Miracle-dz/UniFAR-FTUs huggingface dataset:
rRNA:mRNA pairing alters the length and the symmetry of mRNA-protected fragments in ribosome profiling experiments

Motivation: Ribosome profiling is a new technique that allows monitoring locations of translating ribosomes on mRNA at a whole transcriptome level. A recent ribosome profiling study demonstrated that internal Shine–Dalgarno (SD) sequences have a major global effect on translation rates in bacteria: ribosomes pause at SD sites in mRNA. Therefore, it is important to understand how SD sites effect mRNA movement through the ribosome and generation of ribosome footprints. Results: Here, we provide evidence that in addition to pausing effect, internal SD sequences induce a caterpillar-like movement of mRNA through the ribosome cavity. Once an SD site binds to the ribosome, it remains attached to it while the ribosome decodes a few subsequent codons. This leads to asymmetric progressive elongation of ribosome footprints at the 3′-end. It is likely that internal SD sequences induce a pause not on a single, but on several adjacent codons. This finding is important for our understanding of mRNA movement through the ribosome and also should facilitate interpretation of ribosome profiling data. Contact: brave.oval. pan@gmail.com
Monetary Cost-Aware Checkpointing and Migration on Amazon Cloud Spot Instances

Recently introduced spot instances in the Amazon Elastic Compute Cloud (EC2) offer low resource costs in exchange for reduced reliability; these instances can be revoked abruptly due to price and demand fluctuations. Mechanisms and tools that deal with the cost-reliability tradeoffs under this schema are of great value for users seeking to lessen their costs while maintaining high reliability. We study how mechanisms, namely, checkpointing and migration, can be used to minimize the cost and volatility of resource provisioning. Based on the real price history of EC2 spot instances, we compare several adaptive checkpointing schemes in terms of monetary costs and improvement of job completion times. We evaluate schemes that apply predictive methods for spot prices. Furthermore, we also study how work migration can improve task completion in the midst of failures while maintaining low monetary costs. Trace-based simulations show that our schemes can reduce significantly both monetary costs and task completion times of computation on spot instance.
The Effect of Hip Bracing on Gait in Patients with Medial Knee Osteoarthritis

Objective. Impaired hip motion has been associated with heightened medial knee joint loading in patients with knee osteoarthritis (OA). A hip external rotation strap designed to pull the femur into external rotation and abduction may serve as one protective mechanism. The primary aim of our study is to determine if the strap decreases medial knee joint loading during level walking in people with knee OA. Design. This study is a single-day repeated measures design. Methods. 15 volunteers with medial knee OA underwent motion analysis data collection during two randomly assigned walking conditions: (1) wearing the strap and (2) control (no strap). Primary outcome measures were peak pelvis, hip and knee joint motions, and torques. These outcomes were averaged across five trials for each condition. Results. Hip abduction (P < 0.01), trunk lean towards the stance limb (P = 0.04) and pelvic tilt (P = 0.02) significantly increased with the strap versus control trials. Knee adduction loading did not significantly change with the strap (P = 0.33). Conclusion. The use of the hip external rotation strap resulted in angular changes at the hip and pelvis which may be beneficial for patients with medial knee osteoarthritis.
A randomized controlled trial of auricular acupuncture for cocaine dependence.

BACKGROUND Partly because of a lack of a conventional, effective treatment for cocaine addiction, auricular acupuncture is used to treat this disorder in numerous drug treatment facilities across the country for both primary cocaine-dependent and opiate-dependent populations. OBJECTIVE To evaluate the effectiveness of auricular acupuncture for the treatment of cocaine addiction. METHODS Eighty-two cocaine-dependent, methadone-maintained patients were randomly assigned to 1 of 3 conditions: auricular acupuncture, a needle-insertion control condition, or a no-needle relaxation control. Treatment sessions were provided 5 times weekly for 8 weeks. The primary outcome was cocaine use assessed by 3-times-weekly urine toxicology screens. RESULTS Longitudinal analysis of the urine data for the intent-to-treat sample showed that patients assigned to acupuncture were significantly more likely to provide cocaine-negative urine samples relative to both the relaxation control (odds ratio, 3.41; 95% confidence interval, 1.33-8.72; P =. 01) and the needle-insertion control (odds ratio, 2.40; 95% confidence interval, 1.00-5.75; P =.05). CONCLUSIONS Findings from the current study suggest that acupuncture shows promise for the treatment of cocaine dependence. Further investigation of this treatment modality appears to be warranted.
Combined Mining: Discovering Informative Knowledge in Complex Data

Enterprise data mining applications often involve complex data such as multiple large heterogeneous data sources, user preferences, and business impact. In such situations, a single method or one-step mining is often limited in discovering informative knowledge. It would also be very time and space consuming, if not impossible, to join relevant large data sources for mining patterns consisting of multiple aspects of information. It is crucial to develop effective approaches for mining patterns combining necessary information from multiple relevant business lines, catering for real business settings and decision-making actions rather than just providing a single line of patterns. The recent years have seen increasing efforts on mining more informative patterns, e.g., integrating frequent pattern mining with classifications to generate frequent pattern-based classifiers. Rather than presenting a specific algorithm, this paper builds on our existing works and proposes combined mining as a general approach to mining for informative patterns combining components from either multiple data sets or multiple features or by multiple methods on demand. We summarize general frameworks, paradigms, and basic processes for multifeature combined mining, multisource combined mining, and multimethod combined mining. Novel types of combined patterns, such as incremental cluster patterns, can result from such frameworks, which cannot be directly produced by the existing methods. A set of real-world case studies has been conducted to test the frameworks, with some of them briefed in this paper. They identify combined patterns for informing government debt prevention and improving government service objectives, which show the flexibility and instantiation capability of combined mining in discovering informative knowledge in complex data.
Core filaments of the nuclear matrix

The nuclear matrix is concealed by a much larger mass of chromatin, which can be removed selectively by digesting nuclei with DNase I followed by elution of chromatin with 0.25 M ammonium sulfate. This mild procedure removes chromatin almost completely and preserves nuclear matrix morphology. The complete nuclear matrix consists of a nuclear lamina with an interior matrix composed of thick, polymorphic fibers and large masses that resemble remnant nucleoli. Further extraction of the nuclear matrices of HeLa or MCF-7 cells with 2 M sodium chloride uncovered a network of core filaments. A few dark masses remained enmeshed in the filament network and may be remnants of the nuclear matrix thick fibers and nucleoli. The highly branched core filaments had diameters of 9 and 13 nm measured relative to the intermediate filaments. They may serve as the core structure around which the matrix is constructed. The core filaments retained 70% of nuclear RNA. This RNA consisted both of ribosomal RNA precursors and of very high molecular weight hnRNA with a modal size of 20 kb. Treatment with RNase A removed the core filaments. When 2 M sodium chloride was used directly to remove chromatin after DNase I digestion without a preceding 0.25 M ammonium sulfate extraction, the core filaments were not revealed. Instead, the nuclear interior was filled with amorphous masses that may cover the filaments. This reflected a requirement for a stepwise increase in ionic strength because gradual addition of sodium chloride to a final concentration of 2 M without an 0.25 M ammonium sulfate extraction uncovered core filaments.
Cultural Adaptation Process of the Supportive Care Needs Survey for Mexican Patients with Breast Cancer

Breast cancer (BC) is a significant public health issue in Mexico. The understanding of how to meet patient’s individual needs is essential to guide supportive care and improve quality of life among these patients. One of the most comprehensive tools for needs assessment is the Supportive Care Needs Sur vey Short Form-34 (SCNS-SF34), its validity and reliability has been robustly established in several languages, but there are no studies focusing on specific cultural features concerning Mexican women diagnosed with BC. Our objective was to describe and analyze the process of cultural adaptation of the SCNS-SF34 in Mexican women with BC through a pilot study. This process was performed following standardized procedures: a forward and backward translation by experts was undertaken in both lan guages and the translated version was piloted in 21 women with BC diagnosis. The results showed that appropriate adaptation of the SCNS-SF34 required both literal and sociocultural modifications, and highlighted that appropriate adaptation requires rigorous development methodology that takes into account cultural conditions as well as conceptual, linguistic and metric properties.
In Search of the Self: A Positron Emission Tomography Study

Previous work using positron emission tomography (PET) has shown that memory encoding processes are associated with preferential activation of left frontal regions of the brain, whereas retrieval processes are associated predominantly with right frontal activations. One possible reason for the asymmetry is that episodic retrieval necessarily involves reference to the self, and the self-concept may be represented (at least partially) in right frontal regions. Accordingly, the present study investigated the possibility that encoding of self-related material might also activate right frontal areas. Eight right-handed volunteers judged trait adjectives under four separate PET scan conditions: (a) relevance to self, (b) relevance to a well-known public figure, (c) social desirability, and (d) number of syllables. The results showed that self-related encoding yielded left frontal activations similar to those associated with other types of semantic encoding, but also specific activations in the right frontal lobe. It is concluded that the concept of self involves both general schematic structures and further specific components involved in episodic memory retrieval.
DEVELOPING EXTENSIVE READING PROJECT BASED LEARNING(PJBL) TO IMPROVE STUDENTS’ READING COMPREHENSIONIN EFL CLASS

This research was conducted at the second semester of English Study Program of STKIP PGRI Bandar Lampung 2015/2016 academic year. The research data were collected by using test of multiple choice and observation. The population of this research was the students of English Study Program of STKIP PGRI Bandar Lampung. The samples were the students of II B chosen by using purposive sampling. The data of this research were analyzed by using SPSS. The result reveals Extensive Reading PjBL technique can be used to promote the students’ reading comprehension achievement in second semester of the students of STKIP PGRI Bandar Lampung. From the result of correlation test, it shows that among the five aspects of Project Based Learning, there are only two aspects which correlate to the reading score of the students. The correlation coefficient shows the positive trends. They are listening to the discussion and time management aspects. The implementation of Extensive Reading Project Based Learning in English teaching and learning process of reading was successful to improve the students’ reading skills. The qualitative data shows that the students’ reading improved better in the aspects of main ideas and vocabulary. Key words: reading comprehension, extensive reading, project based learning
CookiExt: Patching the browser against session hijacking attacks

Session cookies constitute one of the main attack targets against client authentication on the Web. To counter these attacks, modern web browsers implement native cookie protection mechanisms based on the HttpOnly and Secure ags. While there is a general understanding about the eectiveness of these defenses, no formal result has so far been proved about the security guarantees they convey. With the present paper we provide the rst such result, by presenting a mechanized proof of noninterference assessing the robustness of the HttpOnly and Secure cookie ags against both web and network attackers with the ability to perform arbitrary XSS code injection. We then develop CookiExt, a browser extension that provides client-side protection against session hijacking, based on appropriate agging of session cookies and automatic redirection over HTTPS for HTTP requests carrying these cookies. Our solution improves over existing client-side defenses by combining protection against both web and network attacks, while at the same time being designed so as to minimise its eects on the user's browsing experience. Finally, we report on the experiments we carried out to practically evaluate the eectiveness of our approach.
Atomistic predictions of substrate orientation impact during SiGe alloys solid phase epitaxial regrowth

Coupled effects of substrate orientation and germanium concentration during silicon-germanium Solid Phase Epitaxial Regrowth (SPER) is analyzed through lattice kinetic Monte Carlo simulations. Atomistic events depending on the bonding environment allow to replicate the effects of alloying on SPER velocity of (100) substrates. The model is then used to draw predictions of the regrowth anisotropy in SiGe. Whereas Ge increase leads to a well-established SPER rate increase, whatever is the substrate orientation, moving away from (100) substrate orientation leads to a decrease of SPER rate caused by an unavoidable competition between the atomistic recrystallization configurations.
SPECTRAL: A new evolutionary synthesis code. Application to the irregular Galaxy NGC 1560

We have developed a new evolutionary synthesis code, which incorporates the output from chemical evolution models. We compare results of this new code with other published codes, and we apply it to the irregular galaxy NGC 1560 using sophisticated chemical evolution models. The code makes important contributions in two areas: a) the generation of synthetic populations with time-dependent star formation rates and stellar populations of different metallicities; b) the extension of the set of stellar tracks from the Geneva group by adding the AGB phases for $m_{\rm i}/M_\odot \geq 0.8$, as well as the low mass stars. Our code predicts spectra, broad band colors, and Lick indices by using a spectral library, covering a more complete grid of stellar parameters than previous models. The application of the code to the galaxy NGC 1560 constrains the star formation age of its stellar population at around 10.0 Gyr.
The radio luminosity function of radio-loud quasars from the 7C Redshift Survey

We present a complete sample of 24 radio-loud quasars (RLQs) from the new 7C Redshift Survey. Every quasar with a low-frequency (151 MHz) radio flux-density S(sub 151) > 0.5 Jy in two regions of the sky covering 0.013 sr is included; 23 of these have sufficient extended flux to meet the selection criteria, 18 of these have steep radio spectra (hereafter denoted as SSQs). The key advantage of this sample over most samples of RLQs is the lack of an optical magnitude limit. By combining the 7C and 3CRR samples, we have investigated the properties of RLQs as a function of redshift z and radio luminosity L(sub 151). We derive the radio luminosity function (RLF) of RLQs and find that the data are well fitted by a single power-law with slope alpha(sub 1) = 1.9 +/- 0.1 (for H(sub 0) = 50 km/s.Mpc, OMEGA(sub M) = 1, OMEGA(sub DELTA) = 0). We find that there must be a break in the RLQ RLF at log(sub 10)(L(sub 151)/W Hz.sr) approximately < or = 27, in order for the models to be consistent with the 7C and 6C source counts. The z-dependence of the RLF follows a one-tailed gaussian which peaks at z = 1.7 +/- 0.2. We find no evidence for a decline in the co-moving space density of RLQs at higher redshifts. A positive correlation between the radio and optical luminosities of SSQs is observed, confirming a result of Serjeant. We are able to rule out this correlation being due to selection effects or biases in our combined sample. The radio-optical correlation and best-fit model RLF enable us to estimate the distribution of optical magnitudes of quasars in samples selected at low radio frequencies, We con- clude that for samples with S(sub 151) approximately < or = 1 Jy one must use optical data significantly deeper than the POSS-I limit (R approximately equal 20), in order to avoid severe incompleteness.
SmartMeter.KOM: A low-cost wireless sensor for distributed power metering

Most current smart metering solutions aim at increasing user awareness for their household's electrical energy consumption. Although some smart meters make use of wireless data transfers between their sensor and display units, their integration into existing wireless sensor networks is hampered by proprietary communication interfaces and their lack of re-programmability. Furthermore, the sole availability of aggregate consumption values renders current meters insufficient for novel application scenarios like smart home automation, for which information at device-level granularity and high resolution is vital. We address these shortcomings of existing solutions by presenting SmartMeter.KOM, our wireless sensor node capable of determining the current consumption of individual electrical appliances at high resolution. The platform is based on low-power hardware and incorporates a reprogrammable microcontroller which allows developers to easily deploy new algorithms. Its IEEE 802.15. 4-compliant radio transceiver makes its integration with existing sensor networks possible, and thus enables their integration in smart buildings. We demonstrate the versatility of SmartMeter.KOM by presenting prototypical implementations of smart applications and identifying further research directions.
Taxation and Public Finance in a Transition Economy: A Case Study of Russia

Countries that are moving from central planning to a market economy face unique problems in many areas, including taxation and public finance. The methods of collecting the revenue needed to fund government services were much different under a socialist system. Shifting to a market system requires government to create new institutions and methods of collecting revenue. All transition economies face similar problems in this regard and several different approaches have been tried in an attempt to find the solution that is best for each particular country. This paper summarizes the methods the Russian Federation is using and comments on the problems Russia still faces as it attempts to install a system of taxation and public finance that is appropriate for its emerging market economy.
Nap1 regulates proper CENP-B binding to nucleosomes

CENP-B is a widely conserved centromeric satellite DNA-binding protein, which specifically binds to a 17-bp DNA sequence known as the CENP-B box. CENP-B functions positively in the de novo assembly of centromeric nucleosomes, containing the centromere-specific histone H3 variant, CENP-A. At the same time, CENP-B also prevents undesired assembly of the CENP-A nucleosome through heterochromatin formation on satellite DNA integrated into ectopic sites. Therefore, improper CENP-B binding to chromosomes could be harmful. However, no CENP-B eviction mechanism has yet been reported. In the present study, we found that human Nap1, an acidic histone chaperone, inhibited the non-specific binding of CENP-B to nucleosomes and apparently stimulated CENP-B binding to its cognate CENP-B box DNA in nucleosomes. In human cells, the CENP-B eviction activity of Nap1 was confirmed in model experiments, in which the CENP-B binding to a human artificial chromosome or an ectopic chromosome locus bearing CENP-B boxes was significantly decreased when Nap1 was tethered near the CENP-B box sequence. In contrast, another acidic histone chaperone, sNASP, did not promote CENP-B eviction in vitro and in vivo and did not stimulate specific CENP-B binding to CENP-A nucleosomes in vitro. We therefore propose a novel mechanism of CENP-B regulation by Nap1.
Generational "Structural Flexibility" in the United Arab Emirati Family: Lewis Coser's Functions of Social Conflict Revisited

This study examined, to what extent the structure of spousal relationship in United Arab Emirati' (UAE) family has been changed from rigidity to flexibility among a sample of 168 pairs of daughters and mothers (N=336). Three propositions were derived from Coser's theory "functions of social conflict" to measure the structural flexibility: releasing the antagonistic claims, interdependency and reproducing of consensual agreements. Findings revealed that daughters and mothers reported a low level of structural flexibility in terms of the three propositions, however, daughters reported more flexibility than their mothers. This result indicates that the rapid and comprehensive change of the infrastructures didn’t lead to a parallel change in the nontangible elements of UAE culture which are highly rooted in a composition of social traditions and Islamic values.
IgE Production to α-Gal Is Accompanied by Elevated Levels of Specific IgG1 Antibodies and Low Amounts of IgE to Blood Group B

IgE antibodies to gal-α-1,3-gal-β-1,4-GlcNAc (α-gal) can mediate a novel form of delayed anaphylaxis to red meat. Although IgG antibodies to α-gal (anti-α-gal or anti-Gal) are widely expressed in humans, IgE anti-α-gal is not. We explored the relationship between the IgG and IgE responses to both α-gal and the related blood group B antigen. Contradicting previous reports, antibodies to α-gal were found to be significantly less abundant in individuals with blood group B or AB. Importantly, we established a connection between IgE and IgG responses to α-gal: elevated titers of IgG anti-α-gal were found in IgE-positive subjects. In particular, proportionally more IgG1 anti-α-gal was found in IgE-positive subjects against a background of IgG2 production specific for α-gal. Thus, two types of immune response to α-gal epitopes can be distinguished: a ‘typical’ IgG2 response, presumably in response to gut bacteria, and an ‘atypical’, Th2-like response leading to IgG1 and IgE in addition to IgG2. These results suggest that IgE to a carbohydrate antigen can be formed (probably as part of a glycoprotein or glycolipid) even against a background of bacterial immune stimulation with essentially the same antigen.