Miracle-dz/UniFAR-FTUs huggingface dataset:
New staging system and a registry for perihilar cholangiocarcinoma

Perihilar cholangiocarcinoma is one of the most challenging diseases with poor overall survival. The major problem for anyone trying to convincingly compare studies among centers or over time is the lack of a reliable staging system. The most commonly used system is the Bismuth‐Corlette classification of bile duct involvement, which, however, does not include crucial information such as vascular encasement and distant metastases. Other systems are rarely used because they do not provide several key pieces of information guiding therapy. Therefore, we have designed a new system reporting the size of the tumor, the extent of the disease in the biliary system, the involvement of the hepatic artery and portal vein, the involvement of lymph nodes, distant metastases, and the volume of the putative remnant liver after resection. The aim of this system is the standardization of the reporting of perihilar cholangiocarcinoma so that relevant information regarding resectability, indications for liver transplantation, and prognosis can be provided. With this tool, we have created a new registry enabling every center to prospectively enter data on their patients with hilar cholangiocarcinoma (www.cholangioca.org). The availability of such standardized and multicenter data will enable us to identify the critical criteria guiding therapy. (HEPATOLOGY 2011;)
Energy-Dependent Conformational Change in the TolA Protein ofEscherichia coli Involves Its N-Terminal Domain, TolQ, and TolR

ABSTRACT TolQ, TolR, and TolA inner membrane proteins of Escherichia coli are involved in maintaining the stability of the outer membrane. They share homology with the ExbB, ExbD, and TonB proteins, respectively. The last is involved in energy transduction between the inner and the outer membrane, and its conformation has been shown to depend on the presence of the proton motive force (PMF), ExbB, and ExbD. Using limited proteolysis experiments, we investigated whether the conformation of TolA was also affected by the PMF. We found that dissipation of the PMF by uncouplers led to the formation of a proteinase K digestion fragment of TolA not seen when uncouplers are omitted. This fragment was also detected in ΔtolQ, ΔtolR, and tolA(H22P) mutants but, in contrast to the parental strain, was also seen in the absence of uncouplers. We repeated those experiments in outer membrane mutants such as lpp, pal, and Δrfa mutants: the behavior of TolA inlpp mutants was similar to that observed with the parental strain. However, the proteinase K-resistant fragment was never detected in the Δrfa mutant. Altogether, these results suggest that TolA is able to undergo a PMF-dependent change of conformation. This change requires TolQ, TolR, and a functional TolA N-terminal domain. The potential role of this energy-dependent process in the stability of the outer membrane is discussed.
High IL-17E and Low IL-17C Dermal Expression Identifies a Fibrosis-Specific Motif Common to Morphea and Systemic Sclerosis

Background High interleukin (IL)-17A levels are characteristically found in the skin of systemic sclerosis (SSc) individuals. Our aim was to investigate whether the dermal expression of IL-17A and related IL-17 family members (i.e. IL-17C, IL-17E and IL-17F) could distinguish fibrotic from healthy skin and could show similarities in SSc and morphea, two disorders with presumed distinct pathogenesis, but characterized by skin fibrosis. Methods Biopsies were obtained from the involved skin of 14 SSc, 5 morphea and 8 healthy donors (HD) undergoing plastic surgery. Immunohistochemistry/immunofluorescence techniques were coupled to a semi-automated imaging quantification approach to determine the presence of the IL-17 family members in the skin. The in vitro effects induced by the IL-17 family members on fibroblasts from normal and SSc individuals were assessed by ELISA and RIA. Results Positive cells for each of the IL-17 isoforms investigated were present in the dermis of all the individuals tested, though with variable frequencies. SSc individuals had increased frequency of IL-17A+ (p = 0.0237) and decreased frequency of IL-17F+ (p = 0.0127) and IL-17C+ cells (p = 0.0008) when compared to HD. Similarly, morphea individuals had less frequent IL-17C+ cells (p = 0.0186) in their skin but showed similar number of IL-17A+ and IL-17F+ cells when compared to HD. Finally, IL-17E+ cells were more numerous in morphea (p = 0.0109) and tended to be more frequent in SSc than in HD. Fibroblast production of IL-6, MMP-1 and MCP-1 was enhanced in a dose-dependent manner in the presence of IL-17E and IL-17F, but not in the presence of IL-17C. None of the cytokine tested had significant effect on type I collagen production. Of interest, in SSc the frequency of both IL-17A and IL-17F positive cells increased with disease duration. Conclusions The frequency of IL-17A and IL-17F distinguish SSc to morphea individuals while dermal expression of IL-17C (low) and IL-17E (high) identifies a fibrosis-specific motif. The specific IL-17C/IL-17E cytokine combination may thus play a role in the development of fibrosis.
Inaccurate mate recognition as a mating strategy of a ‘pioneer male’

Heterosubspecific mating experiments were carried out between two subspecies of cabbage butterflies, British Pieris rapae rapae and Japanese P. rapae crucivora, to examine how accurately males recognize the mates. The two subspecies are different in that the wings of female P. rapae rapae reflect little UV light, whereas those of female P. rapae crucivora are strongly UV-reflective. The wing colouration of P. rapae crucivora involving UV is believed to be critical in mate recognition. The results showed that males of both subspecies displayed mating behaviours, to and copulated with, females of both subspecies. Furthermore, P. rapae crucivora males exhibited mating behaviours and attempted to copulate with females of Pieris melete with low UV reflectance which are critically different from P. rapae crucivora females with high UV reflectance. Based on these findings, we propose the “pioneer male” hypothesis, which argues that such inaccurate mate recognition may sometimes be selectively beneficial for males and thus an adaptive mating strategy. The “pioneer male” was discussed in terms of its possible role in the evolution.
Effect of Interposed Periosteum in an Animal Physeal Fracture Model

To study the effect of interposed periosteum on physeal fracture healing, 52 skeletally immature female Harlan Sprague-Dawley rats, 4 to 5 weeks of age, were randomized to one of three cohort groups. All animals underwent surgical dissection of the left proximal medial tibia; dissection consisted of superficial exposure and incision of a standard periosteal flap. Animals in Group I (fracture alone) underwent physeal fracture; those in Group II (fracture and periosteum) underwent physeal fracture with interposition of periosteum in the fracture site, and those in Group III (positive control) underwent physeal fracture, excision of 1/2 of the growth plate, and interposition of periosteum in the defect. After histologic examination of serial sections, fracture alone resulted in physeal injury frequently associated with small bar formation without a reduction in leg length. With the addition of interposition of periosteum into the fracture site, a small, but statistically significant, increase in leg length discrepancy frequently associated with small histologic bar formation occurred when compared with fracture alone.
Clarifying the Mechanism of Superantigen Toxicity

Superantigens are bacterial proteins that generate a powerful immune response by binding to Major Histocompatibility Complex class II molecules on antigen-presenting cells and T cell receptors on T cells. A recent article reveals that at least one of the superantigens, staphylococcal enterotoxin B (SEB), also binds the co-stimulatory molecule CD28, suggesting that a much larger and potentially more stable complex is formed at the immunological synapse than was previously thought. This revelation greatly clarifies some of the mystery surrounding how and why these toxins are able to elicit such a toxic immune response at extremely low concentrations. These findings also highlight a novel role for CD28 in microbial pathogenicity.
Changes in vitamin-D metabolites and parathyroid hormone in plasma following cholecalciferol administration to pre- and postmenopausal women in the Netherlands in early spring and to postmenopausal women in Curaçao

To study the effect on plasma 25-hydroxycholecalciferol (25(OH)D), 1,25-dihydroxycholecalciferol (1,25(OH)2D) and parathyroid hormone (PTH) we supplemented premenopausal (aged 30 (SD 7) years) and postmenopausal (aged 61 (SD 2) years) white women living in The Netherlands in late winter/early spring, and elderly black and white women (aged 75 (SD 6) years) living in Curacao (Dutch Antilles) with either 10 or 20µpg cholecalciferol/d for 4, 5 and 9 weeks respectively. Baseline plasma 25(OH)D concentration of Dutch women was lower than that of Curacao women. Postmenopausal Dutch women had a higher PTH concentration in plasma than premenopausal Dutch and postmenopausal Curaçao women. There were no differences in plasma 1,25(OH)2D. Cholecalciferol administration increased 25(OH)D in all groups, 1,25(OH)2D in postmenopausal Curaçao women and PTH in postmenopausal Curaçao women and premenopausal Dutch women. Serum and urinary Ca and phosphate concentrations did not change. There were no response differences between 10 and 20 µg doses. Oral cholecalciferol administration (either 10 or 20 µg/d) to women living at northern latitudes in late winter/early spring increased 25(OH)D levels to the baseline levels of elderly people living in the tropics.
Secrecy energy efficiency optimization for MISO and SISO communication networks

Energy-efficiency, high data rates and secure communications are essential requirements of the future wireless networks. In this paper, optimizing the secrecy energy efficiency is considered. The optimal beamformer is designed for a MISO system with and without considering the minimum required secrecy rate. Further, the optimal power control in a SISO system is carried out using an efficient iterative method, and this is followed by analyzing the trade-off between the secrecy energy efficiency and the secrecy rate for both MISO and SISO systems.
Discrete Load Balancing in Heterogeneous Networks with a Focus on Second-Order Diffusion

In this paper we consider a wide class of discrete diffusion load balancing algorithms. The problem is defined as follows. We are given an interconnection network and a number of load items, which are arbitrarily distributed among the nodes of the network. The goal is to redistribute the load in iterative discrete steps such that at the end each node has (almost) the same number of items. In diffusion load balancing, nodes are only allowed to balance their load with their direct neighbors. We show three main results. Firstly, we present a general framework for randomly rounding the flow generated by continuous diffusion schemes over the edges of a graph in order to obtain corresponding discrete schemes. Compared to the results of Rabani, Sinclair, and Wanka, FOCS'98, which are only valid w.r. t. The class of homogeneous first order schemes, our framework can be used to analyze a larger class of diffusion algorithms, such as algorithms for heterogeneous networks and second order schemes. Secondly, we bound the deviation between randomized second order schemes and their continuous counterparts. Finally, we provide a bound for the minimum initial load in a network that is sufficient to prevent the occurrence of negative load at a node during the execution of second order diffusion schemes. Our theoretical results are complemented with extensive simulations on different graph classes. We show empirically that second order schemes, which are usually much faster than first order schemes, will not balance the load completely on a number of networks within reasonable time. However, the maximum load difference at the end seems to be bounded by a constant value, which can be further decreased if first order scheme is applied once this value is achieved by second order scheme.
Integrating adaptive services in grid resource brokering

Grid computing is highly dynamic in nature where resources are subject to change due to performance degradation and node failure. The resources include processing elements, storage, network, and so on; they come from the interconnection of parallel machines, clusters, or any workstation. One of the main properties of these resources is to have changing characteristics even during the execution of an application. Thus, resource usage by applications cannot be static during run-time; neither can change in resources be considered as faults. Therefore, Grrid application designers must keep in mind that resources and resource management are highly dynamic within Grid architectures. Grdi resource brokering is introduced to simplify resource discovery, selection, and job submission for Grid application. However, it is the responsibility of a Grid resource broker to distribute jobs among heterogeneous resources and optimise the resource usage. As a result, a Grid resource broker should have the capablility to adapt to these changes and take appropriate actions to improve performance of various computing applications. To adapt to the Grid resource changes, an adaptive service is introduced in this research. The adaptive service consists of a monitoring tool, decision manager, and migration engine to ensure the job finishes at the time specified. The adaptive service supports job migration during run-time to ensure timely job completion. Our work in this research shows a Grid test-bed and White Rose Grid implementation of an adaptive service that supports job migration during run-time to ensure timely job completion. Performance prediction is used to estimate expected job completion time and determine whether any onserved performance degradation is likely to result in failure to meet a user specified deadline. A key feature of our approach is that the user is not required to install additional software or make complex alterations to their code requiring specialist Grid computing knowledge. This is achieved using a reflective technique to bind the adaptive service components to the user's code. Also, this research proves the adaptive service overhead is very minimal. The adaptive service is a viable contender for future Grid resource brokering implementation.
Smart article: a scientific crosstalk

An era of the huge expansion of the academic population which is accompanied by the extremely high scientific productivity inevitably causes confusion for scientists who can hardly read all the publications about their topic of interest (Godlee et al., 2000). In the 1980s, a decade which witnessed the explosion of technology, everybody was amazed at the evolution in the research, but nobody could envisage that this evolution would bring its own difficulties. This overwhelming flood of published material may be suggestive of the need for scientists to change their style of producing scholarly articles. The recent increasing trend of data production may even result in discouraging scholars from reading the works of one another thoroughly. This issue can even be exacerbated by the ever-increasing amount of knowledge production and its getting more accessible via the internet (Godlee et al., 2000; Abbott, 2008). In coming years, scientific publications will be totally technology driven and print version of journals will become obsolete (Bailey and Pang, 2004; Liben-Nowell and Kleinberg, 2008). For the very genuine reason, the ecology of information should be changed in the future and our suggestion to solve this crisis of abundance of scholarly publishing is “Smart Article. ” Smart article is actually an interactive searchable screen, a big transformation from print to beyond the screen. The content is not merely a digital version of a printed article; it is a totally new way of literary structure and interface transformation. In fact smart articles are fully organized abstracts with smart backbone comprised of different virtual layers. Although each article is displayed in a single page, details are also available in an interactive question-answer based between manmachine. It means that smart searching of structures and substructures will be facilitated in an enhanced article which leads to mutual understanding between article and reader. The structure of a smart article will be coherent and each segment or paragraph will be logically followed by another one. Unlike the conventional articles, more detailed information about each part including hypothesis, methods, results and the discussion will be available on the platform and the researcher will be able to find all the data he wants to know about, for example the materials and laboratory instruments with access to video, audio, and expandable images. Therefore, by reading just one embedded searchable article, the researcher could obtain much more information compared with reading just one conventional article at the same time. Smart article utilizes digital technology to provide a better research experience. The main objective of this technology is to preserve the message of an article and offer a new way of comprehending the concept in an attractive and unique style and provide researchers with the opportunity to find all the required information on his chosen topic with a simple real-time dialog.
Transplantation of Human Neural Stem Cells Exerts Neuroprotection in a Rat Model of Parkinson's Disease

Neural stem cells (NSCs) possess high potencies of self-renewal and neuronal differentiation. We explored here whether transplantation of human NSCs cloned by v-myc gene transfer, HB1.F3 cells, is a feasible therapeutic option for Parkinson's disease. In vivo, green fluorescent protein-labeled HB1.F3 cells (200,000 viable cells in 3 μl of PBS) when stereotaxically transplanted (same-day lesion-transplant paradigm) into the 6-hydroxydopamine-lesioned striatum of rats significantly ameliorated parkinsonian behavioral symptoms compared with controls (vehicle, single bolus, or continuous minipump infusion of trophic factor, or killed cell grafts). Such graft-derived functional effects were accompanied by preservation of tyrosine hydroxylase (TH) immunoreactivity along the nigrostriatal pathway. Grafted HB1.F3 cells survived in the lesioned brain with some labeled with neuronal marker mitogen-activated protein 2 and decorated with synaptophysin-positive terminals. Furthermore, endogenous neurogenesis was activated in the subventricular zone of transplanted rats. To further explore the neuroprotective mechanisms underlying HB1.F3 cell transplantation, we performed cell culture studies and found that a modest number of HB1.F3 cells were TH and dopamine and cAMP-regulated phosphoprotein 32 positive, although most cells were nestin positive, suggesting a mixed population of mature and immature cells. Administration of the HB1.F3 supernatant to human derived dopaminergic SH-SY5Y cells and fetal rat ventral mesencephalic dopaminergic neurons protected against 6-hydroxydopamine neurotoxicity by suppressing apoptosis through Bcl-2 upregulation, which was blocked by anti-stem cell factor antibody alone, the phosphatidylinositol 3-kinase/Akt inhibitor LY294002 [2-(4-morpholinyl)-8-phenyl-1(4H)-benzopyran-4-one] alone, or a combination of both. These results suggest that HB1.F3 cell transplantation exerts neuroprotective effects against dopaminergic depletion in vitro and in vivo because of trophic factor secretion and neuronal differentiation.
Believability of evidence matters for correcting social impressions

Significance The digital age affords exposure to a staggering amount of information—not all of it true. The extent to which mere exposure to information of uncertain veracity or outright disinformation campaigns shapes our impressions of others, independent of our subjective assessments of its truth value, is thus a key question with important implications, especially because implicit evaluations have been shown to uniquely predict behaviors such as which politician a voter ultimately votes for in an election. This study sheds light on the nature of implicit cognition and the extent to which dissociations between implicit and explicit evaluations can be successfully explained by differential reliance on propositional learning processes. To what extent are we beholden to the information we encounter about others? Are there aspects of cognition that are unduly influenced by gossip or outright disinformation, even when we deem it unlikely to be true? Research has shown that implicit impressions of others are often insensitive to the truth value of the evidence. We examined whether the believability of new, contradictory information about others influenced whether people corrected their implicit and explicit impressions. Contrary to previous work, we found that across seven studies, the perceived believability of new evidence predicted whether people corrected their implicit impressions. Subjective assessments of truth value also uniquely predicted correction beyond other properties of information such as diagnosticity/extremity. This evidence shows that the degree to which someone thinks new information is true influences whether it impacts implicit impressions.
Transcriptional and Genomic Targets of Neural Stem Cells for Functional Recovery after Hemorrhagic Stroke

Hemorrhagic stroke is a life-threatening disease characterized by a sudden rupture of cerebral blood vessels, and it is widely believed that neural cell death occurs after exposure to blood metabolites or subsequently damaged cells. Neural stem cells (NSCs), which maintain neurogenesis and are found in subgranular zone and subventricular zone, are thought to be an endogenous neuroprotective mechanism for these brain injuries. However, due to the complexity of NSCs and their microenvironment, current strategies cannot satisfactorily enhance functional recovery after hemorrhagic stroke. It is well known that transcriptional and genomic pathways play important roles in ensuring the normal functions of NSCs, including proliferation, migration, differentiation, and neural reconnection. Recently, emerging evidence from the use of new technologies such as next-generation sequencing and transcriptome profiling has provided insight into our understanding of genomic function and regulation of NSCs. In the present article, we summarize and present the current data on the control of NSCs at both the transcriptional and genomic levels. Using bioinformatics methods, we sought to predict novel therapeutic targets of endogenous neurogenesis and exogenous NSC transplantation for functional recovery after hemorrhagic stroke, which could also advance our understanding of its pathophysiology.