Miracle-dz/UniFAR-FTUs huggingface dataset:
Definition of a domain of GLVR1 which is necessary for infection by gibbon ape leukemia virus and which is highly polymorphic between species

Expression of human GLVR1 in mouse cells confers susceptibility to infection by gibbon ape leukemia virus (GALV), while the normally expressed mouse Glvr-1 does not. Since human and murine GLVR1 proteins differ at 64 positions in their sequences, some of the residues differing between the two proteins are critical for infection. To identify these, a series of hybrids and in vitro-constructed mutants were tested for the ability to confer susceptibility to infection. The results indicated that human GLVR1 residues 550 to 551, located in a cluster of seven of the sites that differ between the human and mouse proteins, are the only residues differing between the two which must be in the human protein form to allow infection. Sequencing of a portion of GLVR1 from the rat (which is infectible) confirmed the importance of this cluster in that it contained the only notable differences between the rat and mouse proteins. This region, which also differs substantially between the rat and the human proteins, therefore exhibits a pronounced tendency for polymorphism.
SILENT: serialized low energy transmission coding for on-chip interconnection networks

On-chip source-synchronous serial communication has many advantages over multi-bit parallel communication in the aspects of skew, crosstalk area cost, wiring difficulty, and clock synchronization. However, the serial wire tends to dissipate more energy than parallel bus due to the bit multiplexing. We propose a coding method to reduce the transmission energy of the serial communication by minimizing the number of transitions on the serial wire. We demonstrate the significant energy saving in a multimedia application, 3D graphics. We also apply the coding technique to a CMOS SoC implementation which integrates various processing units with packet switched on-chip networks.
The Application of Genomics to Emerging Zoonotic Viral Diseases

Interspecies transmission of pathogens may result in the emergence of new infectious diseases in humans as well as in domestic and wild animals. Genomics tools such as high-throughput sequencing, mRNA expression profiling, and microarray-based analysis of single nucleotide polymorphisms are providing unprecedented ways to analyze the diversity of the genomes of emerging pathogens as well as the molecular basis of the host response to them. By comparing and contrasting the outcomes of an emerging infection with those of closely related pathogens in different but related host species, we can further delineate the various host pathways determining the outcome of zoonotic transmission and adaptation to the newly invaded species. The ultimate challenge is to link pathogen and host genomics data with biological outcomes of zoonotic transmission and to translate the integrated data into novel intervention strategies that eventually will allow the effective control of newly emerging infectious diseases.
Morphological Annotation of Quranic Arabic

The Quranic Arabic Corpus (http://corpus.quran.com) is an annotated linguistic resource with multiple layers of annotation including morphological segmentation, part-of-speech tagging, and syntactic analysis using dependency grammar. The motivation behind this work is to produce a resource that enables further analysis of the Quran, the 1,400 year old central religious text of Islam. This paper describes a new approach to morphological annotation of Quranic Arabic, a genre difficult to compare with other forms of Arabic. Processing Quranic Arabic is a unique challenge from a computational point of view, since the vocabulary and spelling differ from Modern Standard Arabic. The Quranic Arabic Corpus differs from other Arabic computational resources in adopting a tagset that closely follows traditional Arabic grammar. We made this decision in order to leverage a large body of existing historical grammatical analysis, and to encourage online collaborative annotation. In this paper, we discuss how the unique challenge of morphological annotation of Quranic Arabic is solved using a multi-stage approach. The different stages include automatic morphological tagging using diacritic edit-distance, two-pass manual verification, and online collaborative annotation. This process is evaluated to validate the appropriateness of the chosen methodology.
The Oracle Problem in Software Testing: A Survey

Testing involves examining the behaviour of a system in order to discover potential faults. Given an input for a system, the challenge of distinguishing the corresponding desired, correct behaviour from potentially incorrect behavior is called the “test oracle problem”. Test oracle automation is important to remove a current bottleneck that inhibits greater overall test automation. Without test oracle automation, the human has to determine whether observed behaviour is correct. The literature on test oracles has introduced techniques for oracle automation, including modelling, specifications, contract-driven development and metamorphic testing. When none of these is completely adequate, the final source of test oracle information remains the human, who may be aware of informal specifications, expectations, norms and domain specific information that provide informal oracle guidance. All forms of test oracles, even the humble human, involve challenges of reducing cost and increasing benefit. This paper provides a comprehensive survey of current approaches to the test oracle problem and an analysis of trends in this important area of software testing research and practice.
A Framework for Shared Leadership.

Some students seem to understand that the classroom and school communities are in the business of learning together. For instance, when our 9-year-old grandson, Dylan, completes his own work, he observes how other students are progressing. He voluntarily goes to the desks of other students and assists them. Shannon, our 10-year-old granddaughter, serves as a peer mediator at her school in Colorado, helping other students work out solutions to their conflicts.
Optimizing TBox and ABox Reasoning with Pseudo Models

This paper investigates optimization techniques and data structures exploiting the use of so-called pseudo models . These techniques are applied to speed-up TBox and ABox reasoning for the description logic ALCNHR+. The advances are demonstrated by an empirical analysis using the description logic system RACE that implements TBox and ABox reasoning for ALCNHR+.
Subdivision Analysis of the Trilinear Interpolant

Isosurfaces are fundamental volumetric visualization tools and are generated by approximating contours of trilinearly interpolated scalar fields. While a complete set of cases has recently been published by Nielson, the formal proof that these cases are the only ones possible and that they are topologically correct is difficult to follow. We present a more straightforward proof of the correctness and completeness of these cases based on a variation of the Dividing Cubes algorithm. Since this proof is based on topological arguments and a divide-and-conquer approach, this also sets the stage for developing tessellation cases for higher order interpolants and the quadrilinear interpolant in four dimensions. We also demonstrate that apart from degenerate cases, Nielson's cases are, in fact, subsets of two basic configurations of the trilinear interpolant.
Fast Recovery from Dual Link Failures in IP Networks

This paper develops a novel mechanism for recover- ing from dual link failures in IP networks. The highlight of the developed routing approach is that a node re-routes a packet around the failed link without the knowledge of the second link failure. The proposed technique requires three protection addresses for every node, in addition to the normal address. Associated with every protection address of a node is a protection graph. Each link connected to the node is removed in at least one of protection graphs and every protection graph is guaranteed to be two-edge connected. The network recovers from the first failure by tunneling the packet to the next-hop node using one of the protection addresses of the next-hop node; and the packet is routed over the protection graph corresponding to that protection address. We prove that it is sufficient to provide up to three protection addresses per node to tolerate any arbitrary two link failures in a three-edge connected graph. We evaluate the effectiveness of the proposed technique over several network topologies. network recovers from the first failure using IP-in-IP tunneling (RFC2003) using one of the "protection addresses" of the next node in the path. Packets destined to the protection address of a node are routed over a protection graph where the failed link is not present. Every protection graph is guaranteed to be two-edge connected by construction, hence is guaranteed to tolerate another link failure. We develop an elegant technique to compute the protection graphs at a node such that each link connected to the node is removed in at least one of protection graphs, and every protection graph is two-edge connected. The highlight of our approach is that we prove that every node requires at most three protection graphs. The rest of the paper is organized as follows: Section II surveys the techniques developed for fast recovery from single link failures. Section III describes the network model. Sec- tion IV describes our approach for dual link failure recovery, proves the requirement of up to three protection addresses per node, and discusses two different approaches to route using colored trees in the protection (auxiliary) graphs. We evaluate the effectiveness of the proposed approach on several networks and present our results in Section V. Our conclusions are presented in Section VI.
Describing the Cognitive Complexity of Counselors-in-Training Enrolled in a Group Dynamics and Methods Course

Research supports the link between higher levels of cognitive complexity and counseling efficacy. Counselor educators, therefore, strive to promote higher levels of cognitive complexity in different areas of counselor preparation, such as individual counseling and multicultural training. Presently, the research literature lacks studies focused on cognitive complexity in group work training. To address this gap in the literature, this study used content analysis, a qualitative methodology to describe cognitive complexity of 10 counselors-in-training enrolled in a Group Dynamics and Methods course. Using Bloom’s Cognitive Taxonomy to analyze participants’ written reflection assignments, I found that participants demonstrated cognitive complexity primarily in knowledge through application levels. Several categories/themes emerged from a separate analysis, including leader styles/techniques, norms, activities, and sharing/disclosing. I discuss these findings and highlight key aspects of the findings in relation to the broader literature. I identify implications for counselor educators and suggest future studies for counselor education researchers.
SNP Array Karyotyping Allows for the Detection of Uniparental Disomy and Cryptic Chromosomal Abnormalities in MDS/MPD-U and MPD

We applied single nucleotide polymorphism arrays (SNP-A) to study karyotypic abnormalities in patients with atypical myeloproliferative syndromes (MPD), including myeloproliferative/myelodysplastic syndrome overlap both positive and negative for the JAK2 V617F mutation and secondary acute myeloid leukemia (AML). In typical MPD cases (N = 8), which served as a control group, those with a homozygous V617F mutation showed clear uniparental disomy (UPD) of 9p using SNP-A. Consistent with possible genomic instability, in 19/30 MDS/MPD-U patients, we found additional lesions not identified by metaphase cytogenetics. In addition to UPD9p, we also have detected UPD affecting other chromosomes, including 1 (2/30), 11 (4/30), 12 (1/30) and 22 (1/30). Transformation to AML was observed in 8/30 patients. In 5 V617F+ patients who progressed to AML, we show that SNP-A can allow for the detection of two modes of transformation: leukemic blasts evolving from either a wild-type jak2 precursor carrying other acquired chromosomal defects, or from a V617F+ mutant progenitor characterized by UPD9p. SNP-A-based detection of cryptic lesions in MDS/MPD-U may help explain the clinical heterogeneity of this disorder.
Carbon black and lung cancer: Testing a new exposure metric in a German cohort.

BACKGROUND A cohort mortality study of a large carbon black production plant in Germany showed an elevation in lung cancer mortality (SMR 1.81 (95% CI: 1.34-2.39)), although the elevation could not be linked to exposure to carbon black. METHODS In follow up to a British study of carbon black production workers [Sorahan et al., 2007] in which risk of lung cancer progressively declined after cessation of employment-in contrast to an expected upward trend-we evaluated the German cohort with a similar methodology, that is, by focusing on the first 15 years after leaving employment in terms of lung cancer SMR. RESULTS In our SMR analysis of the German cohort of 1,528 men and an inception cohort of 1,271 men, distinctly different results from the British cohort were observed. We observed a rising trend in lung cancer SMR, in contrast to the declining SMR trend noted in the British cohort. In fact, Cox models for lung cancer mortality with attained age as the basic time variable showed negative coefficients for the full and inception cohorts. CONCLUSIONS Our analysis of a large German cohort of carbon black workers does not support the concept of a declining risk of lung cancer following cessation of employment.
Accelerating universe in scalar tensor models – comparison of theoretical predictions with observations

Aims. To study the possibility of the appearance of an accelerated universe in scalar tensor cosmological models. Methods. We consider scalar tensor theories of gravity assuming that the scalar field is not minimally coupled with gravity. We use this theory to study evolution of a flat homogeneous and isotropic universe. In this case the dynamical equations can be derived form a point-like Lagrangian. We study the general properties of dynamics of this system and show that for a wide range of initial conditions such models lead in a natural way to an accelerated phase of expansion of the universe. Assuming that the point-like Lagrangian admits a Noether symmetry, we are able to explicitly solve the dynamical equations. Results. We study one particular model and show that its predictions are compatible with observational data, namely the publicly available data on type Ia supernovae, the parameters of large scale structure determined by the 2-degree Field Galaxy Redshift Survey (2dFGRS), the measurements of cosmological distances with the Sunyaev-Zel’dovich effect and the rate of growth of density perturbations. This model produces in a natural way an epoch of accelerated expansion. With an appropriate choice of parameters our model is fully compatible with several observed characteristics of the universe.
Prophylactic efficacy of lithium carbonate in manic-depressive illness. Report of the Veterans Administration and National Institute of Mental Health collaborative study group.

In an 18 hospital study, 205 patients hospitalized with a diagnosis of manic-depressive illness, manic type, were treated upon discharge with lithium carbonate or placebo for a two-year period. Lithium carbonate was significantly more effective than placebo in preventing relapses (ie, affective episodes severe enough to require hospitalization or use of nonstudy drugs). The difference in treatment outcome between lithium carbonate and placebo was due mainly to the lower incidence of manic relapses on lithium carbonate. Patients on lithium carbonate also had a lower incidence of depressive relapses than patients on placebo but the limited incidence of severe depression in this sample makes it difficult to draw any conclusions regarding the prophylactic efficacy of lithium carbonate in depressive illness. The results from this trial coupled with those from other studies indicate that lithium carbonate combined with regular clinical appraisals is a safe and effective treatment for preventing relapse in manic-depressive illness.
Comparison of Digestion Methods for the Determination of Metal Levels in Soils in Itakpe, Kogi State, Nig eria

The analysis of agricultural soil of Itakpe, Kogi S tate, Nigeria to ascertain levels of concentration of total metal co ntent of cadmium, copper, magnesium, nickel, lead and zinc and comparison of digestion methods , using % extractability was carried out by use of atomic abs orption spectroscopy technique. The digestion methods used were HNO 3, HCl and different combinations of acids (HClO 4, HCl, HNO 3 and HF). Results show that the concentration values obtained were as follows: Cd ranged 0.17-0.36, Cu ranged 0.0 8-1.09, Mg ranged 0.04-0.13, Ni ranged 0.04-0.12, Pb ranged 0.05-0.42 and Zn 0.0 4-0.11 µg/g. The most efficient digestion methods are the combination of HNO 3, and HCl (1:3) (aquaregia) and HCl. The combination of HNO 3, HClO 4 and HF (3:2:1) is most efficient for Cd extraction; HNO 3, combination of HNO 3, HClO 4 and HF (3:2:1), HCl and combination of HClO 4 and HF (1:5) were most efficient for Cu extraction ; HNO 3 and HCl were most efficient for Mg extraction; combinat ion of HClO 4 and HF (1:5) were most efficient for Ni; combination of HNO 3, HClO 4 and HF (3:2:1), combination of HNO 3 and HCl (1:3), HCl and combination of HClO 4 and HF (1:5) were most efficient for Pb and most efficient for Z n combination of HNO 3, HClO 4 and HF (3:2:1), combination of HNO 3 and HCl (1:3), and combination of HClO 4 and HF (1:5). The possible reasons for variation in % extractability of some metals are given.
The Life Cycle of Alumni Donations

It is common knowledge that “old grads” are more generous than young alumni and that donations are higher for reunion-year classes than for others, but what is the quantitative impact of these factors? This paper studies life cycle and reunion-year effects on participation rates and gift size using a 73,000-gift sample over a ten-year period to a small state university. The author estimates time patterns of the life cycles by means of regression equations, whose potential use he demonstrates by simulations.
Canonical Wnt signaling is required for development of embryonic stem cell-derived mesoderm

Formation of mesoderm from the pluripotent epiblast depends upon canonical Wnt/β-catenin signaling, although a precise molecular basis for this requirement has not been established. To develop a robust model of this developmental transition, we examined the role of Wnt signaling during the analogous stage of embryonic stem cell differentiation. We show that the kinetics of Wnt ligand expression and pathway activity in vitro mirror those found in vivo. Furthermore, inhibition of this endogenous Wnt signaling abrogates the functional competence of differentiating ES cells, reflected by their failure to generate Flk1+ mesodermal precursors and subsequent mature mesodermal lineages. Microarray analysis at various times during early differentiation reveal that mesoderm- and endoderm-associated genes fail to be induced in the absence of Wnt signaling, indicating a lack of germ layer induction that normally occurs during gastrulation in vivo. The earliest genes displaying Wnt-dependent expression, however, were those expressed in vivo in the primitive streak. Using an inducible form of stabilized β-catenin, we find that Wnt activity, although required, does not autonomously promote primitive streak-associated gene expression in vitro. Our results suggest that Wnt signaling functions in this model system to regulate the thresholds or stability of responses to other effector pathways and demonstrate that differentiating ES cells represent a useful model system for defining complex regulatory interactions underlying primary germ layer induction.
Detecting and visualizing inter-worksheet smells in spreadsheets

Spreadsheets are often used in business, for simple tasks, as well as for mission critical tasks such as finance or forecasting. Similar to software, some spreadsheets are of better quality than others, for instance with respect to usability, maintainability or reliability. In contrast with software however, spreadsheets are rarely checked, tested or certified. In this paper, we aim at developing an approach for detecting smells that indicate weak points in a spreadsheet's design. To that end we first study code smells and transform these code smells to their spreadsheet counterparts. We then present an approach to detect the smells, and to communicate located smells to spreadsheet users with data flow diagrams. To evaluate our apporach, we analyzed occurrences of these smells in the Euses corpus. Furthermore we conducted ten case studies in an industrial setting. The results of the evaluation indicate that smells can indeed reveal weaknesses in a spreadsheet's design, and that data flow diagrams are an appropriate way to show those weaknesses.
Unraveling the dynamics of community-associated methicillin-resistant Staphylococcus aureus.

Since the first description of the community-associated methicillin-resistant Staphylococcus aureus (CA-MRSA) strain USA300 [1] in the 1990s, this pathogen has emerged worldwide [2]. Within a decade, USA300 has become the most prevalent cause of community-acquired S. aureus infections in many settings in the United States [3]. Originally causing infections mainly in individuals without recent healthcare exposure, USA300 is increasingly causing hospital-acquired infections. There is, therefore, an urgent need for infection control measures. Although person-to-person transmission in the community must be the driving force of this epidemic [4], transmission dynamics and risk factors for colonization are still not well understood [5]. The study of Popovich et al in this issue of Clinical Infectious Diseases [6] is a next step in elucidating the dynamics of USA300. In their study they demonstrate that, compared to individuals not infected with human immunodeficiency virus (HIV), patients with HIV are more likely to be colonized with USA300 at hospital admission and that they are carrying USA300 at multiple body sites, such as the nares, throat, axillae, inguinal regions, and perirectal area, and in wounds, if present. Importantly, 38.5% of the USA300 carriers would have remained undetected if only nasal cultures had been obtained. This study emphasizes 2 important aspects in the transmission dynamics of USA300.