Miracle-dz/UniFAR-FTUs huggingface dataset:
Tractability of Parameterized Completion Problems on Chordal, Strongly Chordal, and Proper Interval Graphs

We study the parameterized complexity of three NP-hard graph completion problems. The minimum fill-in problem asks if a graph can be triangulated by adding at most k edges. We develop O(ck m) and O(k2mn+f(k)) algorithms for this problem on a graph with n vertices and m edges. Here f(k) is exponential in k and the constants hidden by the big-O notation are small and do not depend on k. In particular, this implies that the problem is fixed-parameter tractable (FPT). The proper interval graph completion problem, motivated by molecular biology, asks if a graph can be made proper interval by adding no more than k edges. We show that the problem is FPT by providing a simple search-tree-based algorithm that solves it in O(ck m)-time. Similarly, we show that the parameterized version of the strongly chordal graph completion problem is FPT by giving an O(ck m log n)-time algorithm for it. All of our algorithms can actually enumerate all possible k-completions within the same time bounds.
Evaluation of the Presence of a Face Search Advantage in Chernoff Faces

Chernoff faces (Chernoff, 1973) are an early attempt at large scale multivariate data representation and are based on underlying assumptions that have not been empirically tested. This study investigated i) whether data coded as Chernoff faces benefit from face perception, and ii) whether each feature of a Chernoff face is equally salient. We tested four pairs of oppositely coded Chernoff faces (e.g. smile, frown) in an oddball search paradigm with set sizes of 5, 10 and 15. To evaluate whether face perception aided search, we used a control condition with inverted faces, a manipulation known to diminish holistic face processing. Equivalent search efficiencies for upright and inverted Chernoff faces demonstrates that they do not receive any significant benefit from face perception. Additionally, none of the features tested together produced significantly different search efficiencies from one another. It also appears that overall Chernoff faces do not allow for particularly efficient visual search.
Improving Wayfinding for Older Users With Selective Attention Deficits

Older adults experience difficulties with navigating their environments and may need to rely on signs more heavily than younger adults. However, older adults also experience difficulties with focusing their visual attention, which suggests that signs need to be designed with the goal of making it as easy as possible to attend to them. This article discusses some design principles that may be especially important to compensate for declining attentional focus. These principles include distinctiveness, consistent appearance and location, standardized images, simplicity, isolation from other elements of the environment, and reassurance about the current route.
Modulation of Yersinia Type Three Secretion System by the S1 Domain of Polynucleotide Phosphorylase*

Both low temperatures and encounters with host phagocytes are two stresses that have been relatively well studied in many species of bacteria. Previous work has shown that the exoribonuclease polynucleotide phosphorylase (PNPase) is required for Yersiniae to grow at low temperatures. Here, we show that PNPase also enhances the ability of Yersinia pseudotuberculosis and Yersinia pestis to withstand the killing activities of murine macrophages. PNPase is required for the optimal functioning of the Yersinia type three secretion system (TTSS), an organelle that injects effector proteins directly into host cells. Unexpectedly, the effect of PNPase on the TTSS is independent of its ribonuclease activity and instead requires its S1 RNA binding domain. In contrast, catalytically inactive enzyme does not enhance the low temperature growth effect of PNPase. Surprisingly, wild-type-like TTSS functioning was restored to the pnp mutant strain by expressing just the ∼70 amino acid S1 domains from either PNPase, RNase R, RNase II, or RpsA. Our findings suggest that PNPase plays multifaceted roles in enhancing Yersinia survival in response to stressful conditions.
Deliberation on Design Strategies of Automatic Harvesting Systems: A Survey

In Asia, decreasing farmer and labor populations due to various factors is a serious problem that leads to increases in labor costs, higher harvesting input energy consumption and less resource utilization. To solve these problems, researchers are engaged in providing long term and low-tech alternatives in terms of mechanization and automation of agriculture by way of efficient, low cost and easy to use solutions. This paper reviews various design strategies in recognition and picking systems, as well as developments in fruit harvesting robots during the past 30 years in several countries. The main objectives of this paper are to gather all information on fruit harvesting robots; focus on the technical developments so far achieved in picking devices; highlight the problems still to be solved; and discuss the future prospects of fruit harvesting robots.
Different Patterns of Cytokines and Chemokines Combined with IFN-γ Production Reflect Mycobacterium tuberculosis Infection and Disease

Background IFN-γ is presently the only soluble immunological marker used to help diagnose latent Mycobacterium tuberculosis (M.tb) infection. However, IFN-γ is not available to distinguish latent from active TB infection. Moreover, extrapulmonary tuberculosis, such as tuberculous pleurisy, cannot be properly diagnosed by IFN-γ release assay. As a result, other disease- or infection-related immunological biomarkers that would be more effective need to be screened and identified. Methodology A panel of 41 soluble immunological molecules (17 cytokines and 24 chemokines) was tested using Luminex liquid array-based multiplexed immunoassays. Samples, including plasma and pleural effusions, from healthy donors (HD, n = 12) or patients with latent tuberculosis infection (LTBI, n = 20), pulmonary tuberculosis (TB, n = 12), tuberculous pleurisy (TP, n = 15) or lung cancer (LC, n = 15) were collected and screened for soluble markers. Peripheral blood mononuclear cells (PBMCs) and pleural fluid mononuclear cells (PFMCs) were also isolated to investigate antigen-specific immune factors. Principal Findings For the 41 examined factors, our results indicated that three patterns were closely associated with infection and disease. (1) Significantly elevated plasma levels of IL-2, IP-10, CXCL11 and CXCL12 were present in both patients with tuberculosis and in a sub-group participant with latent tuberculosis infection who showed a higher level of IFN-γ producing cells by ELISPOT assay compared with other latently infected individuals. (2) IL-6 and IL-9 were only significantly increased in plasma from active TB patients, and the two factors were consistently highly secreted after M.tb antigen stimulation. (3) When patients developed tuberculous pleurisy, CCL1, CCL21 and IL-6 were specifically increased in the pleural effusions. In particular, these three factors were consistently highly secreted by pleural fluid mononuclear cells following M.tb-specific antigen stimulation. In conclusion, our data imply that the specific secretion of soluble immunological factors, in addition to IFN-γ, may be used to evaluate M.tb infection and tuberculosis disease.
SIMULATION OF THE AERONAUTICAL RADIO CHANNEL FOR TELEMETRY APPLICATIONS

The aeronautical channel is an air to ground channel characterized by multipath, high doppler shifts, Rayleigh fading and noise. Use of a channel sounder ensures proper estimation of the parameters associated with the impulse response of the channel. These estimates help us to characterize the radio channels associated with aeronautical telemetry. In order to have a satisfactory channel characterization, the amplitudes, phase shifts and delays associated with each multipath component in the channel model must be determined.
Recursive Diffeomorphism-Based Regression for Shape Functions

This paper proposes a recursive diffeomorphism based regression method for one-dimensional generalized mode decomposition problem that aims at extracting generalized modes $\alpha_k(t)s_k(2\pi N_k\phi_k(t))$ from their superposition $\sum_{k=1}^K \alpha_k(t)s_k(2\pi N_k\phi_k(t))$. First, a one-dimensional synchrosqueezed transform is applied to estimate instantaneous information, e.g., $\alpha_k(t)$ and $N_k\phi_k(t)$. Second, a novel approach based on diffeomorphisms and nonparametric regression is proposed to estimate wave shape functions $s_k(t)$. These two methods lead to a framework for the generalized mode decomposition problem under a weak well-separation condition. Numerical examples of synthetic and real data are provided to demonstrate the fruitful applications of these methods.
Metagenome Sequencing of the Microbial Community of a Solar Saltern Crystallizer Pond at Cáhuil Lagoon, Chile

ABSTRACT Cáhuil Lagoon in central Chile harbors distinct microbial communities in various solar salterns that are arranged as interconnected ponds with increasing salt concentrations. Here, we report the metagenome of the 3.0- to 0.2-µm fraction of the microbial community present in a crystallizer pond with 34% salinity.
The ever-surprising chemistry of boron: enhanced acidity of phosphine.boranes.

The acidity-enhancing effect of BH(3) in gas-phase phosphineboranes compared to the corresponding free phosphines is enormous, between 13 and 18 orders of magnitude in terms of ionization constants. Thus, the enhancement of the acidity of protic acids by Lewis acids usually observed in solution is also observed in the gas phase. For example, the gas-phase acidities (GA) of MePH(2) and MePH(2)BH(3) differ by about 118 kJ mol(-1) (see picture). The gas-phase acidity of a series of phosphines and their corresponding phosphineborane derivatives was measured by FT-ICR techniques. BH(3) attachment leads to a substantial increase of the intrinsic acidity of the system (from 80 to 110 kJ mol(-1)). This acidity-enhancing effect of BH(3) is enormous, between 13 and 18 orders of magnitude in terms of ionization constants. This indicates that the enhancement of the acidity of protic acids by Lewis acids usually observed in solution also occurs in the gas phase. High-level DFT calculations reveal that this acidity enhancement is essentially due to stronger stabilization of the anion with respect to the neutral species on BH(3) association, due to a stronger electron donor ability of P in the anion and better dispersion of the negative charge in the system when the BH(3) group is present. Our study also shows that deprotonation of ClCH(2)PH(2) and ClCH(2)PH(2)BH(3) is followed by chloride departure. For the latter compound deprotonation at the BH(3) group is found to be more favorable than PH(2) deprotonation, and the subsequent loss of Cl(-) is kinetically favored with respect to loss of Cl(-) in a typical S(N)2 process. Hence, ClCH(2)PH(2)BH(3) is the only phosphineborane adduct included in this study which behaves as a boron acid rather than as a phosphorus acid.
EORTC Receptor and Biomarker Study Group Report: A Sandwich Enzyme-Linked Immunosorbent Assay for Vascular Endothelial Growth Factor in Blood and Tumor Tissue Extracts

A four-antibody sandwich enzyme-linked immunosorbent assay (ELISA) for vascular endothelial growth factor (VEGF) for application in blood (serum and plasma) and tumor tissue extracts was set up within the framework of the EORTC Receptor and Biomarker Study Group (RBSG). Polyclonal antibodies against VEGF165 were raised in chickens and rabbits, and used in a previously described assay format. The assay was validated and characterized for use in serum, plasma and tumor tissue extracts. The resulting VEGF ELISA was found to be specific for VEGF165 and VEGF121, the main isoforms of VEGF. The assay showed good precision and parallelism in serial dilutions of samples. The assay was not susceptible to interference by heterophilic antibodies because avian antibodies (duck anti-chicken and chicken anti-VEGF) were used in the pre-analyte stage and mammalian antibodies (rabbit anti-VEGF and goat anti-rabbit) in the post-analyte stage. In conclusion, a sensitive, robust and specific VEGF ELISA has been developed. Research into the prognostic value of VEGF employing this assay is currently underway.
ClawHMMER: A Streaming HMMer-Search Implementatio

The proliferation of biological sequence data has motivated the need for an extremely fast probabilistic sequence search. One method for performing this search involves evaluating the Viterbi probability of a hidden Markov model (HMM) of a desired sequence family for each sequence in a protein database. However, one of the difficulties with current implementations is the time required to search large databases. Many current and upcoming architectures offering large amounts of compute power are designed with data-parallel execution and streaming in mind. We present a streaming algorithm for evaluating an HMM’s Viterbi probability and refine it for the specific HMM used in biological sequence search. We implement our streaming algorithm in the Brook language, allowing us to execute the algorithm on graphics processors. We demonstrate that this streaming algorithm on graphics processors can outperform available CPU implementations. We also demonstrate this implementation running on a 16 node graphics cluster.
Universal Dependencies Parsing for Colloquial Singaporean English

Singlish can be interesting to the ACL community both linguistically as a major creole based on English, and computationally for information extraction and sentiment analysis of regional social media. We investigate dependency parsing of Singlish by constructing a dependency treebank under the Universal Dependencies scheme, and then training a neural network model by integrating English syntactic knowledge into a state-of-the-art parser trained on the Singlish treebank. Results show that English knowledge can lead to 25% relative error reduction, resulting in a parser of 84.47% accuracies. To the best of our knowledge, we are the first to use neural stacking to improve cross-lingual dependency parsing on low-resource languages. We make both our annotation and parser available for further research.
MAPTRAITS 2014 - The First Audio/Visual Mapping Personality Traits Challenge - An Introduction: Perceived Personality and Social Dimensions

The Audio/Visual Mapping Personality Challenge and Workshop (MAPTRAITS) is a competition event that is organised to facilitate the development of signal processing and machine learning techniques for the automatic analysis of personality traits and social dimensions. MAPTRAITS includes two sub-challenges, the continuous space-time sub-challenge and the quantised space-time sub-challenge. The continuous sub-challenge evaluated how systems predict the variation of perceived personality traits and social dimensions in time, whereas the quantised challenge evaluated the ability of systems to predict the overall perceived traits and dimensions in shorter video clips. To analyse the effect of audio and visual modalities on personality perception, we compared systems under three different settings: visual-only, audio-only and audio-visual. With MAPTRAITS we aimed at improving the knowledge on the automatic analysis of personality traits and social dimensions by producing a benchmarking protocol and encouraging the participation of various research groups from different backgrounds.
CD5 and CD23 expression on B cells in peripheral blood and synovial fluid of rheumatoid arthritis patients: relationship with interleukin-4, soluble CD23 and tumour necrosis factor alpha levels.

METHODS We have studied in peripheral blood (PB) and synovial fluid (SF) of 31 patients diagnosed with rheumatoid arthritis (RA), the expression of CD5 and CD23 antigens on B cells, and the levels of soluble CD23 (sCD23), interleukin-4 (IL-4) and tumour necrosis factor alpha (TNF-alpha). We have also correlated the results with the disease activity index. RESULTS CD5+ B cells are expanded in SF and, moreover, show higher expression of CD23 than CD5 - B cells. Twelve patients had detectable levels of IL-4 in plasma and 10 in SF (nine patients in both samples); the absence of IL-4 was related to a higher expression of CD23 on CD5 + B cells and with higher levels of sCD23. A negative correlation was found in SF between TNF-alpha and sCD23 levels. CONCLUSION There is no correlation between disease activity index and the different parameters studied (expression of CD5 and CD23 on B cells, sCD23, IL-4 and TNF-alpha levels) either in plasma/PB or in SF.
A Metadata Workload Generator for Data-Intensive File Systems

Large-scale data-intensive computing [2, 3] has posed numerous challenges to the underlying distributed file system, due to the unprecedented amount of data, the large number of users, the intense competition on cost and service quality, and the emergence of new applications. As a result, there has been an increasing amount of research on scalable metadata management [4, 6], high availability [6], efficient scheduling [7], and dynamic data replication and placement [1]. The performance of the proposed solutions depends on the characteristics of the metadata workload, which describes file operations with respect to the underlying namespace, and captures correlation across time and file system structures. One example where realistic metadata workloads are highly desirable is the design of peta and exascale data-intensive file systems [5, 6]. The large scale of the system requires partitioning of the namespace, whose performance depends on the nature of the workload. Existing micro-benchmarks such as mdtest assume uniform data access patterns across all files, while realistic workloads, such as those we analyzed, exhibit highly skewed access patterns both in terms of file sizes and time since creation. The discrepancy in assumptions can cause ineffective namespace partitioning. Currently there exist no publicly available traces from large-scale data-intensive systems. Designers and evaluators often rely on proprietary traces and disclose only the characteristics of workloads that are interesting to that particular work. Comparisons of solutions to the same problem are difficult as the characteristics of one workload are difficult to verify in others. Within the Internet-services data-intensive community a few benchmark tools have emerged, but they have targeted other layers of the infrastructure (e.g., Gridmix for map-reduce and YCSB for key-value stores). We present a tool that generates representative workloads based on trace studies on two large production clusters at Yahoo! , and user-configurable workloads based on proprietary traces and/or user-specified parameters. The synthetic workloads generated are guaranteed to be statistically realistic with respect to the original traces, and conform to parameters set by users.
The Genesis of Pedophilia

Abstract Many male sex offenders against children say they themselves were sexually abused in childhood. This observation has supported several variations of what has come to be known as the “abuse-to-abuser hypothesis. ” This study tested three versions of the abuse-to-abuser hypothesis: (a) the age men are abused determines the age of their sexual victims; (b) sexually abused men are likely to reenact the type of abuse they experienced; (c) men who were sexually abused as children are more likely to sexually abuse same-sexed victims. A consecutive series was retrospectively reviewed consisting of 100 men accused of sexually abusing children. Subjects completed a standardized, semi-structured interview. Men with personal histories of sexual abuse (Assaulted offenders) and men without sexual abuse histories (Non-Assaulted offenders) were compared in terms of victim age, type of offense, and sex of victim using t-tests, correlation coefficients and Chi-square tests. Twenty percent of the sample reported pas.
Incremental Dependency Parsing Using Online Learning

We describe an incremental parser that was trained to minimize cost over sentences rather than over individual parsing actions. This is an attempt to use the advantages of the two top-scoring systems in the CoNLL-X shared task. In the evaluation, we present the performance of the parser in the Multilingual task, as well as an evaluation of the contribution of bidirectional parsing and beam search to the parsing performance.
Mechanism and Bicoid‐dependent control of hairy stripe 7 expression in the posterior region of the Drosophila embryo

Pair‐rule gene hairy (h) expression in seven evenly spaced stripes, along the longitudinal axis of the Drosophila blastoderm embryo, is mediated by a modular array of separate stripe enhancer elements. The minimal enhancer element, which generates reporter gene expression in place of the most posterior h stripe 7 (h7‐element), contains a dense array of binding sites for factors providing the trans‐acting control of h stripe 7 expression as revealed by genetic analyses. The h7‐element mediates position‐dependent gene expression by sensing region‐specific combinations and concentrations of both the maternal homeodomain transcriptional activators, Caudal and Bicoid, and of transcriptional repressors encoded by locally expressed zygotic gap genes. Caudal and Bicoid, which form complementing concentration gradients along the longitudinal axis of the embryo, function as redundant activators, indicating that the anterior determinant Bicoid is able to activate gene expression in the most posterior region of the embryo. The spatial limits of the h stripe 7 domain are brought about by the local activities of repressors which prevent activation. The results suggest that the gradients of Bicoid and Caudal combine their activities to activate segmentation genes along the entire axis of the embryo.
AIB1 Polymorphisms Predict Aggressive Ovarian Cancer Phenotype

Purpose: The androgen receptor (AR) harbors a polymorphic CAG repeat sequence in exon 1, coding for a polyglutamine tract whose length inversely correlates with AR transactivation function. AIB1, an AR coactivator, expresses a similar polymorphic glutamine sequence within the carboxyl-terminal coding region. We hypothesized that genotypic variations in the androgen-signaling pathway promote aggressive epithelial ovarian cancer biology, and sought to examine the effect of AIB1 genotype on clinical outcome. Experimental Design: Genotype analysis of the AIB1 CAG repeat region was done on 89 patients with epithelial ovarian cancer. Medical records were reviewed for clinicopathologic factors and survival. Data were examined using the χ2 test and Kaplan-Meier survival and Cox regression analyses. Results: We identified four AIB1 genotypes, with glutamine codon lengths of 26, 28, 29, and 30. Patients with a short AIB1 genotype (with ≤28 CAG repeats) showed statistically shorter time to disease recurrence compared to those with a long genotype (≥29 CAG repeats; 15.0 versus 30.0 months; P = 0.01). Patients with short AIB1 also showed decreased overall survival (57.0 months) compared to those with a long genotype (median survival not yet reached; P = 0.02). When controlling for established prognostic factors, multivariate analysis identified the presence of a short AIB1 genotype as an independent poor prognostic factor for overall survival (P = 0.05). Conclusions: These data suggest that short AIB1 genotypes may promote aggressive malignant phenotypes of epithelial ovarian cancer. (Cancer Epidemiol Biomarkers Prev 2005;14(12):2919–22)