Miracle-dz/UniFAR-FTUs huggingface dataset:
Increasing protein stability by improving beta‐turns

Our goal was to gain a better understanding of how protein stability can be increased by improving β‐turns. We studied 22 β‐turns in nine proteins with 66–370 residues by replacing other residues with proline and glycine and measuring the stability. These two residues are statistically preferred in some β‐turn positions. We studied: Cold shock protein B (CspB), Histidine‐containing phosphocarrier protein, Ubiquitin, Ribonucleases Sa2, Sa3, T1, and HI, Tryptophan synthetase α‐subunit, and Maltose binding protein. Of the 15 single proline mutations, 11 increased stability (Average = 0.8 ± 0.3; Range = 0.3–1.5 kcal/mol), and the stabilizing effect of double proline mutants was additive. On the basis of this and our previous work, we conclude that proteins can generally be stabilized by replacing nonproline residues with proline residues at the i + 1 position of Type I and II β‐turns and at the i position in Type II β‐turns. Other turn positions can sometimes be used if the φ angle is near −60° for the residue replaced. It is important that the side chain of the residue replaced is less than 50% buried. Identical substitutions in β‐turns in related proteins give similar results. Proline substitutions increase stability mainly by decreasing the entropy of the denatured state. In contrast, the large, diverse group of proteins considered here had almost no residues in β‐turns that could be replaced by Gly to increase protein stability. Improving β‐turns by substituting Pro residues is a generally useful way of increasing protein stability. Proteins 2009. © 2009 Wiley‐Liss, Inc.
Markov models of specular and diffuse scattering in restoration of medical ultrasound images

Observed medical ultrasound images are degraded representations of the true tissue reflectance. The specular reflections at boundaries between regions of different tissue types are blurred, and the diffuse scattering within such regions also contains speckle. This reduces the diagnostic value of such images. In order to remove both blur and speckle, the authors develop a maximum a posteriori deconvolution algorithm for two-dimensional (2-D) ultrasound radio frequency (RF) images based on a new Markov random field image model incorporating spatial smoothness constraints and physical models for specular reflections and diffuse scattering. During stochastic relaxation, the algorithm alternates steps of restoration and segmentation, and includes estimation of reflectance parameters. The smoothness constraints regularize the overall procedure, and the algorithm uses the specular reflection model to locate region boundaries. The resulting restorations of some simulated and real RF images are significantly better than those produced by Wiener filtering.
Title : Optimization of the Flapping Wing Systems for a Micro Air Vehicle

The flapping wing of a micro air vehicle is optimized to enhance performance while some rigidity is kept with minimum mass. A work flow for the design of the flapping wing is defined. The performances to be enhanced are thrust coefficient and propulsive efficiency. The flapping kinematics of the flapping wing is determined by solving a path optimization problem which maximizes the performances. The optimization process is carried out based on a well defined surrogate model. The surrogate model is made from the results of two-dimensional fluid dynamic analysis. The Kriging method is employed to establish the surrogate model and a genetic algorithm is utilized for the multi-objective function problem. Dynamic topology optimization is performed to find the distribution of reinforcement. Certain rigidity can be kept by the results of topology optimization. A dynamic topology optimization method is developed by modification of the equivalent static loads method for non linear static response structural optimization. Three-dimensional computational fluid dynamic analysis is performed based on the optimum values of the path optimization to evaluate the external loads for the topology optimization process. It is found that the topology results are quite similar to the practical product. The process of the defined work flow is materialized by interfacing various software systems. Nomenclature AR = aspect ratio a = dimensionless length from the leading edge to the pivot point b = design variable vector ) (b C = viscous damping matrix CFD = computational fluid dynamics CD = drag coefficient CL = lift coefficient CT = thrust coefficient CM = pitch moment coefficient D C = time average drag coefficient L C = time average lift coefficient T C = time average thrust coefficient c = chord, m E = Young’s modulus Fx = x component of the resulting aerodynamics force acting on the airfoil, N Fy = y component of the resulting aerodynamics force acting on the airfoil, N f = frequency, Hertz ) (s eq f = equivalent static loads vector h = reduced plunging amplitude with respect to the chord k = reduced frequency ) (b K = stiffness matrix ) (b M = mass matrix Ma = mach number Re = Reynolds number S = reference area St = Strouhal number T = period, second u = far field flow velocity, m/s e v = volume of each element V = total volume of the structure ) (t z = dynamic displacement vector ) (s z = static displacement vector  = phase angle of pitching motion leading plunging motion ρ = density of fluid around the airfoil, kg/m m ρ = density of the material, kg/m 3 θ = angle between the chord and the far field flow speed direction η = propulsive efficiency ω = angular frequency, rad/s 1  = specified value of density 2  = percent of the total design variable 3  = density value of design update
Primary epithelioid angiosarcoma of the lung presenting as left-sided shoulder pain.

Dear Editor, Primary angiosarcoma of the lung is a rare, often difficult to diagnose disorder with non-specific respiratory manifestations. Angiosarcoma involving the lung is usually a result of metastatic disease. Among the commonest presentation of this rare disease is pulmonary haemorrhage, which has been described in a handful of cases.1,2 We report a unique presentation of primary pulmonary angiosarcoma in a 23-year-old man who presented with a metastatic leftsided shoulder and chest pain. The diagnosis was confirmed by a computer tomography (CT)-guided biopsy of the left lung mass. Immunohistochemical studies were positive for Vimentin, CD34, CD31 and Factor VIII and negative for CK, CK7, epithelial membrane antigen (EMA), thyroid transcription factor 1 (TTF1), Calretinin, smooth muscle actin (SMA), Desmin, leukocyte common antigen (LCA) and human melanoma black (HMB)45.
Changes in the gene expression of adiponectin and adiponectin receptors ( AdipoR 1 and AdipoR 2 ) in ovarian follicular cells of dairy cow at different stages of development

Adiponectin is one of the most important, recently discovered adipocytokines that acts at various levels to control male and female fertility through central effects on the hypothalamus-pituitary axis or through peripheral effects on the ovary, uterus, and embryo. We studied simultaneous changes in the gene expression pattern of adiponectin and adiponectin receptors 1 and 2 (AdipoR1 and AdipoR2) in granulosa and theca cells, cumulus-oocyte complex, and in corpus luteum in healthy bovine (Bos tarus) follicles at different stages of development. The expression levels of adiponectin, AdipoR1, and AdipoR2 mRNA were lower (P < 0.05) in granulosa and cumulus cells in comparison with that in theca cells and oocyte. In contrast with the oocyte, AdipoR1 in granulosa, theca, and luteal cells was expressed (P < 0.05) more than AdipoR2. Adiponectin expression increased (P < 0.05) in granulosa cells and in cumulus-oocyte complex during follicular development from small to large follicles. Opposite results were observed in theca cells. Expression of adiponectin was highest in the late stages of corpus luteum (CL) regression, whereas lower expression was recorded in active CL (P < 0.05). AdipoR1 and AdipoR2 expression increased during the terminal follicular growth in granulosa and theca cells (P < 0.05) and during the luteal phase progress in CL. There was positive correlation between adiponectin mRNA level in granulosa cells from large follicles and follicular fluid estradiol concentration (r = 0.48, P < 0.05) and negative correlation between adiponectin mRNA abundance in theca cells and follicular fluid progesterone concentration (r = – 0.44, P < 0.05). In conclusion, we found that the physiologic status of the ovary has significant effects on the natural expression patterns of adiponectin and its receptors in follicular and luteal cells of bovine ovary. # 2010 Elsevier Inc. All rights reserved.
Cellular therapies supplement: strategies for improving transplant efficiency in the context of cellular therapeutics

The field of hematopoietic stem cell transplantation (HSCT) has overcome many obstacles that have led to our current clinical ability to utilize cells collected from marrow, mobilized peripheral blood, or umbilical cord blood for the treatment of malignant and nonmalignant hematologic diseases. It is in this context that it becomes evident that future progress will lie in our development of an understanding of the biology by which the process of HSCT is regulated. By understanding the cellular components and the mechanisms by which HSCT is either enhanced or suppressed it will then be possible to design therapeutic strategies to improve rates of engraftment that will have a positive impact on immune reconstitution post‐HSCT. In this review we focus primarily on allogeneic hematopoietic stem cell transplantation (allo‐HSCT), the current challenges associated with allo‐HSCT, and some developing strategies to improve engraftment in this setting.
How to minimize the TCP effect in a UMTS-HSDPA system?

This paper focuses on the interaction between the transmission control protocol (TCP) layer and the radio interface in a 3G wireless system. An analytical model to evaluate the impact of TCP on the UMTS-HSDPA capacity is presented. A method to minimize the effect of TCP on wireless networks using shared channels is also proposed. High speed downlink packet access (HSDPA) is an evolution of the UMTS standard over the air interface to achieve higher aggregate bit rates through the introduction of adaptive modulation and coding, hybrid automatic repeat request (ARQ), fast scheduling, fast cell selection, and multiple input multiple output (MIMO) (space time coding and blast) techniques. The proposed model is used to evaluate the effect of the TCP protocol on the bit rate of various data services (at 64 and 128 kbps). As expected, the bit rate per flow decreases strongly if the congestion frequency in the wired network increases. However, the overall capacity achieved by HSDPA is not as affected by the TCP layer. Using this result, a method to maintain the bit rate per TCP flow at a given value without loosing much cell capacity is proposed. The findings are supported by simulation results. Copyright © 2005 John Wiley & Sons, Ltd.
Reduced survival in patients with early-stage non-small-cell lung cancer is associated with high pleural endothelial progenitor cell levels.

OBJECTIVES Endothelial progenitor cells are capable of contributing to neovascularization in tumours. In patients with either malignant or transudative pleural effusion, we tested the presence of pleural endothelial progenitor cells. We also measured the number of endothelial progenitor cells in post-surgery pleural drainage of either patients with early non-small-cell lung cancer or control patients with benign lung disease undergoing pulmonary resection. The prospective influence of post-surgery pleural-drainage endothelial progenitor cells on cancer recurrence/survival was investigated. METHODS Pleural endothelial progenitor cell levels were quantified by fluorescence-activated cell sorting analysis in pleural effusion of 15 patients with late-stage non-small-cell lung cancer with pleural involvement and in 15 control patients with congestive heart failure. Also, pleural-drainage endothelial progenitor cells were measured in pleural-drainage fluid 48 h after surgery in 64 patients with early-stage non-small-cell lung cancer and 20 benign lung disease patients undergoing pulmonary resection. Cancer recurrence and survival was evaluated in patients with high pleural-drainage endothelial progenitor cell levels. RESULTS The number of pleural endothelial progenitor cells was higher in non-small-cell lung cancer pleural effusion than in transudative pleural effusion. Also, pleural-drainage endothelial progenitor cell levels were higher in patients with non-small-cell lung cancer than in patients with benign lung disease undergoing pulmonary resection (P < 0.05). Non-small-cell lung cancer patients with high pleural-drainage endothelial progenitor cell levels had a significantly 4.9 higher rate of cancer recurrence/death than patients with lower pleural-drainage endothelial progenitor cell levels, irrespective of confounders. CONCLUSIONS Endothelial progenitor cells are present in the pleural effusion and are higher in patients with late-stage non-small-cell lung cancer with pleural involvement than in congestive heart failure patients. Endothelial progenitor cell levels are higher in the post-surgery pleural drainage of patients with non-small-cell lung cancer than in non-neoplastic pleural-drainage fluid. High pleural-drainage endothelial progenitor cell levels in patients undergoing pulmonary resection for early non-small-cell lung cancer predict an increased risk of cancer recurrence and death.
Trust in Online Prescription Filling

This paper examines the impact of trust and uncertainty on online prescription filling. Drawing on prior research in consumer trust and theory of transaction cost economics, this paper proposes a research model to investigate the precedents of trust, the sources of uncertainty, and their relationships with the consumer’s intention to adopt online prescription filling. The model was empirically tested using a large sample. It is found that (1) calculative, knowledge-based, and institutional antecedents of trust significantly affect trust, (2) information asymmetry and online drug retailers’ opportunistic behavior contribute to perceived uncertainty of online prescription filling, (3) trust reduces uncertainty and positively affects intention, and (4) uncertainty has a negative influence on intention. A major contribution of this paper is that the understanding of trust on consumer intention is augmented by including uncertainty and its sources explicitly in the research model.
Tools for analyzing and mapping scholarly publications not indexed by the Web of Science: the case of fruit and vegetable publications by the French National Institute for Agricultural Research (INRA)

Introduction. The fruit and vegetable sector group of the French National Institute for Agricultural Research (INRA) carried out a bibliometric analysis of INRA publications on fruits and vegetables produced between 2002 and 2006. While a previous study focused on scientific publications indexed by the Web of Science, this study took into account the remaining INRA publications, i.e., gray literature, technical papers and scientific papers not indexed by the Web of Science. Materials and methods. Different steps were taken to constitute and process a corpus of INRA researchers' publication data. The citation corpus gathering bibliographic data was mainly constituted using the INRA institutional repository (ProdINRA). To ensure exhaustivity, a survey was carried out to collect INRA researchers' publications. Due to the different types of publications involved, we had to develop an original method to constitute a complete database which could allow bibliometric analysis. The Sphinx Plus(2) Survey program was used to analyze publications and Pajek software was used to visualize networks. Results. A total of 2,224 publications were authored by INRA between 2002 and 2006. We analyzed the typology of fruits and vegetables studied at INRA, the INRA research centers and research divisions involved, the main research topics, and the national and international partners of INRA authors. Graphic visualizations allowed an attractive presentation of relationships between authors within and outside INRA. Conclusion. This study led to the mapping of INRA fruit and vegetable research publications. It confirmed that INRA plays an active role in the field of fruit and vegetable research. French research is carried out in the main INRA research centers located in horticultural and/or fruit regions, particularly in South-Eastern France. Despite the fact that the nature of these publications provides less opportunity for co-publication, this study highlights the relationships between INRA and French partners or foreign countries.
Distributed neuronal networks for encoding category‐specific semantic information: the mismatch negativity to action words

Mismatch negativity (MMN), an index of experience‐dependent memory traces, was used to investigate the processing of action‐related words in the human brain. Responses to auditorily presented movement‐related English words were recorded in a non‐attend odd‐ball protocol using a high‐density electroencephalographic (EEG) set‐up. MMN was calculated using responses to the same words presented as standard and deviant stimuli in different sessions to avoid contamination from phonetic–acoustic differences. The topography of the mismatch negativity to action words revealed an unusual centro‐posterior distribution of the responses, suggesting that activity was at least in part generated posterior to usually observed frontal MMNs. Moreover, responses to hand‐related word stimulus (pick) had a more widespread lateral distribution, whereas leg‐related stimulus (kick) elicited a more focal dorsal negativity. These differences, remarkably reminiscent of sensorimotor cortex topography, were further assessed using distributed source analysis of the EEG signal (L2 minimum‐norm current estimates). The source analysis also confirmed differentially distributed activation for the two stimuli. We suggest that these results indicate activation of distributed neuronal assemblies that function as category‐specific memory traces for words and may involve sensorimotor cortical structures for encoding action words.
The Ankrd13 Family of Ubiquitin-interacting Motif-bearing Proteins Regulates Valosin-containing Protein/p97 Protein-mediated Lysosomal Trafficking of Caveolin 1*

Caveolin 1 (Cav-1) is an oligomeric protein that forms flask-shaped, lipid-rich pits, termed caveolae, on the plasma membrane. Cav-1 is targeted for lysosomal degradation in ubiquitination- and valosin-containing protein (VCP)-dependent manners. VCP, an ATPase associated with diverse cellular activities that remodels or segregates ubiquitinated protein complexes, has been proposed to disassemble Cav-1 oligomers on the endosomal membrane, facilitating the trafficking of Cav-1 to the lysosome. Genetic mutations in VCP compromise the lysosomal trafficking of Cav-1, leading to a disease called inclusion body myopathy with Paget disease of bone and/or frontotemporal dementia (IBMPFD). Here we identified the Ankrd13 family of ubiquitin-interacting motif (UIM)-containing proteins as novel VCP-interacting molecules on the endosome. Ankrd13 proteins formed a ternary complex with VCP and Cav-1 and exhibited high binding affinity for ubiquitinated Cav-1 oligomers in an UIM-dependent manner. Mass spectrometric analyses revealed that Cav-1 undergoes Lys-63-linked polyubiquitination, which serves as a lysosomal trafficking signal, and that the UIMs of Ankrd13 proteins bind preferentially to this ubiquitin chain type. The overexpression of Ankrd13 caused enlarged hollow late endosomes, which was reminiscent of the phenotype of the VCP mutations in IBMPFD. Overexpression of Ankrd13 proteins also stabilized ubiquitinated Cav-1 oligomers on the limiting membrane of enlarged endosomes. The interaction with Ankrd13 was abrogated in IMBPFD-associated VCP mutants. Collectively, our results suggest that Ankrd13 proteins cooperate with VCP to regulate the lysosomal trafficking of ubiquitinated Cav-1.
The Effects of Technology Readiness Index and IT-based Services on the Service Quality in the Hotel Industry

In the past the hotel primarily focused on the personnel services. Nowadays they gradually use information technology to provide the services, for example, on-line room reservation, free Internet services and so on. However, whether the customer accepts these IT-based services or not? How IT-based services influence service quality, customer's satisfaction, and loyalty? These issues need further discussion. This study explores the effects of customer's technology readiness index and IT-based services on the total service quality in the hotel industry. We investigate the customer of five-star international hotel and use LISREL software to test our hypotheses. The results indicate that when the customer has higher technology readiness index, he (she) will perceive better IT-based services and total service quality. That is, the more the customer accepts technology, the more he (she) has positive attitude about IT-based services and total service quality. Next, when the customer perceives better about IT-based services, he (she) will feel better about total service quality. Finally, when the customer perceives better about IT-based services and total service quality, he (she) will be more satisfied and more royal to the hotel.
Laparoscopic Common Bile Duct Exploration for Retrieval of Impacted Dormia Basket following Endoscopic Retrograde Cholangiopancreatography with Mechanical Failure: Case Report with Literature Review

Dormia baskets are commonly used during endoscopic retrograde cholangiopancreatography (ERCP). One complication is basket retention, through impaction with a gallstone or wire fracture. We describe a case where the external handle of the basket snapped causing retained basket plus large gallstone impacted in the common bile duct (CBD). Following laparoscopic cholecystectomy, laparoscopic CBD exploration allowed direct stone fragmentation under vision with the choledochoscope. Fragments were removed using a choledochoscopic basket and Fogarty catheter, and the basket was withdrawn. Literature search identified 114 cases of retained baskets with management including shockwave lithotripsy (27%), papillary balloon dilatation (22%), open CBD exploration (11%), and one laparoscopic case.
Homeostatic Expansion and Phenotypic Conversion of Human T Cells Depend on Peripheral Interactions with APCs

Immune recovery in lymphopenic hosts depends largely on homeostatic peripheral expansion, especially when thymopoiesis is insufficient, as is often the case in human adults. Although it has been well studied in mice, the study of homeostatic peripheral expansion of human T cells has been limited by the lack of an appropriate in vivo model. In this study, we use T cell-deficient humanized mice and an adoptive transfer approach to demonstrate that two distinct proliferative responses of autologous T cells occur in vivo in a lymphopenic setting. Human naive CD4 and CD8 T cells that undergo rapid proliferation acquire a memory-like phenotype and the ability to rapidly produce IFN-γ, whereas those undergoing slow proliferation retain naive phenotypic and functional characteristics. Recovery of both populations depends on the extent of human non-T cell chimerism in the periphery of recipient humanized mice. Furthermore, memory conversion of CD4 and CD8 T cells correlates with the level of human CD14+ and CD19+ chimerism in recipient mice, respectively, suggesting that different types of APCs support memory conversion of CD4 and CD8 T cells. Because lymphopenia affects clinical outcomes, this model, which will allow detailed investigation of the effects of lymphopenia in patients, is of clinical significance.