Miracle-dz/UniFAR-FTUs huggingface dataset:
Association between the DICER rs1057035 polymorphism and cancer risk: evidence from a meta-analysis of 1,2675 individuals.

BACKGROUND DICER, one of the microRNA (miRNA) biogenesis proteins, is involved in the maturation of miRNAs and is implicated in cancer development and progression. The results from previous epidemiological studies on associations between DICER rs1057035 polymorphism and cancer risk were inconsistent. Thereforewe performed this meta-analysis to summarize possible associations. MATERIALS AND METHODS We searched all relevant articles on associations between DICER rs1057035 polymorphism and cancer risk from PubMed, EMBASE, Chinese Biomedical Literature and Chinese National Knowledge Infrastructure until August 2014. Odds ratios (ORs) with 95% confidence intervals (CIs) were calculated to assess any associations. Heterogeneity tests, sensitivity analyses and publication bias assessments were also performed in this meta-analysis. All analyses were conducted using STATA software. RESULTS Seven case-control studies, including 4,875 cancer cases and 7,800 controls were included in the meta-analysis. Overall, the results indicated that the C allele of DICER rs1057035 polymorphism was significantly associated with decreased cancer risk in allelic comparison, heterozygote and dominant genetic models (C vs T: OR=0.88, 95%CI 0.81-0.95, p=0.002; TC vs TT: OR=0.85, 95%CI 0.77-0.93, p=0.001; CC/TC vs TT: OR=0.86, 95%CI 0.78-0.94, p=0.001). In the subgroup analysis by ethnicity, a significantly decreased cancer risk was found in Asian but not Caucasian populations. CONCLUSIONS The present meta-analysis suggests that the C allele of the DICER rs1057035 polymorphism probably decreases cancer risk. However, this association may be Asian-specific and the results should be treated with caution. Further well-designed studies based on larger sample sizes and group of populations are needed to validate these findings.
Returning Individuals with Mild to Moderate Brain Injury Back to Work: A Systematic Client Centered Approach

the of the individual living the brain injury when rehabilitation of intervention programmes. are occupational therapy the lived of brain The intervention centred. My exploration of the literature also revealed only one study that focused on the best practice for maintaining employment. [33] The study described the best practice for gaining and employing people with brain injuries from a developed world perspective. the study lacked information on how brain injured individuals adapt different working environments and it lacked the incorporation of the personal perspectives of the brain injured individuals themselves.
Corrective Classification: Classifier Ensembling with Corrective and Diverse Base Learners

Empirical studies on supervised learning have shown that ensembling methods lead to a model superior to the one built from a single learner under many circumstances especially when learning from imperfect, such as biased or noise infected, information sources. In this paper, we provide a novel corrective classification (C2) design, which incorporates error detection, data cleansing and Bootstrap sampling to construct base learners that constitute the classifier ensemble. The essential goal is to reduce noise impacts and eventually enhance the learners built from noise corrupted data. We further analyze the importance of both the accuracy and diversity of base learners in ensembling, in order to shed some light on the mechanism under which C2 works. Experimental comparisons will demonstrate that C2 is not only superior to the learner built from the original noisy sources, but also more reliable than bagging or the aggressive classifier ensemble (ACE), which are two degenerate components/variants of C2.
Pattern Recognition Receptors and Cytokines in Mycobacterium tuberculosis Infection—The Double-Edged Sword?

Tuberculosis, an infectious disease caused by Mycobacterium tuberculosis (Mtb), remains a major cause of human death worldwide. Innate immunity provides host defense against Mtb. Phagocytosis, characterized by recognition of Mtb by macrophages and dendritic cells (DCs), is the first step of the innate immune defense mechanism. The recognition of Mtb is mediated by pattern recognition receptors (PRRs), expressed on innate immune cells, including toll-like receptors (TLRs), complement receptors, nucleotide oligomerization domain like receptors, dendritic cell-specific intercellular adhesion molecule grabbing nonintegrin (DC-SIGN), mannose receptors, CD14 receptors, scavenger receptors, and FCγ receptors. Interaction of mycobacterial ligands with PRRs leads macrophages and DCs to secrete selected cytokines, which in turn induce interferon-γ- (IFNγ-) dominated immunity. IFNγ and other cytokines like tumor necrosis factor-α (TNFα) regulate mycobacterial growth, granuloma formation, and initiation of the adaptive immune response to Mtb and finally provide protection to the host. However, Mtb can evade destruction by antimicrobial defense mechanisms of the innate immune system as some components of the system may promote survival of the bacteria in these cells and facilitate pathogenesis. Thus, although innate immunity components generally play a protective role against Mtb, they may also facilitate Mtb survival. The involvement of selected PRRs and cytokines on these seemingly contradictory roles is discussed.
Correcting for the study bias associated with protein–protein interaction measurements reveals differences between protein degree distributions from different cancer types

Protein–protein interaction (PPI) networks are associated with multiple types of biases partly rooted in technical limitations of the experimental techniques. Another source of bias are the different frequencies with which proteins have been studied for interaction partners. It is generally believed that proteins with a large number of interaction partners tend to be essential, evolutionarily conserved, and involved in disease. It has been repeatedly reported that proteins driving tumor formation have a higher number of PPI partners. However, it has been noticed before that the degree distribution of PPI networks is biased toward disease proteins, which tend to have been studied more often than non-disease proteins. At the same time, for many poorly characterized proteins no interactions have been reported yet. It is unclear to which extent this study bias affects the observation that cancer proteins tend to have more PPI partners. Here, we show that the degree of a protein is a function of the number of times it has been screened for interaction partners. We present a randomization-based method that controls for this bias to decide whether a group of proteins is associated with significantly more PPI partners than the proteomic background. We apply our method to cancer proteins and observe, in contrast to previous studies, no conclusive evidence for a significantly higher degree distribution associated with cancer proteins as compared to non-cancer proteins when we compare them to proteins that have been equally often studied as bait proteins. Comparing proteins from different tumor types, a more complex picture emerges in which proteins of certain cancer classes have significantly more interaction partners while others are associated with a smaller degree. For example, proteins of several hematological cancers tend to be associated with a higher number of interaction partners as expected by chance. Solid tumors, in contrast, are usually associated with a degree distribution similar to those of equally often studied random protein sets. We discuss the biological implications of these findings. Our work shows that accounting for biases in the PPI network is possible and increases the value of PPI data.
Long-term suppression of neurodegeneration in chronic experimental optic neuritis: antioxidant gene therapy.

PURPOSE To test in mice with experimental autoimmune encephalomyelitis (EAE) a strategy designed to treat patients at risk for axonal degeneration and persistent visual loss from optic neuritis and multiple sclerosis. METHODS The authors cloned the human extracellular superoxide dismutase (ECSOD) or catalase (CAT) gene into recombinant adenoassociated virus (AAV). Transgene expression was evaluated by immunochemistry of infected RGC-5 cells and after intravitreal injection of AAV-ECSOD or AAV-CAT, or both, into the right eyes of DBA/1J mice. Control cells and left eyes were inoculated with AAV-GFP. Animals were sensitized for EAE, followed by serial contrast-enhanced MRI for 6 months, and then were euthanatized. The effects of ECSOD and CAT modulation on the EAE optic nerve were gauged by computerized analysis of optic nerve volume, myelin fiber area, axonal cell loss, and retinal ganglion cell (RGC) loss. RESULTS Western blot analysis of infected RGC-5 cells revealed that expression of ECSOD increased 15-fold and that of CAT increased 3.5-fold. One month after intraocular injections, transgene expression increased 4-fold for AAV-ECSOD and 3.3-fold for AAV-CAT. Six months after intraocular injections and EAE sensitization, combination therapy with ECSOD and catalase decreased RGC loss by 29%, optic nerve demyelination by 36%, axonal loss by 44%, and cellular infiltration by 34% compared with the contralateral control eyes inoculated with AAV-GFP. Compared with the normal optic nerve, it limited RGC loss to 9%. CONCLUSIONS Viral-mediated delivery of antioxidant genes provides long-lasting suppression against neuronal and axonal loss associated with permanent visual disability in patients with optic neuritis and multiple sclerosis.
Further Explorations of the Facing Bias in Biological Motion Perception: Perspective Cues, Observer Sex, and Response Times

The human visual system has evolved to be highly sensitive to visual information about other persons and their movements as is illustrated by the effortless perception of point-light figures or ‘biological motion’. When presented orthographically, a point-light walker is interpreted in two anatomically plausible ways: As ‘facing the viewer’ or as ‘facing away’ from the viewer. However, human observers show a ‘facing bias’: They perceive such a point-light walker as facing towards them in about 70-80% of the cases. In studies exploring the role of social and biological relevance as a possible account for the facing bias, we found a ‘figure gender effect’: Male point-light figures elicit a stronger facing bias than female point-light figures. Moreover, we also found an ‘observer gender effect’: The ‘figure gender effect’ was stronger for male than for female observers. In the present study we presented to 11 males and 11 females point-light walkers of which, very subtly, the perspective information was manipulated by modifying the earlier reported ‘perspective technique’. Proportions of ‘facing the viewer’ responses and reaction times were recorded. Results show that human observers, even in the absence of local shape or size cues, easily pick up on perspective cues, confirming recent demonstrations of high visual sensitivity to cues on whether another person is potentially approaching. We also found a consistent difference in how male and female observers respond to stimulus variations (figure gender or perspective cues) that cause variations in the perceived in-depth orientation of a point-light walker. Thus, the ‘figure gender effect’ is possibly caused by changes in the relative locations and motions of the dots that the perceptual system tends to interpret as perspective cues. Third, reaction time measures confirmed the existence of the facing bias and recent research showing faster detection of approaching than receding biological motion.
A need for incentivizing field hydrology, especially in an era of open data: discussion of “The role of experimental work in hydrological sciences – insights from a community survey”*

ABSTRACT The sharing of data and collection of new data are both essential, but they are not inherently complementary. When data are openly available, researchers may be motivated to use those data rather than collect more because field work has costs and risks. The competitive advantage to those who do not put resources towards fieldwork may discourage field hydrology. Allocating efforts towards generating field data, which benefits hydrological sciences, is not necessarily best for individual hydrologists, especially in an era of open data. The objective of this work is to open a conversation on whether individuals’ best interests may contrast with the community’s desire for new observations. If the community wants new field observations, there is a need to consider the shifting balance of incentives and disincentives for pursuing field studies in hydrology.
Intelligent Machines in the 21st Century: Automating the Processes of Inference and Inquiry

The last century saw the application of Boolean algebra toward the construction of computing machines, which work by applying logical transformations to information contained in their memory. The development of information theory and the generalization of Boolean algebra to Bayesian inference have enabled these computing machines. in the last quarter of the twentieth century, to be endowed with the ability to learn by making inferences from data. This revolution is just beginning as new computational techniques continue to make difficult problems more accessible. However, modern intelligent machines work by inferring knowledge using only their pre-programmed prior knowledge and the data provided. They lack the ability to ask questions, or request data that would aid their inferences. Recent advances in understanding the foundations of probability theory have revealed implications for areas other than logic. Of relevance to intelligent machines, we identified the algebra of questions as the free distributive algebra, which now allows us to work with questions in a way analogous to that which Boolean algebra enables us to work with logical statements. In this paper we describe this logic of inference and inquiry using the mathematics of partially ordered sets and the scaffolding of lattice theory, discuss the far-reaching implications of the methodology, and demonstrate its application with current examples in machine learning. Automation of both inference and inquiry promises to allow robots to perform science in the far reaches of our solar system and in other star systems by enabling them to not only make inferences from data, but also decide which question to ask, experiment to perform, or measurement to take given what they have learned and what they are designed to understand.
Transcriptome analysis provides insight into venom evolution in a seed‐parasitic wasp, Megastigmus spermotrophus

One of the most striking host range transitions is the evolution of plant parasitism from animal parasitism. Parasitoid wasps that have secondarily evolved to attack plants (ie gall wasps and seed‐feeders) demonstrate intimate associations with their hosts, yet the mechanism of plant–host manipulation is currently not known. There is, however, emerging evidence suggesting that ovipositional secretions play a role in plant manipulation. To investigate whether parasites have modified pre‐existing adaptations to facilitate dramatic host shifts we aimed to characterize the expression of venom proteins in a plant parasite using a collection of parasitoid venom sequences as a guide. The transcriptome of a seed‐feeding wasp, Megastigmus spermotrophus, was assembled de novo and three putative venoms were found to be highly expressed in adult females. One of these putative venoms, aspartylglucosaminidase, has been previously identified as a major venom component in two distantly related parasitoid wasps (Asobara tabida and Leptopilina heterotoma) and may have originated via gene duplication within the Hymenoptera. Our study shows that M. spermotrophus, a specialized plant parasite, expresses putative venom transcripts that share homology to venoms identified in Nasonia vitripennis (both superfamily Chalcidoidea), which suggests that M. spermotrophus may have co‐opted pre‐existing machinery to develop as a plant parasite.
The 'E' in NIME: Musical Expression with New Computer Interfaces

Is there a distinction between New Interfaces for Musical Expression and New Interfaces for Controlling Sound? This article begins with a brief overview of expression in musical performance, and examines some of the characteristics of effective "expressive" computer music instruments. It becomes apparent that sophisticated musical expression requires not only a good control interface but also virtuosic mastery of the instrument it controls. By studying effective acoustic instruments, choosing intuitive but complex gesture-sound mappings that take advantage of established instrumental skills, designing intelligent characterizations of performance gestures, and promoting long-term dedicated practice on a new interface, computer music instrument designers can enhance the expressive quality of computer music performance.
On Automating XSEDE User Ticket Classification

The XSEDE ticket system, which is a help desk ticketing system, receives email and web-based problem reports (i.e., tickets) from users and these tickets can be manually grouped into predefined categories either by the ticket submitter or by operations staff. This manual process can be automated by using text classification algorithms such as Multinomial Naive Bayes (MNB) or Softmax Regression Neural Network (SNN). Ticket subjects, rather than whole tickets, were used to make an input word list along with a manual word group list to enhance accuracy. The text mining algorithms used the input word list to select input words in the tickets. Compared with the Matlab svm() function, MNB and SNN showed overall better accuracy (up to ~85.8% using two simultaneous category selection). Also, the service provider resource (i.e., system name) information could be extracted from the tickets with ~90% accuracy.
Grasping the Changes Seen in Older Adults When Reaching for Objects of Varied Texture

Old age is associated with reduced mobility of the hand. To investigate age related decline when reaching-to-lift an object we used sophisticated kinematic apparatus to record reaches carried out by healthy older and younger participants. Three objects of different widths were placed at three different distances, with objects having either a high or low friction surface (i.e. rough or slippery). Older participants showed quantitative differences to their younger counterparts – movements were slower and peak speed did not scale with object distance. There were also qualitative differences with older adults showing a greater propensity to stop the hand and adjust finger position before lifting objects. The older participants particularly struggled to lift wide slippery objects, apparently due to an inability to manipulate their grasp to provide the level of precision necessary to functionally enclose the object. These data shed light on the nature of age related changes in reaching-to-grasp movements and establish a powerful technique for exploring how different product designs will impact on prehensile behavior.
Undeveloped land: development opportunity or planning problem?

Land policies have become prioritised in the political agenda in many nations in a way that ensures the sustainability of supply within urban boundaries. This is due to the negative implications of sprawling cities. While many studies regard undeveloped land as a development opportunity (whether for the present or the future), it can be argued that the existence of undeveloped land can, in dissimilar urban contexts with dissimilar situations, be a planning problem. The city of Riyadh is chosen as a case study to show how undeveloped land can be a planning problem. It was established that undeveloped land can be divided into three categories; undeveloped land that is located in the urban-rural fringe, currently undeveloped brownfield land (i.e. it has been previously developed) and undeveloped white land (i.e. virgin land). While the first two categories can be a development opportunity, the undeveloped white land can be a sign of a planning problem. It is vital to explain this as future studies should deal with the issue of undeveloped land differently (i.e. whether it is a development opportunity or a planning problem).
Studies on the role of the host immune response in recovery from Friend virus leukemia. I. Antiviral and antileukemia cell antibodies

The humoral immune response to Friend virus leukemia was studied in congenic F1 mice differing in their incidence of recovery from leukemia. Antiviral neutralizing antibodies rose in titer in vivo concurrently with disappearance of viremia and fall in spleen virus levels. Cytotoxic antileukemia cell antibodies also appeared at this time. Passive transfer of these antibodies could inactivate low numbers of leukemia cells in vivo; however, mice of both high and low recovery genotypes produced antibodies in equal titer and recovered from viral infection in spite of striking differences in recovery from leukemic splenomegaly. Mice lacking C57BL genes did not produce antibodies or recover from viremia except in rare instances. Recovery from splenomegaly was found to be influenced by three or more C57BL genes independent of the H-2 complex.
Diagnostic Value of Transesophageal Echocardiography in Cardiac Surgery

The aim of this study was to assess the diagnostic value of intraoperative 2-D color Doppler transesophageal echocardiography (ITEE) for the surgeon and anesthesiologist in patients undergoing coronary bypass surgery or heart valve replacement. Information given by ITEE in 100 cardiac operations was documented. We judged the ITEE information, considering to what extent it was not to be obtained by other methods and to what extent it influenced the operation itself. The value was classified as dispensable (0), informative (1), valuable (2), or essential (3). In 50 consecutive patients with heart-valve replacement (25 aortic valve prostheses, 25 mitral valve prostheses) ITEE was 38 x (0), 8 x (1), 4 x (2). In 50 consecutive patients undergoing coronary artery bypass graft surgery it was 33 x (0), 11 x (1), 4 x (2), 2 x (3). The two essential diagnoses referred to undetected vein graft occlusions. Information classified as valuable mainly referred to left and right ventricular function or valvular and prosthetic valve function when difficulties occurred during and after extracorporeal circulation. In conclusion, information given by ITEE, although generally regarded as dispensable in the procedures considered, was valuable in 10% of cases and in 2% even essential.
Climate Factors Leading to Asymmetric Extreme Capture in the Tree‐Ring Record

Paleoclimate data play a critical role in contextualizing recent hydroclimate extremes, but asymmetries in tree‐ring responses to extreme climate conditions pose challenges for reconstruction and interpretation of past climate. Here we establish the extent to which existing tree‐ring records capture precipitation extremes in western North America and evaluate climate factors hypothesized to lead to asymmetric extreme capture, including timing of precipitation, seasonal temperatures, snowpack, and atmospheric river events. We find that while there is dry‐biased asymmetry in one third of western North American tree‐ring records, 45% of sites capture wet extremes as well as or better than dry extremes. Summer extremes are rarely captured at any sites. Latitude and elevation affect site‐level extreme responses, as do seasonal climate conditions, particularly in the autumn and spring. Directly addressing asymmetric extreme value capture in tree‐ring records can aid our interpretation of past climate and help identify alternative avenues for future reconstructions.