Miracle-dz/UniFAR-FTUs huggingface dataset:
Caenorhabditis elegans Predation on Bacillus anthracis: Decontamination of Spore Contaminated Soil with Germinants and Nematodes

Remediation of Bacillus anthracis-contaminated soil is challenging and approaches to reduce overall spore levels in environmentally contaminated soil or after intentional release of the infectious disease agent in a safe, low-cost manner are needed. B. anthracis spores are highly resistant to biocides, but once germinated they become susceptible to traditional biocides or potentially even natural predators such as nematodes in the soil environment. Here, we describe a two-step approach to reducing B. anthracis spore load in soil during laboratory trials, whereby germinants and Caenorhabditis elegans nematodes are applied concurrently. While the application of germinants reduced B. anthracis spore load by up to four logs depending on soil type, the addition of nematodes achieved a further log reduction in spore count. These laboratory based results suggest that the combined use of nematodes and germinants could represent a promising approach for the remediation of B. anthracis spore contaminated soil. Originality-Significance Statement: This study demonstrates for the first time the successful use of environmentally friendly decontamination methods to inactivate Bacillus anthracis spores in soil using natural predators of the bacterium, nematode worms.
Shape and spatial working memory capacities are mostly independent

Whether visual working memory (WM) consists of a common storage resource or of multiple subsystems has been a controversial issue. Logie (1995) suggested that it can be divided into visual (for color, shape, objects, etc.) and spatial WM (for location). However, a recent study reported evidence against this hypothesis. Using a dual task paradigm, Wood (2011) showed interference between shape and spatial WM capacities, suggesting that they share a common resource limitation. We re-examined this finding controlling possible confounding factors, including the way to present spatial location cues, task order, and type of WM load to be manipulated. The same pattern of results was successfully reproduced, but only in a highly powered experiment (N = 90), and therefore the size of interference was estimated to be quite small (d = 0.24). Thus, these data offer a way to reconcile seemingly contradicting previous findings. On the one hand, some part of the storage system is genuinely shared by shape and spatial WM systems, confirming the report of Wood (2011). On the other hand, the amount of the overlap is only minimal, and therefore the two systems should be regarded as mostly independent from each other, supporting the classical visuo-spatial separation hypothesis.
Clavision: visual automatic piano music transcription

One important problem in Musical Information Retrieval is Automatic Music Transcription, which is an automated conversion process from played music to a symbolic notation such as sheet music. Since the accuracy of previous audio-based transcription systems is not satisfactory, we propose an innovative visual-based automatic music transcription system named claVision to perform piano music transcription. Instead of processing the music audio, the system performs the transcription only from the video performance captured by a camera mounted over the piano keyboard. claVision can be used as a transcription tool, but it also has other applications such as music education. The claVision software has a very high accuracy (over 95%) and a very low latency in real-time music transcription, even under different illumination conditions.
Degrees of freedom of general symmetric MIMO interference broadcast channels

In this paper, we study the maximal achievable degrees of freedom (DoF) for G-cell, K-user M×N symmetric multi-input-multi-output (MIMO) interference broadcast channel (MIMO-IBC) with constant coefficients by linear interference alignment (IA). We start by analyzing the sufficient and necessary conditions of the IA feasibility, which are associated with generalized Fibonacci sequences. Except for the well-known proper condition, we find another condition necessary to ensure a kind of irreducible interference to be eliminated, denoted as irreducible condition. We proceed to find the minimal number of antennas at each base station and each user to support a required number of interference-free data streams, from which we obtain the maximal achievable DoF. We find that the feasibility conditions in terms of the required antenna resources can be divided into two regions according the ratio of ρ = M/N. If ρ falls into the region that characterized by the proper condition, the achievable DoF per user with spatial extension is (M + N)/(GK + 1). If ρ lies in the region that characterized by the irreducible condition, the DoF is a piecewise linear function of M or N alternately.
Have Baryonic Acoustic Oscillations in the galaxy distribution really been measured

Recent publications claim that there is no convincing evidence for measurements of the baryonic acoustic oscillation (BAO) feature in galaxy samples using either monopole or radial information. Different claims seem contradictory: data are either not consistent with the BAO model or data are consistent with both the BAO model and featureless models without BAO. We investigate this point with a set of 216 realistic mock galaxy catalogues extracted from MICE 7680, one of the largest volume dark matter simulation run to date, with a volume of 1300 cubical gigaparsecs. Our mocks cover similar volume, densities and bias as the real galaxies and provide 216 realizations of the lambda or ω=−1 cold dark matter (ωCDM) BAO model. We find that only 20 per cent of the mocks show a statistically significant (3σ) preference for the true (input) ωCDM BAO model as compared to a featureless (non-physical) model without BAO. Thus the volume of current galaxy samples is not yet large enough to claim that the BAO feature has been detected. Does this mean that we cannot locate the BAO position? Using a simple (non-optimal) algorithm we show that in 50 per cent (100 per cent) of the mocks, we can find the BAO position within 5 per cent (20 per cent) of the true value. These two findings are not in contradiction: the former is about model selection and the later is about parameter fitting within a model. We conclude that current monopole and radial BAO measurements can be used as standard rulers if we assume ωCDM type of models.
Social Stories to Increase Verbal Initiation in Children With Autism and Asperger’s Disorder

Abstract. Individuals with autism spectrum disorders experience pervasive social and communication skill deficits. One of the most popular treatment recommendations to address these deficits is the use of social stories. Although social stories are beneficial at reducing many disruptive behaviors, empirical evidence for their use to increase social and communication behaviors is limited. The present study, conducted in a natural setting, investigated the use of social stories to increase the prosocial behaviors of verbal initiations and contingent responses in students with either autism or Asperger\'s disorder. Results suggested that the efficaciousness of this widely accepted intervention is questionable and in need of further research.
The role of urine trypsinogen-2 test in the differential diagnosis of acute pancreatitis in the Emergency Department.

BACKGROUND The aim of the study was to investigate the role and importance of the urine trypsinogen-2 dipstick test in the differential diagnosis of acute pancreatitis in the Emergency Department and to compare results with those of conventional tests. METHODS The study was performed prospectively in the patients admitting to the Emergency Department due to upper abdominal pain. Thirty-two of the 87 patients included in the study had acute pancreatitis diagnosis. Serum amylase, lipase, C-reactive protein (CRP) and urine trypsinogen-2 using Actim pancreatitis dipstick were studied in all patients. The statistical analysis was performed using SPSS 11.5 package program. RESULTS Urine trypsinogen-2 was found positive in 21 (65.6%) of 32 patients. The sensitivity of the test for pancreatitis was identified as 64%, specificity as 85%, positive predictive value as 72%, and negative predictive value as 81%. These values were statistically significant compared to the control group (p<0.01). CONCLUSION Although it has lower sensitivity and specificity compared to amylase and lipase, we suggest that urine trypsinogen-2 test may be an important diagnostic tool in excluding the diagnosis of acute pancreatitis, since it provides results within 5 minutes in the Emergency Department, is cheaper, has a higher negative predictive value, and is easy to use.
On the Relative Value of Multiple-Choice, Constructed Response, and Examinee-Selected Items on Two Achievement Tests. Program Statistics Research Technical Report No. 93-28.

Using analyses based on fitting item response models to data from the College Board's Advanced Placement exams in chemistry and United States history, we found that the constructed response portion of the tests yielded little information over and above that provided by the multiple-choice sections. These tests also allow examinees to select subsets of the constructed response items; we found that scoring on the basis of the selections themselves provided almost as much information as did scoring on the basis of the answers. One goal of the Advanced Placement (AP) testing program of the College Board is to determine the proficiency attained by high school students in college level courses. Such courses are offered at more than 40% of the 21,000 secondary schools in this country, including 80% of those having a junior class larger than 250 students. With few exceptions, AP exams are made up of one section consisting of multiple-choice (MC) items and a second section of constructed response
When Null Hypothesis Significance Testing Is Unsuitable for Research: A Reassessment

Null hypothesis significance testing (NHST) has several shortcomings that are likely contributing factors behind the widely debated replication crisis of psychology, cognitive neuroscience and biomedical science in general. We review these shortcomings and suggest that, after about 60 years of negative experience, NHST should no longer be the default, dominant statistical practice of all biomedical and psychological research. Different inferential methods (NHST, likelihood estimation, Bayesian methods, false-discovery rate control) may be most suitable for different types of research questions. Whenever researchers use NHST they should justify its use, and publish pre-study power calculations and effect sizes, including negative findings. Studies should optimally be pre-registered and raw data published. The current statistics lite educational approach for students that has sustained the widespread, spurious use of NHST should be phased out. Instead, we should encourage either more in-depth statistical training of more researchers and/or more widespread involvement of professional statisticians in all research.
Whole genome sequencing and variant discovery in the ASPIRE autism spectrum disorder cohort

Autism spectrum disorder (ASD) is a highly heterogeneous genetic disorder with strong evidence of ASD‐association currently available only for a small number of genes. This makes it challenging to identify the underlying genetic cause in many cases of ASD, and there is a continuing need for further discovery efforts. We sequenced whole genomes of 119 deeply phenotyped ASD probands in order to identify likely pathogenic variants. We prioritized variants found in each subject by predicted damage, population frequency, literature evidence, and phenotype concordance. We used Sanger sequencing to determine the inheritance status of high‐priority variants where possible. We report five novel de novo damaging variants as well as several likely damaging variants of unknown inheritance; these include two novel de novo variants in the well‐established ASD gene SCN2A. The availability of rich phenotypic information and its concordance with the literature allowed us to increase our confidence in pathogenicity of discovered variants, especially in probands without parental DNA. Our results contribute to the documentation of potential pathogenic variants and their associated phenotypes in individuals with ASD.
Deformation due to the 17 August 1999 Izmit, Turkey, earthquake measured from SPOT images

The geometry of the ruptured areas and the coseismic slip distribution data are key to highlighting the behavior of seismic faults. This information is generally retrieved from field investigations and geodetic measurements or synthetic aperture radar (SAR) interferometry. Here we show that SPOT images can also be used to accurately map the fault zone and to determine the slip distribution by subpixel correlation of images acquired before and after an earthquake. The measured slip includes the contribution of possible distributed shear that might not be clearly expressed in surface ruptures and smoothes out possible along-strike variability due to near-surface fault complexities. We apply the technique to the M_s = 7.4, 1999, Izmit earthquake. Our results reveal a <100-m-wide and very linear fault zone that can be traced for 70 km from Golcuk to Akyazi, along which supershear rupture has been inferred. The obtained slip distribution compares well with the field measurements and is consistent with ground deformation measured at some distance from the fault zone using SAR images. Very little deformation was accommodated off the main fault plane. Maximum slip is observed near Sapanca lake at a small fault jog that has probably influenced rupture propagation.
A General Asymptotic Expansion Formula for Integrals Involving High-Order Orthogonal Polynomials

A new method of evaluating overlap integrals involving orthogonal polynomials is proposed. The technique relies on purely algebraic manipulation of the associated recurrence coefficients. For a large class of polynomials and for sufficiently large orders, these coefficients can be written explicitly as Taylor series in terms of powers of $\epsilon=1/n$, where n is the polynomial order. Such decompositions are perfectly suited to the accurate numerical evaluation of integrals involving high-order polynomials. Examples include the numerical evaluation of integrals involving classical orthogonal polynomials such as Laguerre, Jacobi, and Gegenbauer.
MIT Open Access

An analytical Mason equivalent circuit is derived for a circular, clamped plate piezoelectric micro-machined ultrasonic transducer (pMUT) design in 31 mode considering an arbitrary electrode conﬁguration at any axisymmetric vibration mode. The explicit deﬁnition of lumped parameters based entirely on geometry, material properties and deﬁned constants enables straightforward and wide ranging model implementation for future pMUT design and optimization. Beyond pMUTs, the acoustic impedance model is developed for universal application to any clamped, circular plate system and operating regimes including relevant simpliﬁcations are identiﬁed via the wave number-radius product ka . For the single electrode fundamental vibration mode case, sol-gel Pb ( Zr 0 . 52 ) Ti 0 . 48 O 3 (PZT) pMUT cells are micro-fabricated with varying electrode size to conﬁrm the derived circuit model with electrical impedance measurements. For the ﬁrst time, experiment and ﬁnite element simulation results are successfully applied to validate extensive electrical, mechanical and acoustic analytical modeling of a pMUT cell for wide ranging applications including medical ultrasound, non-destructive testing, and range ﬁnding.
From Epidemiology to Daily Life: Linking Daily Life Stress Reactivity to Persistence of Psychotic Experiences in a Longitudinal General Population Study

Subclinical psychotic experiences at the level of the general population are common, forming an extended psychosis phenotype with clinical psychosis. Persistence of subclinical experiences is associated with transition to later mental disorder. Increased daily life stress reactivity is considered an endophenotype for psychotic disorders. We examined, in a longitudinal framework, whether baseline momentary assessment markers of stress reactivity would predict persistence of subclinical psychotic experiences over time. In a general population sample of female twins (N = 566), the Experience Sampling Method (ESM; repetitive random sampling of momentary emotions, psychotic experiences and context) was used to assess (emotional and psychotic) daily life stress reactivity. Persistence of subclinical psychotic experiences was based on the Community Assessment of Psychic Experiences (CAPE), assessed three times over 14 months post-baseline. It was investigated whether baseline daily life emotional and psychotic stress reactivity predicted persistence of psychotic experiences over time. Higher levels of emotional stress reactivity (a decrease in positive and an increase in negative affect in response to stress), and increased psychotic reactivity to daily stress was found in individuals with persistent psychotic experiences over time compared to individuals with transient psychotic experiences. The results suggest that markers of daily life stress reactivity may predict “macro-level” persistence of normally transient expression of psychotic liability over time. Linking daily life markers of altered reactivity in terms of emotions and psychotic experiences to longitudinal persistence of psychotic experiences, associated with increased risk of transition to overt mental disorder, may contribute to earlier and more accurate diagnosis of risk.
Effect of Wenxin Granule on Ventricular Remodeling and Myocardial Apoptosis in Rats with Myocardial Infarction

Aim. To determine the effect of a Chinese herbal compound named Wenxin Granule on ventricular remodeling and myocardial apoptosis in rats with myocardial infarction (MI). Methods. Male Sprague-Dawley (SD) rats were randomly divided into four groups: the control group, the model group, the metoprolol group, and the Wenxin Granule group (WXKL group) with sample size (n) of 7 rats in each group. An MI model was established in all rats by occlusion of the left anterior descending coronary artery (the control group was without occlusion). Wenxin Granule (1.35 g/kg/day), metoprolol (12 mg/kg/day), and distilled water (5 mL/kg/day for the control and model groups) were administered orally for 4 weeks. Ultrasonic echocardiography was used to examine cardiac structural and functional parameters. Myocardial histopathological changes were observed using haematoxylin and eosin (H&E) dyeing. Myocardial apoptosis was detected by terminal deoxynucleotidyl transferase mediated dUTP nick end labeling (TUNEL) staining. Serum angiotensin II (Ang II) concentration was measured using the enzyme-linked immunosorbent assay (ELISA). Results. It was found that Wenxin Granule could partially reverse ventricular remodeling, improve heart function, alleviate the histopathological damage, inhibit myocardial apoptosis, and reduce Ang II concentration in rats with MI. Conclusions. The results of the current study suggest that Wenxin Granule may be a potential alternative and complementary medicine for the treatment of MI.
Data mapping for unreliable memories

Future digital signal processing (DSP) systems must provide robustness on algorithm and application level to the presence of reliability issues that come along with corresponding implementations in modern semiconductor process technologies. In this paper, we address this issue by investigating the impact of unreliable memories on general DSP systems. In particular, we propose a novel framework to characterize the effects of unreliable memories, which enables us to devise novel methods to mitigate the associated performance loss. We propose to deploy specifically designed data representations, which have the capability of substantially improving the system reliability compared to that realized by conventional data representations used in digital integrated circuits, such as 2's-complement or sign-magnitude number formats. To demonstrate the efficacy of the proposed framework, we analyze the impact of unreliable memories on coded communication systems, and we show that the deployment of optimized data representations substantially improves the error-rate performance of such systems.
Alternative Splicing Coupled Nonsense-Mediated Decay Generates Neuronal Cell Type-Specific Expression of SLM Proteins

The unique physiological and morphological properties of neuronal populations are crucial for the appropriate functioning of neuronal circuits. Alternative splicing represents an attractive mechanism for generating cell type-specific molecular repertoires that steer neuronal development and function. However, the mechanisms that link neuronal identity to alternative splicing programs are poorly understood. We report that cell type-specific, mutually exclusive expression of two alternative splicing regulators, SLM1 and SLM2, in the mouse hippocampus is achieved by a cross-repression mechanism. Deletion of SLM2 in vivo modifies alternative splicing of its paralog Slm1 and stabilizes its mRNA, resulting in expression of SLM1 in previously SLM2-expressing cells. Despite this ectopic upregulation of SLM1, loss of SLM2 severely disrupts the alternative splicing regulation of Nrxn1, Nrxn2, and Nrxn3, highlighting that the two SLM paralogs have partially divergent functions. Our study uncovers a hierarchical, SLM2-dependent mechanism for establishing cell type-specific expression of neuronal splicing regulators in vivo.
Sphingosine kinase 1 is a reliable prognostic factor and a novel therapeutic target for uterine cervical cancer

Sphingosine kinase 1 (SPHK1), an oncogenic kinase, has previously been found to be upregulated in various types of human malignancy and to play a crucial role in tumor development and progression. Although SPHK1 has gained increasing prominence as an important enzyme in cancer biology, its potential as a predictive biomarker and a therapeutic target in cervical cancer remains unknown. SPHK1 expression was examined in 287 formalin-fixed, paraffin-embedded cervical cancer tissues using immunohistochemistry, and its clinical implications and prognostic significance were analyzed. Cervical cancer cell lines including HeLa and SiHa were treated with the SPHK inhibitors SKI-II or FTY720, and effects on cell survival, apoptosis, angiogenesis, and invasion were examined. Moreover, the effects of FTY720 on tumor growth were evaluated using a patient-derived xenograft (PDX) model of cervical cancer. Immunohistochemical analysis revealed that expression of SPHK1 was significantly increased in cervical cancer compared with normal tissues. SPHK1 expression was significantly associated with tumor size, invasion depth, FIGO stage, lymph node metastasis, and lymphovascular invasion. Patients with high SPHK1 expression had lower overall survival and recurrence-free survival rates than those with low expression. Treatment with SPHK inhibitors significantly reduced viability and increased apoptosis in cervical cancer cells. Furthermore, FTY720 significantly decreased in vivo tumor weight in the PDX model of cervical cancer. We provide the first convincing evidence that SPHK1 is involved in tumor development and progression of cervical cancer. Our data suggest that SPHK1 might be a potential prognostic marker and therapeutic target for the treatment of cervical cancer.