Miracle-dz/UniFAR-FTUs huggingface dataset:
CREME: a framework for identifying cis-regulatory modules in human-mouse conserved segments

MOTIVATION The binding of transcription factors to specific regulatory sequence elements is a primary mechanism for controlling gene transcription. Recent findings suggest a modular organization of binding sites for transcription factors that cooperate in the regulation of genes. In this work we establish a framework for finding recurrent cis-regulatory modules in the promoters of a selected set of genes and scoring their statistical significance. RESULTS Proceeding from a database of identified binding site motifs and their genomic locations we seek motifs whose frequency in the selected promoters is different than in a background promoter set. We present several statistical tests designed for this purpose. We provide a hashing algorithm for detecting combinations of these motifs that co-occur in clusters within the selected promoters. The significance of such co-occurrences is evaluated using novel statistical scores. Our methods are combined in CREME, a suite of software which includes a browser for viewing the pattern of occurrence of selected cis-regulatory modules. We applied our methodology to find modules within human-mouse conserved promoter segments, focusing on cell cycle regulated genes and stress response related genes. To validate the biological significance of the identified modules we tested whether the associated genes tended to be co-expressed or share similar function. In the cell cycle set five of the seven identified sets of genes were coherently expressed. On the stress response data four of the six detected sets fell predominantly into well-defined functional sub-categories.
THE NOVEL FLAVONOID CHEMISTRY AND PHYLOGENETIC ORIGIN OF PHLOX FLORIDANA

The utility of comparative flavonoid analysis in determining amphiploid ancestry has been established in studies where the amphiploid chemistry is a summation of the parental constituents (e.g., Smith and Levin, 1963). Major departures from additivity have been termed "enigmatic" (Levin, 1968) or "not . an acceptable basis for . clarifying the status or relation of taxa" (Stromnaes and Garber, 1963). However, studies of hybrids of Baptisia (Alston et al., 1965), Dicentra (Fahselt and Ownbey, 1968), Lasthenia (Ornduff et al., 1973), Saccharum (Williams et al., 1974), and Phlox (Levy and Levin, 1971, 1974) have demonstrated that non-additivity may arise from novel (hybrid) compound production and the displacement of the usual parental end products. Apparent non-additivity also may result from subsequent diversification of either the ancestral or derived taxa or from unrecognized introgression. It may also reflect an erroneous phylogenetic framework. Phlox floridana Bentham has been judged to be an allotetraploid (2n = 28) derivative of hybridization between the diploids (2n = 14) P. pilosa ssp. pilosa Wherry and P. carolina ssp. angusta Wherry on bases of comparative morphology, karyology, and ecogeography (Levin, 1968). Subsequent considerations of seed protein chemistry (Levin and Schaal, 1970) were compatible with this assessment. However, Levin's analysis also indicated that P. floridana contained less than half of the putative parental flavonoids and exhibited numerous "new" flavonoids. The purpose of the present study was to determine whether the novel compounds could be traced to the putative progenitors and, if so, how they may have originated. Investigation involved the characterization of the nonanthocyanin flavonoids in an extensive geographical survey of P. floridana, its putative progenitors, and one additional taxon, P. pilosa ssp. detonsa Wherry. The potential role of this taxon in the evolution of P. floridana will become apparent in the following systematic summary. Phlox pilosa ssp. pilosa and P. carolina ssp. angusta differ conspicuously in (1) morphology, especially in stature, vesture, and style length (Wherry, 1955), (2) karyology, in both symmetry and location of chromosomal satellites (Smith and Levin, 1967), and (3) seed protein chemistry, each taxon exhibiting taxon-specific electrophoretic markers (Levin and Schaal, 1970). Phlox floridana exhibits (1) a morphology that is intermediate between or a mosaic of diploid features, (2) a karyotype that essentially is a summation of the diploids, and (3) a seed protein chemistry of 13 markers, one specific to P. pilosa ssp. pilosa, four specific to P. carolina ssp. angusta, and eight common to both diploids. According to Wherry (1955), the diploids are sympatric throughout the range of P. carolina including all four subspecies, angusta, carolina, alta, and turritella. The range of P. floridana overlaps this sympatric zone in northwestern Florida and surrounding areas of southern Alabama and Georgia. While the above features seem to provide strong support for the stated phylogeny,
Effect of Ochratoxin A on Escherichia coli–Challenged Broiler Chicks

Abstract A study was conducted to evaluate the effects of ochratoxin A (OA) on Escherichia coli–challenged broiler chickens. Day-old broiler chicks were separated into two groups of 92 chicks each, with one group fed a control mash diet, and the other fed a mash diet containing 2 ppm OA. On day 14, each group was further separated into two groups, with one group inoculated with E. coli O78 (1 × 107 colony-forming units/0.5 ml), whereas the other group was not inoculated with E. coli. After E. coli inoculation on day 14, four birds from each group were euthanatized at 1, 2, 3, 5, 7, 10, 14, and 21 days postinoculation. Escherichia coli infection caused dullness, depression, huddling, and diarrhea. Mortality was 14.3% in chicks infected with E. coli but fed no OA. Mortality increased to 35.7% in chicks fed OA and infected with E. coli. Decreased body weight and reduced feed intake were observed in chicks fed OA, and the effects were more pronounced in chicks fed OA and infected with E. coli. Increased serum levels of aspartate aminotransferase, alanine aminotransferase, uric acid, and creatinine and decreased levels of total proteins, albumin, globulins, calcium, and phosphorus were observed in OA-fed birds. Escherichia coli infection did not cause significant alteration in any of the serum biochemical parameters. The presence of OA in poultry rations increased mortality and the severity of an E. coli infection.
Autoimmune liver diseases and antiphospholipid antibodies positivity: a meta-analysis of literature studies.

BACKGROUND AND AIMS Several studies reported an association between autoimmune liver diseases (AiLD) and antiphospholipid antibodies (aPL) positivity. We performed a meta-analysis of studies evaluating the association of primary biliary cirrhosis (PBC), autoimmune hepatitis (AIH), and primary sclerosing cholangitis (PSC) with aPL positivity and with aPL-related thrombotic events. METHODS Studies evaluating the association of AiLD with aPL (anticardiolipin [aCL], anti-β2 glycoprotein-I [anti-β2GPI], lupus anticoagulant [LA] antibodies) and with aPL-related thrombotic complications were systematically searched in the PubMed, Web of Science, Scopus and EMBASE databases. RESULTS A total of 10 studies (750 patients with AiLD and 1,244 healthy controls) were included in the analysis on the prevalence of aPL and showed that AiLD are significantly associated with the presence of aCL and anti-β2GPI. The association with aCL positivity was consistently confirmed in PBC (OR: 13.93, 95%CI: 4.69-41.38), AIH (OR: 23.50, 95%CI: 4.28-129.13), and PSC (OR: 18.21, 95%CI: 7.05-47.08). Similarly, anti-β2GPI were found more frequently in PBC (OR: 25.10, 95%CI: 4.77-132.11), AIH (OR: 48.57, 95%CI: 11.07-213.09), and PSC (OR: 36.30, 95%CI: 6.55-201.31). These findings are confirmed when separately analyzing IgM, IgG, and IgA directed against phospholipids. Two of the 10 included articles and 1 further study (67 cases and 75 controls) showed a trend - not achieving statistical significance - towards a higher prevalence of thrombotic complications in AIH patients with aPL as compared to those with only AIH (OR: 1.67, 95%CI: 0.46-6.05). CONCLUSION PBC, AIH, and PSC are significantly associated with aPL positivity. The association with aPL-related thrombotic complications should be further studied.
Effect of chronic stress on running wheel activity in mice

Acute and chronic stress have been reported to have differing effects on physical activity in rodents, but no study has examined a chronic stress protocol that incorporates stressors often experienced by rodents throughout a day. To examine this, the effects of the Unpredictable Chronic Mild Stress (UCMS) protocol on voluntary running wheel activity at multiple time points, and/or in response to acute removal of chronic stress was determined. Twenty male Balb/c mice were given access and accustomed to running wheels for 4 weeks, after which they were randomized into 2 groups; exercise (EX, n = 10) and exercise with chronic stress using a modified UCMS protocol for 7 hours/day (8:00 a.m.-3:00p.m.), 5 days/week for 8 weeks (EXS, n = 10). All mice were given access to running wheels from approximately 3:30 p.m. to 7:30 a.m. during the weekday, however during weekends mice had full-time access to running wheels (a time period of no stress for the EXS group). Daily wheel running distance and time were recorded. The average running distance, running time, and work each weekday was significantly lower in EXS compared to EX mice, however, the largest effect was seen during week one. Voluntary wheel running deceased in all mice with increasing age; the pattern of decline appeared to be similar between groups. During the weekend (when no stress was applied), EXS maintained higher distance compared to EX, as well as higher daily distance, time, and work compared to their weekday values. These results indicate that mild chronic stress reduces total spontaneous wheel running in mice during the first week of the daily stress induction and maintains this reduced level for up to 8 consecutive weeks. However, following five days of UCMS, voluntary running wheel activity rebounds within 2–3 days.
Rheumatoid arthritis after Chikungunya fever: a prospective follow-up study of 21 cases

In 2005–6, more than 1.5 million people in the Indian Ocean area were infected with Chikungunya fever. In Reunion Island, 38.3% of the population, approximately 300 000 people, were infected.1 Only 6% of the cases were asymptomatic. Chikungunya fever is a viral infection transmitted to humans by Aedes mosquitoes.2,3 Chikungunya infection usually causes a syndrome characterised by fever, headaches, chills, conjunctivitis, rash, myalgia and severe joint pain with or without swelling. Joint symptoms vary from polyarthralgia to symmetrical polyarthritis. The outcome is usually benign, but persistent joint pain and stiffness may occur.3,4,5,6,7,8 We report 21 cases …
Preserving privacy in social networking systems: Policy-based control and anonymity

Social Networking Systems (SNSs), such as Facebook, are complex information systems involving a huge number of active entities that provide and consume enormous amounts of information. Such information can be mainly attributed to the users of SNSs and hence, can be considered privacy-sensitive. Therefore, in contrast to traditional systems where access control is governed by system policies, enabling individual users to specify their privacy control policies becomes a natural requirement. The intricate semantic relationships among data objects, users, and between data objects and users further add to the complexity of privacy control needs. Moreover, there is immense interest in studying social network data that is collected by SNSs for various research purposes. Anonymization is a solution to preserve user privacy in this case. However, anonymizing social network datasets effectively and efficiently is a much more challenging task than anonymizing tabular datasets due to the connectedness of the users in a social network graph. In this dissertation, we propose approaches and methods that facilitate preserving user privacy in terms of providing both fine-grained control of information and utility-preserving anonymization. In particular, we propose an ontology-based privacy control framework that enables fine-grained specification and enforcement of privacy control policies by both users and SNS providers. Our framework allows an SNS provider to determine privacy control policy authorities for SNS information, and allows users to specify advanced policies, that in addition to fine-grained policy specification, enables sharing of authority over protected resources. Based on such an ontology-based foundation, we also propose a framework to support novel privacy policy analysis tasks in SNSs. Furthermore, we propose a framework to enhance anonymization algorithms for social network datasets in terms of preserving their structural properties without sacrificing privacy requirements set for the algorithms. The proposed approaches direct the behavior of anonymization algorithms based on concepts in social network theory. We evaluate our proposed methods and approaches by implementing a prototype of the privacy control framework, carrying out a policy analysis case study for a real-world SNS, and performing an extensive set of experiments on improving social network anonymization in terms of preserving data utility.
Sequential Monte Carlo Methods in Practice

Sequential importance sampling (cid:2)SIS(cid:3) was (cid:4)rst developed in (cid:5)(cid:6)(cid:7)(cid:8)s for molecular simulation(cid:9) Although half a century has passed by(cid:10) the SIS methodology remains one of the most versatile and power(cid:11) ful means for the simulation and optimization of chain polymers(cid:9) In (cid:5)(cid:6)(cid:6)(cid:8)s(cid:10) statisticians reinvented the same methodology in a more gen(cid:11) eral form(cid:10) brought forth a number of enhancements(cid:10) and applied it to a much broader spectrum of problems(cid:9) In this article(cid:10) along with a historical account of the methodology(cid:10) we present a theoretical frame(cid:11) work for the SIS with resampling(cid:9) We emphasize the basic concept of a weighted sample(cid:10) the fundamental idea of sequential build(cid:2)up(cid:10) the important technique of reweighting and resampling(cid:10) and various other methods(cid:10) e(cid:9)g(cid:9)(cid:10) the partial rejection control and marginalization(cid:10) for im(cid:11) proving a sequential importance sampler(cid:9) To illustrate(cid:10) we show how to analyze a state(cid:11)space model with SIS and how to treat the con(cid:11) ditional dynamic linear model with marginalization(cid:10) resampling(cid:10) and rejection control techniques(cid:9) We report some simulation results for two(cid:11)dimensional target tracking in clutter(cid:9)
Specificity of the Tuberculin Skin Test Is Modified by Use of a Protein Cocktail Containing ESAT-6 and CFP-10 in Cattle Naturally Infected with Mycobacterium bovis

ABSTRACT The mycobacterial immunodominant ESAT-6 and CFP-10 antigens are strongly recognizable in tuberculosis-infected cattle, and they do not elicit a response in cattle without infection. In addition, they are absent in most environmental mycobacterial species, and therefore, their use can be an alternative to purified protein derivative (PPD) tuberculin in the development of a more specific skin diagnostic test in cattle. The aim of the current study was to assess the potential of an ESAT-6 and CFP-10 (E6-C10) protein cocktail in a skin test format in naturally tuberculosis-infected and paratuberculosis-infected cattle. We also included MPB83 as a third component in one of the protein cocktail preparations. The protein cocktail was tested at different dose concentrations (5, 10, and 15 μg per protein). The best skin response to the E6-C10 protein cocktail was obtained with 10 μg. Subsequently, this concentration was tested in 2 herds with high and low bovine tuberculosis prevalence, the latter with paratuberculosis coinfection. Our data show that the E6-C10 cocktail allows identification of an important proportion of animals that PPDB is not able to recognize, especially in low-prevalence herds. The protein cocktail did not induce reactions in tuberculosis-free cattle or in paratuberculosis-infected cattle. Addition of MPB83 to the protein cocktail did not make any difference in the skin reaction.
SMT-centric power-aware thread placement in chip multiprocessors

In Simultaneous Multi-Threading (SMT) chip multiprocessors (CMPs), thread placement is performed today in a largely power-unaware manner. For example, consolidation of active threads into fewer cores exposes opportunities for power savings that have not been addressed in prior work. The savings opportunity is especially high in the emerging context where percore power gating (PCPG) is becoming viable. The use of the optimum combination of core-wise SMT level and number of active cores to achieve a desired power-performance efficiency is a knob which has not been explored in prior work nor implemented as part of the operating system task scheduler.
Parallel Dimers and Anti-parallel Tetramers Formed by Epidermal Growth Factor Receptor Pathway Substrate Clone 15 (EPS15)*

The recently discovered localization of epidermal growth factor receptor pathway substrate clone 15 (Eps15) to plasma membrane clathrin-coated pits and its constitutive association with the endocytic clathrin adaptor protein complex, AP-2, strongly suggest that Eps15 has an important role in the pathway of clathrin-dependent endocytic traffic. We report here that Eps15 forms dimers and tetramers of distinct shape. The Eps15 dimer is an elongated molecule, 32 nm in length. There is a globular “head” at one end of the molecule and an extended “stalk” of 25 nm which is kinked at about 17 nm away from the head. In the Eps15 dimer, two subunits are arranged parallel to each other, so that the head corresponds to two side by side copies of the N-terminal region I, which contains the three Eps15 homology domains. The proximal part of the stalk is the coiled-coil central region II containing 20 heptad repeats. The kink is at the boundary between region II and the C-terminal region III, which contains the AP-2 binding site, 15 aspartic-proline-phenylalanine repeats, and proline-rich Src homology domain ligand sites. The Eps15 tetramer has a “dumbbell” shape, ∼31 nm in length; it is formed by the anti-parallel association of two Eps15 dimers. Formation of these Eps15 tetramers appears to require contacts between regions I of one dimer and regions III of a second apposing dimer. The extended shapes of the Eps15 dimers and tetramers suggest how Eps15 oligomers are located in the clathrin coat. We discuss the implications for accessibility to partners and for proposed functions of Eps15.
Nerve Growth Factor-Dependent Activation of NF-κB Contributes to Survival of Sympathetic Neurons

Neurotrophins activate multiple signaling pathways in neurons. However, the precise roles of these signaling molecules in cell survival are not well understood. In this report, we show that nerve growth factor (NGF) activates the transcription factors NF-κB and AP-1 in cultured sympathetic neurons. Activated NF-κB complexes were shown to consist of heterodimers of p50 and Rel proteins (RelA, as well as c-Rel), and NF-κB activation was found to occur independently ofde novo protein synthesis but in a manner that required the action of the proteasome complex. Treatment with the NF-κB inhibitory peptide SN50 in the continuous presence of NGF resulted in dose-dependent induction of cell death. Under the conditions used, SN50 was shown to selectively inhibit NF-κB activation but not the activation of other cellular transcription factors such as AP-1 and cAMP response element-binding protein. Cells treated with SN50 exhibited morphological and biochemical hallmarks of apoptosis, and the kinetics of cell killing were accelerated relative to death induced by NGF withdrawal. Finally, experiments were conducted to test directly whether NF-κB could act as a survival factor for NGF-deprived neurons. Microinjection of cells with an expression plasmid encoding NF-κB (c-Rel) resulted in enhanced neuronal survival after withdrawal of NGF, whereas cells that were transfected with a vector encoding a mutated derivative of c-Rel lacking the transactivation domain underwent cell death to the same extent as control cells. Together, these findings suggest that the activation of NF-κB/Rel transcription factors may contribute to the survival of NGF-dependent sympathetic neurons.
No-look flick: single-handed and eyes-free japanese text input system on touch screens of mobile devices

We present a single-handed and eyes-free Japanese kana text input system on touch screens of mobile devices. We first conducted preliminary experiments to investigate the accuracy with which subjects could single-handedly point to and flick without using their eyes. We found from the results that users can point at a screen that was divided into 2 x 2 with 100% accuracy and that users can flick at a 2 x 2 grid without using their eyes with 96.1% accuracy using our algorithm for flick recognition. The system used kana letter input based on two-stroke input with three keys to enable accurate eyes-free typing. First, users flick for consonant input, and then similarly flick for vowel input. We conducted a long-term user study to measure basic text entry speed and error rate performance under eyes-free conditions, and readability of transcribed phrases. As a result, the mean text entry speed was 51.2 characters per minute (cpm) in the 10th session of the user study and the mean error rate was 0.6% of all characters. The mean text entry speed was 33.9 cpm in the 11th session, which was conducted under totally eyes-free conditions and the mean error rate was 4.8% of all characters. We not only measured cpm and error rate, but also measured error rate of reading, which we devised as a novel metric to measure how accurately users can read transcribed phrases. The mean error rate of reading in the 11th session was 5.7% of all phrases.