Miracle-dz/UniFAR-FTUs huggingface dataset:
Enhanced Phenotypic Alterations of Alveolar Type II Cells in Response to Aflatoxin G1‐Induced Lung Inflammation

Recently, we discovered that Aflatoxin G1 (AFG1) induces chronic lung inflammatory responses, which may contribute to lung tumorigenesis in Balb/C mice. The cancer cells originate from alveolar type II cells (AT‐II cells). The activated AT‐II cells express high levels of MHC‐II and COX‐2, may exhibit altered phenotypes, and likely inhibit antitumor immunity by triggering regulatory T cells (Tregs). However, the mechanism underlying phenotypic alterations of AT‐II cells caused by AFG1‐induced inflammation remains unknown. In this study, increased MHC‐II expression in alveolar epithelium was observed and associated with enhanced Treg infiltration in mouse lung tissues with AFG1‐induced inflammation. This provides a link between phenotypically altered AT‐II cells and Treg activity in the AFG1‐induced inflammatory microenvironment. AFG1‐activated AT‐II cells underwent phenotypic maturation since AFG1 upregulated MHC‐II expression on A549 cells and primary human AT‐II cells in vitro. However, mature AT‐II cells may exhibit insufficient antigen presentation, which is necessary to activate effector T cells, due to the absence of CD80 and CD86. Furthermore, we treated A549 cells with AFG1 and TNF‐α together to mimic an AFG1‐induced inflammatory response in vitro, and we found that TNF‐α and AFG1 coordinately enhanced MHC‐II, CD54, COX‐2, IL‐10, and TGF‐β expression levels in A549 cells compared to AFG1 alone. The phenotypic alterations of A549 cells in response to the combination of TNF‐α and AFG1 were mainly regulated by TNF‐α‐mediated induction of the NF‐κB pathway. Thus, enhanced phenotypic alterations of AT‐II cells were induced in response to AFG1‐induced inflammation. Thus, AT‐II cells are likely to suppress anti‐tumor immunity by triggering Treg activity. J. Cell. Physiol. 230: 1199–1211, 2015. © 2014 Wiley Periodicals, Inc., A Wiley Company
Knowledge-based semidefinite linear programming classifiers

In this paper, we present knowledge-based support vector machine (SVM) classifiers using semidefinite linear programming. SVMs are an optimization-based solution method for large-scale data classification problems. Knowledge-based SVM classifiers, where prior knowledge is in the form of ellipsoidal constraints, result in a semidefinite linear programme with a set containment constraint. These problems are reformulated as standard semidefinite linear programming problems by the application of a dual characterization of the set containment under a mild regularity condition. The reformulated semidefinite linear programme is solved by the publicly available solvers. Computational results show that prior knowledge can often improve correctness of the classifier.
Photoconstructs of Nerve Guidance Prosthesis Using Photoreactive Gelatin as a Scaffold

We devised a novel nerve prosthesis composed of an elastomeric gelatinous tube and multifilament gelatinous fibers, both of which were prepared from styrene-derivatized gelatin, which allows in situ formation of a bioactive substance-incorporated gel. An in vitro study showed that the axonal regeneration potential of a photocured gelatin layer impregnated with laminin, fibronectin, and NGF was almost comparable with that of coated Matrigel. A nerve conduit and fibers prepared from photoreactive gelatin was subjected to visible-light irradiation with rotation in the presence of camphorquinone as a photoinitiator using a custom-designed apparatus. A sample of transparent gelatinous conduit with an inner diameter of 1.2 mm and a wall thickness of 0.6 mm and gelatin fibers ranging from 10 to 100 μm in diameter were produced. The photocured elastomeric gelatinous tube was flexible and had structural integrity that allowed mechanical handling without breaking. A novel nerve guidance prosthesis composed of tubes packed with fibers was assembled. This photofabrication technology may enable the design of a tailor-made shape and rapid morphogenesis and functional recovery of damaged nerve tissue.
A Flexible Role- and Resource-Based Access Control Model

RBAC realizes the separation of duty and helps to manage the users with various roles. However, RBAC cannot work well in distributed environment. In this paper, a flexible role- and resource- based access control model (called RRBAC) is proposed. RRBAC introduces role and resource concepts to access control, and provides a flexible approach for many security domains. RRBAC supports different types of resources sharing in open distributed environment. In the paper, we have a detailed description of RRBAC. Thereto, a use case is given to show how the model works, which illustrates that RRBAC is sound and reasonable.
Statistical placement for FPGAs considering

Process variations affecting timing and power is an important issue for modern integrated circuits in nanometre technologies. Field programmable gate arrays (FPGA) are similar to application-specific integrated circuit (ASIC) in their susceptibility to these issues, but face unique challenges in that critical paths are unknown at test time. The first in-depth study on applying statistical timing analysis with cross-chip and on-chip variations to speed-binning and guard- banding in FPGAs has been presented. Considering the uniqueness of re-programmability in FPGAs, the effects of timing-model with guard-banding and speed-binning on statistical performance and timing yield are quantified. A new variation aware statistical placement, which is the first statistical algorithm for FPGA layout and achieves a yield loss of 29.7% of the original yield loss with guard-banding and a yield loss of 4% of the original one with speed-binning for Microelectronics Center of North Carolina (MCNC) and Quartus University Interface Program (QUIP) designs, has also been developed.
Automatic detection of design problems in object-oriented reengineering

The evolution of software systems over many years often leads to unnecessarily complex and inflexible designs which in turn lead to a huge amount of effort for enhancements and maintenance. Thus, the reengineering of object oriented software becomes more and more important as the number, age and size of such legacy systems grow. A key issue during reengineering is the identification and location of design problems which prevent the efficient further development of a system. Up to now this problem area has not been sufficiently supported, either by methods, or by tools. We present a technique for analyzing legacy code, specifying frequent design problems as queries and locating the occurrences of these problems in a model derived from source code. We present our experiences with a tool set which we implemented to support this task by automatically analyzing a given system and detecting the specified problems. We applied our tools to check violations of a number of well known design rules in existing source code taken from several case studies, both from industrial and academic fields. These experiments showed that the task of problem detection in reengineering can be automated to a large degree, and that the technique presented can be efficiently applied to real world code.
Ex Vivo Analysis of Human Antigen-Specific CD8+ T-Cell Responses: Quality Assessment of Fluorescent HLA-A2 Multimer and Interferon-γ ELISPOT Assays for Patient Immune Monitoring

The authors developed a standardized approach for immune monitoring of antigen-specific CD8+ T cells within peripheral blood lymphocytes (PBLs) that combines direct ex vivo analysis of Melan-A/MART-1 and influenza-specific CD8+ T cells with HLA-A2/peptide multimers and interferon-γ ELISPOT assays. Here the authors assessed the quality of results obtained with 180 PBLs from healthy donors and melanoma patients. Reproducibility of the multimer assay was good (average of 15% variation). In the absence of in vivo antigen-specific T-cell responses, physiologic fluctuations of multimer-positive T cells was low, with variation coefficients of 20% for Melan-A and 28% for influenza-specific T cells. In contrast, patients with vaccination-induced T-cell responses had significantly increased T-cell frequencies clearly exceeding physiologic fluctuations. Comparable results were obtained with ELISPOT assays. In conclusion, this approach is well suited to assess T-cell responses as biologic endpoints in clinical vaccine studies.
Functional analysis of the true late human cytomegalovirus pp28 upstream promoter: cis-acting elements and viral trans-acting proteins necessary for promoter activation

As a model for analyzing the regulation of human cytomegalovirus late genes, we investigated the 28-kDa phosphoprotein (pp28) gene region. Transcripts of 1.6 and 1.3 kb were expressed in wild-type human cytomegalovirus-infected cells but not in cells infected with a DNA-negative temperature-sensitive mutant (ts66), indicating that DNA replication is absolutely required for pp28 gene expression. Transient promoter activation studies revealed that the pp28 gene region upstream promoter (pp28US) functioned early when expressed independently of the viral genome. However, the promoter was not efficiently activated by immediate-early (IE) proteins but was activated equally well by both wild-type virus and ts66. Deletion analysis of the pp28US promoter indicated that sequences upstream of the CAP site between -107 and -32 were required for activation of the pp28 promoter. Within that region exist a 10-bp sequence at -90 (AGTGAT CGTG) and its inverted repeat at -32 which positively influence pp28 promoter function. Therefore, in the case of the pp28US promoter, viral proteins interact through discrete sequences to facilitate late gene expression.
HMM-Based Techniques for Intent Recognition in a Simulated Realistic Naval Environment

Activity recognition aims to recognize the actions of one or more agents from a series of observations. Intent recognition is an area of research dedicated to automatically detecting and predicting the intentions of agents in an environment before they are realized. Intent recognition occurs in conjunction with activity recognition, and both may use the same set of low-level features. When applying intent recognition to simulated environments, realism is a key factor for producing systems which are adaptable to real-life settings. This thesis explores techniques for creating intent recognition systems which are readily adaptable to real world scenarios. We seek to develop methods of intent recognition for multiple ships in a realistic naval environment, where the task is complicated by realistic physics and ship movements. Our intent recognition system is primarily based on Hidden Markov Models that have been trained on large datasets of simulated scenarios, where ships are enacting the patterns which we wish to later recognize. These patterns involve ships performing various maneuvers, such as blocking or ramming. Based on the detection of a set of highly discriminatory features extracted from the data, the HMM is able to recognize patterns in order to reliably separate ship actions into various intent classes. Using a temporal window of activities, our system predicts ship intentions before they are realized, potentially allowing for responsive actions.
Risk Factors and Alzheimer's Disease: A Comparative Study of Two Communities

Objective: To determine the association between demographic, lifestyle and medical history factors to Alzheimer's disease (AD), we studied samples of two community dwelling populations with significantly different prevalence rates of AD in Indianapolis, USA (6.24%) and Ibadan, Nigeria (1.4%). Methods: The samples were drawn from African—American community dwelling residents 65 years of age and over in Indianapolis, and Yoruba community-dwelling residents 65 years of age and over in Ibadan. A two-stage epidemiological design was used in which diagnosis of AD was by National Institute of Neurological and Communicative Disorders and Stroke and the Alzheimer's Disease and Related Disorders Association criteria. Results: In Indianapolis, age (odds ratio [OR] = 1.16; 95% confidence interval [Cl] = 1.11-1.21), family history of dementia (OR = 5.40; 95% Cl = 1.99-14.62), low education (0-6 years, OR = 3.49; 95% Cl = 1.06-11.48) and rural residence (OR = 2.49; 95% CI = 1.05-5.88) were associated with a higher risk of AD. In Ibadan, age (OR = 1.15; 95% Cl = 1.12-1.18) and female gender (OR = 13.9; 95% Cl = 3.85-50.28) were associated with a higher risk of AD. Conclusions: The remarkably similar odds ratios between age and AD between sites suggest that biological processes associated with ageing are essential elements in the development of AD but that genetic and environmental risk factors may alter age-specific rates. In our longitudinal study, we intend to investigate in more depth the interaction between these ageing, genetic and environmental factors.
The interaction of charged and uncharged drugs with neutral (HP-beta-CD) and anionically charged (SBE7-beta-CD) beta-cyclodextrins.

PURPOSE The objective of this work was to determine the role that charge might play in the interaction of charged and uncharged drugs with neutral (2-hydroxypropyl-beta-cyclodextrin, HP-beta-CD) and anionically charged (SBE7-beta-CD) modified beta-cyclodextrins. SBE7-beta-CD is a sulfobutyl ether, sodium salt, derivative variably substituted on the 2-, 3- and the 6-positions of beta-cyclodextrin. The number seven refers to the average degree of substitution. METHODS The binding of the acidic drugs, indomethacin, naproxen and warfarin and the basic drugs, papaverine, thiabendazole, miconazole and cinnarizine with the two cyclodextrins was determined at 25 degrees C as a function of pH and cyclodextrin concentration by the phase-solubility method. RESULTS Except for miconazole and cinnarizine (Ap-type diagrams), all other materials studied displayed AL-type diagrams. By comparing the binding constants of both the charged and uncharged forms of the same drugs to both HP-beta-CD and SBE7-beta-CD, the following conclusions could be drawn. The binding constants for the neutral forms of the drugs were always greater with SBE7-beta-CD than with HP-beta-CD. For the anionic agents, the binding constants between SBE7-beta-CD and HP-beta-CD were similar while the binding constants for the cationic agents with SBE7-beta-CD were superior to those of HP-beta-CD, especially when compared with the neutral form of the same drug. CONCLUSIONS A clear charge effect on complexation, attraction in the case of cationic drugs and perhaps inhibition in the case of anionic drugs, was seen with the SBE7-beta-CD.
Early clinical experience with the E-vita thoracic stent-graft system: a single center study.

AIM The aim of this study was to evaluate the safety and efficacy of a new endovascular thoracic stent-graft, which was designed to overcome the restrictions of previously used stent-grafts. METHODS Between May 2004 and March 2008 a prospective evaluation was conducted in 126 consecutive patients (71% men; age 64 [19-86] years). A total of 138 implantations were performed. E-vita stent-grafts were implanted for type-B dissection (N.=56), degenerative aneurysm (N.=25), penetrating aortic ulcer (N.=17), blunt traumatic lesions (N.=10), mobile atheroma (N.=1), suture aneurysms (N.=7) and revisionary surgery following previous endograft implantation (N.=22). All patients eligible for stent-grafting were treated with this system regardless of their clinical status and aortic pathology. The percentage of emergency procedures was 52% (N.=72). Per implantation a mean of 1.3 segments was implanted with an effective total covered length of the aorta of mean 204 mm, median 230 mm (0-450 mm). In 32 of 39 cases with more than one segment, the entire descending aorta was included in the procedure. RESULTS The 30-day mortality rate was 12.3% (17 patients). All deaths but one were in the group of emergency surgery patients. This results in mortality of 1.5% in the elective and 22% in the emergency procedures. Reversible procedure-induced spinal cord ischemia was observed in 2 cases. Stroke occurred in 2.8% (4 patients). Primary technical success was rated at 77 % (106 procedures) and secondary success at 89 % (124 procedures). CONCLUSION All forms of thoracic aortic disease can be treated with this new stent-graft. It has proved particularly valuable in cases of difficult conditions in the aortic arch and extended aneurysms. In particular, it is possible to cover the entire thoracic aorta with two or three stent-graft segments, thus considerably reducing the number of connections.
Characterization of the virA locus of Agrobacterium tumefaciens: a transcriptional regulator and host range determinant.

The virulence (vir) region of Agrobacterium tumefaciens mediates the transfer of a defined segment of plasmid DNA (the T‐DNA) into the plant genome. The vir genes are specifically induced by molecules produced by wounded plant cells, and virA is required for this induction. We have determined the nucleotide sequence of virA loci from limited (pTiAg162) and wide (pTiA6) host range tumor‐inducing (Ti) plasmids, each of which encodes a single protein of 92,000 daltons. Using antibody directed against the virA gene product, we have localized the VirA protein to the bacterial inner membrane. VirA is homologous to at least four bacterial proteins which play a role in the transcriptional regulation of diverse families of genes. Based on its role in vir gene induction, homology to transcriptional regulators and membrane localization, we propose that VirA acts as an environmental sensor of plant‐derived inducer molecules and transmits this information to the level of vir gene expression. The pTiAg162 virA locus was shown to be ineffective at directing vir gene induction, suggesting that this may in part contribute to the narrow host range conferred by this plasmid.
The course of adjustment disorder in Danish male conscripts

Conscription has been employed for more than a century. To evaluate the course and fate of conscripts deemed mentally unfit for immediate continued service, a prospective questionnaire study of conscripts referred for mental evaluation was conducted. Questionnaires were completed at the time of enrolment, time of admittance for evaluation, time of discharge from their evaluation and at 1-year follow-up. Out of a class of 6949 conscripts, 93 were referred for psychiatric evaluation and 69 of those referred decided to enter the study (60 of these were in time deemed unfit for further military service). At the time of admittance, on average after 79 days of service, there was a significant 36%, 34%, 20% and 20% increase in depression, sleep, somatization and interpersonality scores, respectively. At the time of discharge 14 days after admittance, the symptom scores had dropped to a level comparable to scores at the time of enrolment. At 1-year follow-up, the descending trend in scores was maintained, though not reaching statistical significance compared with scores at time of discharge. The scores at 1-year follow-up were also, except for a higher depression score, comparable with the scores of a control group of conscripts evaluated 1 year after service. The psychological profile of conscripts referred for evaluation was different at the time of enrolment compared with conscripts in general, the scores being between 9% (interpersonality) and 29% (depression) higher. They also had a higher prevalence of adverse family events in their history. The course observed is indifferent from other situations of enforced stress.
Functional Evaluation of Complete Sciatic, Peroneal, and Posterior Tibial Nerve Lesions in the Rat

Quantification of peripheral nerve regeneration in animal studies of nerve injury and repair by histologic, morphologic, and electrophysiologic parameters has been controversial because such studies may not necessarily correlate with actual nerve function. This study modifies the previously described sciatic functional index (SFI), tibial functional index (TFI), and peroneal functional index (PFI) based on multiple linear regression analysis of factors derived from measurements of walking tracks in rats with defined nerve injuries. The factors that contributed to these formulas were print-length factor (PLF), toe-spread factor (TSF), and intermediary toe-spread factor (ITF). It was shown that animals with selective nerve injuries gave walking tracks that were consistent, predictable, and based on known neuromuscular deficits. The new formula for sciatic functional index was compared with previously described indices. The sciatic functional index, tibial functional index, and peroneal functional index offer the peripheral nerve investigator a noninvasive quantitative assessment of hindlimb motor function in the rat with selective hindlimb nerve injury.
Evidence for a climate signal in trends of global crop yield variability over the past 50 years

Low variability of crop production from year to year is desirable for many reasons, including reduced income risk and stability of supplies. Therefore, it is important to understand the nature of yield variability, whether it is changing through time, and how it varies between crops and regions. Previous studies have shown that national crop yield variability has changed in the past, with the direction and magnitude dependent on crop type and location. Whilst such studies acknowledge the importance of climate variability in determining yield variability, it has been assumed that its magnitude and its effect on crop production have not changed through time and, hence, that changes to yield variability have been due to non-climatic factors. We address this assumption by jointly examining yield and climate variability for three major crops (rice, wheat and maize) over the past 50 years. National yield time series and growing season temperature and precipitation were de-trended and related using multiple linear regression. Yield variability changed significantly in half of the crop–country combinations examined. For several crop–country combinations, changes in yield variability were related to changes in climate variability.
The coach-coachee relationship in executive coaching: A field study

Numerous authors have suggested that the working relationship between coach and coachee constitutes an essential condition to the success of executive coaching. This study empirically investigated the links between the coach–coachee relationship and the success of a coaching intervention in an organizational setting. Data were collected from two samples: 73 managers who received executive coaching for a period of eight months and 24 coaches. Results from 31 coach–coachee dyads were analyzed. Results indicate that the coach–coachee relationship plays a mediating role between the coaching received and development of the coachees’ self-efficacy. Findings also show four significant correlates to the coach–coachee relationship: the coach’s selfefficacy with regard to facilitating learning and results, the coachee’s motivation to transfer, his or her perception of supervisor support, and the number of coaching sessions received.