Miracle-dz/UniFAR-FTUs huggingface dataset:
Global gene expression in cotton (Gossypium hirsutum L.) leaves to waterlogging stress

Cotton is sensitive to waterlogging stress, which usually results in stunted growth and yield loss. To date, the molecular mechanisms underlying the responses to waterlogging in cotton remain elusive. Cotton was grown in a rain-shelter and subjected to 0 (control)-, 10-, 15- and 20-d waterlogging at flowering stage. The fourth-leaves on the main-stem from the top were sampled and immediately frozen in liquid nitrogen for physiological measurement. Global gene transcription in the leaves of 15-d waterlogged plants was analyzed by RNA-Seq. Seven hundred and ninety four genes were up-regulated and 1018 genes were down-regulated in waterlogged cotton leaves compared with non-waterlogged control. The differentially expressed genes were mainly related to photosynthesis, nitrogen metabolism, starch and sucrose metabolism, glycolysis and plant hormone signal transduction. KEGG (Kyoto Encyclopedia of Genes and Genomes) analysis indicated that most genes related to flavonoid biosynthesis, oxidative phosphorylation, amino acid metabolism and biosynthesis as well as circadian rhythm pathways were differently expressed. Waterlogging increased the expression of anaerobic fermentation related genes, such as alcohol dehydrogenase (ADH), but decreased the leaf chlorophyll concentration and photosynthesis by down-regulating the expression of photosynthesis related genes. Many genes related to plant hormones and transcription factors were differently expressed under waterlogging stress. Most of the ethylene related genes and ethylene-responsive factor-type transcription factors were up-regulated under water-logging stress, suggesting that ethylene may play key roles in the survival of cotton under waterlogging stress.
Immediate implant placement for schizophrenic patient with outpatient general anesthesia

The difficult oral healthcare in intellectually disabled patients with poor behavioral control has led to debate over the cost-effectiveness and validity of implant treatment in these patients. The patient in the present report had schizophrenia that had led to poor oral care and severe dental caries in the full mouth. Tooth extraction and a removable prosthesis were planned, but the guardian wanted an implant procedure. Since the guardian showed strong will and cooperation with regard to the patient's oral healthcare, extraction followed by immediate implant placement was performed across two rounds of general anesthesia. Since the outcome appears successful, we present this case report. Immediate implant placement after tooth extraction requires fewer surgeries and rounds of general anesthesia, reduces horizontal bone resorption, and can achieve better esthetic results. Therefore, as long as a certain degree of oral care is possible, this can be a positive option for restoration of a partially edentulous mouth, even in intellectually disabled patients.
POTASSIUM AND AMINO ACID TRANSPORT IN HUMAN LEUKOCYTES EXPOSED TO PHAGOCYTIC STIMULI

Influxes of potassium and amino acids were measured in suspensions of human polymorphonuclear leukocytes (PMNs) under resting conditions and after various phagocytic stimuli. Both ouabain-sensitive (or pump) and ouabain-insensitive (or leak) influxes of K were determined. In 5 mM external K, mean total K influx was 0.69 nmol/106 cells x min, of which 52% was ouabain-sensitive. Ouabain binding was irreversible, and, as in erythrocytes, was inhibited by K. At external concentrations of 0.1 mM, influxes of lysine and leucine were entirely carrier-mediated, with means of 0.021 nmol/106 cells x min, and 0.019 nmol/106 cells x min, respectively. After incubation of PMNs with zymosan or latex particles, the K pump was reduced more than 60%, whereas amino acid influxes were inhibited only by 30%. PMNs were also exposed to cytochalasin B before challenge by particles: the drug prevented phagocytosis but not surface binding of zymosan, nor did it influence transport of K or amino acids. After pretreatment of PMNs with cytochalasin B, interaction of zymosan with their surface resulted in the same degree of inhibition of influxes of K and amino acids as when the cells were permitted to phagocytose the particles. In contrast, exposure of PMN to latex particles, which do not bind to cytochalasin B-treated cells, after pretreatment of cells with cytochalasin B did not result in inhibition of influxes. Treatment of cells with colchicine had no effect on either membrane transport or its inhibition after exposure to various phagocytic stimuli. These results indicate that the surface membranes of PMNs are functionally heterogeneous with respect to the association of transport sites for the different solutes. Moreover, loss of specific membrane functions from phagocytosing cells may result from the surface-at-tachment phase of particle-cell interactions, since the interactions of zymosan particles with PMNs in the absence of phagocytosis also inhibited transport of solutes.
Bi-directional recurrent neural network with ranking loss for spoken language understanding

This paper presents our latest investigation of recurrent neural networks for the slot filling task of spoken language understanding. We implement a bi-directional Elman-type recurrent neural network which takes the information not only from the past but also from the future context to predict the semantic label of the target word. Furthermore, we propose to use ranking loss function to train the model. This improves the performance over the cross entropy loss function. On the ATIS benchmark data set, we achieve a new state-of-the-art result of 95.56% F1-score without using any additional knowledge or data sources.
Local Parallel Computation of Stochastic Completion Fields

We describe a local parallel method for computing the stochastic completion field introduced in the previous article (Williams and Jacobs, 1997). The stochastic completion field represents the likelihood that a completion joining two contour fragments passes through any given position and orientation in the image plane. It is based on the assumption that the prior probability distribution of completion shape can be modeled as a random walk in a lattice of discrete positions and orientations. The local parallel method can be interpreted as a stable finite difference scheme for solving the underlying Fokker-Planck equation identified by Mumford (1994). The resulting algorithm is significantly faster than the previously employed method, which relied on convolution with large-kernel filters computed by Monte Carlo simulation. The complexity of the new method is O (n3m), while that of the previous algorithm was O(n4m2 (for an n n image with m discrete orientations). Perhaps most significant, the use of a local method allows us to model the probability distribution of completion shape using stochastic processes that are neither homogeneous nor isotropic. For example, it is possible to modulate particle decay rate by a directional function of local image brightnesses (i.e., anisotropic decay). The effect is that illusory contours can be made to respect the local image brightness structure. Finally, we note that the new method is more plausible as a neural model since (1) unlike the previous method, it can be computed in a sparse, locally connected network, and (2) the network dynamics are consistent with psychophysical measurements of the time course of illusory contour formation.
Two-year outcome of preschool children with autism or Asperger's syndrome.

OBJECTIVE DSM-IV specifies that Asperger's disorder is a type of pervasive developmental disorder without clinically significant cognitive or language delay. There are no data, however, on the outcome of children with Asperger's disorder or on whether their outcome differs from that of children with autism. The objectives of this study were to compare the outcome of groups of children with these disorders over a period of 2 years on variables independent of the defining criteria and to identify variables that might account for these differences. METHOD All children 4-6 years of age who came for assessment or were currently in treatment at a pervasive developmental disorder service of one of several centers in a large geographic region were identified. Children who received a diagnosis of autism (N=46) or Asperger's syndrome (N=20) on the basis of a diagnostic interview and had an IQ in the nonretarded range were given a battery of cognitive, language, and behavioral tests. Families were contacted roughly 2 years after the date of their enrollment in the study, and many of the tests were readministered. RESULTS Children with Asperger's syndrome had better social skills and fewer autistic symptoms 2 years after study enrollment than the children with autism. The differences in outcome could not be explained by initial differences in IQ and language abilities. Children with autism who had developed verbal fluency at follow-up were very similar to the children with Asperger's syndrome at study enrollment. CONCLUSIONS Although the exact mechanism for the differences in outcome remain to be determined, it appears that Asperger's disorder and autism represent parallel but potentially overlapping developmental trajectories.
Genetic Dissection of the Ity3 Locus Identifies a Role for Ncf2 Co-Expression Modules and Suggests Selp as a Candidate Gene Underlying the Ity3.2 Locus

Typhoid fever and salmonellosis, which are caused by Salmonella typhi and typhimurium, respectively, are responsible for significant morbidity and mortality in both developed and developing countries. We model typhoid fever using mice infected with Salmonella typhimurium, which results in a systemic disease, whereby the outcome of infection is variable in different inbred strains of mice. This model recapitulates several clinical aspects of the human disease and allows the study of the host response to Salmonella typhimurium infection in vivo. Previous work in our laboratory has identified three loci (Ity, Ity2, and Ity3) in the wild-derived MOLF/Ei mice influencing survival after infection with Salmonella typhimurium. Fine mapping of the Ity3 locus indicated that two sub-loci contribute collectively to the susceptibility of B6.MOLF-Ity/Ity3 congenic mice to Salmonella infection. In the current paper, we provided further evidence supporting a role for Ncf2 (neutrophil cytosolic factor 2 a subunit of NADPH oxidase) as the gene underlying the Ity3.1 sub-locus. Gene expression profiling indicated that the Ity3.1 sub-locus defined a global gene expression signature with networks articulated around Ncf2. Furthermore, based on differential expression and complementation analysis using Selp (selectin-P) knock-out mice, Selp was identified as a strong candidate gene for the Ity3.2 sub-locus.
On the Development of the Complementation System in English and its Relation to Switch-Reference

In this paper, we show that many of the dramatic changes that took place in the course of the history of the English complementation system are the result of a simple morphological change in the determiner system. We propose that Old English (OE) evolved from a system in which ‘complements’ clauses, relatives clauses and DPs were interpreted as adverbials to a system in which they are interpreted as arguments of the verb (in a sense to be defined below). As the determiner acquired certain type of morphological features, a complementation system developed. This hypothesis allows us to resolve the traditional tension between the idea that the passage from OE system to the New English (NE) system is a change from parataxis to hypotaxis, and the conception according to which complementation was already there (see among many others, Small, 1924; Curme, 1911). The common view on complementation considers it as a primitive of the linguistic system, in the sense that it is identified by a specific grammatical category (e.g. complementizer, subordinator). This view, which is shared by the two apparently opposite conceptions of complementation, is in fact misleading. Complementation, we claim, is derivative of the configurational properties of the structure. An important implication of our hypothesis is that, while the structures required for complementation are always present, complementation involves computational mechanisms that may be blocked, leaving as the only option the interpretation of the structure as an ‘adverbial’. Our hypothesis provides a possible account for the apparent directionality of linguistic change without recourse to the controversial increasing ‘(structural) complexity hypothesis’. In fact the latter hypothesis is incompatible with our analysis. The analysis developed here suggests that linguistic change is far more restricted and involves only changes in the features of elements which determine the level of projections of these elements. In the conclusion, we show that this claim is reinforced by the fact that apparently unrelated changes (i.e. meaning change of prepositions, emergence of genitive constructions) all follow from the nature of the determiner system of OE, which is reminiscent of similar systems found in typologically unrelated languages. 1. The role of the Determiner in the Licensing of Complementation The basis of our proposal is that DPs, relative clauses and complement clauses, all share the same basic structure in which a D° determiner licenses a CP complement, a proposal reminiscent of what Kayne (1994), has suggested for the structure of relative clauses and nominals involving overt predication such as genitives, possessives and related constructions. The LF configurations that we propose for NE are illustrated in (1.b), (2.b) and (3.b) for nominals, complement clauses and relative clauses respectively:
Preimplantation Human Blastocyst‐Endometrial Interactions: The Role of Inflammatory Mediators

Immune factors such as cytokines, chemokines, and growth factors are known to play important roles in the preimplantation interactions and communication between the blastocyst and receptive endometrium. This crucial dialog occurs during the stages when the blastocyst is in the uterine cavity immediately preceding implantation and the establishment of pregnancy. Human preimplantation processes are difficult to study due to restrictions on tissue availability. This review focuses on the expression and role of immune factors in human blastocyst‐endometrial dialog during the very early stages of implantation. It highlights the importance of immune regulators and the need to develop new models to study human implantation.
Using phone-based activity monitors to promote physical activity in older adults: A pilot study

Physical inactivity is a leading risk factor in a number of chronic diseases. Older adults are at the highest risk because they are the least inactive of all age groups. Smartphone-based intervention techniques present the opportunity to support cost-effective behavioral intervention to promote physical activity. We present a pilot study that examines the feasibility of utilizing the “Strive” smartphone-based passive sensing application to motivate older adults to stay active. Eight participants aged between 50 and 80 years used the application over a period of three weeks to track their daily activity habits. Participants carried smartphones to track daily activities and introspected about their lifestyles as part of weekly check-in sessions. The value that 24×7 smartphone-based sensors provided to this population was an easy-to-use and always available companion to promote awareness about their physical activity. The main motivations for participants to stay active were to prevent loss of personal health due ageing and the need to stay young. Participants increased their daily physical activity by 15% over the first week. This increase was mainly driven by the younger participants. Participants were willing to bear the inconvenience of physical activity tracking due a phone if it meant that they would obtain a better report of their daily physical activities. Any application that tracks physical activity using smartphones needs to address the wearability of the phone.
Modeling trust and distrust information in recommender systems via joint matrix factorization with signed graphs

We propose an efficient recommendation algorithm, by incorporating the side information of users' trust and distrust social relationships into the learning process of a Joint Non-negative Matrix Factorization technique based on Signed Graphs, namely JNMF-SG. The key idea in this study is to generate clusters based on signed graphs, considering positive and negative weights for the trust and distrust relationships, respectively. Using a spectral clustering approach for signed graphs, the clusters are extracted on condition that users with positive connections should lie close, while users with negative ones should lie far. Then, we propose a Joint Non-negative Matrix factorization framework, by generating the final recommendations, using the user-item and user-cluster associations over the joint factorization. In our experiments with a dataset from a real-world social media platform, we show that we significantly increase the recommendation accuracy, compared to state-of-the-art methods that also consider the trust and distrust side information in matrix factorization.
Forest Delineation Based on Airborne LIDAR Data

The delineation of forested areas is a critical task, because the resulting maps are a fundamental input for a broad field of applications and users. Different national and international forest definitions are available for manual or automatic delineation, but unfortunately most definitions lack precise geometrical descriptions for the different criteria. A mandatory criterion in forest definitions is the criterion of crown coverage (CC), which defines the proportion of the forest floor covered by the vertical projection of the tree crowns. For loosely stocked areas, this criterion is especially critical, because the size and shape of the reference area for calculating CC is not clearly defined in most definitions. Thus current forest delineations differ and tend to be non-comparable because of different settings for checking the criterion of CC in the delineation process. This paper evaluates a new approach for the automatic delineation of forested areas, based on airborne laser scanning (ALS) data with a clearly defined method for calculating CC. The new approach, the ‘tree triples’ method, is based on defining CC as a relation between the sum of the crown areas of three neighboring trees and the area of their convex hull. The approach is applied and analyzed for two study areas in Tyrol, Austria. The selected areas show a loosely stocked forest at the upper timberline and a fragmented forest on the hillside. The fully automatic method presented for delineating forested areas from ALS data shows promising results with an overall accuracy of 96%, and provides a beneficial tool for operational applications.
Switched-Power Two-Layer Superposition Coding in Cooperative Decode-Forward Relay Systems

In this paper, we consider a decode-forward relay system with a source, a relay, and a destination, where two-layer superposition codes are used at the source and the relay. An equivalent squared minimum distance (ESMD) that determines the error performance is derived by using an upper bound on the pair-wise error probability. Without deriving error probabilities, the error performance level for each of superimposed symbols can be shown in a straightforward manner by the ESMD. An optimal superposition-coded relay scheme and a suboptimal switched-power superposition coding scheme are proposed by improving the ESMD. Closed-form power allocation that maximizes the ESMD for the switched scheme is derived for 2-ary pulse amplitude modulation (PAM). An M-ary PAM generalization for the switched-power superposition-coded relay scheme is also presented. Simulation results show that significant signal-to-noise ratio gains are achieved in the optimal and switched-power superposition coding strategies for 2-ary and 4-ary PAM over the Rayleigh fading channel.
Who Is Performing Hip Arthroscopy?: An Analysis of the American Board of Orthopaedic Surgery Part-II Database

Background: Hip arthroscopy utilization has increased dramatically over the last decade. However, the lack of a formal training curriculum raises concern that inconsistent technical performance may be an issue for early-career hip arthroscopists. The purpose of the present study was to investigate hip arthroscopy utilization by early-career orthopaedic surgeons while focusing on fellowship training status to better guide future development of a hip arthroscopy training curriculum. Methods: The American Board of Orthopaedic Surgery (ABOS) Part-II database was used to identify candidates who had performed ≥1 hip arthroscopy procedures between 2006 and 2015. Procedures were categorized using Common Procedural Terminology (CPT) codes, and candidates were categorized by fellowship training experience. Trends in hip arthroscopy utilization were evaluated using univariate and regression analyses while stratifying by fellowship training experience. Results: Overall, 9.2% (643) of 6,987 ABOS candidates had performed ≥1 hip arthroscopy procedures. Over the study period, both the proportion of candidates performing hip arthroscopy and the proportion of hip arthroscopy procedures performed (relative to all procedures performed, of any type) increased (p < 0.001). Candidates performing hip arthroscopy most frequently reported sports medicine fellowship training (74.5%; 479 of 643). Also, among the candidates who performed hip arthroscopy, the proportion who had sports medicine fellowship training increased over the study period (p = 0.001). The majority of candidates performing hip arthroscopy (67.2%; 432 of 643) performed ⩽5 hip arthroscopy procedures, while a small number of high-volume hip arthroscopists (6.5%; 42 of 643) performed 34.6% (1,403 of 4,054) of all hip arthroscopy procedures. Conclusions: The increase in hip arthroscopy utilization in this cohort appears to have been driven primarily by the increased number of candidates performing hip arthroscopy and less by an increasing number of hip arthroscopy procedures being performed by individual candidates. The majority of candidates performing hip arthroscopy were sports-medicine-fellowship trained. This information is valuable for both trainees and educators interested in improving education and defining a curriculum for future hip arthroscopy training.
A Sequential Model for Classifying Temporal Relations between Intra-Sentence Events

We present a sequential model for temporal relation classification between intra-sentence events. The key observation is that the overall syntactic structure and compositional meanings of the multi-word context between events are important for distinguishing among fine-grained temporal relations. Specifically, our approach first extracts a sequence of context words that indicates the temporal relation between two events, which well align with the dependency path between two event mentions. The context word sequence, together with a parts-of-speech tag sequence and a dependency relation sequence that are generated corresponding to the word sequence, are then provided as input to bidirectional recurrent neural network (LSTM) models. The neural nets learn compositional syntactic and semantic representations of contexts surrounding the two events and predict the temporal relation between them. Evaluation of the proposed approach on TimeBank corpus shows that sequential modeling is capable of accurately recognizing temporal relations between events, which outperforms a neural net model using various discrete features as input that imitates previous feature based models.