Miracle-dz/UniFAR-FTUs huggingface dataset:
Personal UV Dosimetry by Bacillus subtilis Spore Films

Background: Ultraviolet radiation (UVR) is known to be the most important risk factor for melanoma and non-melanoma skin cancers. Until today it has been impossible to measure reliably UVR in the frame of epidemiological studies. The recent development of a spore film containing spores of Bacillus subtilis resulted in a new method of UV measurement by personal dosimetry. Methods: The practical application of dosimeters was tested in 18 study persons under different circumstances of UV exposure and in 4 different geographical regions. Results: Eleven children carried dosimeters on their shoulders for 1 day, playing in- and outdoors on a sunny day in summertime. Their whole-day values ranged from 0.1 to 1.5 minimal erythema doses (MED) per day with a mean of 0.71 MED (±0.44). Four lifeguards in a public swimming-pool carried dosimeters on their shoulders for 11 days and received UV exposures ranging from 3.6 to 9.5 MED (mean 5.9 ± 1.88). Three mountain guides with dosimeters attached to the lateral head in different mountain regions at 23 mountaineering activities received daily exposures of 4.44–17.07 MED (mean 11.9 ± 3.8). Conclusion: B. subtilis spore film dosimeters can be applied to different study persons including children and mountain guides under different climatic conditions. A broad range of UV exposures can reliably be measured with this method.
Combining drugs and radiotherapy: from the bench to the bedside

Purpose of reviewThe current standard care of treatment for glioblastoma multiforme (GBM) is never curative and exclusively involves the use of cytoxics upfront (e.g., radiation and chemotherapy). Current clinical protocols involve the use of single-agent targeted therapies, which inhibit specific pathways. Given the functional redundancies present in human tumors and escape mechanisms, it is highly unlikely that such a monotherapy approach will be successful in the treatment of GBM. Future directions of therapy for GBMs will likely involve the use of therapeutic cocktails, including more than one target specific inhibitors based on tumor escape mechanism, genetic, epigenetic and molecular signatures. This review addresses some of the relevant issues. Recent findingsCorrelative clinical studies from various clinical trials and preclinical studies have provided the meticulous use of chemotherapeutics and radiation based on molecular profiling of tumors. Alkylating agents such as temozolomide lose their efficacy if DNA repair enzyme expression is upregulated. The alternative strategies include targeting the enzyme or one can use poly (ADP) ribose inhibitor to inhibit base excision repair pathway rather than mismatch repair pathway. Currently, several inhibitors in this category are in clinical trials. Next, we have addressed new avenues including radiosensitizers, hypoxia, metabolism, angiogenesis, invasive and infiltrative nature of tumors and potential molecular targets, which can be exploited for clinical trials. Finally, we have included some aspect of genome-wide association studies and correlative analysis and the lessons learned to design better clinical trials. SummaryAdvances in profiling the noncoding RNAs, genetic, epigenetic profiles, metabolomics, genomics and proteomics may uncover important resistance mechanisms in GBM. Personalized therapy using various therapeutic cocktails targeting these resistance mechanisms may prove even more effective in the future management of GBMs.
Topological Properties of Large-Scale Cortical Networks Based on Multiple Morphological Features in Amnestic Mild Cognitive Impairment

Previous studies have demonstrated that amnestic mild cognitive impairment (aMCI) has disrupted properties of large-scale cortical networks based on cortical thickness and gray matter volume. However, it is largely unknown whether the topological properties of cortical networks based on geometric measures (i.e., sulcal depth, curvature, and metric distortion) change in aMCI patients compared with normal controls because these geometric features of cerebral cortex may be related to its intrinsic connectivity. Here, we compare properties in cortical networks constructed by six different morphological features in 36 aMCI participants and 36 normal controls. Six cortical features (3 volumetric and 3 geometric features) were extracted for each participant, and brain abnormities in aMCI were identified by cortical network based on graph theory method. All the cortical networks showed small-world properties. Regions showing significant differences mainly located in the medial temporal lobe and supramarginal and right inferior parietal lobe. In addition, we also found that the cortical networks constructed by cortical thickness and sulcal depth showed significant differences between the two groups. Our results indicated that geometric measure (i.e., sulcal depth) can be used to construct network to discriminate individuals with aMCI from controls besides volumetric measures.
On the Design of Turbo Packet Combining Schemes for Relay-Assisted Systems over Multi-Antenna Broadband Channels

This paper focuses on turbo packet combining strategies for multi-relay-assisted systems operating over multiple-input-multiple-output (MIMO) broadband channel. We propose a frequency domain minimum mean square error (MMSE)-based turbo packet combining scheme where all slots received signals and their corresponding channel frequency responses (CFR)s are used to decode the data packet. We also provide an efficient recursive implementation way for the proposed scheme, and show that both its computational complexity and memory requirements are quite insensitive to the number of relays in the system. For the special case of cooperative automatic repeat request (ARQ) systems, we introduce an adaptive packet combining algorithm that enable to reduce the receiver implementation cost. Block error rate (BLER) performance are provided to demonstrate the gains offered by the proposed combining scheme over the conventional soft information-based combining.
Dependent nonparametric trees for dynamic hierarchical clustering : Supplementary material

There exist a wide variety of distributions over trees with infinitely many nodes, including the nested Chinese restaurant process (Blei et al., 2004), the Dirichlet diffusion tree (Neal, 2003), and Kingman’s coalescent (Kingman, 1982). These models differ from the TSSBP in that data can only be associated with a leaf node, or equivalently a full path from root to leaf. We chose to base our clustering model on the TSSBP because, in many applications, it makes sense to associate data with internal nodes. For example, a document may be narrowly about Physics or Biology, or may be a more broad article on the sciences in general.
User-representative feature selection for keystroke dynamics

Continuous user authentication with keystroke dynamics uses characters sequences as features. Since users can type characters in any order, it is imperative to find character sequences (n-graphs) that are representative of user typing behavior. The contemporary feature selection approaches do not guarantee selecting frequently-typed features which may cause less accurate statistical user-representation. Furthermore, the selected features do not inherently reflect user typing behavior. We propose four statistical-based feature selection techniques that mitigate limitations of existing approaches. The first technique selects the most frequently occurring features. The other three consider different user typing behaviors by selecting: n-graphs that are typed quickly; n-graphs that are typed with consistent time; and n-graphs that have large time variance among users. We use Gunetti's keystroke dataset and k-means clustering algorithm for our experiments. The results show that among the proposed techniques, the most-frequent feature selection technique can effectively find user-representative features. We further substantiate our results by comparing the most-frequent feature selection technique with three existing approaches (popular Italian words, common n-graphs, and least frequent n-graphs). We find that it performs better than the existing approaches after selecting a certain number of most-frequent n-graphs.
On the Nature of Immersion During Study Abroad: Some Participant Perspectives

The Valcourt program founded in 1990 with the aim of supplementing existing semester and academic-year programs available through Collegiate University and providing an opportunity for students with as little as two semesters of language instruction to study in France. In this article, perspectives from Molise and Ashley, who along with five other participants from Collegiate, agreed to serve as informants in a qualitative research project which sought to understand–from their point of view–the transition they were making from language learning in an American classroom to language use in Valcourt and back again. The resulting data show, among other things, how truly unique each participant’s perspective can be, even when backgrounds seem similar.
Sorafenib Suppresses JNK-Dependent Apoptosis through Inhibition of ZAK

Sorafenib is U.S. Food and Drug Adminstration–approved for the treatment of renal cell carcinoma and hepatocellular carcinoma and has been combined with numerous other targeted therapies and chemotherapies in the treatment of many cancers. Unfortunately, as with other RAF inhibitors, patients treated with sorafenib have a 5% to 10% rate of developing cutaneous squamous cell carcinoma (cSCC)/keratoacanthomas. Paradoxical activation of extracellular signal–regulated kinase (ERK) in BRAF wild-type cells has been implicated in RAF inhibitor–induced cSCC. Here, we report that sorafenib suppresses UV-induced apoptosis specifically by inhibiting c-jun–NH2–kinase (JNK) activation through the off-target inhibition of leucine zipper and sterile alpha motif–containing kinase (ZAK). Our results implicate suppression of JNK signaling, independent of the ERK pathway, as an additional mechanism of adverse effects of sorafenib. This has broad implications for combination therapies using sorafenib with other modalities that induce apoptosis. Mol Cancer Ther; 13(1); 221–9. ©2013 AACR.
QUANTIFYING THREATS TO IMPERILED SPECIES IN THE UNITED STATES

Biologists are nearly unanimous in their belief that humanity is in the process of extirpating a significant portion of the earth's spe­ cies. The ways in which we are doing so reflect the magnitude and scale of human enterprise. Everything from highway construction to cattle ranch­ ing to leaky bait buckets has been implicated in the demise or endan­ germent of particular species. Ac­ cording to Wilson (1992), most of these activities fall into four major categories, which he terms "the mind­ less horsemen of the environmental apocalypse": overexploitation, habi­ tat destruction, the introduction of non-native (alien) species, and the spread of diseases carried by alien species. To these categories may be added a fifth, pollution, although it can also be considered a form of habitat destruction. Surprisingly, there have been reIa­ tively few analyses of the extent to which each of these factors-much less the more specific deeds encomDavid S. Wilcove is a senior ecologist at the Environmental Defense Fund, Wash­ ington, DC 20009. David Rothstein re­ ceived his J.D. in 1997 from Northeastern
Point spread function estimation and deblurring using code V optical imaging

In order to deal with image blur and distortion it is necessary to have enough knowledge on Point Spread Function (PSF) as the sources of degradation effects which causes blur in images are incorporated in Point spread Function (PSF) so if we have an abundance knowledge on PSF the it becomes easy to recover the original image from blurred image since the PSF defines the system response. As per the earlier survey, the PSF is calculated from Image Transmission Theory using deconvolution method (mathematical method). But PSF can also be calculated from the software tool CODE V more effectively and efficiently. Here is a brief survey on PSF using Code V.
Pregabalin‐withdrawal encephalopathy and splenial edema: A link to high‐altitude illness?

A postherpetic‐neuralgia patient abruptly discontinued pregabalin. Thirty hours later, unexplained nausea, headache, and ataxia developed, progressing to delirium 8 days later. Magnetic resonance imaging indicated T2‐hyperintense lesions of her splenium. Similar magnetic resonance imaging abnormalities, interpreted as focal vasogenic edema, develop in some epileptic patients after rapid anticonvulsant withdrawal. Patients with high‐altitude cerebral edema have similar splenial‐predominant magnetic resonance imaging abnormalities that accompany these same neurological symptoms. This case is the first to associate anticonvulsant‐withdrawal splenial abnormalities with neurological symptoms, with gabapentin‐type anticonvulsants, and is among the first in nonepileptic patients, suggesting that sudden anticonvulsant withdrawal alone, unaccompanied by seizures, can initiate symptomatic focal brain edema. The similarity of this syndrome to high‐altitude cerebral edema suggests a possible common pathophysiology and offers potential therapies. Ann Neurol 2005
Decay Of Correlations In Subcritical Potts And Random-Cluster Models

We prove exponential decay for the tail of the radius R of the cluster at the origin, for subcritical random-cluster models, under an assumption slightly weaker than that E(R d1) < 1 (here, d is the number of dimensions). Speciically, if E(R d1) < 1 throughout the subcritical phase, then P(R n) exp(n) for some > 0. This implies the exponential decay of the two-point correlation function of subcritical Potts models, subject to a hypothesis of (at least) polynomial decay of this function. Similar results are known already for percolation and Ising models, and for Potts models when the number q of available states is suuciently large; indeed the hypothesis of polynomial decay has been proved rigorously for these cases. In two dimensions, the hypothesis that E(R) < 1 is weaker than requiring that the susceptibility be nite, i.e., that the two-point function be summable. The principal new technique is a form of Russo's formula for random-cluster models reported by Bezuidenhout, Grimmett, and Kesten. For the current application, this leads to an analysis of a rst-passage problem for random-cluster models, and a proof that the associated time constant is strictly positive if and only if the tail of R decays exponentially.
Jumping on the Train of Personalized Medicine: A Primer for Non-Geneticist Clinicians: Part 2. Fundamental Concepts in Genetic Epidemiology

With the decrease in sequencing costs, personalized genome sequencing will eventually become common in medical practice. We therefore write this series of three reviews to help non-geneticist clinicians to jump into the fast-moving field of personalized medicine. In the first article of this series, we reviewed the fundamental concepts in molecular genetics. In this second article, we cover the key concepts and methods in genetic epidemiology including the classification of genetic disorders, study designs and their implementation, genetic marker selection, genotyping and sequencing technologies, gene identification strategies, data analyses and data interpretation. This review will help the reader critically appraise a genetic association study. In the next article, we will discuss the clinical applications of genetic epidemiology in the personalized medicine area.
Children as researchers : exploring issues and barriers in English primary schools

This thesis identifies and explores the issues and barriers that appear to influence children's and adults' experiences of children's engagement in self-directed empirical research in five English primary schools associated with the Children's Research Centre at The Open University. As far as is known, this is the first in-depth study of children as independent researchers in the context of English primary schools. A flexible, multimethod research design was adopted. Predominantly qualitative data was generated through focus groups held with, and questionnaires distributed to, the young researchers and their peers and through individual unstructured interviews with adults. The qualitative data generated through these methods was analysed in the style of Grounded Theory (Glaser and Strauss, 1967; Strauss and Corbin, 1998). Quantitative data was subject to exploratory data analysis. This complemented and informed the qualitative analyses. The central categories which emerged from the data and, in particular, the identification of important issues by the children, have together informed the staged construction of a new model. This model illustrates the factors and processes that had an impact on both the children's experiences of research training and the research process and outcomes. The model demonstrates that these are inextricably interrelated. It is hoped that consideration of the issues and barriers identified will provide a basis for the further implementation and evaluation of young researcher initiatives in schools. The findings of the study have been drawn on to make recommendations for policy, practice and future research, particularly in those areas which are identified as significant by, and to, the children involved. It is also hoped that this study will address a gap in our knowledge and understanding of children as researchers and inform critical debate concerning children's voice and participation, adult-child power relationships and children's rights in English primary schools and more widely.
Institutional Origin: Labor Market Signaling in Higher Education

In response to the need for further research on promotion and tenure decisions, this study examined one of the criteria used in these decisions: inbreeding. Based on an analysis of the academic marketplace modifying Spence’s theory of job market signaling behavior, the following research hypothesis guided the study: female inbred faculty have patterns of productivity that are significantly different from the patterns of productivity of male inbred faculty. Significant differences between the groups in the study were found, including the major finding that inbred women are more productive in traditional areas than inbred men.
Robust Optimization: Design in MEMS

Robust Optimization: Design in MEMS by Peter Josef Sedivec Master of Science, Plan II in Mechanical Engineering University of California, Berkeley Professor Andrew Packard, Chair This report introduces a robust design technique for micro-electro-mechanical systems (MEMS) subject to inherent geometric and material uncertainties. Although design has played an important role in MEMS development, little has been done to account for the uncertainties associated with MEMS fabrication. Current fabrication techniques have poor dimensional tolerances and material properties at the microscale are not well characterized. The robust design problem we pose is to minimize the expected variance between the actual and target system performance. After a few assumptions, the robust design problem can be written as a constrained minimization. We consider a subset of these problems and design an algorithm to minimize rational polynomial functions subject to polynomial inequality constraints. In this report we give a detailed outline of the algorithm, verify its performance on two standard optimization test problems. Finally, we conclude with two MEMS design problems that illustrate our robust design technique and optimization algorithm. These examples show that the robust designs nominally meet the target performance and are significantly less sensitive to geometric uncertainties than typical designs.
Indices for bioavailability and biotransformation potential of contaminants in soils

Bioavailability is an important consideration in risk assessment of soil contaminants and in the selection of appropriate remediation technologies for polluted sites. The present study examined the bioavailability and biodegradation potential of phenanthrene with respect to a pseudomonad in 15 different soils through separate measurements of mineralization, transformation, and desorption to a polymeric infinite sink (Tenax®) after 180‐d sterile pre‐equilibration with phenanthrene. Fractions strongly resistant to desorption and mineralization at long times were evident in all cases. After correcting for bioconversion (moles mineralized per mole transformed) determined in aqueous particle‐free soil extracts, a correlation was found between the biotransformation‐resistant fraction and the Tenax desorption‐resistant fraction. Indices are proposed to assess bioavailability (BAt) and biotransformation potential (BTPt) of a compound in a soil based on parallel desorption and degradation studies over a selected period t. The BAt is the ratio of moles biotransformed to moles desorbed to an infinite sink, and it reflects the biotransformation rate relative to the maximal desorption rate. Values of BA30 (30‐d values) ranged from 0.64 (for dark gray silt loam) to 1.12 (Wurtsmith Air Force Base [AFB] 2B, Oscoda, MI, USA). The BTPt is the ratio between moles biotransformed and moles of contaminant remaining sorbed after maximal desorption. The BTPt provides an indication of the maximum extent of biotransformation that may be expected in a system, assuming desorption is a prerequisite for biodegradation. Values of BTP30 ranged between 0.3 (Wurtsmith AFB 1B) and 13 (Mount Pleasant silt loam, NY, USA). The combination of BAt and BTPt provides insights regarding the relationship between physical availability (desorption) and biological processes (biotransformation kinetics, toxicity, other soil factors) that occur during biodegradation and are suggested to represent the remediation potential of the chemical. The BA30 values less than 0.9 and BTP30 values less than five indicate poor potential for site remediation.
Variable presence of 5-methylcytosine in commercial RNA and DNA

Nucleoside methylations and other nucleic acid modifications have recently encountered a surge in interest, prompted, among other things, by the detection of methylation and active demethylation of DNA and mRNA by similar mechanisms. In DNA, deoxycytidine methylation by Dnmt enzymes generates 5-methyldeoxycytidine,1 an important epigenetic mark that typically causes inactivation of transcription of the methylated promoter region. Recent exciting developments have shown that these marks are not concrete-cast, but can be actively removed by the oxidative action of TET enzymes,2 which generate, through a series of 2-electron oxidations, first hydroxymethylcytidine (hm5C), then formyldeoxycytidine (f5C),3 and finally carboxydeoxycytidine (ca5C), which may eventually regenerate deoxycytidine by decarboxylation. The apparent functional homolog in mRNA is m6A, which appears to reduce translation efficiency. Here, too, the methylation can be removed by TET-related enzymes generating first hydroxymethyladenosine (hm6A), then formyladenosine (f6A). 4,5,6 Also, the presence of 5-methylcytidine in mRNA has been reported early on, and has recently raised renewed interest, although its function is as yet unclear and putative conversion into hydroxymethylcytidine is yet to be demonstrated.32 These developments are enhanced by the development of highly sensitive detection methods7,8 including the adaptation of the so-called bisulfite sequencing from DNA, where it is well established,9 to RNA, where its application has significantly contributed to the present high level of interest.10,11,12 However, bisulfite sequencing alone does not yield unassailable results13,14 and we have thus looked to expand the limits of detection of m5C in both DNA and RNA by LC-MS/MS. Here we report a straightforward regimen that provides values for the limit of quantification (LOQ) in the triple digit attomol range. Its application to presumed negative controls, namely synthetic oligonucleotides, surprisingly detected significant amounts of m5C in both types of synthetic nucleic acids.