Miracle-dz/UniFAR-FTUs huggingface dataset:
Sequence Analysis of the Porcine Epidemic Diarrhea Virus Genome between the Nucleocapsid and Spike Protein Genes Reveals a Polymorphic ORF

Abstract In order to investigate the genome organization of the porcine epidemic diarrhea virus (PEDV) further, cDNA clones covering the region between the nucleocapsid and the spike (S) protein genes were independently constructed and sequenced for the two virulent isolates Br1/87 and CV777. Of the three major ORFs identified, two were found to encode the major and minor coronavirus membrane proteins M and sM. A potentially single ORF, designated ORF3 according to the pattern of the viral subgenomic mRNAs, could be identified between the S and sM genes. A striking variability, essentially generated by short deletions clustered in a few loci, was observed in the ORF3 of both isolates. The largest predicted polypeptide of 223 amino acids showed homology with polypeptides potentially encoded by other members of the same genetic subset, including two shorter polypeptides of human respiratory virus HCV 229E and one of transmissible gastroenteritis virus TGEV. This homology suggests that the two HCV ORFs may have originated from a single precursor. The function of these polypeptides is not known, but the predicted products of the PEDV ORF3 and related ORFs share features suggestive of a membrane-associated protein.
Chewing Gum Containing Citric Acid Reduces the Burden of Periodontal Pathogens

Objective: In a preliminary study, we noted that citric acid has the potency to induce human beta defensins (hBD-2) in salivary secretions. As hBDs are thought to ameliorate periodontal disease by suppressing key periodontal pathogens we developed a citric acid-containing chewing gum (CA-gum) to test this hypothesis. Here we report, the effect of CA-gum on three major periodontal pathogens Prevotella intermedia (Pi), Tannerella forsythia (Tf), Treponema denti- cola (Td) and Fusobacterium species (Fb). Methods: A randomized, double-blind, placebo-controlled trial with 61 individuals, was conducted over 14 days. Each subject was allowed to chew CA-gum (31 subjects) or placebo gum (30 subjects) at irregular intervals, but was instructed to eat at least three pieces of gum a day. None had active caries, symptoms of gingivitis or periodontal disease, smoking history, or concurrent medication. To determine the levels of oral carriage of the putative pathogens, saliva was collected from each subject by paraffin chewing in a standard manner and, the number of total cultivative microorganisms (CFUs) determined. Five key periodontal pathogens, Pg, Pi, Tf, Td and Fb present in saliva were determined quantitatively using real-time polymerase chain reaction (PCR) (BML Inc., Saitama, JAPAN). Results: Compared with the placebo chewing gum group the CA-gum group had significantly lower levels of Prevotella intermedia, Tannerella forsythia, and Fusobacterium spp. in their saliva. (Wilcoxon t-test; p 0.05).
Heart Rate during Conflicts Predicts Post-Conflict Stress-Related Behavior in Greylag Geese

Background Social stressors are known to be among the most potent stressors in group-living animals. This is not only manifested in individual physiology (heart rate, glucocorticoids), but also in how individuals behave directly after a conflict. Certain ‘stress-related behaviors’ such as autopreening, body shaking, scratching and vigilance have been suggested to indicate an individual's emotional state. Such behaviors may also alleviate stress, but the behavioral context and physiological basis of those behaviors is still poorly understood. Methodology/Principal Findings We recorded beat-to-beat heart rates (HR) of 22 greylag geese in response to agonistic encounters using fully implanted sensor-transmitter packages. Additionally, for 143 major events we analyzed the behavior shown by our focal animals in the first two minutes after an interaction. Our results show that the HR during encounters and characteristics of the interaction predicted the frequency and duration of behaviors shown after a conflict. Conclusions/Significance To our knowledge this is the first study to quantify the physiological and behavioral responses to single agonistic encounters and to link this to post conflict behavior. Our results demonstrate that ‘stress-related behaviors’ are flexibly modulated by the characteristics of the preceding aggressive interaction and reflect the individual's emotional strain, which is linked to autonomic arousal. We found no support for the stress-alleviating hypothesis, but we propose that stress-related behaviors may play a role in communication with other group members, particularly with pair-partners.
Med8, a subunit of the mediator CTD complex of RNA polymerase II, directly binds to regulatory elements of SUC2 and HXK2 genes.

In a search to identify new factors required for expression of SUC2 gene in Saccharomyces cerevisiae, we have partially purified a 27 kDa protein (p27) that bound both the DRSs of the HXK2 gene and the UASs of SUC2 gene. The amino terminal sequence of p27 identified the MED8 gene (open reading frame YBR193C), located in chromosome II of S. cerevisiae, as the gene coding for the protein. Disruption of this gene has demonstrated that is an essential gene for yeast growth. To determine whether the p27 protein represents the Med8 product, we expressed MED8 gene in E. coli and demonstrated that the heterologous synthesized protein specifically binds to both UASSUC2 and DRS2HXK2. This observation suggests that Med8 may be important for the coupling of the glucose repression pathway of SUC2 gene to the HXK2 gene expression. Med8 has been described as a mediator protein interacting with the CTD of the RNA polymerase II. Thus, the role of Med8 could be to act as coupling factor by linking activating and repressing transcription complexes to the RNA polymerase II holoenzyme transcriptional machinery.
Sharp bends with low losses in dielectric optical waveguides.

A new method is proposed for making sharp bends with low radiation losses in dielectric optical waveguides. By modifying the transverse refractive-index profile at curved sections both the pure bend and the transition losses can be minimized. The optimum gradient-index profile requires an inhomogeneous medium. But in practice this can be replaced by a layered medium. By using four homogeneous layers the permitted radius of curvature of a slab waveguide can be reduced, e.g., from 6400 to only 100 wavelengths.
Pivotal roles for eomesodermin during axis formation, epithelium-to-mesenchyme transition and endoderm specification in the mouse

The T-box transcription factor eomesodermin (Eomes) has been implicated as an important component in germ layer induction and patterning in vertebrate embryos. In the mouse, Eomes is essential for development of the trophectoderm lineage and Eomes loss-of-function mutants arrest at implantation. Here, we have used a novel Eomes conditional allele to test Eomes functions in the embryo proper. Eomes-deficient embryos express both Fgf8 and its downstream target Snail at normal levels but surprisingly fail to downregulate E-cadherin. Eomes functional loss thus efficiently and profoundly blocks EMT and concomitant mesoderm delamination. Marker analysis as well as fate-mapping and chimera studies demonstrate for the first time that Eomes is required for specification of the definitive endoderm lineage. We also describe developmental abnormalities in Eomes/Nodal double heterozygotes, and demonstrate that these phenotypes reflect Eomes and Nodal interactions in different tissue sites. Collectively, our experiments establish that Eomes is a key regulator of anteroposterior axis formation, EMT and definitive endoderm specification in the mouse.
Bidding Languages for Combinatorial Auctions

Combinatorial auctions provide a valuable mechanism for the allocation of goods in settings where buyer valuations exhibit complex structure with respect to substitutabilityand complementarity. Most algorithms are designed to work with explicit bids for concrete bundles of goods. However, logical bidding languages allow the expression of complex utility functions in a natural and concise way. We introduce a new, generalized language where bids are given by propositional formulae whose subformulae can be annotated with prices. This language allows bidder utilities to be formulated more naturally and concisely than existing languages. Furthermore, we outline a general algorithmic technique for winner determination for auctions that use this bidding language.
Incidence and determinants of lower extremity running injuries in long distance runners: a systematic review

The purpose of this study was to present a systematic overview of published reports on the incidence and associated potential risk factors of lower extremity running injuries in long distance runners. An electronic database search was conducted using the PubMed–Medline database. Two observers independently assessed the quality of the studies and a best evidence synthesis was used to summarise the results. The incidence of lower extremity running injuries ranged from 19.4% to 79.3%. The predominant site of these injuries was the knee. There was strong evidence that a long training distance per week in male runners and a history of previous injuries were risk factors for injuries, and that an increase in training distance per week was a protective factor for knee injuries.
Routine immunologic tests in systemic lupus erythematosus: is there a need for more studies?

OBJECTIVE To evaluate the sensitivity, specificity, and likelihood ratios of anti-dsDNA, C3, C4, and Clq binding tests for predicting flares in systemic lupus erythematosus (SLE) and to evaluate the conflicting results reported in the recent literature. METHODS Test results from 9 to 3 months preceding 83 flares among 53 patients from a cohort study of 202 patients with SLE were assessed for their ability to predict renal and nonrenal flares and all flares combined. A flare was defined as a 6 point rise in a modified SLE Disease Activity Index. RESULTS For all 4 tests, sensitivity approximated 50% and specificity was less than 75%. For anti-dsDNA, Clq binding, and C4, both positive and negative likelihood ratios were close to 1.0, suggesting little clinical value for routine testing. For C3, likelihood ratios for a positive test approximated 2.0, meeting the minimal level for clinical significance. Review of previous studies suggested that sample size, the use of a standardized disease activity measure to define a flare, the severity of the flare, and the study duration could not explain the discrepant results among studies. The 2 studies with testing every 4 to 6 weeks found that a rising anti-dsDNA predicted flares, while those with less frequent testing did not. CONCLUSION While our study provided no major support for routine testing with anti-dsDNA, C3, C4, or Clq binding, additional longitudinal studies are needed to assess monthly testing of anti-dsDNA as a predictor of flare in SLE.
Mitochondrial and nuclear genetic relationships among Pacific Island and Asian populations.

Mitochondrial and autosomal short tandem-repeat (STR) genetic distances among 28 Pacific Island and Asian populations are significantly correlated (r=.25, P<.01) but describe distinct patterns of relationships. Maternally inherited-mtDNA data suggest that Remote Oceanic Islanders originated in island Southeast Asia. In contrast, biparental STR data reveal substantial genetic affinities between Remote Oceanic Islanders and Near Oceanic populations from highland Papua New Guinea and Australia. The low correlation between maternal and biparental genetic markers from the same individuals may reflect differences in genome-effective population sizes or in sex-biased gene flow. To explore these possibilities, we have examined genetic diversity, gene flow, and correlations among genetic, linguistic, and geographic distances within four sets of populations representing potential geographic and cultural spheres of interaction. GST estimates (a measure of genetic differentiation inversely proportional to gene flow) from mtDNA sequences vary between 0.13 and 0.39 and are typically five times greater than GST estimates from STR loci (0.05-0.08). Significant correlations (r>.5, P<.05) between maternal genetic and linguistic distances are coincident with high mtDNA GST estimates (>0.38). Thus, genetic and linguistic distances may coevolve, and their correspondence may be preserved under conditions of genetic isolation. A significant correlation (r=.65, P<.01) between biparental genetic and geographic distances is coincident with a low STR GST estimate (0.05), indicating that isolation by distance is observed under conditions of high nuclear-gene flow. These results are consistent with an initial settlement of Remote Oceania from island Southeast Asia and with extensive postcolonization male-biased gene flow with Near Oceania.
When Friends Have Other Friends

Children rarely have their friends to themselves. At all ages, but especially in late childhood and early adolescence, friendship experiences are normally embedded in the wider relational context of group interaction and networks of peer relationships (Cairns, Xie, L Fletcher, Hunter, & Eanes, 2006; Sabongui, Bukowski, & Newcomb, 1998; South & Haynie, 2004). For example, studies employing diaries, observations, surveys, or other techniques that assess time use indicate that children’s opportunities for interaction with their friends are almost overwhelmingly public in that other children are present and interacting as well (e.g., Crockett, Losoff, & Petersen, 1984; Larson & Richards, 1991; Montemayor & Van-Komen, 1985; see Brown, Larson, & Saraswathi, 2002). In addition, most children have several friends and are aware that their specific friends like or have friendships with other, outside children (e.g., George & Hartmann, 1996; Parker & Seal, 1996). Isolated friendships, it seems, are the exception not the rule. The public nature of friendship in late childhood and early adolescence is a potentially important but often underappreciated consideration in understanding why these relationships form, have certain qualities, and take specific directions. In particular, by serving as the broader context in which friendship experiences unfold, outsiders and outside relationships shape children’s experiences within friendships in important ways. At times, outsiders have a positive influence on specific friendships (see Milardo & Helms-Erikson, 2000). For example, when third parties and other friends recognize and respond to pairs of children as friends, this can have an important ‘‘audience effect’’ that cements the partners’ identification with and commitment to one another (McCall, 1988). Outsiders can also positively influence friendships in more direct ways. For example, if motivated to do so, outsiders can be effective at helping members resolve disputes or rectify perceived injustices (e.g., Simmons, 2002). Hart: Handbook of Jealousy, Theory, Research, and Multidisciplinary Approaches 9781405185790_4_022 Final Proof page 516 12.2. 2010 3:03pm
Graph-based text classiﬁcation: learn from your neighbors

Automatic classiﬁcation of data items, based on training samples, can be boosted by considering the neighborhood of data items in a graph structure (e.g., neighboring documents in a hyperlink environment or co-authors and their publications for bibliographic data entries). This paper presents a new method for graph-based classiﬁcation, with particular emphasis on hyperlinked text documents but broader applicability. Our approach is based on iterative relaxation labeling and can be combined with either Bayesian or SVM classiﬁers on the feature spaces of the given data items. The graph neighborhood is taken into consideration to exploit locality patterns while at the same time avoiding overﬁtting. In contrast to prior work along these lines, our approach employs a number of novel techniques: dynamically inferring the link/class pattern in the graph in the run of the iterative relaxation labeling, judicious pruning of edges from the neighborhood graph based on node dissimilarities and node degrees, weighting the inﬂuence of edges based on a distance metric between the classiﬁcation labels of interest and weighting edges by content similarity measures. Our techniques considerably improve the robustness and accuracy of the classiﬁcation outcome, as shown in systematic experimental comparisons with previously published methods on three diﬀerent real-world datasets.
Analysis of the initiation of nuclear pore assembly by ectopically targeting nucleoporins to chromatin

Nuclear pore complexes (NPCs) form the gateway to the nucleus, mediating virtually all nucleocytoplasmic trafficking. Assembly of a nuclear pore complex requires the organization of many soluble sub-complexes into a final massive structure embedded in the nuclear envelope. By use of a LacI/LacO reporter system, we were able to assess nucleoporin (Nup) interactions, show that they occur with a high level of specificity, and identify nucleoporins sufficient for initiation of the complex process of NPC assembly in vivo. Eleven nucleoporins from different sub-complexes were fused to LacI-CFP and transfected separately into a human cell line containing a stably integrated LacO DNA array. The LacI-Nup fusion proteins, which bound to the array, were examined for their ability to recruit endogenous nucleoporins to the intranuclear LacO site. Many could recruit nucleoporins of the same sub-complex and a number could also recruit other sub-complexes. Strikingly, Nup133 and Nup107 of the Nup107/160 subcomplex and Nup153 and Nup50 of the nuclear pore basket recruited a near full complement of nucleoporins to the LacO array. Furthermore, Nup133 and Nup153 efficiently targeted the LacO array to the nuclear periphery. Our data support a hierarchical, seeded assembly pathway and identify Nup133 and Nup153 as effective “seeds” for NPC assembly. In addition, we show that this system can be applied to functional studies of individual nucleoporin domains as well as to specific nucleoporin disease mutations. We find that the R391H cardiac arrhythmia/sudden death mutation of Nup155 prevents both its subcomplex assembly and nuclear rim targeting of the LacO array.
Automatic Tune Set Generation for Machine Translation with Limited Indomain Data

Many effective adaptation techniques for statistical machine translation crucially rely on in-domain development sets to learn model parameters. In this paper we present a novel method that automatically generates the matching tune set for Arabic-to-English MT with limited indomain data 1 . This technique improves our MT system over two baselines (tuned on data from the same domain but different genres) by 1.2 and 3.5 BLEU points using significantly less tuning data (1/6 and 1/2 of the baselines). Lexical and morphological features contribute to the success of our method in different ways. Generating tune sets using length distribution also improves the system significantly. Finally, our method obtains competitive results in experiments where ingenre tune sets are available.
How Peroxisomes Affect Aflatoxin Biosynthesis in Aspergillus Flavus

In filamentous fungi, peroxisomes are crucial for the primary metabolism and play a pivotal role in the formation of some secondary metabolites. Further, peroxisomes are important site for fatty acids β-oxidation, the formation of reactive oxygen species and for their scavenging through a complex of antioxidant activities. Oxidative stress is involved in different metabolic events in all organisms and it occurs during oxidative processes within the cell, including peroxisomal β-oxidation of fatty acids. In Aspergillus flavus, an unbalance towards an hyper-oxidant status into the cell is a prerequisite for the onset of aflatoxin biosynthesis. In our preliminary results, the use of bezafibrate, inducer of both peroxisomal β-oxidation and peroxisome proliferation in mammals, significantly enhanced the expression of pex11 and foxA and stimulated aflatoxin synthesis in A. flavus. This suggests the existence of a correlation among peroxisome proliferation, fatty acids β-oxidation and aflatoxin biosynthesis. To investigate this correlation, A. flavus was transformed with a vector containing P33, a gene from Cymbidium ringspot virus able to induce peroxisome proliferation, under the control of the promoter of the Cu,Zn-sod gene of A. flavus. This transcriptional control closely relates the onset of the antioxidant response to ROS increase, with the proliferation of peroxisomes in A. flavus. The AfP33 transformant strain show an up-regulation of lipid metabolism and an higher content of both intracellular ROS and some oxylipins. The combined presence of a higher amount of substrates (fatty acids-derived), an hyper-oxidant cell environment and of hormone-like signals (oxylipins) enhances the synthesis of aflatoxins in the AfP33 strain. The results obtained demonstrated a close link between peroxisome metabolism and aflatoxin synthesis.
Transitional Justice Processes, Shared Narrative Memory about Past Collective Violence and Reconciliation

Perceptions of the “Truth and Reconciliation” and “Political Imprisonment and Torture” commissions and related beliefs, emotions and socio-emotional climate were analyzed in population affected and unaffected by past political violence in Chile (N=1278). Those with a positive evaluation of commissions’ goal of creation of an inclusive narrative, by comparison to people that disagree report higher negative emotions such as shame, as well as positive ones such as pride and hope by respect to collective past, agree more with social forgiveness, stress more learning of past collective misdeeds, perceives a more positive emotional climate, intergroup trust, confidence in institutions – however they did not share more universalistic values. A positive evaluation of the commissions’ goal of helps to prevent violence, supports justice and to know the truth about past collective violence, low exposure to past political violence, low negative emotions and high positive emotions predict positive socio-emotional climate in multiple regression analyses. Results suggest that commissions play a relatively successful role as transitional justice rituals, reinforcing reconciliation, but that the creation of an inclusive narrative or shared collective memory is less successful and less relevant that the preventive, helps to justice and to know the truth TC’ s functions.
Parallelization of Wavelet Filters Using Simd Extensions

Much work has been done to optimize wavelet transforms for SIMD extensions of modern CPUs. However, these approaches are mostly restricted to the vertical part of 2-D transforms with line-wise organized memory layouts because this leads to a rather straight forward SIMD-implementation. This work shows for an example of a common wavelet filter new approaches to use SIMD operations on 1-D transforms that are able to produce reasonable speedups. As a result, the performance of algorithms that use wavelet transforms, such as JPEG2000, can be increased significantly. Various variants of parallelization are presented and compared. Their advantages and disadvantages for general filters are discussed.