Miracle-dz/UniFAR-FTUs huggingface dataset:
Excystation of in vitro-derived Giardia lamblia cysts

This is the first in-depth analysis of the excystation of Giardia lamblia cysts prepared in vitro. Its goals were both to achieve efficient excystation and to gain insights into this crucial but poorly understood process. To identify the critical elements of excystation, we tested the sequential low-pH induction and protease treatments which had been reported to be important for excystation of fecal cysts. The optimal pH for induction of excystation was 4.0. Emergence was greatly (approximately 10-fold) stimulated by subsequent exposure of in vitro-derived cysts to chymotrypsin, trypsin, or human pancreatic fluid. The stimulatory activity of each was abolished by soybean trypsin inhibitor, demonstrating that the activity of pancreatic fluid was due to these proteases. Excystation of in vitro-derived cysts was approximately 10 to 38%. Although the walls of in vitro-derived cysts were partially digested by protease treatment, trophozoites emerged only from one pole, as observed with fecal cysts. The conditions of encystation also determined the efficiency of excystation. Specifically, encystation in the presence of lactic acid, a major metabolite of colonic bacteria, stimulated excystation approximately fourfold, although it did not increase the total numbers of cysts. These experiments have shown that excystation of in vitro-derived cysts reflects that of cysts purified from human feces in that it is dependent upon conditions which simulate the passage of cysts through the human stomach (low pH) and into the small intestine (pancreatic proteases).
Finding the semantic-level precursors on a blog network

In this work, we study semantic-level precedence relationships between participants in a blog network. Our methodology has two steps: a process to identify units of discussion at the semantic level and a probabilistic framework to estimate temporal relationships between blogs, in terms of the order in which they arrive at those units of discussion. We propose dyadic precursor scores that can be used to construct semantic-level precedence networks. From these scores, we derive global precursor and laggard scores. Dyadic precursor scores are compared with URL linking to show that the semantic-level temporal relationships we estimate are an indicator of influence. Global scores are compared to traditional link degree and PageRank metrics, and we uncover relationships between semantic-level temporal behaviour and popularity. We show that our method reveals information about the network that could not be obtained from structural links alone.
Protein Stability and Dynamics Modulation: The Case of Human Frataxin

Frataxin (FXN) is an α/β protein that plays an essential role in iron homeostasis. Apparently, the function of human FXN (hFXN) depends on the cooperative formation of crucial interactions between helix α1, helix α2, and the C-terminal region (CTR) of the protein. In this work we quantitatively explore these relationships using a purified recombinant fragment hFXN90–195. This variant shows the hydrodynamic behavior expected for a monomeric globular domain. Circular dichroism, fluorescence, and NMR spectroscopies show that hFXN90–195 presents native-like secondary and tertiary structure. However, chemical and temperature induced denaturation show that CTR truncation significantly destabilizes the overall hFXN fold. Accordingly, limited proteolysis experiments suggest that the native-state dynamics of hFXN90–195 and hFXN90–210 are indeed different, being the former form much more sensitive to the protease at specific sites. The overall folding dynamics of hFXN fold was further explored with structure-based protein folding simulations. These suggest that the native ensemble of hFXN can be decomposed in at least two substates, one with consolidation of the CTR and the other without consolidation of the CTR. Explicit-solvent all atom simulations identify some of the proteolytic target sites as flexible regions of the protein. We propose that the local unfolding of CTR may be a critical step for the global unfolding of hFXN, and that modulation of the CTR interactions may strongly affect hFXN physiological function.
Nuclear Pore-Like Structures in a Compartmentalized Bacterium

Planctomycetes are distinguished from other Bacteria by compartmentalization of cells via internal membranes, interpretation of which has been subject to recent debate regarding potential relations to Gram-negative cell structure. In our interpretation of the available data, the planctomycete Gemmata obscuriglobus contains a nuclear body compartment, and thus possesses a type of cell organization with parallels to the eukaryote nucleus. Here we show that pore-like structures occur in internal membranes of G.obscuriglobus and that they have elements structurally similar to eukaryote nuclear pores, including a basket, ring-spoke structure, and eight-fold rotational symmetry. Bioinformatic analysis of proteomic data reveals that some of the G. obscuriglobus proteins associated with pore-containing membranes possess structural domains found in eukaryote nuclear pore complexes. Moreover, immuno-gold labelling demonstrates localization of one such protein, containing a β-propeller domain, specifically to the G. obscuriglobus pore-like structures. Finding bacterial pores within internal cell membranes and with structural similarities to eukaryote nuclear pore complexes raises the dual possibilities of either hitherto undetected homology or stunning evolutionary convergence.
Effects of Insulin and St. John's Wort Treatments on Anxiety, Locomotory Activity, Depression, and Active Learning Parameters of Streptozotocin-Diabetic Rats

The aim of this work was to investigate the effects of St. John's Wort (SJW) extract treatment on behavioral changes arising in streptozotocin (STZ)-diabetic rats. Plus-maze, activity cage, modified forced swimming, and active avoidance tests were performed for evaluating exploratory behaviors, spontaneous locomotor activities, depression levels, and learning parameters of animals, respectively. Obtained data exhibited a diabetes mellitus (DM)-induced increase in anxiety and depression levels, decrease in spontaneous locomotor activities, and impairment of learning parameters in rats even in the early stages of the disease. Daily insulin replacement (2 IU/kg/day) could not restore these impaired parameters completely, indicating the need of novel therapeutic approaches. SJW extract (125 and 250 mg/kg) treatments for seven days provided significant improvement in all of the impaired parameters observed in this study, probably due to its antidiabetic and central nervous system (CNS)-related effects. Based on the findings of the present study, it may be suggested that SJW extracts may be of help to diabetic patients suffering from depressive moods, sleeping disturbances, and cognitive deficits and may provide a new potential alternative for the treatment of psychiatric complications of diabetes.
Effect of lift-off conditions on micropatterning of nanocrystalline quantum dot films

A micropatterning of nanocrystalline quantum dots (NQD) films using lift-off process has been proposed and experimentally demonstrated earlier. In this paper, the conditions of patterning process are investigated in order to define process parameters window for the lift-off procedure. The patterning of NQD CdSe/ZnS films using lift-off is studied in terms of photoresist thickness, solvent composition, and substrate material. The outcome of the process is monitored by means of fluorescence microscopy, atomic force microscope, and optical microscopy. The results show that patterns less than 1 μm can be resolved in NQD films with minimal alteration of the film characteristics, provided the photoresist layer is thicker than about 100 nm and acetone used as a solvent is spiked with toluene up to 10% of the solvent volume. The performance of the process in terms of resolution and film quality was found to be independent of the substrate used.
Adding Flexible Input Device Support to a Web Browser with MundoMonkey

Computer applications are increasingly used in non-desktop settings, e.g. at a public kiosk systems or on mobile phones. Thanks to the widespread availability of web browsers for different platforms, web interfaces are often employed in these settings. However, current browsers lack sufficient support for flexibly adapting to non-desktop settings, e.g. ad-hoc changes of input devices. A use case for this is, e.g., an interactive shopping window that presents a web interface for buying products. If the browser in the shopping window supported ad-hoc changes of input devices, the customer could dynamically attach carried input devices, e.g., a mobile phone, to the browser and interact with it. In this paper, we present a solution to the problem of dynamically connecting input devices in a non-desktop setting to a browser, based on the MundoMonkey Firefox extension for interactive spaces. Using our approach, the unmodified web user interface can be used with arbitrary input devices in ways that cannot be realized by synthesizing mouse and keyboard events. In our approach, the customization to the device at hand is performed transparently to the application developer by the end-user.
EVALUATION OF PRECONDITIONED KRYLOV SUBSPACE METHODS FOR NAVIER-STOKES EQUATIONS

The purpose of this work is to compare the performance of some preconditioned iterative methods for solving the linear systems of equations, formed at each time-integration step of two-dimensional incompressible NavierStokes equations of fluid flow. The Navier-Stokes equations are discretized in an implicit and upwind control volume formulation. The iterative methods used in this paper include BiCG, CGS and GMRES. These Krylov subspace methods are equipped with incomplete LU factorization preconditioning. To increase the convergence rate, a scaling technique is used. Our numerical results show that the preconditioned GMRES method performs better than other preconditioned Krylov subspace methods.
Assessment of techniques used to evaluate the effect of posture and cardiac output on Cerebral Autoregulation

In this study, the role of cardiac output in Cerebral Autoregulation was assessed. Mean arterial pressure, cerebral blood flow velocity (middle and anterior cerebral artery), stroke volume, cardiac output, total peripheral resistance and cerebral autoregulatory index were assessed in 3 healthy young males and 4 healthy young females during seated and upright thigh cuff testing. Two different methods (long axis left ventricular echocardiography and Modelflow) of evaluating stroke volume and cardiac output were compared. The results showed that cerebral autoregulation was less effective in the upright posture in all subjects. Females had better autoregulation in the anterior cerebral artery, whereas males had better autoregulation in the middle cerebral artery. Cardiac output does not appear to play an important role in cerebral autoregulation during thigh cuff testing. Estimations of cardiac output and stroke volume did not strongly correlate between Modeflow and long axis left ventricular echocardiography.
Investigation of Coated Cutting Tool Performance during Machining of Super Duplex Stainless Steels through 3D Wear Evaluations

In this study, the wear mechanisms and tribological performance of uncoated and coated carbide tools were investigated during the turning of super duplex stainless steel (SDSS)—Grade UNS S32750, known commercially as SAF 2507. The tool wear was evaluated throughout the cutting tests and the wear mechanisms were investigated using an Alicona Infinite Focus microscope and a scanning electron microscope (SEM) equipped with energy dispersive spectroscopy (EDS). Tribo-film formation on the worn rake surface of the tool was analyzed using X-ray Photoelectron Spectroscopy (XPS). In addition, tribological performance was evaluated by studying chip characteristics such as thickness, compression ratio, shear angle, and undersurface morphology. Finally, surface integrity of the machined surface was investigated using the Alicona microscope to measure surface roughness and SEM to reveal the surface distortions created during the cutting process, combined with cutting force analyses. The results obtained showed that the predominant wear mechanisms are adhesion and chipping for all tools investigated and that the AlTiN coating system exhibited better performance in all aspects when compared with CVD TiCN + Al2O3 coated cutting insert and uncoated carbide insert; in particular, built-up edge formation was significantly reduced.
Mesoporous Aluminum Hydroxide Synthesized by a Single‐Source Precursor‐Decomposition Approach as a High‐Quantum‐Yield Blue Phosphor for UV‐Pumped White‐Light‐Emitting Diodes

Strongly emissive (photoluminescence quantum yield up to 65%), thermally stable aluminum hydroxide blue phosphors are synthesized by a single-source precursor-decomposition approach. Blue-emitting UV-pumped light-emitting diodes (LEDs) based on the aluminum hydroxide phosphor reach luminous efficiency of 27.5 lm W-1 , while UV-white-LEDs integrating blue-emitting aluminum hydroxide and red-emitting CuInS2 nanocrystals achieve high color-rendering-index values of 94.3 and luminous efficiency of 23.5 lm W-1 .
The Lymphocyte

diagnostic methods includes fine illustrations and instructions for preparing thick and thin blood films, distinct reproductions describing the morphologic characteristics of the erythrocytic stages of the four human malaria plasmodia, and a current evaluation of serological tests, including ELISA (enzyme-linked immunosorbent assay). In a separate chapter, Anopheles vectors are covered in truly sufficient detail for the non-malariologist. This incorporates a nice section on entomological methods, e.g., the dissection of the midgut and salivary glands of mosquitos. The large chapter on epidemiology is informative, including discussions on malaria surveys, quantitative epidemiology, and cognizant summaries of malarious regions of the world. The chapter on the chemotherapy and chemoprophylaxis of malaria is up-todate and inclusive. The chapter on malaria control is the longest of the book. Drawing upon his years of experience as a malariologist, the author delves into crucial topics in the selection of proper methods of control, e.g., chemical and biological methods against adult and larval forms, prevention by environmental/hygiene practices in the community, and specific preventive measures effectively utilized on an individual basis. The current and future status of success in malaria eradication is commented upon in the last chapter. I especially recommend this readable and informative book for two groups of health care providers: (1) those who are non-malariologists by training but have some interest in tropical infectious diseases and (2) those whose interests lie within public health, international health, or preventive medicine and epidemiology.
Filling the void—enriching the feature space of successful stopping

The ability to inhibit behavior is crucial for adaptation in a fast changing environment and is commonly studied with the stop signal task. Current EEG research mainly focuses on the N200 and P300 ERPs and corresponding activity in the theta and delta frequency range, thereby leaving us with a limited understanding of the mechanisms of response inhibition. Here, 15 functional networks were estimated from time–frequency transformed EEG recorded during processing of a visual stop signal task. Cortical sources underlying these functional networks were reconstructed, and a total of 45 features, each representing spectrally and temporally coherent activity, were extracted to train a classifier to differentiate between go and stop trials. A classification accuracy of 85.55% for go and 83.85% for stop trials was achieved. Features capturing fronto‐central delta‐ and theta activity, parieto‐occipital alpha, fronto‐central as well as right frontal beta activity were highly discriminating between trial‐types. However, only a single network, comprising a feature defined by oscillatory activity below 12 Hz, was associated with a generator in the opercular region of the right inferior frontal cortex and showed the expected associations with behavioral inhibition performance. This study pioneers by providing a detailed ranking of neural features regarding their information content for stop and go differentiation at the single‐trial level, and may further be the first to identify a scalp EEG marker of the inhibitory control network. This analysis allows for the characterization of the temporal dynamics of response inhibition by matching electrophysiological phenomena to cortical generators and behavioral inhibition performance. Hum Brain Mapp 38:1333–1346, 2017. © 2016 Wiley Periodicals, Inc.
Continuously Tunable Pore Size for Gas Separation via a Bilayer Nanoporous Graphene Membrane

Pore size is a crucial factor impacting gas separation, but difficult to control for a single-layer nanoporous graphene membrane. Here, we propose a bilayer design of a nanoporous graphene membrane with a continuously tunable effective pore size, by shifting the lateral position of one graphene layer against the other. Molecular dynamics simulations of gas permeation reveal that selective separation of gases, such as CO2, N2, and CH4, of 3–4 A in kinetic diameter can be achieved for a bilayer membrane from single-layer pores as large as 25 A in size. Hence, this bilayer design allows both great flexibility of pore sizes in a single layer of graphene and continuous variation of the effective pore size through the bilayer at a sub-angstrom level.
Theoretical calculations of rotationally inelastic collisions of He with NaK(A (1)Σ(+)): Transfer of population, orientation, and alignment.

We have performed extensive calculations to investigate thermal energy, rotationally inelastic collisions of NaK (A(1)Σ(+)) with He. We determined a potential energy surface using a multi-reference configuration interaction wave function as implemented by the GAMESS electronic structure code, and we have performed coupled channel scattering calculations using the Arthurs and Dalgarno formalism. We also calculate the Grawert coefficients B(λ)(j, j') for each j → j' transition. These coefficients are used to determine the probability that orientation and alignment are preserved in collisions taking place in a cell environment. The calculations include all rotational levels with j or j' between 0 and 50, and total (translational and rotational) energies in the range 0.0002-0.0025 a.u. (∼44-550 cm(-1)). The calculated cross sections for transitions with even values of Δj tend to be larger than those for transitions with odd Δj, in agreement with the recent experiments of Wolfe et al. (J. Chem. Phys. 134, 174301 (2011)). The calculations of the energy dependence of the cross sections and the calculations of the fraction of orientation and alignment preserved in collisions also exhibit distinctly different behaviors for odd and even values of Δj. The calculations also indicate that the average fraction of orientation or alignment preserved in a transition becomes larger as j increases. We interpret this behavior using the semiclassical model of Derouard, which also leads to a simple way of visualizing the distribution of the angles between the initial and final angular momentum vectors j and j'. Finally, we compare the exact quantum results for j → j' transitions with results based on the simpler, energy sudden approximation. That approximation is shown to be quite accurate.
Molecular models of human visual pigments: insight into the atomic bases of spectral tuning

Abstract The cycle of vision is a chain of biochemical reactions that occur after exposure of the pigments to the light. The known mechanisms of the transduction of the light pulse derive mainly from studies on bovine rhodopsin. The objective of this work is to construct molecular models of human rhodopsin and opsins, for which three-dimensional structures are not available, to analyze the retinal environment and identify the similarities and differences that characterize the human visual pigments. One of the main results of this work is the identification of Glu102 as the probable second counterion of the Schiff base in M opsin (green pigments) and L opsin (red pigments). Further, the analysis of the molecular models allows uncovering the molecular bases of the different absorption maxima of M and L opsins with respect to rhodopsin and S opsin. These differences appear to be due to both an increase in the polarity of the retinal environment and specific electrostatic interactions, which determine a reorganization of the electronic distribution of retinal by selectively stabilizing one of the two resonance forms.
Type III Secretion Decreases Bacterial and Host Survival following Phagocytosis of Yersinia pseudotuberculosis by Macrophages

ABSTRACT Yersinia pseudotuberculosis uses a plasmid (pYV)-encoded type III secretion system (T3SS) to translocate a set of effectors called Yops into infected host cells. YopJ functions to induce apoptosis, and YopT, YopE, and YopH act to antagonize phagocytosis in macrophages. Because Yops do not completely block phagocytosis and Y. pseudotuberculosis can replicate in macrophages, it is important to determine if the T3SS modulates host responses to intracellular bacteria. Isogenic pYV-cured, pYV+ wild-type, and yop mutant Y. pseudotuberculosis strains were allowed to infect bone marrow-derived murine macrophages at a low multiplicity of infection under conditions in which the survival of extracellular bacteria was prevented. Phagocytosis, the intracellular survival of the bacteria, and the apoptosis of the infected macrophages were analyzed. Forty percent of cell-associated wild-type bacteria were intracellular after a 20-min infection, allowing the study of the macrophage response to internalized pYV+Y. pseudotuberculosis. Interestingly, macrophages restricted survival of pYV+ but not pYV-cured or ΔyopB Y. pseudotuberculosis within phagosomes: only a small fraction of the pYV+ bacteria internalized replicated by 24 h. In addition, ∼20% of macrophages infected with wild-type pYV+Y. pseudotuberculosis died of apoptosis after 20 h. Analysis of yop mutants expressing catalytically inactive effectors revealed that YopJ was important for apoptosis, while a role for YopE, YopH, and YopT in modulating macrophage responses to intracellular bacteria could not be identified. Apoptosis was reduced in Toll-like receptor 4-deficient macrophages, indicating that cell death required signaling through this receptor. Treatment of macrophages harboring intracellular pYV+Y. pseudotuberculosis with chloramphenicol reduced apoptosis, indicating that the de novo bacterial protein synthesis was necessary for cell death. Our finding that the presence of a functional T3SS impacts the survival of both bacterium and host following phagocytosis of Y. pseudotuberculosis suggests new roles for the T3SS in Yersinia pathogenesis.