Miracle-dz/UniFAR-FTUs huggingface dataset:
Computational Design of an Enzyme Catalyst for a Stereoselective Bimolecular Diels-Alder Reaction

Biocatalytic Boost Enzymes tend to direct reactions toward specific products much more selectively than synthetic catalysts. Unfortunately, this selectivity has evolved for cellular purposes and may not promote the sorts of reactions chemists are seeking to enhance (see the Perspective by Lutz). Siegel et al. (p. 309) now describe the design of enzymes that catalyze the bimolecular Diels-Alder reaction, a carbon-carbon bond formation reaction that is central to organic synthesis but unknown in natural metabolism. The enzymes display high stereoselectivity and substrate specificity, and an x-ray structure of the most active enzyme confirms that the structure matches the design. Savile et al. (p. 305, published online 17 June) applied a directed evolution approach to modify an existing transaminase enzyme so that it recognized a complex ketone in place of its smaller native substrate, and could tolerate the high temperature and organic cosolvent necessary to dissolve this ketone. This biocatalytic reaction improved the production efficiency of a drug that treats diabetes. Synthetic enzymes catalyze a carbon-carbon bond-forming reaction with high stereoselectivity and substrate specificity. The Diels-Alder reaction is a cornerstone in organic synthesis, forming two carbon-carbon bonds and up to four new stereogenic centers in one step. No naturally occurring enzymes have been shown to catalyze bimolecular Diels-Alder reactions. We describe the de novo computational design and experimental characterization of enzymes catalyzing a bimolecular Diels-Alder reaction with high stereoselectivity and substrate specificity. X-ray crystallography confirms that the structure matches the design for the most active of the enzymes, and binding site substitutions reprogram the substrate specificity. Designed stereoselective catalysts for carbon-carbon bond-forming reactions should be broadly useful in synthetic chemistry.
An empirically validated method for characterizing pelagic habitats in the Gulf of Mexico using ocean model data

Mesoscale oceanic features such as eddies generate considerable environmental heterogeneity within the pelagic oceans, but their transient nature makes it difficult to identify both their spatial and temporal extent and their effects on the distribution of pelagic fauna. Simplifying these complex features using a biologically meaningful classification system will likely be a useful first step in understanding the extent of their influence in structuring open‐ocean ecosystems. In this study, we present a tool to classify the pelagic environment in the Gulf of Mexico using sea‐surface height and temperature‐at‐depth data from the 1/25° GOM HYbrid Coordinate Ocean Model (HYCOM). Three “water types” were identified: Loop Current‐origin water (LCOW), Gulf common water (CW), and mixed (MIX) water, where the latter represents an intermediate state during the degradation of LCOW to CW. The HYCOM‐derived classifications were validated against in situ CTD data and microbial samples collected through 2015–2016 by the Deep Pelagic Nekton Dynamics of the Gulf of Mexico (DEEPEND) consortium. The validation data comprised classifications derived from both temperature‐depth (TD) and temperature‐salinity (TS) profiles and from microbial community analyses from the surface to mesopelagic depths. The HYCOM classifications produced an overall agreement rate of 77% with the TS/TD classifications, and 79% with the microbial classifications. With applicability across a wide range of spatial and temporal scales, we believe that the system provides a useful, complementary tool for biological oceanographers and resource managers interested in better understanding the effects of major mesoscale features on the pelagic biota.
Fatty Acid Labeling from Glutamine in Hypoxia Can Be Explained by Isotope Exchange without Net Reductive Isocitrate Dehydrogenase (IDH) Flux

Background: Cancer cells in hypoxia were claimed to rely on reductive isocitrate dehydrogenase (IDH) for lipogenesis based on increased isotopic labeling of fatty acids from glutamine. Results: Oxidative IDH flux persists in hypoxia, whereas acetyl-CoA demand drops. Conclusion: Reductive IDH flux may not be a net contributor to acetyl-CoA production. Significance: Isotopic label incorporation is indicative of flux, although not necessarily of net flux. Acetyl-CoA is an important anabolic precursor for lipid biosynthesis. In the conventional view of mammalian metabolism, acetyl-CoA is primarily derived by the oxidation of glucose-derived pyruvate in mitochondria. Recent studies have employed isotope tracers to show that in cancer cells grown in hypoxia or with defective mitochondria, a major fraction of acetyl-CoA is produced via another route, reductive carboxylation of glutamine-derived α-ketoglutarate (catalyzed by reverse flux through isocitrate dehydrogenase, IDH). Here, we employ a quantitative flux model to show that in hypoxia and in cells with defective mitochondria, oxidative IDH flux persists and may exceed the reductive flux. Therefore, IDH flux may not be a net contributor to acetyl-CoA production, although we cannot rule out net reductive IDH flux in some compartments. Instead of producing large amounts of net acetyl-CoA reductively, the cells adapt by reducing their demand for acetyl-CoA by importing rather than synthesizing fatty acids. Thus, fatty acid labeling from glutamine in hypoxia can be explained by spreading of label without net reductive IDH flux.
Value and limits of surgery in acute pancreatitis – forensic dilemma in case of death in acute pancreatitis

Acute pancreatitis is one of the pathological conditions known as surgical abdominal emergencies, in which surgery is reserved only for lithiasic etiology and / or local complications of the disease. The risk of death is still high, despite the big understanding progress of the etiopathogenic mechanisms of the disease. It is forensic the one who is called in those situations with medical failure find the death-generating causes that can be attributed to medical and surgical gesture.
Subthreshold oscillations and resonant frequency in guinea‐pig cortical neurons: physiology and modelling.

1. Intracellular recordings were made from neurons in slices from guinea‐pig frontal cortex. In 50% of the cells, sustained subthreshold voltage oscillations were evoked by long (> 6 s) depolarizing pulses. The peak‐to‐peak amplitude of these oscillations was less than 5 mV and the frequency was voltage dependent, increasing with depolarization from 4 (near rest) to 20 Hz (at 30 mV depolarization). 2. The impedance‐frequency relationship of both oscillating and non‐oscillating cells was studied by intracellular injection of sinusoidal current with linearly changing frequency. In most cells, a peak in the impedance magnitude (resonant behaviour) was observed at depolarized levels. The frequency of the peak impedance (peak frequency) increased with depolarization from 3 (near rest) to 15 Hz (at 30 mV depolarization). 3. Application of TTX (10(‐6) M) significantly decreased the impedance magnitude near the peak frequency. The subthreshold oscillations, however, as well as the action potentials, were fully blocked by TTX. On the other hand, TEA (15 mM) and Cs+ (5 mM) abolished both the subthreshold oscillations and the resonant behaviour. Replacing Ca2+ with Co2+ (5 mM) or Ni2+ (1 mM) did not abolish the subthreshold oscillations. The peak in the frequency‐response curve was only slightly reduced. 4. An isopotential membrane model, consisting of a leak current, a fast persistent sodium current, a slow non‐inactivating potassium current (with the kinetics of the M‐current) and membrane capacitance, is sufficient to produce both voltage oscillations and resonant behaviour. The kinetics of the K+ current by itself is sufficient to produce resonance behaviour. The Na+ current amplifies the peak impedance magnitude and is essential for the generation of subthreshold oscillation. The model correctly predicted the behaviour of the frequency response before and after TTX and TEA application, as well as the relation between the expected passive impedance and the experimental impedance. 5. We speculate that the tendency of the neurons to generate voltage signals at a certain frequency (as a result of the subthreshold oscillations) and to preferentially respond to inputs arriving at the same frequency (the resonance behaviour) promotes population activity at that preferred frequency.
Multi-Source Inverter for Power-Split Hybrid Electric Powertrains

Some electrified vehicles, for example the Toyota Prius, integrate a dc–dc converter between the battery pack and the traction inverter to increase the powertrain efficiency. However, adding this extra converter adversely affects the cost and power density of the powertrain due to the additional components, such as the switches and the inductor, that are expensive and heavy in high-power converters. The concept of the multi-source inverter was previously introduced as an alternative solution to reduce the power rating of the dc–dc converter while keeping similar powertrain performance. In this paper, the implementation of the multi-source inverter in a hybrid power-split powertrain is discussed. The operating modes during both dc–ac and ac–dc conversions are detailed and a prototype is experimentally tested with a load. New control strategies of the proposed powertrain show that three out of five operating modes bring new opportunities in terms of battery charging and power rating reduction of the dc–dc converter. A vehicle-level simulation model is developed in MATLAB/Simulink to quantify the benefits of the proposed topology. Simulations are performed for four drive cycles to compare the power profile of the dc–dc converter of the suggested powertrain with the Toyota Prius. The average power transferred by the dc–dc converter can be reduced by up to 25$\%$ in most drive cycles tested.
Responses of fibers in the cat's auditory nerve to the cubic difference tone.

Recordings were made of discharges in single fibers of the cat’s auditory nerve using single‐tone and two‐tone signals of varying frequency. The frequency of the single tone was varied stepwise from the fiber’s best frequency to about 1.7 times this value. One component of the two‐tone signal was varied in exactly the same manner while the frequency of the other was increased in such a way that the frequency of the cubic difference tone (CDT, 2f1−f2) generated within the auditory system was kept constant at the fiber’s best frequency. Responses in terms of discharge rate and period histograms were collected for both signals. The difference in spike rate between the response to the single tone and to the two tones could be ascribed to the CDT and was used to estimate the CDT level as a function of the signal level and frequency. It turned out that the CDT level relative to that of the primaries is about 15 dB smaller for frequencies beyond 10 kHz than for lower frequencies, and slighly decreasing for an in.
Rpb7 subunit of RNA polymerase II interacts with an RNA-binding protein involved in processing of transcripts.

Rpb4-Rpb7, a dissociable subcomplex of RNA polymerase II (pol II), is required for transcription initiation. To understand the role of Rpb7 in transcription initiation or other processes in transcription, we carried out a two-hybrid screen for proteins that interact with Rpb7 of the fission yeast Schizosaccharomyces pombe. The screen identified the S.pombe homolog of the Saccharomyces cerevisiae Nrd1, an RNA-binding protein implicated in 3' end formation of small nucleolar and small nuclear RNAs transcribed by pol II. The S.pombe protein, named Seb1 for seven binding, was essential for cell viability, and bound directly to Rpb7 in vitro. Saccharomyces cerevisiae Rpb7 also interacted with Nrd1, indicating that the interaction is conserved in evolution. Glu166 and/or Asp167 of S.pombe Rpb7, residues near the C-terminus of the 172 amino acid protein, were found to be important for its interaction with Seb1. Our results suggest that Rpb7 may function to anchor a processing factor to the pol II apparatus, thereby coupling RNA processing to transcription. The role for Rpb7 is consistent with its location in the pol II complex determined by recent structural studies.
Network Monitoring in Federated Cloud Environment

With a growing number of infrastructure cloud services becoming available there are many benefits to interconnecting several cloud services. However, seamless cloud interoperability is the complex issue, especially when different cloud platforms are interconnected. One of the major aspects of federating clouds resources is network federation. Federated networks must deal not only with heterogeneous cloud platforms, but also with different virtualization technologies and the added complexity of multi-layer virtualization. In order to allow monitoring and analysis of the complex heterogeneous environment, there is a need to present a user with the full aggregated view of the federated network including cloud interconnect and with the match between different layers and platforms. In this paper we present a framework that uses Skydive tool for network monitoring and analysis in BEACON federated network environment.
Effectiveness of TDD on unit testing practice

Background: Several studies report that test driven development (TDD) has effects on the software product e.g. code quality and developers’ productivity. In recent literature reviews, the impact of TDD on source code quality is seen as a more focused area in empirical research compared to unit testing. However, the quality of production code is tightly coupled with the quality of test code. Objective: The aim of this study is to investigate the impact of test driven development approach compared to an incremental test last development (ITLD), on unit test case quality. The impact is measured in terms of code coverage and mutation score metrics. The hypotheses test the differences in the quality of test cases produced using TDD and ITLD approaches. Method: We conducted an experiment in an industrial setting with 24 professionals in five consecutive days. Three programing tasks, i.e. one task using ITLD and two tasks using TDD, are selected for the experiment. We extracted unit test case quality attributes i.e. mutation score and code coverage from the data collected on each day of the experiment. For the code coverage, we used the metrics; instruction, branch, method, cyclomatic complexity and line coverage. The difference of mutation score and code coverage metrics are then evaluated using non-parametric significance tests. Results: The results indicate that except three metrics i.e. branch coverage, method coverage, mutation score, we could not find significant differences in terms of unit test case quality between the treatments. Subjects wrote test cases that cover more branches during TDD practice on a green-field (as a new development) task, compared to ITLD and TDD practice on a brown-field (modifications on an existing code base) task. In terms of method coverage, test cases produced using ITLD covered more methods than both TDD tasks; whereas no significant difference is found for method coverage between the both TDD tasks. In terms of mutation score, test cases written during TDD practice on a green-field task have more defect detection abilities than test cases written during ITLD practice and TDD practice on a brown-field task. Conclusion: Our finding are different from previous studies performed at academic settings. We believe that other factors (i.e. task’s complexity, experiment duration and participant’s interest towards tasks) could influence the results. Therefore, future studies could be designed by minimizing the impact of these factors to get more generalizable results.
Structural-functional organisation of the bone marrow hematopoietic stem cells niches

This article focuses on (1) the analysis of the structural-functional organization of bone marrow niches of the hematopoietic stem cells, (2) the role of the intercellular contact interactions and humoral regulation factors in these niches, in particular CXCL12, SCF and TGFβ, and (3) the intracellular signal pathways: Notch, Wnt and Shh. The two types of niches, switching from one into another: endosteal niches located on the endost surface at the borderline with bone marrow cavity and the vascular niches included into bone marrow parenchyma. It is emphasized that the main role in the formation of the niches of both types is ascribed to the multipotent stromal cells, which serve as a base for differentiation of the osteoblasts, spindle-shaped N-cadherin+CD45osteoblasts (SNO-cells), nestin-expressing cells (Nes+ cells), cells with leptin receptor (Lepr+ cells), abundant producing CXCL12 reticular cells (CAR-cells) and NG2-pericytes. The endothelial cells are no less important. Also, the adipocytes, osteoclasts, macrophages and megakaryocytes, regulatory T-cells and neuronal cells are involved in the niche functioning. It is postulated that osteoblasts and CAR-cells play a crucial role in the genesis of immune system cells: common lymphoid precursors, B-lymphocytes, natural killer and dendritic cells.
Class B Gene Expression and the Modified ABC Model in Nongrass Monocots

The discovery of the MADS-box genes and the study of model plants such as Arabidopsis thaliana and Antirrhinum majus have greatly improved our understanding of the molecular mechanisms driving the diversity in floral development. The class B genes, which belong to the MADS-box gene family, are important regulators of the development of petals and stamens in flowering plants. Many nongrass monocot flowers have two whorls of petaloid organs, which are called tepals. To explain this floral morphology, the modified ABC model was proposed. This model was exemplified by the tulip, in which expansion and restriction of class B gene expression is linked to the transition of floral morphologies in whorl 1. The expression patterns of class B genes from many monocot species nicely fit this model; however, those from some species, such as asparagus, do not. In this review, we summarize the relationship between class B gene expression and floral morphology in nongrass monocots, such as Liliales (Liliaceae) and Asparagales species, and discuss the applicability of the modified ABC model to monocot flowers.
Analysis of a high‐throughput cone‐and‐plate apparatus for the application of defined spatiotemporal flow to cultured cells

The shear stresses derived from blood flow regulate many aspects of vascular and immunobiology. In vitro studies on the shear stress‐mediated mechanobiology of endothelial cells have been carried out using systems analogous to the cone‐and‐plate viscometer in which a rotating, low‐angle cone applies fluid shear stress to cells grown on an underlying, flat culture surface. We recently developed a device that could perform high‐throughput studies on shear‐mediated mechanobiology through the rotation of cone‐tipped shafts in a standard 96‐well culture plate. Here, we present a model of the three‐dimensional flow within the culture wells with a rotating, cone‐tipped shaft. Using this model we examined the effects of modifying the design parameters of the system to allow the device to create a variety of flow profiles. We first examined the case of steady‐state flow with the shaft rotating at constant angular velocity. By varying the angular velocity and distance of the cone from the underlying plate we were able to create flow profiles with controlled shear stress gradients in the radial direction within the plate. These findings indicate that both linear and non‐linear spatial distributions in shear stress can be created across the bottom of the culture plate. In the transition and “parallel shaft” regions of the system, the angular velocities needed to provide high levels of physiological shear stress (5 Pa) created intermediate Reynolds number Taylor‐Couette flow. In some cases, this led to the development of a flow regime in which stable helical vortices were created within the well. We also examined the system under oscillatory and pulsatile motion of the shaft and demonstrated minimal time lag between the rotation of the cone and the shear stress on the cell culture surface. Biotechnol. Bioeng. 2013; 110: 1782–1793. © 2013 Wiley Periodicals, Inc.
Providing prescription drug coverage to the elderly: America's experiment with Medicare Part D.

The federal government's Medicare program did not provide general prescription drug coverage for the first 40 years of its existence. Thus, more than 30 percent of the 44 million elderly and disabled beneficiaries of the program lacked insurance coverage for prescribed medications. The Medicare Prescription Drug, Improvement, and Modernization Act of 2003 established a voluntary outpatient prescription drug benefit known as Medicare Part D. This program took effect in 2006 and represents the largest expansion of an entitlement program since the start of Medicare itself. The design of Part D is of particular interest to economists for at least three reasons: First, the program has the potential to affect significantly both the health and the economic well-being of the more than 44 million individuals currently enrolled in Medicare. Second, Part D has substantially increased government spending on health care despite the projections that such spending was already on an unsustainable path. Third, Part D represents an ambitious attempt to use market mechanisms in the delivery of a large-scale entitlement program. Part D has been controversial. In this paper, we aim to shed light on the various issues raised by the Part D program, including the incentives inherent in the competition among plans, the forces that affect drug prices, and the sustainability of Part D in the face of adverse selection and moral hazard. We conclude that Part D has succeeded in a number of important ways, however, substantial room for improvement remains.
Invariant features for dice recognition across illumination

A system is proposed for the recognition of the dot numbers on dice in general table game settings. Different from previous dice recognition systems which use a single top-view camera and work only under controlled illumination, the proposed one uses multiple cameras and works for uncontrolled illumination. The proposed system exploits the local invariant features robust to illumination variation and good for building the homographies between multiple viewpoints. The homographies can enhance coplanar features and weaken non-coplanar features, giving a way to segment the top surfaces of the dice. A coarse-to-fine search with a shape-dependent local descriptor is designed to identify the dots on the segmented top surfaces and recognize their spatial distribution patterns. Experiments show that the proposed system can achieve a superb recognition rate for various uncontrolled illumination conditions.