Miracle-dz/UniFAR-FTUs huggingface dataset:
Resource utilization and interspecific relations of sympatric bobcats and coyotes

We used scat analysis and radiotelemetry to characterize use of foods and habitats by sympatric bobcats and coyotes, and evaluated these in the context of spatial and temporal relationships to assess the potential for, and evidence of, interspecific competition. Bobcats and coyotes exhibited broad and overlapping diets. However, diets of the two predators differed in the relative contributions of small and large prey, with bobcats consuming relatively more rodent and lagomorph biomass and coyotes consuming relatively more ungulate biomass. Consumption among rodent prey species was highly correlated between bobcats and coyotes, indicating no evidence of prey partitioning within this group. Habitat selection by the two predators differed slightly at the landscape scale but not within home ranges. Bobcats and coyotes occupied small, overlapping home ranges, such that the likelihood of interspecific encounters (direct or indirect) was high. Bobcats displayed slight avoidance of overlapping coyote core areas during coyote reproductive seasons (winter and spring), when coyotes are typically most territorial (toward conspecifics), but displayed slight attraction during times of year when coyotes were not engaged in reproductive activities. Relative to coyotes, which were strongly nocturnal, diel activity patterns of bobcats were more diurnal and variable. However, activity patterns were not inversely correlated. Overall, these predators appeared to use resources independently and we found little evidence of negative interactions. Differences in resource use by bobcats and coyotes appeared to relate to fundamental niche differences as opposed to competition-related resource partitioning.
Increasing frame rate in ultrasound imaging by temporal morphing using tissue Doppler

The diagnostic value of echocardiographic images seems to diminish when the frame rate is low. In this work, morphing based on velocity information was used to improve the perceived smoothness of B-mode cine-loops with low frame rate. Based on an estimate of the velocity field calculated from B-mode speckle tracking and tissue Doppler measurements, morphed cine-loops with arbitrarily high frame rate were created. Morphing was applied to cardiac ultrasound cine-loops with apical insonation. The quality of the morphed data was evaluated by removing frames from duplex B-mode and tissue Doppler recordings, then replacing the removed B-mode frames with morphed ones. The decimated and morphed sequences were compared to the original ones. Wall motion scoring, a subjective evaluation technique for regional viability of the myocardium, was applied to data from 20 patients with varying pathology. Sixty cine-loops were scored twice, first with original data and later with morphed data. The results were compared for each recording, and the scorings were identical in the two cases for 94% of the segments. We conclude that much of the diagnostic value is retained in recordings with 15 frames per second when temporal morphing is applied
Integrating color and motion to enhance human detection within aquatic environment

An adaptive spatio-temporal filtering scheme based on a novel concept of motion frequency is proposed as the preprocessing step to enhance human detection under a noisy aquatic environment. In this framework, each pixel is first classified into one of three categories quantified by its motion frequency, each of which is filtered using an appropriate filtering scheme. For regions affected by glistening reflections and glares, a color compensation filter is specially developed to improve partly hidden human detection and minimize errors due to moving background elements. Additionally, a blob-based verification procedure is introduced to remove the target's shadow. Experimental results demonstrate the effectiveness of the algorithm and its role in enhancing the robustness of an aquatic surveillance system for outdoor swimming pools at nighttime
Making Hand Geometry Verification System More Accurate Using Time Series Representation with R-K Band Learning

At present, applications of biometrics are rapidly increasing due to inconveniences in using traditional passwords and physical keys. Hand geometry, one of the most well-known biometrics, is implemented in many verification systems with various feature extraction methods. In recent work, a hand geometry verification system using time series conversion techniques and Dynamic Time Warping (DTW) distance measure with Sakoe-Chiba band has been proposed. This system demonstrates many advantages, especially ease of implementation and small storage space requirement using time series representation. In this paper, we propose a novel hand geometry verification system that exploits DTW distance measure and R-K band learning to further improve the system performance. Finally, our evaluation reveals that our proposed system outperforms the current system by a wide margin, in terms of False Acceptance Rate (FAR), False Rejection Rate (FRR), and Total Success Rate (TSR) at Equal Error Rate (EER).
Transgenic Evaluation of Activated Mutant Alleles of SOS2 Reveals a Critical Requirement for Its Kinase Activity and C-Terminal Regulatory Domain for Salt Tolerance in Arabidopsis thaliana

In Arabidopsis thaliana, the calcium binding protein Salt Overly Sensitive3 (SOS3) interacts with and activates the protein kinase SOS2, which in turn activates the plasma membrane Na+/H+ antiporter SOS1 to bring about sodium ion homeostasis and salt tolerance. Constitutively active alleles of SOS2 can be constructed in vitro by changing Thr168 to Asp in the activation loop of the kinase catalytic domain and/or by removing the autoinhibitory FISL motif from the C-terminal regulatory domain. We expressed various activated forms of SOS2 in Saccharomyces cerevisiae (yeast) and in A. thaliana and evaluated the salt tolerance of the transgenic organisms. Experiments in which the activated SOS2 alleles were coexpressed with SOS1 in S. cerevisiae showed that the kinase activity of SOS2 is partially sufficient for SOS1 activation in vivo, and higher kinase activity leads to greater SOS1 activation. Coexpression of SOS3 with SOS2 forms that retained the FISL motif resulted in more dramatic increases in salt tolerance. In planta assays showed that the Thr168-to-Asp–activated mutant SOS2 partially rescued the salt hypersensitivity in sos2 and sos3 mutant plants. By contrast, SOS2 lacking only the FISL domain suppressed the sos2 but not the sos3 mutation, whereas truncated forms in which the C terminus had been removed could not restore the growth of either sos2 or sos3 plants. Expression of some of the activated SOS2 proteins in wild-type A. thaliana conferred increased salt tolerance. These studies demonstrate that the protein kinase activity of SOS2 is partially sufficient for activation of SOS1 and for salt tolerance in vivo and in planta and that the kinase activity of SOS2 is limiting for plant salt tolerance. The results also reveal an essential in planta role for the SOS2 C-terminal regulatory domain in salt tolerance.
Document structure analysis algorithms: a literature survey

Document structure analysis can be regarded as a syntactic analysis problem. The order and containment relations among the physical or logical components of a document page can be described by an ordered tree structure and can be modeled by a tree grammar which describes the page at the component level in terms of regions or blocks. This paper provides a detailed survey of past work on document structure analysis algorithms and summarize the limitations of past approaches. In particular, we survey past work on document physical layout representations and algorithms, document logical structure representations and algorithms, and performance evaluation of document structure analysis algorithms. In the last section, we summarize this work and point out its limitations.
The Effects of Systematic Reinforcement on Academic Performance in Precision Teaching: An Investigation of Acquisition, Retention, and Endurance

The use of positive reinforcement in acquisition programming is a hallmark of Applied Behavior Analysis; however, the Precision Teaching literature reveals a lack of reporting on the use of reinforcement. The present study utilized a groups design and single case analyses to investigate the effect of programming systematic tangible reinforcement on acquisition performance, retention and endurance of academic skills with 10 typically developing students ranging from 5-7 years of age. Results indicate that for both control and experimental participants, an increase in accuracy on both See/Say sight words and math problems occurred; however, the experimental group performed better on See/Say sight words and both groups performed the same with See/Say math problems.
Analyzing structure–function relationships of artificial and cancer-associated PARP1 variants by reconstituting TALEN-generated HeLa PARP1 knock-out cells

Genotoxic stress activates PARP1, resulting in the post-translational modification of proteins with poly(ADP-ribose) (PAR). We genetically deleted PARP1 in one of the most widely used human cell systems, i.e. HeLa cells, via TALEN-mediated gene targeting. After comprehensive characterization of these cells during genotoxic stress, we analyzed structure–function relationships of PARP1 by reconstituting PARP1 KO cells with a series of PARP1 variants. Firstly, we verified that the PARP1\E988K mutant exhibits mono-ADP-ribosylation activity and we demonstrate that the PARP1\L713F mutant is constitutively active in cells. Secondly, both mutants exhibit distinct recruitment kinetics to sites of laser-induced DNA damage, which can potentially be attributed to non-covalent PARP1–PAR interaction via several PAR binding motifs. Thirdly, both mutants had distinct functional consequences in cellular patho-physiology, i.e. PARP1\L713F expression triggered apoptosis, whereas PARP1\E988K reconstitution caused a DNA-damage-induced G2 arrest. Importantly, both effects could be rescued by PARP inhibitor treatment, indicating distinct cellular consequences of constitutive PARylation and mono(ADP-ribosyl)ation. Finally, we demonstrate that the cancer-associated PARP1 SNP variant (V762A) as well as a newly identified inherited PARP1 mutation (F304L\V762A) present in a patient with pediatric colorectal carcinoma exhibit altered biochemical and cellular properties, thereby potentially supporting human carcinogenesis. Together, we establish a novel cellular model for PARylation research, by revealing strong structure–function relationships of natural and artificial PARP1 variants.
Assessing sequence comparison methods with reliable structurally identified distant evolutionary relationships.

Pairwise sequence comparison methods have been assessed using proteins whose relationships are known reliably from their structures and functions, as described in the SCOP database [Murzin, A. G. , Brenner, S. E. , Hubbard, T. & Chothia C. (1995) J. Mol. Biol. 247, 536-540]. The evaluation tested the programs BLAST [Altschul, S. F. , Gish, W. , Miller, W. , Myers, E. W. & Lipman, D. J. (1990). J. Mol. Biol. 215, 403-410], WU-BLAST2 [Altschul, S. F. & Gish, W. (1996) Methods Enzymol. 266, 460-480], FASTA [Pearson, W. R. & Lipman, D. J. (1988) Proc. Natl. Acad. Sci. USA 85, 2444-2448], and SSEARCH [Smith, T. F. & Waterman, M. S. (1981) J. Mol. Biol. 147, 195-197] and their scoring schemes. The error rate of all algorithms is greatly reduced by using statistical scores to evaluate matches rather than percentage identity or raw scores. The E-value statistical scores of SSEARCH and FASTA are reliable: the number of false positives found in our tests agrees well with the scores reported. However, the P-values reported by BLAST and WU-BLAST2 exaggerate significance by orders of magnitude. SSEARCH, FASTA ktup = 1, and WU-BLAST2 perform best, and they are capable of detecting almost all relationships between proteins whose sequence identities are >30%. For more distantly related proteins, they do much less well; only one-half of the relationships between proteins with 20-30% identity are found. Because many homologs have low sequence similarity, most distant relationships cannot be detected by any pairwise comparison method; however, those which are identified may be used with confidence.
Morphometric Features and Glycoconjugate Pattern of Rabbit Intestine are Affected by Particle Size of Pelleted Diets

Feed particle size effects on morphology and glycoconjugate pattern was investigated in the rabbit intestine. Rabbits fed with fine particles (2 mm) displayed more irregularly shaped, higher duodenal villi and deeper crypts in distal colon as well as higher number of goblet cells than coarse (8 mm) fed ones. Brush border expressed: (i) in duodenum, neutral/sulfated glycoconjugates and glycans binding MAL II, SNA, Con A than KOH‐sialidase‐PNA and DBA reactivity in fine and coarse fed rabbits, respectively, (ii) in cecum, mainly sulfoglycans in coarse fed rabbits, MAL II and PNA staining in all samples, and (iii) in distal colon few sulfoglycans and MAL II reactivity. Enterocytes bound MAL II in duodenum, Con A in cecum, DBA, and Con A in distal colon of all rabbits, SNA in distal colon of coarse fed ones. Brunner's glands displayed high presence of acidic/sulfated mucins in fine fed rabbits, neutral glycoconjugates and reactivity with MAL II, SNA, PNA, KOH‐sialidase‐PNA, and Con A in all rabbits. Goblet cells exhibited: (i) in duodenum neutral and sulfomucins as well as MAL II and KOH‐sialidase‐PNA staining, than SNA and DBA in fine and coarse fed rabbits, respectively, (ii) in cecum sulfated glycans, MAL II, SNA, KOH‐sialidase‐PNA, DBA reactivity, and (iii) in distal colon acidic/sulfomucins, MAL II and SNA staining, and DBA reactivity in fine fed specimens. Crypt cells exhibited neutral and PNA reactive glycoconjugates in the cecum. In the distal colon also acidic/sulfated glycans, and MAL II, KOH‐sialidase‐PNA, DBA; SNA staining showed weaker reactivity in fine fed rabbits, which bound Con A. Anat Rec, 2011. © 2011 Wiley‐Liss, Inc.
Improving health literacy: use of an informational brochure improves parents' understanding of their child's fluoroscopic examination.

OBJECTIVE The purpose of this study was to determine parents' knowledge about pediatric fluoroscopic procedures and potential risk from ionizing radiation before and after being given an informational brochure. SUBJECTS AND METHODS We reviewed responses from 120 randomly selected participants who were parents or guardians of pediatric patients undergoing diagnostic fluoroscopic examinations. A questionnaire assessed participants' knowledge of the procedure, radiation exposure, and whether their child had a prior examination before and after receiving an informational brochure. In a feedback survey, participants rated the brochure. A repeated measures mixed model was used to evaluate the effect of the brochure on the participants' knowledge. RESULTS Participant demographics were women (79%), English speaking (99%), white (90%), and education higher than 12th grade (76%). The median age of patients undergoing the fluoroscopic examination was 4 years. Participant knowledge increased (p < 0.0001) between pre- and postbrochure (least-squares means) for those without a previous examination from 38.3 to 63.4 (total test score) and from 46.3 to 61.8 for those with a prior examination. The proportion of correct answers was higher (p < 0.0001) postbrochure compared with pre-brochure in areas of examination name (99% vs 93%), procedure details (97% vs 87%); use of radiation (100% vs 68%), and radiation dose comparison (79% vs 25%). Overall, 99% (119/120) rated the brochure "good" or "great" (p < 0.0001). CONCLUSION An informational brochure given to participants before their child's fluoroscopic procedure improved their knowledge of the examination and radiation exposure. No participants refused their child's examination.
Effectiveness of Online Professional Development for Rural Special Educators

Retaining teachers and accessing professional development have been long-standing struggles for rural school districts, particularly with respect to teachers with special education endorsements. This study examined the effect of asynchronous online professional development in secondary special education and transition for 86 rural special education teachers. In addition, the study compared results of teachers in rural and non-rural settings. Results indicated that rural special education teachers who participated in the online professional development gained knowledge, increased personal capacity to apply research-based practices, and implemented research-based transition practices within their classrooms. Furthermore, participants developed meaningful, collaborative relationships with rural colleagues across the country. While rural and non-rural educators both experienced gains as a result of the professional development, rural educators initially rated their competency in providing transition services much lower than their non-rural peers; however, both groups rated their competency at the same levels at the conclusion of the online professional development.
Hierarchical routing with soft-state replicas in TerraDir

Summary form only given. Recent work on peer-to-peer systems has demonstrated the ability to deliver low latencies and good load balance when demand for data is relatively uniform. We describe an adaptive replication protocol that delivers low latencies, good load balance even when demand is heavily skewed. The protocol can withstand arbitrary and instantaneous changes in demand distribution. Our approach also addresses classical concerns related to topological constraints of asymmetrical namespaces, such as hierarchical bottlenecks in the context of hierarchical namespaces. The protocol replicates routing state in an ad-hoc manner based on profiled information, is lightweight, scalable, and requires no replica consistency guarantees.
Recent Advancements in Speech Enhancement

Speech enhancement is a long standing problem with numerous applications ranging from hearing aids, to coding and automatic recognition of speech signals. In this survey paper we focus on enhancement from a single microphone, and assume that the noise is additive and statistically independent of the signal. We present the principles that guide researchers working in this area, and provide a detailed design example. The example focuses on minimum mean square error estimation of the clean signal’s log-spectral magnitude. This approach has attracted significant attention in the past twenty years. We also describe the principles of a Monte-Carlo simulation approach for speech enhancement.
A role of topoisomerase II in linking DNA replication to chromosome condensation

The condensin complex and topoisomerase II (topo II) have different biochemical activities in vitro, and both are required for mitotic chromosome condensation. We have used Xenopus egg extracts to investigate the functional interplay between condensin and topo II in chromosome condensation. When unreplicated chromatin is directly converted into chromosomes with single chromatids, the two proteins must function together, although they are independently targeted to chromosomes. In contrast, the requirement for topo II is temporarily separable from that of condensin when chromosome assembly is induced after DNA replication. This experimental setting allows us to find that, in the absence of condensin, topo II becomes enriched in an axial structure within uncondensed chromatin. Subsequent addition of condensin converts this structure into mitotic chromosomes in an ATP hydrolysis–dependent manner. Strikingly, preventing DNA replication by the addition of geminin or aphidicolin disturbs the formation of topo II–containing axes and alters the binding property of topo II with chromatin. Our results suggest that topo II plays an important role in an early stage of chromosome condensation, and that this function of topo II is tightly coupled with prior DNA replication.
Joint Matrix Factorization and Manifold-Ranking for Topic-Focused Multi-Document Summarization

Manifold-ranking has proved to be an effective method for topic-focused multi-document summarization. As basic manifold-ranking based summarization method constructs the relationships between sentences simply by the bag-of-words cosine similarity, we believe a better similarity metric will further improve the effectiveness of manifold-ranking. In this paper, we propose a joint optimization framework, which integrates the manifold-ranking process with a similarity metric learning process. The joint framework aims at learning better sentence similarity scores and better sentence ranking scores simultaneously. Experiments on DUC datasets show the proposed joint method achieves better performance than the manifold-ranking baselines and several popular methods.
Lost in translation? Empirical analysis of mapping compositions for large ontologies

When three or more ontologies have been aligned, longer chains of mapped concepts start to appear. In this paper, we empirically study the nature of these composite mappings, focusing on chains of (near) equivalence links of length two. We ask human experts to evaluate samples of composite mappings, taken from large real life data sets. Based on these evaluations, we analyze the features of mappings produced by composition in three different domains (bio-medicine, cultural heritage, and library subject headings), among ontologies in multiple languages (English, Dutch, German, and French), and using existing mappings that were created by different methods (lexical and instance-based methods). We examine the quality of the composite mappings relative to the quality of the input mappings and analyze how characteristics of the input mappings and the ontologies influence the composition.
Not all Risk is Born Equal: The Behavioral Agency Model & Firm Efficacy

We examine the relationship between agent (CEO) risk bearing and the quality of executive risk taking outcomes, by examining the contingency effect of CEO perceived firm efficacy. In doing so, we extend the behavioral agency model (BAM) beyond predictions of risk magnitude to examining how CEO risk taking outcomes differ qualitatively in response to risk bearing. We argue that CEO risk bearing (due to stock options or cash compensation) will positively influence performance outcomes in the presence of higher perceived firm efficacy. However, this positive influence reverses when efficacy is lower. We demonstrate the utility of firm efficacy in exploring the effect of agent risk bearing upon performance outcomes and provide the insight that the CEO pay-performance relationship is influenced by the CEO’s perception of firm efficacy.