Miracle-dz/UniFAR-FTUs huggingface dataset:
Hilbert Space Multidimensional Theory

A general theory of measurement context effects, called Hilbert space multidimensional (HSM) theory, is presented. A measurement context refers to a subset of psychological variables that an individual evaluates on a particular occasion. Different contexts are formed by evaluating different but possibly overlapping subsets of variables. Context effects occur when the judgments across contexts cannot be derived from a single joint probability distribution over the complete set of values of the observed variables. HSM theory provides a way to model these context effects by using quantum probability theory, which represents all the variables within a low dimensional vector space. HSM models produce parameter estimates that provide a simple and informative interpretation of the complex collection of judgments across contexts. Comparisons of HSM model fits with Bayesian network model fits are reported for a new large experiment, demonstrating the viability of this new model. We conclude that the theory is broadly applicable to measurement context effects found in the social and behavioral sciences.
ULTRASOUND FOCUSING IN SPHERICAL BUBBLE CLOUD

HIFU (High Intensity Focused Ultrasound) applications have attracted much attention recently because they are less invasive. However, the behavior of acoustic cavitation caused by high pressure amplitude at the focal region has not been clarified. In this study, it is assumed that the acoustic cavitation forms a spherical bubble cloud which consists of many micro bubbles, and ultrasound focusing in the cloud is investigated numerically. The compressibility of liquid, the evaporation and condensation of liquid at the bubble wall, heat transfer through the bubble wall are considered in the simulation. Initial cloud radius is equal to 0.5 mm, bubble radius is 1 µm, void fraction is 0.1 %, and the frequency of ultrasound extends from 5 kHz to 10 MHz for amplitudes of 10 kPa, 25 kPa, 50 kPa, 75 kPa, 100 kPa or 125 kPa. The pressure wave focuses to the center of the cloud and the pressures inside bubbles increase extremely when the frequency is near the 1 st mode frequency of the cloud estimated from a small amplitude approximation. Especially, in the case of 100 kPa and 125 kPa pressure amplitudes, the high pressures appear even when the frequency is much lower than the 1 st mode frequency.
Convolutional neural networks for classification of alignments of non-coding RNA sequences

Motivation The convolutional neural network (CNN) has been applied to the classification problem of DNA sequences, with the additional purpose of motif discovery. The training of CNNs with distributed representations of four nucleotides has successfully derived position weight matrices on the learned kernels that corresponded to sequence motifs such as protein‐binding sites. Results We propose a novel application of CNNs to classification of pairwise alignments of sequences for accurate clustering of sequences and show the benefits of the CNN method of inputting pairwise alignments for clustering of non‐coding RNA (ncRNA) sequences and for motif discovery. Classification of a pairwise alignment of two sequences into positive and negative classes corresponds to the clustering of the input sequences. After we combined the distributed representation of RNA nucleotides with the secondary‐structure information specific to ncRNAs and furthermore with mapping profiles of next‐generation sequence reads, the training of CNNs for classification of alignments of RNA sequences yielded accurate clustering in terms of ncRNA families and outperformed the existing clustering methods for ncRNA sequences. Several interesting sequence motifs and secondary‐structure motifs known for the snoRNA family and specific to microRNA and tRNA families were identified. Availability and implementation The source code of our CNN software in the deep‐learning framework Chainer is available at http://www.dna. bio.keio. ac.jp/cnn/, and the dataset used for performance evaluation in this work is available at the same URL.
Endophytic fungi from Dracaena cambodiana and Aquilaria sinensis and their antimicrobial activity

Single mycelium method was used to isolate endophytic fungi from surface-sterilized tissues of two medicinal plants. Of the 300 isolates recovered, 172 were from Dracaena cambodiana and 128 from Aquilaria sinensis. According to morphological characteristics, 174 (58%) isolates were identified and belonged to 41 taxa in 30 genera. The remaining 126 (42%) isolates did not sporulate and were segregated into 8 morphological groups. There were colonization rates (34 - 80%) and isolation rates (0.62 - 2.06) in two plants. And some endophytes showed certain level of host specificity or organs specificity. 21 (8.3%) isolates showed antimicrobial activity, moreover, some of them exhibited broadspectrum antimicrobial activity and the inhibition zones ranged from 7 to 27 mm. The active isolates were identified to 17 taxa. Fusarium spp. were the most dominant genera in two plants and showed the most potent antimicrobial activity.
Tolerogenic Dendritic Cells Reduce Airway Inflammation in a Model of Dust Mite Triggered Allergic Inflammation

Purpose The use of tolerogenic dendritic cells (TolDCs) to control exacerbated immune responses may be a prophylactic and therapeutic option for application in autoimmune and allergic conditions. The objective of this work was to evaluate the effects of TolDC administration in a mouse model of allergic airway inflammation caused by mite extract. Methods Mouse bone marrow-derived TolDCs were induced by incubation with granulocyte-macrophage colony-stimulating factor (GM-CSF) and dexamethasone, and then characterized by flow cytometry and cytokine production by enzyme-linked immunosorbent assay (ELISA). For the in vivo model of Blomia tropicalis-induced allergy, mice transplanted with antigen-pulsed TolDCs were sensitized intraperitoneally with B. tropicalis mite extract (BtE) adsorbed to aluminium hydroxide. After challenge by nasal administration of BtE, bronchoalveolar lavage fluid (BALF), lungs, spleen and serum were collected for analysis. Results Induction of TolDCs was efficiently achieved as shown by low expression of major histocompatibility complex (MHC) II, programmed death-ligand (PD-L) 2 and pro-inflammatory cytokine production, and up-regulation of interleukin (IL)-10, upon LPS stimulation in vitro. Transplantation of 1 or 2 doses of BtE-pulsed TolDCs reduced the number of inflammatory cells in BALF and lungs as well as mucus deposition. Moreover, compared to saline-injected controls, TolDC-treated mice showed lower serum levels of anti-BtE immunoglobulin E (IgE) antibodies as well as reduced Gata3 and IL-4 gene expression in the lungs and decreased IFN-γ levels in the supernatant of splenocyte cultures Transplantation of TolDCs increased the percentage of the regulatory T cells in the spleen and the lungs. Conclusions Preventive treatment with TolDCs protects against dust mite-induced allergy in a mouse model, reinforcing the use of tolerogenic dendritic cells for the management of allergic conditions.
Is it just the hip?

Hailer, Y. D. 2014. Legg-Calvé-Perthes Disease – Is it just the hip? Epidemiological, Clinical and Psychosocial Studies with special focus on Etiology. Digital Comprehensive Summaries of Uppsala Dissertations from the Faculty of Medicine 979. 65 pp. Uppsala: Acta Universitatis Upsaliensis. ISBN 978-91-554-8899-4. The overall aim of the thesis was to add some pieces to the etiological puzzle of LCPD with special focus on vascular origin and hyperactivity. Furthermore we wanted to evaluate some consequences of LCPD in adulthood. Swedish registry data were used to identify a cohort of patients with the diagnosis of LCPD. This cohort was compared with a general population– based cohort without LCPD to assess the relative risk of cardiovascular diseases, blood or coagulation defects, injury, ADHD, depression and mortality. In a clinical study we assessed health-related quality of life (EQ-5D-3L), physical activity level (IPAQ) and screened for ADHD (ASRSv1.1) in 116 patients with a history of LCPD who were diagnosed or treated in Uppsala University Hospital between 1978 and 1995. The results confirmed our hypothesis: Patients with a history of LCPD had a 1.7-fold higher risk of cardiovascular diseases, and a 1.4-fold higher risk for blood or coagulation defects compared with genderand age-matched individuals without LCPD. We found a 1.2-fold higher risk for injuries requiring hospital admission than in genderand age-matched individuals without LCPD. The risk was more pronounced among females. Furthermore, we found a 1.5fold higher risk for ADHD. Stratified analysis revealed a 2.1-fold higher risk for ADHD among females with LCPD than among females without LCPD. The risk for depression was 1.3-fold higher, and more pronounced among females with LCPD. Patients with LCPD had a slightly higher mortality risk with higher risk for death from suicide and cardiovascular causes. Patients with a history of LCPD reported a lower health-related quality of life and were more physically active than the Swedish population norm. 28% of 116 patients were likely to have ADHD or had already been diagnosed with ADHD. Both vascular and blood diseases could be present even in childhood and could, in combination with hyperactive behavior pattern and a high physical activity level, contribute to the etiology of LCPD. The lower health-related quality of life and higher risk for depression might reflect the mental burden of LCPD. Patients with LCPD have a higher mortality risk with higher risk for death from suicide and cardiovascular causes.
Matrix Completion from Non-Uniformly Sampled Entries

In this paper, we consider matrix completion from non-uniformly sampled entries including fully observed and partially observed columns. Specifically, we assume that a small number of columns are randomly selected and fully observed, and each remaining column is partially observed with uniform sampling. To recover the unknown matrix, we first recover its column space from the fully observed columns. Then, for each partially observed column, we recover it by finding a vector which lies in the recovered column space and consists of the observed entries. When the unknown $m\times n$ matrix is low-rank, we show that our algorithm can exactly recover it from merely $\Omega(rn\ln n)$ entries, where $r$ is the rank of the matrix. Furthermore, for a noisy low-rank matrix, our algorithm computes a low-rank approximation of the unknown matrix and enjoys an additive error bound measured by Frobenius norm. Experimental results on synthetic datasets verify our theoretical claims and demonstrate the effectiveness of our proposed algorithm.
Automatic Control: How Experts Act Without Thinking

Experts act without thinking because their skill is hierarchical. A single conscious thought automatically produces a series of lower-level actions without top-down monitoring. This article presents a theory that explains how automatic control is possible in skilled typing, where thinking of a word automatically produces a rapid series of keystrokes. The theory assumes that keystrokes are selected by a context retrieval process that matches the current context to stored contexts and retrieves the key associated with the best match. The current context is generated by the typist’s own actions. It represents the goal (“type DOG”) and the motor commands for the keys struck so far. Top-down control is necessary to start typing. It sets the goal in the current context, which initiates the retrieval and updating processes, which continue without top-down control until the word is finished. The theory explains phenomena of hierarchical control in skilled typing, including differential loads on higher and lower levels of processing, the importance of words, and poor explicit knowledge of key locations and finger-to-key mappings. The theory is evaluated by fitting it to error corpora from 24 skilled typists and predicting error probabilities, magnitudes, and patterns. Some of the fits are quite good. The theory has implications beyond typing. It argues that control can be automatic and shows how it is possible. The theory extends to other sequential skills, like texting or playing music. It provides new insights into mechanisms of serial order in typing, speaking, and serial recall.
A Systematic Review of Cognitive Training for Schizophrenia in Developing Countries

The majority of programmes created to improve cognitive difficulties in schizophrenia were developed in Europe and the United States. To our knowledge, very few studies on this area were conducted in developing nations. We conducted a systematic review of the literature in search for studies on cognitive training in schizophrenia in developing countries and discussed the possible difficulties involved in this type of research. Seven different databases were searched for studies on cognitive training in schizophrenia in developing nations. Only 5 studies were found. The main difficulties in conducting this type of research identified by us involve low budget, a lack of necessary infrastructure (trained professionals to deliver the intervention and to carry out assessments, cost of training programmes and availability of space), hurdles to publishing results in larger indexed journals. Despite all the difficulties encountered, we believe it is important that more programmes to treat cognitive deficits in schizophrenia are created in developing countries, as they can be adapted to the cultural differences and different needs of these nations. We also believe cognitive training can be constructed in a low cost manner, requiring minimal infrastructure, adequate to developing nations’ reality.
PHYSICAL SIDE EFFECTS OF PSYCHOACTIVE MEDS

Introduction: Antipsychotics represent a large portion of the psychotropics that may induce hyperprolactinemia. Clinical psychiatric pharmacists must be adept in stratifying the relative risk of hyperprolactinemia among psychotropics, identifying patient risk factors, recognizing differential diagnoses, and recommending therapeutic alternatives and treatment strategies. High-potency, typical antipsychotics are more likely to elevate prolactin although exceptions to the rule exist. Methods: A literature search of PubMed and Google Scholar was performed to identify English language articles on the treatment of antipsychotic-induced hyperprolactinemia in humans. Methodological rigor is summarized for compiled studies in addition to feasibility and limitations of application to clinical practice. Results: There is an absence of robust evidence for the management of antipsychotic-induced hyperprolactinemia. Among the pharmacological treatments studied, aripiprazole (switching or augmentation) possessed the strongest evidence. Pharmacological treatments with less evidence encompassed dose reduction, switching to lower potency antipsychotics, and adding dopamine agonists. To date, no head-tohead studies have been published on the above approaches. Discussion: Atypical antipsychotics with low affinity for dopamine (D2) receptors, such as olanzapine, are logical alternatives for the patient experiencing drug-induced hyperprolactinemia. When augmentation is clinically preferred to switching, a viable option is the addition of a full or partial dopamine agonist, such as bromocriptine or aripiprazole, respectively. Patient-specific risk of psychiatric decompensation and the severity of symptomatic hyperprolactinemia should be weighed when formulating treatment strategies.
Random forest based similarity learning for single cell RNA sequencing data

Motivation Genome-wide transcriptome sequencing applied to single cells (scRNA-seq) is rapidly becoming an assay of choice across many fields of biological and biomedical research. Scientific objectives often revolve around discovery or characterization of types or sub-types of cells, and therefore obtaining accurate cell–cell similarities from scRNA-seq data is critical step in many studies. While rapid advances are being made in the development of tools for scRNA-seq data analysis, few approaches exist that explicitly address this task. Furthermore, abundance and type of noise present in scRNA-seq datasets suggest that application of generic methods, or of methods developed for bulk RNA-seq data, is likely suboptimal. Results Here we present RAFSIL, a random forest based approach to learn cell–cell similarities from scRNA-seq data. RAFSIL implements a two-step procedure, where feature construction geared towards scRNA-seq data is followed by similarity learning. It is designed to be adaptable and expandable, and RAFSIL similarities can be used for typical exploratory data analysis tasks like dimension reduction, visualization, and clustering. We show that our approach compares favorably with current methods across a diverse collection of datasets, and that it can be used to detect and highlight unwanted technical variation in scRNA-seq datasets in situations where other methods fail. Overall, RAFSIL implements a flexible approach yielding a useful tool that improves the analysis of scRNA-seq data. Availability and Implementation The RAFSIL R package is available online at www.kostkalab. net/software.html
Exploitation of Stragglers in Coded Computation

In cloud computing systems slow processing nodes, often referred to as “stragglers”, can significantly extend the computation time. Recent results have shown that error correction coding can be used to reduce the effect of stragglers. In this work we introduce a scheme that, in addition to using error correction to distribute mixed jobs across nodes, is also able to exploit the work completed by all nodes, including stragglers. We first consider vector-matrix multiplication and apply maximum distance separable (MDS) codes to small blocks of sub-matrices. The worker nodes process blocks sequentially, working block-by-block, transmitting partial per-block results to the master as they are completed. Sub-blocking allows a more continuous completion process, which thereby allows us to exploit the work of a much broader spectrum of processors and reduces computation time. We then apply this technique to matrix-matrix multiplication using product code. In this case, we show that the order of computing sub-tasks is a new degree of design freedom that can be exploited to reduce computation time further. We propose a novel approach to analyze the finishing time, which is different from typical order statistics. Simulation results show that the expected computation time decreases by a factor of at least two in compared to previous methods.
Glycinergic signaling in the human nervous system: An overview of therapeutic drug targets and clinical effects

Glycine and related endogenous compounds (d-serine, d-alanine, sarcosine) serve critical roles in both excitatory and inhibitory neurotransmission and are influenced by a multitude of enzymes and transporters, including glycine transporter 1 and 2 (GlyT1 and GlyT2), d-amino acid oxidase (DAAO), serine racemase (SRR), alanine-serine-cysteine transporter 1 (Asc-1), and kynurenine aminotransferase (KAT). MEDLINE, Web of Science, and PsychINFO were searched for relevant human trials of compounds. Many studies utilizing exogenous administration of small molecule agonists of the glycineB site of n-methyl-d-aspartate receptor have been studied as have a growing number of glycine transporter type 1 (GlyT1) inhibitors. The clinical effects of these compounds are reviewed as are the potential effects of newer novel compounds.
Can the ego be depleted? : Attempts to replicate the ego depletion effect and integrate its explanations

Although self-control is so important that no one from any corner of the world would dispute, it is often difficult and vulnerable. Continuous exertion is one of the most influential factors that are detrimental to self-control, which leads to a state called “ego depletion”. Before 2016, the ego depletion effect had been a hot topic for a long time. After a multi-lab replication that reported a non-significant result in 2016, however, it became highly controversial regarding whether the ego depletion effect is a true effect. In the first three articles presenting reanalyses of data from the multi-lab replication, conducting an updated meta-analysis, and implementing a pre-registered large-scale experiment, I demonstrate that the non-significant result found in the multi-lab replication may be due to the ineffectiveness of the depleting task, and there is a reliable ego depletion effect when an effective depleting task is used. Further, Iintroduce and compare several explanations of the ego depletion effect, by analyzing the pros and cons of each explanation. On the basis of this work, I propose a fine-grained new model (i.e., the CoMo model) that integrates various lines of research and is able to explain almost all counterintuitive findings in this area. The last two articles provide evidence in support of the new model but contradict other theories. The limitations and future directions are discussed. (Less)
Making Great Leaps Forward: Accounting for Detectability in Herpetological Field Studies

Abstract Detecting individuals of amphibian and reptile species can be a daunting task. Detection can be hindered by various factors such as cryptic behavior, color patterns, or observer experience. These factors complicate the estimation of state variables of interest (e.g., abundance, occupancy, species richness) as well as the vital rates that induce changes in these state variables (e.g., survival probabilities for abundance; extinction probabilities for occupancy). Although ad hoc methods (e.g., counts uncorrected for detection, return rates) typically perform poorly in the face of no detection, they continue to be used extensively in various fields, including herpetology. However, formal approaches that estimate and account for the probability of detection, such as capture-mark-recapture (CMR) methods and distance sampling, are available. In this paper, we present classical approaches and recent advances in methods accounting for detectability that are particularly pertinent for herpetological data sets. Through examples, we illustrate the use of several methods, discuss their performance compared to that of ad hoc methods, and we suggest available software to perform these analyses. The methods we discuss control for imperfect detection and reduce bias in estimates of demographic parameters such as population size, survival, or, at other levels of biological organization, species occurrence. Among these methods, recently developed approaches that no longer require marked or resighted individuals should be particularly of interest to field herpetologists. We hope that our effort will encourage practitioners to implement some of the estimation methods presented herein instead of relying on ad hoc methods that make more limiting assumptions.