Miracle-dz/UniFAR-FTUs huggingface dataset:
The Cell Cycle Regulated Transcriptome of Trypanosoma brucei

Progression of the eukaryotic cell cycle requires the regulation of hundreds of genes to ensure that they are expressed at the required times. Integral to cell cycle progression in yeast and animal cells are temporally controlled, progressive waves of transcription mediated by cell cycle-regulated transcription factors. However, in the kinetoplastids, a group of early-branching eukaryotes including many important pathogens, transcriptional regulation is almost completely absent, raising questions about the extent of cell-cycle regulation in these organisms and the mechanisms whereby regulation is achieved. Here, we analyse gene expression over the Trypanosoma brucei cell cycle, measuring changes in mRNA abundance on a transcriptome-wide scale. We developed a “double-cut” elutriation procedure to select unperturbed, highly synchronous cell populations from log-phase cultures, and compared this to synchronization by starvation. Transcriptome profiling over the cell cycle revealed the regulation of at least 430 genes. While only a minority were homologous to known cell cycle regulated transcripts in yeast or human, their functions correlated with the cellular processes occurring at the time of peak expression. We searched for potential target sites of RNA-binding proteins in these transcripts, which might earmark them for selective degradation or stabilization. Over-represented sequence motifs were found in several co-regulated transcript groups and were conserved in other kinetoplastids. Furthermore, we found evidence for cell-cycle regulation of a flagellar protein regulon with a highly conserved sequence motif, bearing similarity to consensus PUF-protein binding motifs. RNA sequence motifs that are functional in cell-cycle regulation were more widespread than previously expected and conserved within kinetoplastids. These findings highlight the central importance of post-transcriptional regulation in the proliferation of parasitic kinetoplastids.
Pure oxygen ventilation during general anaesthesia does not result in increased postoperative respiratory morbidity but decreases surgical site infection. An observational clinical study

Background. Pure oxygen ventilation during anaesthesia is debatable, as it may lead to development of atelectasis. Rationale of the study was to demonstrate the harmlessness of ventilation with pure oxygen. Methods. This is a single-centre, one-department observational trial. Prospectively collected routine-data of 76,784 patients undergoing general, gynaecological, orthopaedic, and vascular surgery during 1995–2009 were retrospectively analysed. Postoperative hypoxia, unplanned ICU-admission, surgical site infection (SSI), postoperative nausea and vomiting (PONV), and hospital mortality were continuously recorded. During 1996 the anaesthetic ventilation for all patients was changed from 30% oxygen plus 70% nitrous oxide to 100% oxygen in low-flow mode. Therefore, in order to minimize the potential of confounding due to a variety of treatments being used, we directly compared years 1995 (30% oxygen) and 1997 (100%), whereas the period 1998 to 2009 is simply described. Results. Comparing 1995 to 1997 pure oxygen ventilation led to a decreased incidence of postoperative hypoxic events (4.3 to 3.0%; p < 0.0001) and hospital mortality (2.1 to 1.6%; p = 0.088) as well as SSI (8.0 to 5.0%; p < 0.0001) and PONV (21.6 to 17.5%; p < 0.0001). There was no effect on unplanned ICU-admission (1.1 to 0.9; p = 0.18). Conclusions. The observed effects may be partly due to pure oxygen ventilation, abandonment of nitrous oxide, and application of low-flow anesthesia. Pure oxygen ventilation during general anaesthesia is harmless, as long as certain standards are adhered to. It makes anaesthesia simpler and safer and may reduce clinical morbidity, such as postoperative hypoxia and surgical site infection.
Evaluation of the Effectiveness of EMG Parameters in the Study of Neurogenic Diseases-A Statistical Approach Using Clinical and Simulated Data

Of interest here is the problem of determining to what extent combinations of parameters derived from the EMG signal allow 1) discriminating two subclasses of neurogenic myopathies, and 2) recognizing different morphologies of the motor unit action potential underlying a measured EMG signal. EMG signals measured on clinical subjects and computer-simulated EMG signals were collected in a database and used cooperatively in this study. Suitable statistical models were developed which allow testing hypotheses on the role of accepted EMG parameters for the two purposes named above, and deriving new suitable combinations of EMG parameters. Results support the hypothesis that frequency-domain parameters are very clearly related to the morphology of the motor unit action potential. However, the attempt to use them in order to discriminate the two pathologic subclasses considered appears to be jeopardized by the fact that the signal may be measured in territories which do not reflect the morphology of the motor unit action potential dominant in such subclasses. On the basis of time-domain parameters, a significant discrimination was obtained between the two subclasses, and such discrimination is related mainly to a time-domain parameter which has already proved successful in the discrimination between myopathic and normal subjects. Data corroborate the hypothesis that the diagnostic yield improves when time-domain EMG parameters are measured at recruitment.
Home Availability and the Impact of Weekly Stressful Events Are Associated with Fruit and Vegetable Intake among African American and Hispanic/Latina Women

Background. Mediating and moderating variables may interfere with the association between neighborhood availability of grocery stores (NAG) and supermarkets (NAS) and fruit and vegetable (FV) intake. Objective. The purpose of this study was to test mediation of home availability of FV (HAFV) and moderation of impact of weekly stressful events (IWSE) on the association between NAG and NAS with FV consumption among African American (AA) and Hispanic/Latina (HL) women. Methods. Three hundred nine AA and HL, 25–60 year old women in the Health Is Power (HIP) randomized controlled trial completed validated measures of HAFV, IWSE, and FV intake at baseline. Trained field assessors coded NAG and NAS. Institutional Review Board approval was obtained. Results. NAG and NAS were not associated with FV intake or HAFV, so HAFV was not a mediator. HAFV (std. Beta = .29, P < 0.001) and IWSE (std. Beta = .17; P < 0.05) were related to FV intake (R2 = 0.17; P < 0.001), but IWSE was not a moderator. Conclusion. Increasing HAFV and decreasing the IWSE should increase FV consumption. The extent to which the neighborhood environment is related to the home food environment and diet, and the mechanisms for the association between IWSE and diet should be examined in future research.
The Importance of Higher Education and the Role of Noncognitive Attributes in College Success La importancia de la educación superior y el rol de los atributos no cognitivos en el éxito en dichas instituciones

Higher education is valuable; not everyone is ready for higher education. Although readiness has traditionally been defined as academic, “noncognitive” skills can be considered as important and sometimes more important for success. Noncognitive skills assessments can be used in admissions, also placement, self assessment, and student learning outcomes. In this paper I elaborate on the full range of student attributes that are important for success in college and that ought to be considered for college readiness. I argue that on the basis of educator and employer surveys, prediction studies, and studies focusing on 21st century skills there is now an emerging consensus on what the most important noncognitive skills are, and a variety of approaches to measuring them have been developed and evaluated. Abstract
PATTERNS OF NUCLEOTIDE DIVERSITY IN TWO SPECIES OF MIMULUS ARE AFFECTED BY MATING SYSTEM AND ASYMMETRIC INTROGRESSION

Abstract The evolutionary transition from outcrossing to self-fertilization has far-reaching implications for patterns of intraspecific genetic diversity and the potential for speciation. Using DNA sequence variation at two nuclear loci, we examined the divergence history of two closely related species of Mimulus. To investigate the effects of mating system and introgressive hybridization on the outcrossing M. guttatus and the selfing M. nasutus, we inspected nucleotide diversity within and between natural populations spanning the species' geographic ranges. High sequence similarity among populations of the selfing M. nasutus points to a single evolutionary origin for the species. Consistent with their distinct mating systems, all genetic variation in M. nasutus is distributed among populations, whereas M. guttatus exhibits appreciable levels of nucleotide diversity within populations. Silent genetic diversity is extensive in M. guttatus (mean θsil/site = 0.077) and greatly exceeds the predicted twofold elevation in neutral variation for outcrossers relative to selfers. The finding of several M. guttatus sequences that share complete identity with sequences from M. nasutus suggests that recent asymmetric introgression may have occurred. We argue that exceptionally high nucleotide diversity in M. guttatus is consistent with a long-term history of directional introgression from M. nasutus to M. guttatus throughout the divergence of these two species.
Pedestrian Visibility at Night: Effects of Pedestrian Clothing, Driver Age, and Headlamp Beam Setting

ABSTRACT Reduced visibility is believed to be a major contributor to night-time pedestrian fatalities. In thisstudy, the ability of drivers to recognize the presence of roadside pedestrians was determined andrecognition distances measured using a parallax-based device. Ten young and ten older participants drove atnight around a closed road circuit and pressed a button whenever they recognized a pedestrian. Fourpedestrian clothing conditions were tested (black, white, retroreflective vest and retroreflective material inthe ‘biomotion’ configuration) in both low and high beam conditions. Two pedestrians walked in place onthe shoulder of the road, one in darkness (primary) and one in a high glare position (secondary). Responsedistances were recorded for the primary pedestrian. Overall, drivers identified only 61% of pedestrians inthe presence of glare and 76% in the absence of glare, with only 5% of darkly clad pedestrians beingidentified in the glare condition. Averaged across conditions, the primary pedestrian was identified at 76.5m(251ft), with distances being shortest for darkly clad pedestrians (13m (43ft)), and greatest for the‘biomotion’ pedestrian condition, which improved response distances by up to 50X. The vest conditionfailed to produce similar benefits, despite having an equivalent amount of retroreflective material. Overall,older driver response distances were 58% of those of the younger drivers. These results demonstrate thatwhile all drivers have significant difficulty recognizing pedestrians at night, elderly drivers experience evengreater difficulty. The results also demonstrate the value of clothing configurations that enhance theperception of biological motion.
A New Scheme for Annotating Semantic Relations between Named Entities in Corpora

Although several studies have developed models and type hierarchies for named entity annotation, no such resource is available for semantic relation annotation, despite its utility for various applications (e.g. question answering, information extraction). In this paper, we show that there are two issues in semantic relation description, one concerning knowledge engineering (what to annotate? ) and the other concerning language engineering (how to deal with modality and modifiers? ). We propose a new annotation scheme, making it possible to have both a precise and tractable annotation. A practical experiment shows that annotators using our scheme were able to quickly annotate a large number of sentences with very high inter-annotator agreement.
Locality and availability of array codes constructed from subspaces

Ever-increasing amounts of data are created and processed in internet-scale companies such as Google, Facebook, and Amazon. The efficient storage of such copious amounts of data has thus become a fundamental and acute problem in modern computing. No single machine can possibly satisfy such immense storage demands. Therefore, distributed storage systems (DSS), which rely on tens of thousands of storage nodes, are the only viable solution. Such systems are broadly used in all modern internet-scale systems. However, the design of a DSS poses a number of crucial challenges, markedly different from single-user storage systems. Such systems must be able to reconstruct the data efficiently, to overcome failure of servers, to correct errors, etc. Lots of research was done in the last few years to answer these challenges and the research is increasing in parallel to the increasing amount of stored data. The main goal of this paper is to consider codes which have two of the most important features of distributed storage systems, namely, locality and availability. Our codes are array codes which are based on subspaces of a linear space over a finite field. We present several constructions of such codes which are q-analog to some of the known block codes. Some of these codes possess independent intellectual merit. We examine the locality and availability of the constructed codes. In particular we distinguish between two types of locality and availability, node vs. symbol, locality and availability. To our knowledge this is the first time that such a distinction is given in the literature.
A weight-based map matching method in moving objects databases

In location management, the trajectory represents the motion of a moving object in 3D space-time, i.e., a sequence (x, y, t). Unfortunately, location technologies, cannot guarantee error-freedom. Thus, map matching (a.k.a. snapping), matching a trajectory to the roads on the map, is necessary. We introduce a weight-based map matching method, and experimentally show that, for the offline situation, on average, our algorithm can get up to 94% correctness depending on the GPS sampling interval.
Identification of Frequency of Biased Harmonic Signal

We consider a problem of identification of unknown frequency of a biased sinusoidal signal y(t) = σ0 + σ sin(ωt + φ) + δ(t) with bounded disturbance or harmonic noise δ(t). A new proposed approach to estimation of frequency of biased sinusoidal signal is robust with regard to unaccounted disturbances, which are present in measurement of effective signal. Unlike known analogs, this approach allows to regulate time of estimation of unknown frequency ω. The proposed approach also allows online amplitude and bias estimation. The proposed identification algorithm has smaller dimension than other known analogs.
A Partial Searching Algorithm and Its Application for Polyphonic Music Transcription

This paper proposes an algorithm for studying spectral contents of pitched sounds in real-world recordings. We assume that the 2-order difference, w.r. t. partial index, of a pitched sound is bounded by some small positive value, rather than equal to 0 in a perfect harmonic case. Given a spectrum and a fundamental frequency f0, the algorithm searches the spectrum for partials that can be associated with f0 by dynamic programming. In section 3 a background-foreground model is plugged into the algorithm to make it work with reverberant background, such as in a piano recording. In section 4 we illustrate an application of the algorithm in which a multipitch scoring machine, which involves special processing for close or shared partials, is coupled with a tree searching method for polyphonic transcription task. Results are evaluated on the traditional note level, as well as on a partial-based sub-note level.
Role of Urokinase Receptor in Tumor Progression and Development

Elevated level of urokinase receptor (uPAR) is detected in various aggressive cancer types and is closely associated with poor prognosis of cancers. Binding of uPA to uPAR triggers the conversion of plasminogen to plasmin and the subsequent activation of metalloproteinases. These events confer tumor cells with the capability to degrade the components of the surrounding extracellular matrix, thus contributing to tumor cell invasion and metastasis. uPA-uPAR interaction also elicits signals that stimulate cell proliferation/survival and the expression of tumor-promoting genes, thus assisting tumor development. In addition to its interaction with uPA, uPAR also interacts with vitronectin and this interaction promotes cancer metastasis by activating Rac and stimulating cell migration. Although underlying mechanisms are yet to be fully elucidated, uPAR has been shown to facilitate epithelial-mesenchymal transition (EMT) and induce cancer stem cell-like properties in breast cancer cells. The fact that uPAR lacks intracellular domain suggests that its signaling must be mediated through its co-receptors. Indeed, uPAR interacts with diverse transmembrane proteins including integrins, ENDO180, G protein-coupled receptors and growth factor receptors in cancer cells and these interactions are proven to be critical for the role of uPAR in tumorigenesis. Inhibitory peptide that prevents uPA-uPAR interaction has shown the promise to prolong patients' survival in the early stage of clinical trial. The importance of uPAR's co-receptor in uPAR's tumor-promoting effects implicate that anti-cancer therapeutic agents may also be developed by disrupting the interactions between uPAR and its functional partners.
14 Wavelet Analysis and Neural Networks for Bearing Fault Diagnosis

Today, most maintenance actions are carried out by either corrective (run to failure) or preventive (scheduled or predetermined) strategy. In Corrective Maintenance (CM) the components are maintained after obvious faults or actual breakdown has occurred. With this maintenance strategy the associated costs are usually high due to the production losses, fault occurrence damages, restoring equipment until is being used at failure condition, and the safety/health hazards presented by the fault. However, the Preventive Maintenance (PM) approach has been developed to overcome the CM deficiencies. Traditionally, PM is a time driven process which is performed at regular time intervals, commonly termed the maintenance cycle, regardless of the components actual condition, in order to prevent component or systems breakdown. For example, changing the car engine oil at every 5000 KMs traveled distance, where no concern as to the actual condition and performance capability of the replaced oil.
Bridging Data in the Clouds: An Environment-Aware System for Geographically Distributed Data Transfers

Today's continuously growing cloud infrastructures provide support for processing ever increasing amounts of scientific data. Cloud resources for computation and storage are spread among globally distributed datacenters. Thus, to leverage the full computation power of the clouds, global data processing across multiple sites has to be fully enabled. However, managing data across geographically distributed data enters is not trivial as it involves high and variable latencies among sites which come at a high monetary cost. In this work, we propose a uniform data management system for scientific applications running across geographically distributed sites. Our solution is environment-aware, as it monitors and models the global cloud infrastructure, and offers predictable data handling performance for transfer cost and time. In terms of efficiency, it provides the applications with the possibility to set a trade off between money and time and optimizes the transfer strategy accordingly. The system was validated on Microsoft's Azure cloud across the 6 EU and US data enters. The experiments were conducted on hundreds of nodes using both synthetic benchmarks and the real life A-Brain application. The results show that our system is able to model and predict well the cloud performance and to leverage this into efficient data dissemination. Our approach reduces the monetary costs and transfer time by up to 3 times.
Clinical and microbiologic outcomes in patients receiving treatment for Mycobacterium abscessus pulmonary disease.

BACKGROUND Mycobacterium abscessus can produce a chronic pulmonary infection for which little is known regarding optimal treatment and long-term outcomes. METHODS We performed a retrospective observational study (2001-2008) including all patients who met American Thoracic Society criteria for M. abscessus pulmonary disease. Our aim was the evaluation of clinical and microbiologic outcomes in patients treated with combined antibiotic and surgical therapy, compared with antibiotic therapy alone. RESULTS A total of 107 patients were included in the analysis. Patients were predominantly female (83%) and never-smokers (60%), with a mean age of 60 years. Fifty-nine (55%) of 107 patients had coexistent or previous history of Mycobacterium avium complex pulmonary infection. High-resolution chest CT showed bronchiectasis and nodular opacities in 98% of patients and cavities in 44%. Sixty-nine (46 medical, 23 surgical) patients were followed up for a mean duration of 34 months (standard deviation, 21.1 months, range, 2-82 months). Cough, sputum production, and fatigue remained stable, improved, or resolved in 80%, 69%, and 59% of patients, respectively. Twenty (29%) of 69 patients remained culture positive, 16 (23%) converted but experienced relapse, 33 (48%) converted to negative and did not experience relapse, and 17 (16%) died during the study period. There were significantly more surgical patients than medical patients whose culture converted and remained negative for at least 1 year (57% vs 28%; P = .022). CONCLUSIONS Patients with M. abscessus pulmonary disease who are treated with multidrug antibiotic therapy and surgery or antibiotic therapy alone had similar clinical outcomes. However, surgical resection, in addition to antibiotics, may offer a prolonged microbiologic response.
Topic Identification in Discourse

This paper proposes a corpus-based language model for topic identification. We analyze the association of noun-noun and noun-verb pairs in LOB Corpus. The word association norms are based on three factors: 1) word importance, 2) pair co-occurrence, and 3) distance. They are trained on the paragraph and sentence levels for noun-noun and noun-verb pairs, respectively. Under the topic coherence postulation, the nouns that have the strongest connectivities with the other nouns and verbs in the discourse form the preferred topic set. The collocational semantics then is used to identify the topics from paragraphs and to discuss the topic shift phenomenon among paragraphs.
Analysis of Pull-in Range Limit by Charge Pump Mismatch in a Linear Phase-Locked Loop

In this paper, we show the relationship between the pull-in range of a linear phase-locked loop (PLL) and the current mismatch of the charge pump that controls the frequency of the oscillator in the PLL. We evaluate the pull-in range of the PLL based on a nonlinear behavioral model of the pull-in process with three types of phase detectors. We introduce the mismatch error to the charge pump current in the PLL and study the impact of this error on the pull-in range. We also apply the mismatch error to a nonlinear differential equation that describes the loop dynamics of the PLL and calculate the pull-in range under this mismatch condition. We validate the limitations of the pull-in range due to the current mismatch by a numerical simulation with MATLAB.