmitter Regulation of Vasopressin Gene Expression in the Rat Suprachiasmatic Nucleus In Vitro

Vasopressin (VP) transcription in the rat suprachiasmatic nucleus (SCN) in organotypic culture was studied by in situ hybridization histochemistry using an intron-specific VP heteronuclear RNA probe. The circadian peak of VP gene transcription in the SCN in vitro is completely blocked by a 2 h exposure to tetrodotoxin (TTX) in the culture medium, and this TTX inhibition of VP gene transcription is reversed by exposure of the SCN to either forskolin or potassium depolarization. This suggests that an intrinsic, spontaneously active neuronal mechanism in the SCN is responsible for the cAMP- and depolarization-dependent pathways involved in maintaining peak VP gene transcription. In this paper, we evaluate a variety of neurotransmitter candidates, membrane receptors, and signal-transduction cascades that might constitute the mechanisms responsible for the peak of VP gene transcription. We find that vasoactive intestinal peptide (VIP) and a VPAC2 (VIP receptor subtype 2) receptor-specific agonist, Ro-25-1553, are the most effective ligands tested in evoking a cAMP–mitogen-activated protein kinase signal transduction cascade leading to an increase in VP gene transcription in the SCN. In addition, a second independent pathway involving depolarization activating L-type voltage-gated calcium channels and a Ca-dependent kinase pathway [inhibited by KN62 (1-[N,O-bis(5-isoquinolinesulphonyl)-N-methyl-l-tyrosyl]-4-phenylpiperazine)] rescues VP gene transcription in the presence of TTX. In the absence of TTX, these independent pathways appear to act in a cooperative manner to generate the circadian peak of VP gene transcription in the SCN.
Carbon metabolism and bacteroid respiration in nodules of chick-pea (Cicer arietinum L.) plants grown under saline conditions

ABSTRACT The present work investigates the relationships between nitrogen fixation, carbon metabolism and oxygen consumption by bacteroids of Mesorhizobium ciceri in root nodules of chick-pea plants. Its aim was to establish whether some of the compounds which accumulate under salt stress may be used as respiratory substrates by bacteroids to fuel their own metabolism and nitrogenase activity. Plants were grown in a growth chamber, and salt stress was induced by adding 50 mM NaCl to the nutrient solution at sowing. The data presented here show a rise in fermentative metabolism in nodules of chick-pea plants exposed to high salinity, and suggest that proline, lactate or ethanol, may play an important role as energy-yielding substrates for bacteroids in this plant species. The bacteroids could utilize glucose as a respiratory substrate both under control and saline conditions, while malate did not appear to be the preferred substrate in the presence of salt.
Towards Enabling Overture as a Platform for Formal Notation IDEs

Formal Methods tools will never have as many users as tools for popular programming languages and so the effort spent on constructing Integrated Development Environments (IDEs) will be orders of magnitudes lower than that of programming languages such as Java. This means newcomers to formal methods do not get the same user experience as with their favourite programming IDE. In order to improve this situation it is essential that efforts are combined so it is possible to reuse common features and thus not start from scratch every time. This paper presents the Overture platform where such a reuse philosophy is present. We give an overview of the platform itself as well as the extensibility principles that enable much of the reuse. The paper also contains several examples platform extensions, both in the form of new features and a new IDE supporting a new language.
Exploration of the binding of DNA binding ligands to Staphylococcal DNA through QM/MM docking and molecular dynamics simulation

DNA binding ligands (DBL) were reported to bind the minor groove of bacterial DNA. In the present study, DBL were analyzed and screened for their Staphylococcus inhibitory activity by inhibiting the Staphylococcal DNA replication. The orientation and the ligand-receptor interactions of DBL within the DNA-binding pocket were investigated applying a multi-step docking protocol using Glide and QM/MM docking. The polarization of ligands with QM/MM for DNA-ligand docking with Staphylococcal DNA minor groove was performed in order to understand their possible interactions. Molecular dynamics simulation techniques were employed to obtain the dynamic behavior of the DBL with Staphylococcal DNA. Computational docking and simulation represented a promising alternative to bridge the gap, and so that DNA and gyrase interactions were blocked by DBL. The results revealed the importance of the DBL for strong interactions with the DNA minor groove region and blocking the bacterial replication.
Bilingual Event Extraction: a Case Study on Trigger Type Determination

Event extraction generally suffers from the data sparseness problem. In this paper, we address this problem by utilizing the labeled data from two different languages. As a preliminary study, we mainly focus on the subtask of trigger type determination in event extraction. To make the training data in different languages help each other, we propose a uniform text representation with bilingual features to represent the samples and handle the difficulty of locating the triggers in the translated text from both monolingual and bilingual perspectives. Empirical studies demonstrate the effectiveness of the proposed approach to bilingual classification on trigger type determination.
Describing Reflectances for Color Segmentation Robust to Shadows, Highlights, and Textures

The segmentation of a single material reflectance is a challenging problem due to the considerable variation in image measurements caused by the geometry of the object, shadows, and specularities. The combination of these effects has been modeled by the dichromatic reflection model. However, the application of the model to real-world images is limited due to unknown acquisition parameters and compression artifacts. In this paper, we present a robust model for the shape of a single material reflectance in histogram space. The method is based on a multilocal creaseness analysis of the histogram which results in a set of ridges representing the material reflectances. The segmentation method derived from these ridges is robust to both shadow, shading and specularities, and texture in real-world images. We further complete the method by incorporating prior knowledge from image statistics, and incorporate spatial coherence by using multiscale color contrast information. Results obtained show that our method clearly outperforms state-of-the-art segmentation methods on a widely used segmentation benchmark, having as a main characteristic its excellent performance in the presence of shadows and highlights at low computational cost.
Use of Graded Exercise Testing in Concussion and Return-to-Activity Management

AbstractConcussion is a physiologic brain injury that produces systemic and cognitive symptoms. The metabolic and physiologic changes of concussion result in altered autonomic function and control of cerebral blood flow. Evaluation and treatment approaches based upon the physiology of concussion may therefore add a new dimension to concussion care. In this article, we discuss the use of a standard treadmill test, the Buffalo Concussion Treadmill Test (BCTT), in acute concussion and in postconcussion syndrome (PCS). The BCTT has been shown to diagnose physiologic dysfunction in concussion safely and reliably, differentiate it from other diagnoses (e.g., cervical injury), and quantify the clinical severity and exercise capacity of concussed patients. It is used in PCS to establish a safe aerobic exercise treatment program to help speed recovery and return to activity. The use of a provocative exercise test is consistent with world expert consensus opinion on establishing physiologic recovery from concussion.
Timing yield estimation using statistical static timing analysis

As process variations become a significant problem in deep sub-micron technology, a shift from deterministic static timing analysis to statistical static timing analysis for high-performance circuit designs could reduce the excessive conservatism that is built into current timing design methods. We address the timing yield problem for sequential circuits and propose a statistical approach to handle it. We consider the spatial and path reconvergence correlations between path delays, set-up time and hold time constraints, and clock skew due to process variations. We propose a method to get the timing yield based on the delay distributions of register-to-register paths in the circuit On average, the timing yield results obtained by our approach have average errors of less than 1.0% in comparison with Monte Carlo simulation. Experimental results show that shortest path variations and clock skew due to process variations have considerable impact on circuit timing, which could bias the timing yield results. In addition, the correlation between longest and shortest path delays is not significant.
Risk-neutral modelling with affine and non-affine models

Option prices provide a great deal of information regarding the market’s expectations of future asset price dynamics. But, the implied dynamics are under the risk-neutral measure rather than the physical measure under which the price of the underlying asset itself evolves. This paper demonstrates new techniques for joint analysis of the physical and risk-neutral models using data from both the underlying asset and options. While much of the prior work in this area has focused on affine and affine-jump models because of their analytical tractability, the techniques used in this paper are straightforward to apply to a broad class of models of potential interest. The techniques are based on evaluating various integrals of interest using Monte Carlo sums over simulated volatility paths. In an application using S&P 500 index data, we find that log volatility models perform dramatically better than affine models, but that some evidence of misspecification remains.
An Introduction to Multi-Valued Model Checking

Nowadays computer systems have become ubiquitous. Most of the resources in the development of such systems, and especially in the fail-safe ones, are allocated into the simulation and verification of their behavior. One such automated method of verification is model checking. Given a mathematical description of the real system and a specification usually in the form of temporal logics, a model checker verifies whether the specification is satisfied on the model of the system. Recently, a multi-valued extension to the classical model checking has been proposed. In this approach both the model of the system and the specification take truth values over lattices with more then just two values. Such an extension enhances the expressive power of temporal logics and allows reasoning under uncertainty. Some of the applications that can take advantage of the multi-valued model checking are abstraction techniques, reasoning about conflicting viewpoints and temporal logic query checking. In this paper, we present three different approaches to the multi-valued model checking problem. The first is a reduction from multi-valued CTL∗ to CTL∗, the second a multi-valued CTL symbolic model checking algorithm and, finally, a reduction technique from multi-valued μ-calculus to the classical one.
Dynamic self-scheduling of a fuel and emission constrained power producer under uncertainties

This work addresses a new framework for self-scheduling of a price-taker fuel and emission constrained power producer in a day-ahead market. The goal is determination of a trade-off between the expected profit and the risk when the power producer participates in day-ahead energy and spinning reserve markets. In this paper, a set of uncertainties including price forecasting uncertainty and available fuel uncertainty are contemplated. The latter uncertainty is raised due to the uncertainty of calling the power plant to generate in the spinning reserve market as well as forced outages of power plant. With considering of these uncertainties, a new framework for self-scheduling problem is proposed which is called dynamic self-scheduling. This risk-constrained dynamic self-scheduling framework is therefore formulated and solved as a mixed integer non-linear programming problem. Numerical results for a case study are discussed.
Different roles of cyclic electron flow around photosystem I under sub-saturating and saturating light intensities in tobacco leaves

In higher plants, the generation of proton gradient across the thylakoid membrane (ΔpH) through cyclic electron flow (CEF) has mainly two functions: (1) to generate ATP and balance the ATP/NADPH energy budget, and (2) to protect photosystems I and II against photoinhibition. The intensity of light under which plants are grown alters both CEF activity and the ATP/NADPH demand for primary metabolic processes. However, it is unclear how the role of CEF is affected by the level of irradiance that is applied during the growth and measurement periods. We studied the role of CEF at different light intensities in leaves from sun- and shade-grown plants. At 849 μmol photons m-2 s-1, both types of leaves had nearly the same degree of CEF activation. Modeling of the ATP/NADPH demand revealed that, at this light intensity, the contribution of CEF toward supplying ATP was much higher in the sun leaves. Meanwhile, the shade leaves showed higher levels of non-photochemical quenching and the P700 oxidation ratio. Therefore, at 849 μmol photons m-2 s-1, CEF mainly helped in the synthesis of ATP in the sun leaves, but functioned in photoprotection for the shade leaves. When the light intensity increased to 1976 μmol photons m-2 s-1, CEF activation was greatly enhanced in the sun leaves, but its contribution to supplying ATP changed slightly. These results indicate that the main role of CEF is altered flexibly in response to light intensity. In particular, CEF mainly contributes to balancing the ATP/NADPH energy budget under sub-saturating light intensities. When exposed to saturating light intensities, CEF mainly protects photosynthetic apparatus against photoinhibition.
Integrated Signals Between IL-13, IL-4, and IL-5 Regulate Airways Hyperreactivity

In this investigation, we have examined the integrated relationship between IL-13, IL-4, and IL-5 for the development of airways hyperreactivity (AHR) in a model of asthma in BALB/c mice. Sensitization and aeroallergen challenge of both wild-type (WT) and IL-13 gene-targeted (IL-13−/−) mice induced allergic disease that was characterized by pulmonary eosinophilia and AHR to β-methacholine. Although these responses in IL-13−/− mice were heightened compared with WT, they could be reduced to the level in nonallergic mice by the concomitant neutralization of IL-4. Mice in which both IL-4 and IL-13 were depleted displayed a marked reduction in tissue eosinophils, despite the development of a blood eosinophilia. Similar neutralization of IL-4 in WT mice only partially reduced AHR with no effect on tissue eosinophilia. In addition, neutralization of IL-5 in IL-13−/− mice, but not in WT mice, inhibited AHR, suggesting that tissue eosinophilia is linked to the mechanism underlying AHR only in the absence of IL-13. Additionally, mucus hypersecretion was attenuated in IL-13−/− mice, despite the persistence of AHR. Taken together, our data suggest both a modulatory role for IL-13 during sensitization and a proinflammatory role during aeroallergen challenge. The latter process appears redundant with respect to IL-4.
Local Constraint-Based General Surface Deformation

This paper develops a framework for locally deforming either a parametric surface or hierarchical subdivision surface to match a set of positional and energy minimizing constraints. The positional constraints can be obtained from a wide variety of existing interfaces, and the framework produces a smooth, local and stable deformation through solving a simple local least-squares. We use an indexing scheme to localize optimization to only contributing control points. These points are found and measured by using basis functions or by tracking subdivision mask operations. We demonstrate our framework on B-spline and Loop subdivision surfaces.
Genes Involved in Long-Term Memory Are Expressed in Testis of Cryptorchid Boys and Respond to GnRHa Treatment

It has been known for many years that boys with unilateral or bilateral undescended testis (cryptorchidism) tend to have a low IQ, and those who belong to the high infertility risk (HIR) group perform less well at school than low infertility risk (LIR) patients. However, the molecular biological processes underlying this phenomenon are not understood. In this study, we report the outcome of testicular RNA profiling for genes involved in long-term memory formation. We analyzed the histology and the transcriptome of testicular biopsies from bilateral HIR cryptorchid boys, comparing those who received GnRHa treatment for 6 months after the first surgery with those who did not receive GnRHa before the second surgery. We found that GnRHa treatment alters the testicular mRNA levels of neuronal genes that are involved in long-term memory and testosterone synthesis. These data highlight a possible molecular link between cryptorchidism, impaired mini-puberty, and diminished cognitive functions. Our results are consistent with the hypothesis that hypogonadotropic hypogonadism in cryptorchid boys with altered mini-puberty may affect neuronal genes important for memory and learning, which could help explaining the negative correlation between cryptorchidism and intellectual abilities.
The low-paid worker and the low-paying employer: characterisations using WERS98

Low pay is concentrated in lower-skilled occupations. But the factors that affect pay levels in these occupations are different from those that affect the pay of the higher skilled. The paper used the 1998 Workplace Employee Relations Survey to examine the determinants of pay in lower-skilled jobs. It finds a wide range of employer and workplace characteristics that depress pay levels in these jobs. In only a small minority of them does trade union bargaining attenuate these effects. Human capital and individual characteristics are less important than features of the job and employer.