Miracle-dz/UniFAR-FTUs huggingface dataset:
Ki-67 protein concentrations in urothelial bladder carcinomas are related to Ki-67-specific RNA concentrations in urine.

The Ki-67 protein is a nuclear and nucleolar protein that is strictly associated with cell proliferation. Recently it has been suggested to play a role in the control of the higher order chromatin structure (1). Because the protein is produced only in dividing cells, the anti Ki-67 antibody MIB-1 has been widely used in histopathologic studies to estimate the growth fraction of human neoplastic tissue samples in situ. For a variety of human tumors, including bladder carcinomas, the Ki-67 labeling index has been shown to be of prognostic value for tumor recurrence and for patient survival (2)(3)(4). We investigated whether Ki-67 RNA in total urine of bladder tumor patients is correlated with the Ki-67 labeling index of the corresponding tumor tissue. Spontaneously voided clean-catch urines from 68 patients were collected with informed consent, stored at 4 °C, and processed within 4 h of collection. Approval was obtained from the Ethikkommission of the University of Luebeck. Three groups of patients were included: ( a ) healthy donors (n = 14); ( b ) patients with urinary tract infection as detected by analysis of urine sediment (n = 28); and ( c ) patients with bladder carcinoma (n = 26). All urine samples from patients with tumors were checked for significant bacteriuria or leukocyturia (>10/μL) as well as for the presence of erythrocytes (>10/μL). The specific weights of all urine samples were in the range 1.010–1.015 kg/L, showing that there were no major differences in urine concentration. After routine diagnostics were completed, 1 mL of urine was mixed 1:1 with lysis buffer [5.64 mol/L guanidinium thiocyanate, 5 g/L sarcosyl, 50 mmol/L sodium acetate (pH 6.5), 1 mmol/L β-mercaptoethanol], the pH was adjusted to 7 by addition of 1.5 mol/L HEPES (pH 8.0), and samples were frozen at −80 °C until RNA extraction was performed. …
The Footnote: A Curious History

Preface Acknowledgments 1. Footnotes: The Origin of a Species 2. Ranke: A Footnote about Scientific History 3. How the Historian Found His Muse: Ranke's Path to the Footnote 4. Footnotes and Philosophie: An Enlightenment Interlude 5. Back to the Future, 1: De Thou Documents the Details 6. Back to the Future, 2: The Antlike Industry of Ecclesiastical Historians and Antiquaries 7. Clarity and Distinctness in the Abysses of Erudition: The Cartesian Origins of the Modern Footnote Epilogue: Some Concluding Footnotes Index
Façade apertures optimization: integrating cross-ventilation performance analysis in fluid dynamics simulation

Performance-oriented design has as a primary aim to introduce spaces that achieve acceptable levels of human comfort. Wind-induced airflow plays a significant role in the improving occupants' comfort in a building. This paper explores the extent to which simulation of natural airflow can potentially be a contributing parameter in the conception of performance-aware designs. Testing the natural ventilation performance of a pavilion, the study employs Fast Fluid Dynamics simulation. A performance analysis is conducted, whereby an array of automated feedback loops carried out by a genetic algorithm can produce a number of acceptable solutions as regards the optimization of facades' openings. The experimentation conducted proves the ability of the model to yield design instances that fulfill a number of environmental criteria related to airflow and human comfort. In this light, the paper suggests that the aforementioned method can be used as an experimentation platform to influence the direction a designer may take when considering a design proposal.
Identification of distinct quantitative trait Loci affecting length or weight variability at birth in humans.

CONTEXT The variability of human fetal growth is multifactorial. Twin and family studies demonstrate that genetic determinants influence normal fetal growth, but the responsible genetic polymorphisms are unknown. OBJECTIVE The objective of the study was the mapping of quantitative trait loci (QTLs) for birth length and weight. DESIGN AND METHODS To approach the genetic factors implicated in the normal variation of birth length and weight, we conducted a genome-wide approach of these two quantitative traits in 220 French Caucasian pedigrees (412 sibling pairs) using a variance components method. RESULTS We observed evidence for several QTLs influencing birth length or birth weight independently. Whereas birth length and weight showed a close correlation (r = 0.76, P < 0.0001), their genetic variability appeared largely determined by distinct genomic loci. Birth length was influenced by two major QTLs located in 2p21 and 2q11 (LOD scores 2.69 and 3.57). The variability of birth weight was linked to another QTL on 7q35 (LOD score 3.1). Several other regions showed more modest evidence for linkage with LOD score values of 1-2 on chromosomes 7, 8, 10, 13, and 17 for birth length and chromosomes 1, 2, 6, 8, 10, 13, 14, 15, 17, and 20 for birth weight. CONCLUSION These preliminary QTLs provide a first step toward the identification of the genomic variants involved in the variability of human fetal growth. Our results should, however, be considered preliminary until they are replicated in other studies.
A compressing method for genome sequence cluster using sequence alignment

After identifying the function of a protein, biologists produce new useful proteins by substituting some residues of the identified protein. These new proteins have high sequence homology (similarity). We define a sequence cluster as a cluster that is constituted of similar sequences. As another example of a sequence cluster, we consider a SNP (single nucleotide polymorphism) cluster. A SNP is a DNA sequence variation occurring when a single nucleotide in the genome (or other shared sequence) differs between members of a species (or between paired chromosomes in an individual). We suggest a new compressing technique for these sequence clusters using a sequence alignment method. We select a representative sequence which has a minimum sequence distance in the cluster by scanning distances of all sequences. The distances are obtained by calculating a sequence alignment score. The result of this sequence alignment is utilized to author conversion information called an edit-script between the two sequences. We only stored representative sequences and edit-scripts of each cluster into a database. Member sequences of each cluster can then be easily created using representative sequences and edit-scripts.
ICFHR 2012 Competition on Automatic Forensic Signature Verification (4NsigComp 2012)

This paper presents the results of the ICFHR2012 Competition on Automatic Forensic Signature Verification jointly organized by PR-researchers and Forensic Handwriting Examiners (FHEs). The aim is to bridge the gap between recent technological developments and forensic casework. A forensic like training set containing disguised signatures along with skilled forgeries and genuine signatures was provided to the participants. They were motivated to report the results in Likelihood Ratios (LR). This has made the systems even more interesting for application in forensic casework. For evaluation we used both the traditional Equal Error Rate (EER) and forensically substantial Cost of Log Likelihood Ratios (Ĉllr). The system having the best Minimum Cost of Log Likelihood Ratio ( Ĉllrmin) is declared winner. Various experiments both including and excluding disguised signatures from the test set are reported.
Navigating the wards: teaching medical students to use their moral compasses

The upsurge in formal medical ethics training stems from the desire for more compassionate, less “dehumanized” physicians who can competently face the ethical dilemmas posed by technologic advances and resource constraints. How best to encourage ethical thinking and behavior among medical students remains an open question. However, the authors argue that medical ethics education suffers from an overreliance on strategies that target ethical thinking, with relative inattention to students as ethical actors in specific clinical contexts. In order to produce ethically competent physicians, medical educators must not only teach students to understand and learn from the dilemmas that shape their moral world but also train them to respond to those dilemmas appropriately. The authors discuss current practices in ethics education and how traditional approaches may not equip students with the types of moral “navigating skills” they need to become ethical physicians. They illustrate how medical students can and do learn norms of ethical behavior on the wards and argue why medical education ought to focus more explicitly on this aspect of clinical training. They conclude by recommending ways medical educators can encourage ethical thinking and behavior throughout the entire course of medical training.
An overview of achieving energy efficiency in on-chip networks

Due to the increasing bandwidth demand for the network-on-chip (NoC), interconnection networks become a dominant source of energy consumption in systems-on-chip (SoCs) and chip multi processors (CMPs). Therefore, energy efficient NoC is key to a successful SoC development. This paper presents an overview of different techniques to achieve energy efficiency at the different levels of NoC design including: a) component level where dynamic voltage scaling (DVS) and dynamic link shutdown (DLS) techniques are reviewed; b) circuit level, e.g., voltage swinging of signals; c) architectural level, where specialised tools, such as Wattch and Orion are discussed. We also summarise research on thermal optimisation issues. To the best of our knowledge, this is the first survey of recent research results on the area.
Training with Computer-Supported Motor Imagery in Post-Stroke Rehabilitation

Converging lines of evidence suggest that motor imagery (the mental simulation of a motor act within working memory) is associated with subliminal activation of the motor system. This observation has led to the hypothesis that cortical activation during motor imagery may affect the acquisition of specific motor skills and help the recovery of motor function. In this paper, we describe a clinical protocol in which we use interactive tools to stimulate motor imagery in hemiplegic stroke patients, thereby helping them to recover lost motor function. The protocol consists of an inpatient and an outpatient phase, combining physical and mental practice. In the inpatient phase, patients are trained in a laboratory setting, using a custom-made interactive workbench (VR Mirror). After discharge, patients use a portable device to guide mental and physical practice in a home setting. The proposed strategy is based on the hypotheses that: (a) combined physical and mental practice can make a cost-effective contribution to the rehabilitation of stroke patients, (b) effective mental practice is not possible without some form of support, from a therapist (as in our inpatient phase) or from technology (as in the outpatient phase), (c) the inclusion of an outpatient phase will allow the patient to practice more often than would otherwise be possible, therefore increasing the speed and/or effectiveness of learning, and (d) the use of interactive technology will reduce the patient's need for skilled support, therefore improving the cost-effectiveness of training.
Globally Coherent Text Generation with Neural Checklist Models

Recurrent neural networks can generate locally coherent text but often have difﬁculties representing what has already been generated and what still needs to be said – especially when constructing long texts. We present the neural checklist model , a recurrent neural network that models global coherence by storing and updating an agenda of text strings which should be mentioned somewhere in the output. The model generates output by dynamically adjusting the interpolation among a language model and a pair of attention models that encourage references to agenda items. Evaluations on cooking recipes and dialogue system responses demonstrate high coherence with greatly improved semantic coverage of the agenda.
Assessment using the P scales: best fit – fit for the purpose?

In this article, Andrew Martin, deputy headteacher at Greenside School in Stevenage, provides an outline of the development of the P scales as an assessment tool for pupils working below Level 1 of the National Curriculum. He recounts the difficulties his school found in using P scales to track pupil progress from year to year and describes and evaluates a computer package which he devised in order to fulfil this function. He goes on to discuss current issues in the use of P scales, many of which were highlighted through use of the computer package. These issues include inconsistency in the use of the P scales; variations in pupil profiles; difficulties over making ‘best fit’ judgements; the need for moderation; and relationships with other curriculum and assessment systems in the school years and in the Foundation Stage. Andrew Martin closes his article with a call for consistency in approaches to assessment, particularly in view of the fact that P scale assessments are to be collected as part of statutory end of key stage data collection arrangements in future.
Toward a framework for evaluating extreme programming

Software organizations are progressively adopting the development practices associated with the Extreme Programming (XP) methodology. Most reports on the efficacy of these practices are anecdotal. This paper provides a benchmark measurement framework for researchers and practitioners to express concretely the XP practices the organization has selected to adopt and/or modify, and the outcome thereof. The framework enables the necessary meta-analysis for combining families of case studies. The results of running framework-based case studies in various contexts will eventually constitute a body of knowledge of systematic, empirical evaluations of XP and its practices. Additionally,this benchmark provides a baseline framework that can be adapted for industrial case studies of other technologies and processes. To provide a foundation on the use of the framework, we present the initial validation of our XP evaluation framework based upon a year-long study of an IBM team that adopted a subset of XP practices.
Towards Enriching Linked Open Data via Open Information Extraction

The descriptions of various entities on Linked Data repositories are subject to constant renewals and modifications, with respect to both the descriptions of concepts and relations and entities realizing their instantiations. Thus, the underlying ontologies have to be updated accordingly in order to reflect these changes. This paper presents a system for examining the possibilities of discovering new relations and updating/verifying existing ones for entities described in Linked Data repositories by using Open Information Extraction techniques. These are applied to web content. The process aims to the enrichment of the examined datasets and the expansion of the ontologies with newly-discovered concepts and relations. Towards this target, the paper discusses the intricacies, pitfalls and challenges present.
SPARSE COMPONENT ANALYSIS FOR BLIND SOURCE SEPARATION WITH LESS SENSORS THAN SOURCES

A sparse decomposition approach of observed data matrix is presented in this paper and the approach is then used in blind source separation with less sensors than sources. First, sparse representation (factorization) of a data matrix is discussed. For a given basis matrix, there exist infinite coefficient matrices (solutions) generally such that the data matrix can be represented by the product of the basis matrix and coefficient matrices. However, the sparse solution with minimum1-norm is unique with probability one, and can be obtained by using linear programming algorithm. The basis matrix can be estimated using gradient type algorithm or Kmeans clustering algorithm. Next, blind source separation is discussed based on sparse factorization approach. The blind separation technique includes two steps, one is to estimate a mixing matrix (basis matrix in the sparse representation), the second is to estimate sources (coefficient matrix). If the sources are sufficiently sparse, blind separation can be carried out directly in the time domain. Otherwise, blind separation can be implemented in time-frequency domain after applying wavelet packet transformation preprocessing to the observed mixtures. Three simulation examples are presented to illustrate the proposed algorithms and reveal algorithms performance. Finally, concluding remarks review the developed approach and state the open problems for further studying.
Proving the adulteration of ewe and goat cheeses with cow milk using the reference method of isoelectric focusing of γ-casein.

One of the main problems in cheese production is the adulteration of cheese produced from ewe and goat milk with less expensive cow milk, the presence of which is however not stated on the product declaration. Cow milk is most often used to adulterate cheeses made from ewe and goat milk due to its lower price and availability throughout the year. The addition of cow milk does not only change the organoleptic properties of the final product, but also affects its quality related to its suitability in terms of health intolerance, and thus deceives the consumers (Spuergin et al., 1997; Borková and Snášelová, 2005). Furthermore, the adulteration of products creates Summary
Adenovirus Specific Pre-Immunity Induced by Natural Route of Infection Does Not Impair Transduction by Adenoviral Vaccine Vectors in Mice

Recombinant human adenovirus serotype 5 (HAd5V) vectors are gold standards of T-cell immunogenicity as they efficiently induce also humoral responses to exogenous antigens, in particular when used in prime-boost protocols. Some investigators have shown that pre-existing immunity to adenoviruses interferes with transduction by adenoviral vectors, but the actual extent of this interference is not known since it has been mostly studied in mice using unnatural routes of infection and virus doses. Here we studied the effects of HAd5V-specific immune responses induced by intranasal infection on the transduction efficiency of recombinant adenovirus vectors. Of interest, when HAd5V immunity was induced in mice by the natural respiratory route, the pre-existing immunity against HAd5V did not significantly interfere with the B and T-cell immune responses against the transgene products induced after a prime/boost inoculation protocol with a recombinant HAd5V-vector, as measured by ELISA and in vivo cytotoxic T-cell assays, respectively. We also correlated the levels of HAd5V-specific neutralizing antibodies (Ad5NAbs) induced in mice with the levels of Ad5NAb titers found in humans. The data indicate that approximately 60% of the human serum samples tested displayed Ad5NAb levels that could be overcome with a prime-boost vaccination protocol. These results suggest that recombinant HAd5V vectors are potentially useful for prime-boost vaccination strategies, at least when pre-existing immunity against HAd5V is at low or medium levels.
Wirelessly Powered Mobile Computation Offloading: Energy Savings Maximization

Achieving long battery lives or even self sustainability has been a long standing challenge for designing mobile devices. This paper seamlessly integrates two promising energy-saving technologies, namely mobile computation offloading (MCO) and microwave power transfer (MPT), and proposes a novel design framework of wirelessly powered MCO. Consider a single-user system where a base station (BS) either transfers power to or offloads computation from a mobile. Two mobile operation modes, namely local computation and offloading, are optimized separately for maximizing the mobile energy savings. For local computation, the non-convex problem of optimizing the CPU- cycle frequencies under the deadline and energy causality constraints is solved via convex relaxation. The optimal CPU- cycle frequencies are shown to have different forms depending on the BS transmission power. For offloading, the time duration before the deadline is divided for separate MPT and offloading and the optimal division is derived in a closed form. By combining above results, the optimal offloading decision is analyzed with respect to the deadline, data-input size and BS transmission power and validated by simulation.
TT2NE: a novel algorithm to predict RNA secondary structures with pseudoknots

We present TT2NE, a new algorithm to predict RNA secondary structures with pseudoknots. The method is based on a classification of RNA structures according to their topological genus. TT2NE is guaranteed to find the minimum free energy structure regardless of pseudoknot topology. This unique proficiency is obtained at the expense of the maximum length of sequences that can be treated, but comparison with state-of-the-art algorithms shows that TT2NE significantly improves the quality of predictions. Analysis of TT2NE's incorrect predictions sheds light on the need to study how sterical constraints limit the range of pseudoknotted structures that can be formed from a given sequence. An implementation of TT2NE on a public server can be found at http://ipht.cea. fr/rna/tt2ne.php.
Diagnosing depression in patients with physical diseases using the Beck Depression Inventory (BDI).

443 patients (21-74 yrs old) with a physical illness (355 with coronary heart disease and 88 with chronic pain), 150 unemployed persons (18-63 yrs old) and 623 people (30-59 yrs old) from the normal population in Jamtland, Sweden were tested using the Beck Depression Inventory (BDI). The aim of the study was to investigate whether scores on the physical and non-physical components of the BDI differed between patients and other groups, or if only the physical component was significantly higher in the patient group, and if that could be interpreted as symptomatic of physical disease and not of depression. The patients' scores were significantly higher than those of the other 2 groups on the physical component but only higher than the normal population sample on the non-physical component. This supports the idea that the items for physical symptoms in the BDI might be confounding when determining depression in patients with physical diseases. The non-physical component seems to be the best indicator of depression.
Teacher Dispositions for Effective Education in the Borderlands

Abstract Teacher dispositions, attitudes, and motivation play important roles in educating students so that they are highly successful in school. This is particularly true for students in borderland areas who frequently need to negotiate two cultures, two languages, and two worlds. Using grounded theory with extant data from Tijuana and San Diego-area teachers who participated in a border pedagogy training institute, characteristics that are critical to teacher dispositions—which can make significant differences in effectiveness with students in the borderlands—have been identified.