Miracle-dz/UniFAR-FTUs huggingface dataset:
Virtual Laboratories

At the frontier of most areas in science, computer simulations play a central role. The traditional division of natural science into experimental and theoretical investigations is now completely outdated. Instead, theory, simulation, and experimentation form three equally essential aspects, each with its own unique flavor and challenges. Yet, education in computational science is still lagging far behind, and the number of text books in this area is minuscule compared to the many text books on theoretical and experimental science. As a result, many researchers still carry out simulations in a haphazard way, without properly setting up the computational equivalent of a well equipped laboratory. The art of creating such a virtual laboratory, while providing proper extensibility and documentation, is still in its infancy. A new approach is described here, Open Knowledge, as an extension of the notion of Open Source software. Besides open source code, manuals, and primers, an open knowledge project provides simulated dialogues between code developers, thus sharing not only the code, but also the motivations behind the code.
Consistency of Multiclass Empirical Risk Minimization Methods Based on Convex Loss

The consistency of classification algorithm plays a central role in statistical learning theory. A consistent algorithm guarantees us that taking more samples essentially suffices to roughly reconstruct the unknown distribution. We consider the consistency of ERM scheme over classes of combinations of very simple rules (base classifiers) in multiclass classification. Our approach is, under some mild conditions, to establish a quantitative relationship between classification errors and convex risks. In comparison with the related previous work, the feature of our result is that the conditions are mainly expressed in terms of the differences between some values of the convex function.
The management of parapneumonic effusions and empyema.

Background: In normal subjects, and patients with obstructive and restrictive lung defects, flows during an FVC manoeuver are higher after a fast inspiration without an end-inspiratory pause as compared to a slow inspiration with an end-inspiratory pause of approximately 5 s (time dependence of FVC). Objective: In the present study, we investigated the influence of these two manoeuvres on PEF and FEV 1 in asthmatic patients during methacholine challenge testing. Methods: Thirteen patients who were positive according to routine (non-standardized) methacholine challenge tests (PD20£1.57 mg) were studied. Their average(SD) lung function data were: FVC%pred=94(15), FEV 1 %pred=76(17) and FEV 1 /FVC%=68(12). The patients performed the two types of FVC manoeuvres in random order before and at the last methacholine dose. Results: Using the standardized FVC manoeuvres (fast before/fast after and slow before/slow after), only 10 patients (77%) had a positive test, while all 13 patients were positive with the routine test. Conclusion: These data indicate that different results can be obtained, if instead of the standardized, the non-standardized manoeuvres during methacholine challenge tests are used. The use of non-standardized FVC manoeuvres may lead to over-, or at least theoretically, to underestimation of patients with bronchial hyperresponsiveness. Therefore, standardization of FVC manoeuvres during airway challenge testing is required. Pneumon 2002, 15(2)168-175.
Cholesterol and Lipoprotein Dynamics in a Hibernating Mammal

Hibernating mammals cease feeding during the winter and rely primarily on stored lipids to fuel alternating periods of torpor and arousal. How hibernators manage large fluxes of lipids and sterols over the annual hibernation cycle is poorly understood. The aim of this study was to investigate lipid and cholesterol transport and storage in ground squirrels studied in spring, summer, and several hibernation states. Cholesterol levels in total plasma, HDL and LDL particles were elevated in hibernators compared with spring or summer squirrels. Hibernation increased plasma apolipoprotein A-I expression and HDL particle size. Expression of cholesterol 7 alpha-hydroxylase was 13-fold lower in hibernators than in active season squirrels. Plasma triglycerides were reduced by fasting in spring but not summer squirrels. In hibernators plasma β-hydroxybutyrate was elevated during torpor whereas triglycerides were low relative to normothermic states. We conclude that the switch to a lipid-based metabolism during winter, coupled with reduced capacity to excrete cholesterol creates a closed system in which efficient use of lipoproteins is essential for survival.
First Japanese Record of Uropterygius fasciolatus (Muraenidae: Uropterygiinae) Collected from Yonaguni-jima Island, Ryukyu Archipelago

1 The Kagoshima University Museum, 1-21-30 Korimoto, Kagoshima 890-0065, Japan E-mail: hatampo@gmail.com 2 Present address: National Museum of Marine Biology & Aquarium, 2 Houwan Road, Checheng, Pingtung, 94450, Taiwan 3 Fisheries Research Laboratory, Mie University, 4190-172 Wagu, Shima, Mie 517-0703, Japan 4 Present address: Laboratory of Fisheries Biology, Faculty of Agriculture, Kyushu University, 6-10-1 Hakozaki, Higashi-ku, Fukuoka 812-8581, Japan 5 Corresponding author
Kinetics of NH3‐oxidation, NO‐turnover, N2O‐production and electron flow during oxygen depletion in model bacterial and archaeal ammonia oxidisers

Ammonia oxidising bacteria (AOB) are thought to emit more nitrous oxide (N2 O) than ammonia oxidising archaea (AOA), due to their higher N2 O yield under oxic conditions and denitrification in response to oxygen (O2 ) limitation. We determined the kinetics of growth and turnover of nitric oxide (NO) and N2 O at low cell densities of Nitrosomonas europaea (AOB) and Nitrosopumilus maritimus (AOA) during gradual depletion of TAN (NH3 + NH4+) and O2 . Half-saturation constants for O2 and TAN were similar to those determined by others, except for the half-saturation constant for ammonium in N. maritimus (0.2 mM), which is orders of magnitudes higher than previously reported. For both strains, cell-specific rates of NO turnover and N2 O production reached maxima near O2 half-saturation constant concentration (2-10 μM O2 ) and decreased to zero in response to complete O2 -depletion. Modelling of the electron flow in N. europaea demonstrated low electron flow to denitrification (≤1.2% of the total electron flow), even at sub-micromolar O2 concentrations. The results corroborate current understanding of the role of NO in the metabolism of AOA and suggest that denitrification is inconsequential for the energy metabolism of AOB, but possibly important as a route for dissipation of electrons at high ammonium concentration.
The Response of the Lamb Ductus Venosus to Prostaglandins and Inhibitors of Prostaglandin and Thromboxane Synthesis

Rings of the umbilical end of the ductus venosus (the so-called sphincter) from nearterm fetal and newborn (1–3 days of age) lambs were studied in vitro at low (17–31 mm Hg) and high (504–705 mm Hg) Po2. Tissues developed a modest contraction upon exposure to a high Po2; however, this contraction generally was not sustained and tended to be greater in the fetus than in the newborn. In contrast, excess potassium (55 min) produced a sustained contraction whose magnitude was greater in the newborn. The cyclooxygenase inhibitor, indomethacin, contracted both the fetal and the neonatal ductus venosus; however, responses in the newborn were often not maintained. Furthermore, indomethacin enhanced the potassium response in the fetus, whereas it had no significant effect in the newborn. The thromboxane synthesis inhibitor, compound OKY 1581, was ineffective in either age group. Prostaglandin (PG) E2 and PGI2 relaxed the ductus venosus, the former being slightly more potent. Conversely, stable PG endoperoxide analogs (9α,llα-epoxymethano and 9α,llα-methano-epoxy compounds) and PGF2α were contractile agents. Endoperoxide analogs were more effective in the newborn than the fetus and their action consistently exceeded that of PGF2α. We conclude that the ductus venosus sphincter is endowed with functional muscle cells. These cells are under the influence of a relaxing product of the cyclooxygenase reaction which may be identified with either PGE2 or PGI2. This prostaglandin-mediated relaxing mechanism may contribute to prenatal patency of the vessel. Postnatal closure of the ductus venosus is unlikely to be a direct effect of oxygen on the sphincter muscle. The prostaglandin endoperoxides, however, are well suited for playing a role in the latter process.
Lymphatic Mapping and Sentinel Lymph Node Biopsy

▪ Abstract: The status of the regional nodal basin remains the most important prognostic indicator of survival. The current standard of care for the management of invasive breast cancer is the complete removal of the tumor, with documentation of negative margins by either mastectomy or lumpectomy, followed by complete axillary lymph node dissection. Data suggest that complete lymph node dissection (CLND) provides better local control of the disease and may actually offer a survival advantage. Lymphatic mapping and sentinel lymph node (SLN) biopsy are clearly changing this long‐held paradigm and have the potential to change the standard of surgical care of the breast cancer patient. The purpose of this report is to describe the lymphatic mapping experience at the H. Lee Moffitt Cancer Center and Research Institute. From April 1994 to January 1999, 1,147 consecutive breast cancer patients were enrolled in an institutional review board‐approved lymphatic mapping protocol. Lymphatic mapping was performed using Tc99m‐labeled sulfur colloid and isosulfan blue dye. An SLN was defined as any blue node and/or any hot node with ex vivo radioactivity counts 10 times an excised non‐SLN or in situ radioactivity counts 3 times the background counts. Lymphatic mapping was successful in identifying the SLN in 1,098 of 1,147 (95.7%) cases. In the first 186 patients, all of whom underwent CLND following SLN biopsy, one false‐negative biopsy was encountered for a false‐negative rate of 0.83%. The method of diagnosis (excisional versus minimally invasive) does not appear to impact on lymphatic mapping. Tumor size, however, is directly related to the probability of axillary lymph node involvement. Advances in technology and the development of minimally invasive surgical techniques have heralded a new era in surgery. Lymphatic mapping and SLN biopsy may actually prove to be a more accurate method of identifying metastases to the axilla by allowing a more focused pathologic examination of the axillary node(s) at highest risk for metastasis. With adequate training, this technique can be readily implemented as a valuable tool in the surgical treatment of breast cancer. ▪
Graph-based consensus clustering for class discovery from gene expression data

MOTIVATION Consensus clustering, also known as cluster ensemble, is one of the important techniques for microarray data analysis, and is particularly useful for class discovery from microarray data. Compared with traditional clustering algorithms, consensus clustering approaches have the ability to integrate multiple partitions from different cluster solutions to improve the robustness, stability, scalability and parallelization of the clustering algorithms. By consensus clustering, one can discover the underlying classes of the samples in gene expression data. RESULTS In addition to exploring a graph-based consensus clustering (GCC) algorithm to estimate the underlying classes of the samples in microarray data, we also design a new validation index to determine the number of classes in microarray data. To our knowledge, this is the first time in which GCC is applied to class discovery for microarray data. Given a pre specified maximum number of classes (denoted as K(max) in this article), our algorithm can discover the true number of classes for the samples in microarray data according to a new cluster validation index called the Modified Rand Index. Experiments on gene expression data indicate that our new algorithm can (i) outperform most of the existing algorithms, (ii) identify the number of classes correctly in real cancer datasets, and (iii) discover the classes of samples with biological meaning. AVAILABILITY Matlab source code for the GCC algorithm is available upon request from Zhiwen Yu.
Can Iodo-GTS-21 Be a Model to Develop New Tracer for Imaging Central Nicotinic Receptors?

Background: Change of the nicotinic acetylcholine receptors (nAChR) concentration has been proven to be correlated with several neurodegenerative disorders. Subtype α7 nAChR density declines significantly in Alzheimer's disease patients. GTS-21 was reported to show moderate binding affinity to α7 nAChR. Although GTS-21 has capability to bind to α7 nAChR, however, it binds to α4β2 subtype as well. Several studies have attempted to improve the binding affinity and subtype selectivity of GTS-21 by modifying its functional groups. In the present study, we evaluated a novel derivative of GTS-21, iodo-GTS-21, for its binding affinity and selectivity to two subtypes of nAChR, and determine if iodo-GTS-21 can be a chemical model for developing radioiodinated tracer to image central α7 nAChR. Methods: GTS-21 and iodo-GTS-21 were synthesized for the study. In vitro competition binding assay was performed to estimate the binding affinity of iodo-GTS-21 using rat brain homogenates. Several known cold ligands were used as parallel comparison and methodology confirmation. Results: Iodo-GTS-21 did not increase the binding affinities, as compared to the parent compound GTS- 21, for either α7 nAChR or α4β2 subtype. However, iodo-GTS-21 possessed significant subtype selectivity than that of GTS-21, with K(subscript i) values＞1,000 nM and 13 nM for α7 nAChR and α4β2 subtype, respectively. Conclusion: Iodo-GTS-21 may not be a model to develop new tracer for imaging α7 nAChR. The interesting profile that iodo-GTS-21 showed more selectivity than GTS-21 between bindings to two subtypes of nAChR may be worthwhile for further investigation.
Temporal and spatial distribution, and flight directions of migratory birds in Tsavo West National Park, Kenya: a comparison of radar and ringing data

From 1 November 2013 to 30 April 2014 an avian radar system was operated in Tsavo West National Park, Kenya. The aim of this research was to study the temporal and spatial distribution of migrating birds over Ngulia Safari Lodge and to compare radar data with catching results of grounded birds. Additionally, the general pattern of flight directions during the six-month season is shown. From 25 November to 12 December 2013 more than 21 000 birds of 29 species were caught and ringed under misty conditions, supported by floodlights and sound luring (Pearson 2013). A total of 8564 individuals (41%) were caught during the night. The majority of the birds were Marsh Warblers Acrocephalus palustris (4442 ringed) and Thrush Nightingales Luscinia luscinia (2719). Radar data of bird migration intensities (migration traffic rates, MTR = birds/km/h) show an increase in late November to December, decreasing towards February and rising again in March and April when birds are migrating north to their breeding grounds in Eurasia. These MTRs correlate very well with the numbers of birds on the ground. They also show that birds are still migrating under clear, mist-free conditions, when no attempts were undertaken to catch birds. As expected, the flight directions changed from south in the autumn, to north in March and April. The support of the wind is optimal for migrating birds. At the lower altitudes the wind direction changes from northeast (November – January) to southeast (March, April), thus supporting migrating birds with optimal tailwinds. This means that birds are not obliged to change their flight altitude between seasons. The wind support originated in the calm Intertropical Convergence Zone and is optimal throughout the season from November to April. To our knowledge this is the first time that a study has shown the magnitude of bird migration in eastern Africa and the temporal and spatial distribution for half a year. Keywords: Palaearctic migration, radar, Kenya
Suites of Terpene Synthases Explain Differential Terpenoid Production in Ginger and Turmeric Tissues

The essential oils of ginger (Zingiber officinale) and turmeric (Curcuma longa) contain a large variety of terpenoids, some of which possess anticancer, antiulcer, and antioxidant properties. Despite their importance, only four terpene synthases have been identified from the Zingiberaceae family: (+)-germacrene D synthase and (S)-β-bisabolene synthase from ginger rhizome, and α-humulene synthase and β-eudesmol synthase from shampoo ginger (Zingiber zerumbet) rhizome. We report the identification of 25 mono- and 18 sesquiterpene synthases from ginger and turmeric, with 13 and 11, respectively, being functionally characterized. Novel terpene synthases, (−)-caryolan-1-ol synthase and α-zingiberene/β-sesquiphellandrene synthase, which is responsible for formation of the major sesquiterpenoids in ginger and turmeric rhizomes, were also discovered. These suites of enzymes are responsible for formation of the majority of the terpenoids present in these two plants. Structures of several were modeled, and a comparison of sets of paralogs suggests how the terpene synthases in ginger and turmeric evolved. The most abundant and most important sesquiterpenoids in turmeric rhizomes, (+)-α-turmerone and (+)-β-turmerone, are produced from (−)-α-zingiberene and (−)-β-sesquiphellandrene, respectively, via α-zingiberene/β-sesquiphellandrene oxidase and a still unidentified dehydrogenase.
Alignment-Based Network Coding for Two-Unicast-Z Networks

In this paper, we study the wireline two-unicast-Z communication network over directed acyclic graphs. The two-unicast-$Z$ network is a two-unicast network where the destination intending to decode the second message has a priori side information of the first message. We make three contributions in this paper. First, we describe a new linear network coding algorithm for two-unicast-Z networks over the directed acyclic graphs. Our approach includes the idea of interference alignment as one of its key ingredients. For the graphs of a bounded degree, our algorithm has linear complexity in terms of the number of vertices, and the polynomial complexity in terms of the number of edges. Second, we prove that our algorithm achieves the rate pair (1, 1) whenever it is feasible in the network. Our proof serves as an alternative, albeit restricted to two-unicast-Z networks over the directed acyclic graphs, to an earlier result of Wang et al., which studied the necessary and sufficient conditions for the feasibility of the rate pair (1, 1) in two-unicast networks. Third, we provide a new proof of the classical max-flow min-cut theorem for the directed acyclic graphs.
Estimates of Martian crustal thickness from viscous relaxation of topography

Isostatically compensated crustal thickness variations and associated topographic contrasts at the surface of a planet result in lateral pressure gradients, which may cause the lower crust to flow and reduce the relief. Areas of thicker crust are generally associated with more rapid relaxation of topography. On Mars, topographic features such as impact basins and the hemispheric dichotomy have survived for 4 Gyr. We use a finite difference representation of depth-dependent, non-Newtonian lower crustal flow to investigate how topography decays with time. For a dry diabase rheology, total radiogenic concentrations ≥80% of terrestrial values, and crustal radiogenic concentrations similar to terrestrial basalts, we find that an upper bound on the mean planetary crustal thickness is ∼100 km. In the probably unrealistic case where all the radiogenic elements are in the crust, this maximum crustal thickness can be increased to ∼115 km. The main uncertainty in these results is the total radiogenic abundances on Mars. Comparing our results with the observed shape of the crustal dichotomy provides no evidence that this slope is primarily the result of lower crustal flow. Both Hellas and the dichotomy are isostatically compensated; if the mechanism is Airy isostasy, then the lower bound on mean crustal thickness is ∼30 km. Crustal thicknesses of 30–100 km on Mars can be produced by mid-ocean ridge spreading at potential temperatures of 1350°–1600°C. However, for such crustal thicknesses the lithosphere is likely to be positively buoyant, making subduction difficult.
Lipid Storage and Autophagy in Melanoma Cancer Cells

Cancer stem cells (CSC) represent a key cellular subpopulation controlling biological features such as cancer progression in all cancer types. By using melanospheres established from human melanoma patients, we compared less differentiated melanosphere-derived CSC to differentiating melanosphere-derived cells. Increased lipid uptake was found in melanosphere-derived CSC vs. differentiating melanosphere-derived cells, paralleled by strong expression of lipogenic factors Sterol Regulatory Element-Binding Protein-1 (SREBP-1) and Peroxisome Proliferator-Activated Receptor-γ (PPAR-γ). An inverse relation between lipid-storing phenotype and autophagy was also found, since microtubule-associated protein 1A/1B-Light Chain 3 (LC3) lipidation is reduced in melanosphere-derived CSC. To investigate upstream autophagy regulators, Phospho-AMP activated Protein Kinase (P-AMPK) and Phospho-mammalian Target of Rapamycin (P-mTOR) were analyzed; lower P-AMPK and higher P-mTOR expression in melanosphere-derived CSC were found, thus explaining, at least in part, their lower autophagic activity. In addition, co-localization of LC3-stained autophagosome spots and perilipin-stained lipid droplets was demonstrated mainly in differentiating melanosphere-derived cells, further supporting the role of autophagy in lipid droplets clearance. The present manuscript demonstrates an inverse relationship between lipid-storing phenotype and melanoma stem cells differentiation, providing novel indications involving autophagy in melanoma stem cells biology.