Miracle-dz/UniFAR-FTUs huggingface dataset:
Breathing Life Into Dinosaurs: Tackling Challenges of Soft‐Tissue Restoration and Nasal Airflow in Extinct Species

The nasal region plays a key role in sensory, thermal, and respiratory physiology, but exploring its evolution is hampered by a lack of preservation of soft‐tissue structures in extinct vertebrates. As a test case, we investigated members of the “bony‐headed” ornithischian dinosaur clade Pachycephalosauridae (particularly Stegoceras validum) because of their small body size (which mitigated allometric concerns) and their tendency to preserve nasal soft tissues within their hypermineralized skulls. Hypermineralization directly preserved portions of the olfactory turbinates along with an internal nasal ridge that we regard as potentially an osteological correlate for respiratory conchae. Fossil specimens were CT‐scanned, and nasal cavities were segmented and restored. Soft‐tissue reconstruction of the nasal capsule was functionally tested in a virtual environment using computational fluid dynamics by running air through multiple models differing in nasal soft‐tissue conformation: a bony‐bounded model (i.e., skull without soft tissue) and then models with soft tissues added, such as a paranasal septum, a scrolled concha, a branched concha, and a model combining the paranasal septum with a concha. Deviations in fluid flow in comparison to a phylogenetically constrained sample of extant diapsids were used as indicators of missing soft tissue. Models that restored aspects of airflow found in extant diapsids, such as appreciable airflow in the olfactory chamber, were judged as more likely. The model with a branched concha produced airflow patterns closest to those of extant diapsids. These results from both paleontological observation and airflow modeling indicate that S. validum and other pachycephalosaurids could have had both olfactory and respiratory conchae. Although respiratory conchae have been linked to endothermy, such conclusions require caution in that our re‐evaluation of the reptilian nasal apparatus indicates that respiratory conchae may be more widespread than originally thought, and other functions, such as selective brain temperature regulation, could be important. Anat Rec, 297:2148–2186, 2014. © 2014 Wiley Periodicals, Inc.
Disparity-Based Measurement on Participation Interest and Competition Recommendation Method

Most of the popular recommendation algorithms are providing similar recommendations to users based on their ratings. However, in terms of competition, past records of user ratings do not directly translate to users’ interests in new competitions. Competitions are challenges, and as such, users are unlikely to choose what they have registered before, but instead, prefer challenges that complement the scope of their present abilities. Thus measurements of a user’s interest in competitions should be based on the differences, rather than similarities, in user’s past registration data. In this paper, we propose an alternative recommendation algorithm that measures users’ interests in competitions based on these differences. First, competition differences, such as registrations, stars and browsers records are modeled and calculated. Then, the peak values and the range of users’ interests are attained through such differences. Finally, recommendations of competitions are made if they fall within the range radius. The proposed algorithm proves to be more effective and efficient than conventional recommendation algorithms due to its consideration of competition’s features as well as the user’s psychology.
APRA: Affinity Propagation-Based Resource Allocation Scheme in M2M for System Capacity Maximization

Abstract In this paper, we propose an enhanced affinity propagation (AP)-based resource allocation scheme (APRA) to overcome major issues in machine-to-machine (M2M), such as delay, complexity, throughput, and system capacity. There would be rapid increase of added devices, such as cellular and machine-type devices. It would be difficult for Evolved Node B (eNB) to control all of them. Considering this problem, we propose an AP-based group formation method in which machines make groups with other similar type of machines. After making groups, group members in each group can communicate directly with each other by getting a channel from eNB via their group head. A resource allocation method is proposed for different groups that can use the same channel at the same time. Considering energy constraints, we also propose different methods to rotate the role of a group head among group members, through the modification of AP or the application of Markov chain model. As expected, the group head will drain energy at a higher rate than the group members. Thus, the rotation of the group head will increase the overall performance. Simulation results show that the proposed method can minimize both data delivery delay and operation complexity while increasing the throughput, system capacity, and energy efficiency through the rotation of the group head.
Addition of epirubicin to conventional chemotherapy in patients with advanced ovarian cancer: sequential therapy -a retrospective evaluation. .

AIM To evaluate the effectiveness of the addition of epirubicin to conventional chemotherapy as a first-line therapy for stage III-IV epithelial ovarian cancer. MATERIALS AND METHODS A total of 132 patients who had undergone primary cytoreductive surgery between January 1998 and March 2003 were enrolled in the study. Twenty-four cases were excluded. Out of the remaining 108 subjects, 35 received epirubicin/paclitaxel/ carboplatin (Group EPC) and 73 were treated with paclitaxel/platinum (cisplatin.or carboplatin) (Group PC). RESULTS The median follow-up period was 66.5 months. The clinical complete response was 94% in the EPC group and 97% in the PC group. The recurrence rate in the first 6 months after treatment was significantly higher in the PC than the EPC group (47% vs. 23%, P = 0.018). Triplet chemotherapy was not found to improve 2- and 5-year disease-free survival (DFS) statistically. No significant difference in overall survival was observed between the 2 groups (80% vs. 83% at 2 years and 56% vs. 57% at 5 years for the PC and the EPC group, respectively). The main toxicity in both groups was hematological, and it was particularly severe in the EPC group. CONCLUSION The addition of epirubicin to the standard treatment protocol yielded an improvement in the DFS rate that was not statistically significant and caused a tolerable increase in toxicity.
Development and Clinical Validation of a Multiplex Real-Time Quantitative PCR Assay for Human Infection by Anaplasma phagocytophilum and Ehrlichia chaffeensis

Background: Human granulocytic anaplasmosis (HGA), caused by Anaplasma phagocytophilum, and human monocytic ehrlichiosis (HME), caused by Ehrlichia chaffeensis, often present as undifferentiated fever but are not treated by typical empiric regimens for acute febrile illness. Their role as agents of vector-borne febrile disease in tropical regions is more poorly studied than for other rickettsial infections. Limitations in diagnosis have impaired epidemiologic and clinical research and needless morbidity and mortality occur due to untreated illness. Methods: We designed and clinically validated a multiplex real-time quantitative PCR assay for Anaplasma phagocytophilum and Ehrlichia chaffeensis using samples confirmed by multiple gold-standard methods. Results: Clinical sensitivity and specificity for A. phagocytophilum were 100% (39/39) and 100% (143/143), respectively, and for E. chaffeensis 95% (20/21) and 99% (159/161), respectively. Conclusions: These assays could support early diagnosis and treatment as well as the high-throughput testing required for large epidemiologic studies.
Data Mining : Patterns of User Navigation

We propose a data mining model that captures the user navigation behavior patterns. The user navigation sessions are modeled as a hypertext probabilistic grammar whose higher probability strings correspond to the user's preferred trails. An algorithm to anciently mine such trails is given. We make use of the N gram model which assumes that the last N pages browsed affect the probability of the next page to be visited. The model is based on the theory of probabilistic grammars providing it with a sound theoretical foundation for future enhancements. Moreover, we propose the use of entropy as an estimator of the gram-mar's statistical properties. Extensive experiments were conducted and the results show that the algorithm runs in linear time, the grammar's entropy is a good estimator of the number of mined trails and the real data rules confirm the effectiveness of the model.
Supercritical and Transcritical Real-Fluid Mixing in Diesel Engine Applications

Abstract : A numerical framework for simulating the mixing of supercritical and transcritical fluids with large density ratios is presented. The accurate and robust modeling of real-fluid effects on the fuel/air mixing process is critical in characterizing engine combustion. To describe this mixing process, the double-flux model is extended to systems with real-fluid state equations. For this, an effective specific heat ratio is introduced to eliminate the spurious pressure oscillations that are caused by the nonlinearity of the real-fluid equation of state. High-order WENO spatial discretization scheme is used for the real-fluid flow calculations to account for the large density gradients associated with these flows. One-dimensional single and multicomponent advection test cases and two-dimensional supercritical nitrogen jet mixing and transcritical n-dodecane injection test cases are conducted to show the capability of the present study in application to real-fluid supercritical and transcritical flows. Energy conservation errors, generated due to the double-flux formulation, are acceptable.
Westward Spread of Highly Pathogenic Avian Influenza A(H7N9) Virus among Humans, China

We report infection of humans with highly pathogenic avian influenza A(H7N9) virus in Shaanxi, China, in May 2017. We obtained complete genomes for samples from 5 patients and from live poultry markets or farms in 4 cities. Results indicate that H7N9 is spreading westward from southern and eastern China.
A perturbation-based method for calculating explicit likelihood of evolutionary co-variance in multiple sequence alignments

MOTIVATION The constituent amino acids of a protein work together to define its structure and to facilitate its function. Their interdependence should be apparent in the evolutionary record of each protein family: positions in the sequence of a protein family that are intimately associated in space or in function should co-vary in evolution. A recent approach by Ranganathan and colleagues proposes to look at subsets of a protein family, selected for their sequence at one position, to see how this affects variation at other positions. RESULTS We present a quantitative algorithm for assessing covariation with this approach, based on explicit likelihood calculations. By applying our algorithm to 138 Pfam families with at least one member of known structure, we demonstrate that our method has improved power in finding physically close residues in crystal structures, compared to that of Ranganathan and colleagues. SUPPLEMENTARY INFORMATION www.afodor. net/bioinfosup.html
School-Based Speech-Language Pathologists' Perspectives on Diagnostic Decision Making.

Purpose This study used a structured open interview approach to elicit information from school-based speech-language pathologists (SLPs) regarding their assessment practices for children with suspected language impairment. Method Phone interviews were conducted with 39 school-based SLPs who were employed across the United States. The interviews explored assessment topics related to assessment tool selection and rationale and the integration of assessment data to determine treatment eligibility. Results The results of this study suggest that SLPs use both standardized testing and informal testing for their diagnostic procedures. Standardized testing appears to be the tool that drives diagnostic decisions regarding eligibility and severity. Informal measures, such as parent/teacher interviews and language sampling, were used by school-based SLPs to gather information regarding naturalistic language use; however, they seem less important in the diagnostic decision-making process. Also, SLPs reported completing language sample transcription and analysis in real time while interacting with a child. Conclusions School-based SLPs appear to rely on the results from standardized testing when determining treatment eligibility for children with language impairment. The reliance on standardized testing appears to be driven by institutional policies. We discuss the potential impact of federal/state/district guidelines on diagnostic decisions and consider the research-to-practice gap.
Searching for effective components of cognitive rehabilitation for children and adolescents with acquired brain injury: A systematic review

ABSTRACT Aim. Cognitive rehabilitation is of interest after paediatric acquired brain injury (ABI). The present systematic review examined studies investigating cognitive rehabilitation interventions for children with ABI, while focusing on identifying effective components. Components were categorized as (1) metacognition and/or strategy use, (2) (computerized) drill-based exercises, and (3) external aids. Methods. The databases PubMed (including MEDLINE), PsycInfo, and CINAHL were searched until 22nd June 2017. Additionally, studies were identified through cross-referencing and by consulting experts in the field. Results. A total of 20 articles describing 19 studies were included. Metacognition/strategy use trainings (five studies) mainly improved psychosocial functioning. Drill-based interventions (six studies) improved performance on tasks similar to training tasks. Interventions combining these two components (six studies) benefited cognitive and psychosocial functioning. External aids (two studies) improved everyday memory. No studies combined external aids with drill-based interventions or all three components. Conclusion. Available evidence suggests that multi-component rehabilitation, e.g. combining metacognition/strategy use and drill-based training is most promising, as it can lead to improvements in both cognitive and psychosocial functioning of children with ABI. Intervention setting and duration may play a role. Conclusions remain tentative due to small sample sizes of included studies heterogeneity regarding outcome measures, intervention and therapist variables, and patient characteristics.
Clone Tracker: Tracking Inconsistent Clone Changes in A Clone Group

Source code cloning is a common activity in software development as well as a threat to the maintainability of the source code. Because code clones reduce the reliability of source code and increase the maintenance cost. In maintenance, evolving clones require more attention because of clone changing behavior. In a clone group, all clones are similar and require similar change to keep consistency among those clones. In a scenario where one clone is changed and others remain unchanged may lead to inconsistency. To resolve this issue an approach is proposed and a plugin is developed to track changes in clones. It provides change information with similar clones that may need to be updated accordingly. In the proposed approach, clones are detected and stored in a repository. From that clone groups or classes are created based on those similarities. Clones are mapped into files so that it requires less time to search clones of a fragment. Based on the editor events fragments are queried from the repository. After comparison with an edited fragment, this provides real-time change information. The plugin is incorporated with the IntelliJ Idea so that it can help developer to maintain cloned codes in maintenance time. In study with three open source software, it performs well in accuracy. Although the source code is changed manually to know how it performs in different scenario like insertion, deletion or modification. It can detect changes in a clone fragment and shows other clones of the clone group which may require change to adapt the functionality. However, some requirements to use the plugin may limit the usability.
Little Cross-Feeding of the Mycorrhizal Networks Shared Between C3-Panicum bisulcatum and C4-Panicum maximum Under Different Temperature Regimes

Common mycorrhizal networks (CMNs) formed by arbuscular mycorrhizal fungi (AMF) interconnect plants of the same and/or different species, redistributing nutrients and draining carbon (C) from the different plant partners at different rates. Here, we conducted a plant co-existence (intercropping) experiment testing the role of AMF in resource sharing and exploitation by simplified plant communities composed of two congeneric grass species (Panicum spp.) with different photosynthetic metabolism types (C3 or C4). The grasses had spatially separated rooting zones, conjoined through a root-free (but AMF-accessible) zone added with 15N-labeled plant (clover) residues. The plants were grown under two different temperature regimes: high temperature (36/32°C day/night) or ambient temperature (25/21°C day/night) applied over 49 days after an initial period of 26 days at ambient temperature. We made use of the distinct C-isotopic composition of the two plant species sharing the same CMN (composed of a synthetic AMF community of five fungal genera) to estimate if the CMN was or was not fed preferentially under the specific environmental conditions by one or the other plant species. Using the C-isotopic composition of AMF-specific fatty acid (C16:1ω5) in roots and in the potting substrate harboring the extraradical AMF hyphae, we found that the C3-Panicum continued feeding the CMN at both temperatures with a significant and invariable share of C resources. This was surprising because the growth of the C3 plants was more susceptible to high temperature than that of the C4 plants and the C3-Panicum alone suppressed abundance of the AMF (particularly Funneliformis sp.) in its roots due to the elevated temperature. Moreover, elevated temperature induced a shift in competition for nitrogen between the two plant species in favor of the C4-Panicum, as demonstrated by significantly lower 15N yields of the C3-Panicum but higher 15N yields of the C4-Panicum at elevated as compared to ambient temperature. Although the development of CMN (particularly of the dominant Rhizophagus and Funneliformis spp.) was somewhat reduced under high temperature, plant P uptake benefits due to AMF inoculation remained well visible under both temperature regimes, though without imminent impact on plant biomass production that actually decreased due to inoculation with AMF.
Lenient Execution of C on a Java Virtual Machine: or: How I Learned to Stop Worrying and Run the Code

Most C programs do not conform strictly to the C standard, and often show undefined behaviors, for instance, in the case of signed integer overflow. When compiled by non-optimizing compilers, such programs often behave as the programmer intended. However, optimizing compilers may exploit undefined semantics to achieve more aggressive optimizations, possibly breaking the code in the process. Analysis tools can help to find and fix such issues. Alternatively, a C dialect could be defined in which clear semantics are specified for frequently occurring program patterns with otherwise undefined behaviors. In this paper, we present Lenient C, a C dialect that specifies semantics for behaviors left open for interpretation in the standard. Specifying additional semantics enables programmers to make safe use of otherwise undefined patterns. We demonstrate how we implemented the dialect in Safe Sulong, a C interpreter with a dynamic compiler that runs on the JVM.
Cyclic 3',5' AMP relay in Dictyostelium discoideum. II. Requirements for the initiation and termination of the response

The secretion of 3H-cyclic adenosine 3',5'-monophosphate (cAMP) by prelabeled and suitably differentiated Dictyostelium discoideum amoebae was elicited in a perfusion apparatus by 10(-10) to 10(-5) M [14C]cAMP stimuli of defined magnitude and duration. Exogenous stimuli evoked an immediate increase in the rate of [3H]cAMP secretion which accelerated continuously to reach a peak of up to 100 times the unstimulated rate after 2--3 min of stimulation. Withdrawal of the stimulus at any time during the response led to a rapid decline to basal levels. Furthermore, a spontaneous decline in secretion rate was observed during prolonged cAMP stimulation, with a return to basal levels after 3--8 min of stimulation. After the initial secretory event, cells did not respond further to the continued presence of external [14C]cAMP unless (a) it was interrupted by a brief recovery period or (b) the level of the stimulus was increased sufficiently. Since the second increment could follow the first at any time, continuous secretion of [3H]cAMP could be sustained for up to 30 min by progressively increasing the stimulus between 10(-10) and 10(-5) M cAMP. The total magnitude of spontaneously terminated responses depended on the size of the increment in applied cAMP, larger stimuli evoking both a more rapid acceleration and a slower deceleration in [3H]cAMP secretion rate. The integrated response to a given increment in stimulus level was apparently independent of its "shape" - i.e., the duration, magnitude, and number of sub-steps in the increment. These data support two mechanistic inferences: that amoebae respond in proportion to relative increases in extracellular cAMP concentration, but adapt to the concentration of cAMP itself. The data further suggest that the initiation and termination of the response are mediated by cellular component(s) beyond cAMP-occupied receptors.
Data and Information Visualization Methods, and Interactive Mechanisms: A Survey

availability of enough visualization techniques it can be very confusing to know what and when should be appropriate technique to use in order to convey maximum possible understanding. The basic purpose of visual representation is to efficiently interpret what is insight, as easy as possible. Different available visualization techniques are use for different situation which convey different level of understanding. This document is guide for the young researchers who wants to start work in visualization. The purpose of this piece of document is to collect all visualization techniques with their brief introduction. This paper deals with many definitions and aspects of visualization, how visualization take place i.e. different steps of visualization process, problems that are confront in visualization, categorization of visualization techniques on the bases of distinct perspective, typically known common data and information visualization techniques, basic interactive methods for visualization their advantages and disadvantages, interactivity process, and the scope of visualization up to some extent in different field of research. General Terms Visualization, Visualization techniques, Challenges, Interactive techniques.