Miracle-dz/UniFAR-FTUs huggingface dataset:
Pattern Formation and Optimization in Army Ant Raids

Army ant colonies display complex foraging raid patterns involving thousands of individuals communicating through chemical trails. In this article we explore, by means of a simple search algorithm, the properties of these trails in order to test the hypothesis that their structure reflects an optimized mechanism for exploring and exploiting food resources. The raid patterns of three army ant species, Eciton hamatum, Eciton burchelli, and Eciton rapax, are analyzed. The respective diets of these species involve large but rare, small but common, and a combination of large but rare and small but common food sources. Using a model proposed by Deneubourg et al. [4], we simulate the formation of raid patterns in response to different food distributions. Our results indicate that the empirically observed raid patterns maximize return on investment, that is, the amount of food brought back to the nest per unit of energy expended, for each of the diets. Moreover, the values of the parameters that characterize the three optimal pattern-generating mechanisms are strikingly similar. Therefore the same behavioral rules at the individual level can produce optimal colony-level patterns. The evolutionary implications of these findings are discussed.
Mining Segment-Wise Periodic Patterns in Time-Related Databases

Periodicity search, that is, search for cyclicity in time-related databases, is an interesting data mining problem. Most previous studies have been on finding full-cycle periodicity for all the segments in the selected sequences of the data, that is, if a sequence is periodic, all the points or segments in the period repeat. However, it is often useful to mine segment-wise or point-wise periodicity in time-related data sets. In this study, we integrate data cube and Apriori data mining techniques for mining segment-wise periodicity in regard to a fixed length period and show that data cube provides an efficient structure and a convenient way for interactive mining of multiple-level periodicity.
Copper-catalyzed arylation of alkyl halides with arylaluminum reagents

Summary We report a Cu-catalyzed coupling between triarylaluminum reagents and alkyl halides to form arylalkanes. The reaction proceeds in the presence of N,N,N’,N’-tetramethyl-o-phenylenediamine (NN-1) as a ligand in combination with CuI as a catalyst. This catalyst system enables the coupling of primary alkyl iodides and bromides with electron-neutral and electron-rich triarylaluminum reagents and affords the cross-coupled products in good to excellent yields.
Finding deterministic solution from underdetermined equation: Large-scale performance modeling by least angle regression

The aggressive scaling of IC technology results in high-dimensional, strongly-nonlinear performance variability that cannot be efficiently captured by traditional modeling techniques. In this paper, we adapt a novel L1-norm regularization method to address this modeling challenge. Our goal is to solve a large number of (e.g., 104∼106) model coefficients from a small set of (e.g., 102∼103) sampling points without over-fitting. This is facilitated by exploiting the underlying sparsity of model coefficients. Namely, although numerous basis functions are needed to span the high-dimensional, strongly-nonlinear variation space, only a few of them play an important role for a given performance of interest. An efficient algorithm of least angle regression (LAR) is applied to automatically select these important basis functions based on a limited number of simulation samples. Several circuit examples designed in a commercial 65nm process demonstrate that LAR achieves up to 25× speedup compared with the traditional least-squares fitting.
Immunofluorescent visualization of specifically bound thrombin reveals cellular heterogeneity in number and density of preclustered receptors

Thrombin binding to formaldehyde‐fixed mouse embryo (ME) cells was visualized by indirect immunofluorescence as a dot‐like pattern with dots of approximately 500 nm diameter located over the entire cell surface. Experiments comparing the binding of 125I‐thrombin and dot appearance on parallel cultures indicate that the immunofluorescent pattern is specific for thrombin‐binding to high‐affinity receptors. Similar patterns were observed on cells fixed in ethanol or glutaraldehyde prior to thrombin binding and on cells maintained at 4°C. These patterns were also observed in a number of established cell lines. Thus, thrombin receptors may be clustered prior to thrombin binding on all cells with these receptors. Comparing the amount of 125I‐thrombin bound to CHO cells with the number of fluorescent dots per cell indicated that each dot represents a cluster of over 1000 receptors. On ME cells, the number of thrombin receptor clusters per cell ranged from fewer than 50 to over 5,000. Based on previous studies, this indicates that on ME cells each cluster contains an average of approximately 200 thrombin binding sites with some cells having few, if any, receptors and others having more than a million receptors per cell.
Validity of cardiovascular risk prediction models in Latin America and among Hispanics in the United States of America: a systematic review.

OBJECTIVE To assess the use and validity of prediction models to estimate the risk of cardiovascular disease (CVD) in Latin America and among Hispanic populations in the United States of America. METHODS This was a systematic review of three databases: Ovid MEDLINE (1 January 1950-15 April 2010), LILACS (1 January 1988-15 April 2010), and EMBASE (1 January 1988-15 April 2010). MeSH search terms and domains were related to CVD, prediction rules, Latin America (including the Caribbean), and Hispanics in the United States. Database searches were supplemented by correspondence with experts in the field. RESULTS A total of 1 655 abstracts were identified, of which five cohorts with a total of 13 142 subjects met inclusion criteria. A Mexican cohort showed that the predicted/observed event-rate ratio for coronary heart disease (CHD) according to the Framingham risk score (FRS) was 1.68 (95% CI, 1.26-2.11); incident myocardial infarction, 1.36 (95% CI, 0.90-1.83); and CHD death, 1.21 (95% CI, 0.43-2.00). In Ecuador, a prediction model for CVD and total deaths in hypertensive patients had an area under the curve (AUC) of 0.79 (95% CI, 0.72-0.86), while the World Health Organization method had an AUC of 0.74 (95% CI, 0.67-0.82). A study predicting mortality risk in people with Chagas' disease had an AUC of 0.81 (95% CI, 0.72-0.90). Among a United State s cohort that included Hispanics, FRS overestimated CVD risk for Hispanics with an AUC of 0.69. Another study in the United States that assessed FRS factors predicting CVD death among Mexican-Americans had an AUC of 0.78. CONCLUSIONS The evidence regarding CVD risk prediction rules in Latin America or among Hispanics in the United States is modest at best. It is likely that the FRS overestimates CVD risk in Hispanics when not properly recalibrated.
A global virulence regulator in Acinetobacter baumannii and its control of the phenylacetic acid catabolic pathway.

BACKGROUND Acinetobacter baumannii is one of the most notorious hospital-acquired pathogens, and novel treatment strategies are desperately required. Two-component regulatory systems represent potential therapeutic targets as they mediate microorganism adaptation to changing environments, often control virulence, and are specific to bacteria. Here we describe the first global virulence regulator in A. baumannii. METHODS AND RESULTS Using transcriptional profiling and functional assays of a deletion mutant in the A. baumannii sensor kinase gene, A1S_0574 (termed as gacS), we show that this sensor kinase regulates key virulence characteristics, including pili synthesis, biofilms, and motility, resulting in virulence attenuation in a mammalian septicemia model. Notably, we also identified that GacS regulates an operon novel to A. baumannii (paa operon), which is responsible for the metabolism of aromatic compounds. Deletion of paaE (A1S_1340) confirmed the role of this operon in A. baumannii virulence. Finally, we identified the cognate response regulator (A1S_0236) for GacS and confirmed their interaction. A1S_0236 was shown to regulate 75% of the GacS transcriptome and the same virulence phenotypes. Overexpression of A1S_0236 restored virulence in the gacS mutant. CONCLUSIONS Our study characterizes a global virulence regulator, which may provide an alternate therapeutic target, in one of the most troublesome hospital-acquired pathogens.
Stromal cells control soluble material and cellular transport in lymph nodes

Lymphocytes continuously patrol the secondary lymphoid organs (SLOs) of mammals in search for their cognate antigens. SLOs are composed of leucocytes (~95%) and lymphoid stromal cells (~5%) that form the structural framework of these organs. These sessile cells have been considered for decades as inert elements of the immune system. This simplistic view has dramatically changed in recent years, when it was discovered that these architectural cells are endowed with immuno-regulatory functions. Lymph nodes (LNs) are located at the interface between the blood and lymphatic systems, thus allowing tissue-derived antigen/antigen presenting cells (APCs) to gather with blood-derived lymphocytes. As a typical LN contains ~10 million of tightly packed cells, this accumulation of immune cells and information is probably not sufficient to foster the rare cellular interactions mandatory to the initiation of adaptative immune responses. Herein, I review some of the physicochemical elements of stromal cells that are used to transport and guide immune cells and soluble molecules within LNs.
Image-Based Artefact Removal in Laser Scanning Microscopy

Recent developments in laser scanning microscopy have greatly extended its applicability in cancer imaging beyond the visualization of complex biology, and opened up the possibility of quantitative analysis of inherently dynamic biological processes. However, the physics of image acquisition intrinsically means that image quality is subject to a tradeoff between a number of imaging parameters, including resolution, signal-to-noise ratio, and acquisition speed. We address the problem of geometric distortion, in particular, jaggedness artefacts that are caused by the variable motion of the microscope laser, by using a combination of image processing techniques. Image restoration methods have already shown great potential for post-acquisition image analysis. The performance of our proposed image restoration technique was first quantitatively evaluated using phantom data with different textures, and then qualitatively assessed using in vivo biological imaging data. In both cases, the presented method, comprising a combination of image registration and filtering, is demonstrated to have substantial improvement over state-of-the-art microscopy acquisition methods.
Temporal reasoning in process planning

Computer-aided process planning has been recognized as an important tool for coordinating the different operations involved in making the product. While temporal knowledge is central to the design of efficient and reliable process plans, little attention is given to the integration of process planning and temporal processing and reasoning. To fill the void, we propose in this paper a practical approach, which is inspired by the framework of Temporal Constraint Satisfaction Problem (TCSP), to integrate process planning and temporal reasoning. We show that a TCSP formulation is a subset of a formulation using a reified temporal logic, and discuss the advantages of using such a restricted model. To reflect more realistic process planning encountered in real manufacturing environments, we present a model, called n-TCSP, which is a generalization of the TCSP framework. We envision the proposed temporal reasoning framework as one of the modules in the evolving new intelligent computer-aided process planning.
FDVT: Data Valuation Tool for Facebook Users

The OECD, the European Union and other public and private initiatives are claiming for the necessity of tools that create awareness among Internet users about the monetary value associated to the commercial exploitation of their online personal information. This paper presents the first tool addressing this challenge, the Facebook Data Valuation Tool (FDVT). The FDVT provides Facebook users with a personalized and real-time estimation of the revenue they generate for Facebook. Relying on the FDVT, we are able to shed light into several relevant HCI research questions that require a data valuation tool in place. The obtained results reveal that (i) there exists a deep lack of awareness among Internet users regarding the monetary value of personal information, (ii) data valuation tools such as the FDVT are useful means to reduce such knowledge gap, (iii) 1/3 of the users testing the FDVT show a substantial engagement with the tool.
First- and Second-Generation College Students: A Comparison of Their Engagement and Intellectual Development

Students who are the first in their family to attend college are less likely to graduate compared to students with one or both parents who have baccalaureate degrees. However, surprisingly little is known about the college experiences of first-generation students. This study examined the self-reported college experiences of 1,127 first-year students at a variety of four-year colleges and universities. First-generation students tended to be less engaged and gained less from college than their counterparts with college-educated parents did. These differences were primarily due to first-generation students having lower educational aspirations and living off campus.
Progressive Periodontal Disease and Risk of Very Preterm Delivery

OBJECTIVE: The goal was to estimate whether maternal periodontal disease was predictive of preterm (less than 37 weeks) or very preterm (less than 32 weeks) births. METHODS: A prospective study of obstetric outcomes, entitled Oral Conditions and Pregnancy (OCAP), was conducted with 1,020 pregnant women who received both an antepartum and postpartum periodontal examination. Predictive models were developed to estimate whether maternal exposure to either periodontal disease at enrollment (less than 26 weeks) and/or periodontal disease progression during pregnancy, as determined by comparing postpartum with antepartum status, were predictive of preterm or very preterm births, adjusting for risk factors including previous preterm delivery, race, smoking, social domain variables, and other infections. RESULTS: Incidence of preterm birth was 11.2% among periodontally healthy women, compared with 28.6% in women with moderate-severe periodontal disease (adjusted risk ratio [RR] 1.6, 95% confidence interval [CI] 1.1–2.3). Antepartum moderate-severe periodontal disease was associated with an increased incidence of spontaneous preterm births (15.2% versus 24.9%, adjusted RR 2.0, 95% CI 1.2–3.2). Similarly, the unadjusted rate of very preterm delivery was 6.4% among women with periodontal disease progression, significantly higher than the 1.8% rate among women without disease progression (adjusted RR 2.4, 95% CI 1.1–5.2). CONCLUSION: The OCAP study demonstrates that maternal periodontal disease increases relative risk for preterm or spontaneous preterm births. Furthermore, periodontal disease progression during pregnancy was a predictor of the more severe adverse pregnancy outcome of very preterm birth, independently of traditional obstetric, periodontal, and social domain risk factors. LEVEL OF EVIDENCE: II-2
Randomized Greedy Inference for Joint Segmentation, POS Tagging and Dependency Parsing

In this paper, we introduce a new approach for joint segmentation, POS tagging and dependency parsing. While joint modeling of these tasks addresses the issue of error propagation inherent in traditional pipeline architectures, it also complicates the inference task. Past research has addressed this challenge by placing constraints on the scoring function. In contrast, we propose an approach that can handle arbitrarily complex scoring functions. Specifically, we employ a randomized greedy algorithm that jointly predicts segmentations, POS tags and dependency trees. Moreover, this architecture readily handles different segmentation tasks, such as morphological segmentation for Arabic and word segmentation for Chinese. The joint model outperforms the state-of-the-art systems on three datasets, obtaining 2.1% TedEval absolute gain against the best published results in the 2013 SPMRL shared task. 1
Tau tubulin kinases in proteinopathy

A number of neurodegenerative diseases are characterized by deposition of abnormally phosphorylated tau or TDP‐43 in disease‐affected neurons. These diseases include Alzheimer's disease, frontotemporal lobar degeneration, and amyotrophic lateral sclerosis. No disease‐modifying therapeutics is available to treat these disorders, and we have a limited understanding of the cellular and molecular factors integral to disease initiation or progression. Phosphorylated tau and TDP‐43 are important markers of pathology in dementia disorders and directly contribute to tau‐ and TDP‐43‐related neurotoxicity and neurodegeneration. Here, we review the scope of tau and TDP‐43 phosphorylation in neurodegenerative disease and discuss recent work demonstrating the kinases TTBK1 and TTBK2 phosphorylate both tau and TDP‐43, promoting neurodegeneration.
Emergency department overcrowding and ambulance transport delays for patients with chest pain.

OBJECTIVE Emergency department overcrowding sometimes results in diversion of ambulances to other locations. We sought to determine the resulting prehospital delays for cardiac patients. METHODS Data on consecutive patients with chest pain who were transported to Toronto hospitals by ambulance were obtained for a 4-month period in 1997 and a 4-month period in 1999, which represented periods of low and high emergency department overcrowding respectively. Multivariate analyses were used to model 90th percentile system response (initiation of 9-1-1 call to arrival on scene), on-scene (arrival on scene to departure from scene) and transport (departure from scene to arrival at hospital) intervals. Predictor variables were study period (1997 or 1999), day of the week, time of day, geographic location of the patient, dispatch priority, case severity, return priority and number of other patients with chest pain transported within 2 hours of the index transport. RESULTS A total of 3609 patients (mean age 66.3 years, 50.3% female) who met the study criteria were transported by ambulance during the 2 study periods. There were no significant differences in patient characteristics between the 2 periods, despite the fact that more patients were transported during the second period (p < 0.001). The 90th percentile system response interval increased by 11.3% from the first to the second period (9.7 v. 10.8 min, p < 0.001), whereas the on-scene interval decreased by 8.2% (28.0 v. 25.7 min, p < 0.001). The longest delay was in the transport interval, which increased by 28.4% from 1997 to 1999 (13.4 v. 17.2 min, p < 0.001). In multivariate analyses, the study period (1997 v. 1999) remained a significant predictor of longer transport interval (p < 0.001) and total prehospital interval (p = 0.004). INTERPRETATION An increase in overcrowding in emergency departments was associated with a substantial increase in the system response interval and the ambulance transport interval for patients with chest pain.
Digitally Equalized Doherty RF Front-End Architecture for Broadband and Multistandard Wireless Transmitters

This paper introduces a new architecture of frequency-agile Doherty power amplifier (PA)-based RF front-end. This architecture incorporates a baseband equalizer that is implemented using finite-impulse-response (FIR) digital filters to improve the performance of Doherty PAs when driven with large bandwidth and multiband wireless radios. Depending on the center frequency and bandwidth of the input signal, the FIR filters of the proposed equalizer are synthesized to compensate for the nonideal frequency behavior of the RF building blocks of the Doherty PA. It is shown that the proposed architecture enables the Doherty PA to operate with significantly improved power efficiency and linearity performance beyond its nominal frequency of design, which is suitable for multistandard applications. As a matter of fact, when driven with a 140-MHz bandwidth long-term evolution (LTE) signal centered around 2.30 GHz, the average efficiency of a 2.14-GHz Doherty PA prototype with the proposed digital baseband equalizer is enhanced from 33.5% to 44.7%. Moreover, its linearity performance in terms of adjacent channel leakage ratio (ACLR) is improved from -21 to -26 dB. In addition, when operated in concurrent dual-band mode with two 20-MHz bandwidth LTE signals centered at 1.96 and 2.34 GHz, the proposed Doherty PA enabled a reduction in dc power consumption by nearly 15%. Furthermore, it is demonstrated that the integration of the proposed baseband equalizer does not compromise the linearizability of the Doherty PA. To the best of the authors' knowledge, this is the first demonstration of the use of digital equalization for performance enhancement of RF Doherty PAs.
The interplay of sequence conservation and T cell immune recognition

Predicting which peptides can elicit a T cell response (i.e. are immunogenic) is of great importance for many immunological studies. While it is clear that MHC binding is a necessary requirement for peptide immunogenicity, other variables exist that are incompletely understood. In this study we examined the hypothesis that conservation of a peptide in bacteria that are part of the healthy human microbiome leads to a reduced level of immunogenicity due to tolerization of T cells to the commensal bacteria. This was done by comparing experimentally characterized T cell epitope recognition data from the Immune Epitope Database with their conservation in the human microbiome. Indeed, we did see a lower immunogenicity for conserved peptides conserved. While many aspects how this conservation comparison is done require further optimization, this is a first step towards a better understanding T cell recognition of peptides in bacterial pathogens is influenced by their conservation in commensal bacteria. If the further work proves that this approach is successful, the degree of overlap of a peptide with the human proteome or microbiome could be added to the arsenal of tools available to assess peptide immunogenicity.
System Performance of Fixed Beams with S-CPICH as a Phase Reference in WCDMA

A fixed beam (FB) system that uses a beam specific secondary-common pilot channel (S-CPICH) as a phase reference for channel estimation and demodulation in WCDMA is evaluated in a dynamic radio network simulator. The impact of the angular spread on the downlink (DL) system performance is analyzed. Furthermore, various scrambling code allocation strategies and an adaptive load-dependent power tuning algorithm of the common channels are proposed and evaluated. Extensive simulation results have verified that increasing the number of FB from 1 to 2 or 4 beams per sector in a typical urban radio channel yields significant DL capacity gains