Miracle-dz/UniFAR-FTUs huggingface dataset:
Identification, structural, and biochemical characterization of a group of large Csn2 proteins involved in CRISPR‐mediated bacterial immunity

Many prokaryotic organisms acquire immunity against foreign genetic material by incorporating a short segment of foreign DNA called spacer into chromosomal loci, termed clustered regularly interspaced short palindromic repeats (CRISPRs). The encoded RNAs are processed into small fragments that guide the silencing of the invading genetic elements. The CRISPR‐associated (Cas) proteins are the main executioners of these processes. Herein, we report the crystal structure of Stu0660 of Streptococcus thermophilus, a Cas protein involved in the acquisition of new spacers. By homotetramerization, Stu0660 forms a central channel which is decorated with basic amino acids and binds linear double‐stranded DNA (dsDNA), but not circular dsDNA. Despite undetectably low sequence similarity, two N‐terminal domains of Stu0660 are similar to the entire structure of an Enterococcus faecalis Csn2 protein, which also forms a homotetramer and binds dsDNA. Thus, this work identifies a previously unknown group of Stu0660‐like Csn2 proteins (∼350 residues), which are larger than the known canonical Csn2 proteins (∼220 residues) by containing an extra C‐terminal domain. The commonly present central channel in the two subgroups appears as a design to selectively interact with linear dsDNA. Proteins 2012. © 2012 Wiley Periodicals, Inc.
Research Reports: The Reading Behavior Inventory: An Outcome Assessment Tool

Gregory L. Goodrich, Jennine Kirby, Jennifer Wood, and Laura Peters The Reading Behavior Inventory (RBI) was developed as a targeted outcome measure of a low vision reading rehabilitation program. The Western Blind Rehabilitation Center (WBRC), located at the Veterans Affairs Palo Alto Health Care System in Palo Alto, California, is an inpatient rehabilitation program that serves veterans who are legally blind. The design criteria that were considered in developing the RBI were that the inventory should measure changes in behaviors that are associated with reading: the types of materials that participants read and the participants’ reading performance (speed), satisfaction with reading, reported diffi culty reading, and reported duration of reading. The change in the participants’ reading speed from the beginning to the end of the rehabilitation program was included as the effectiveness measure, while the remaining questions probed the participants’ reading behaviors and perceptions of their ability.
How Planning and Reflection Develop Young Children's Thinking Skills.

THINKING SKILLS oung children ages three to six are capable of making thoughtful decisions about their behavior and keen observations about their environment (as the vignettes at left show). Like Tatiana and Eric, they have insight into their desires, form mental images of the past and future, and attempt to explain their behavior and that of others. Although today's early childhood educators often focus on enhancing reading and mathematics skills to meet ever increasing academic expectations, we must also remain committed to promoting broader thinking abilities. They are the foundation upon which children learn to make decisions, regulate their own behavior, meet complex challenges, and take responsibility for their actions. , reminds us that " key concepts involved in each domain of preschool learning must go hand in hand with information and skill acquisition " (p. 8). It cites research showing that metacognition—higher-level thinking and problem-solving skills—develops when children are encouraged to reflect, predict, question, and hypothesize. How can adults help children exercise these capabilities? There is empirical and practical evidence that we can promote the development of thinking and reasoning in young children in the early years by providing two curriculum components—planning and reflection. Both are thoughtful activities that encourage children to consider what they are doing and what they are learning. They also promote a broad range of other academic, social, and artistic compe-tencies. This article summarizes the research in support of these claims and offers strategies teachers and caregivers can use to encourage planning and reflection in their programs. Michigan. She develops curriculum materials, directs a team of specialists who conduct inservice training across the country and abroad, and conducts research and evaluation on early childhood programs. Last night Tatiana, age four, was telling us [her parents] her plan for the evening as we were eating dinner. She told us she planned to watch her new video, play her memory game with her mom, give her baby doll a bath, and have me read her some books. When I asked her when she was going to brush her teeth and go to bed, she told me that wasnt part of her plan! Today after choice time, three-year-old Eric told me [his teacher] he had watched Goober, the hamster. He reported that at first Goober was asleep, then he woke up and started drinking his water and eating his food. I said Goober must have been hungry. Eric agreed, …
Bimodal Nonrigid Registration of Brain MRI Data With Deconvolution of Joint Statistics

A brain MRI protocol typically includes several imaging contrasts that can provide complementary information by highlighting different tissue properties. The acquired data sets often need to be coregistered or placed in a standard anatomic space before any further processing. Current registration methods particularly for multicontrast data are computationally very intensive, their resolution is lower than that of the images, and their distance metric and its optimization can be limiting. In this paper, a novel and effective nonrigid registration method is proposed that is based on the restoration of the joint statistics of pairs of such images. The registration is performed with the deconvolution of the joint statistics with an adaptive Wiener filter. The deconvolved statistics are forced back to the spatial domain to estimate a preliminary registration. The spatial transformation is also regularized with Gaussian spatial smoothing. The registration method has been compared with the B-Splines method implemented in 3DSlicer and with the SyN method implemented in the ANTs toolkit. The validation has been performed with a simulated Shepp-Logan phantom, a BrainWeb phantom, the real data of the NIREP database, and real multicontrast data sets of healthy volunteers. The proposed method has shown improved comparative accuracy as well as analytical efficiency.
Extreme and conflicting appraisals of activated internal states discriminate remitted bipolar disorder from remitted unipolar depression and non-clinical controls.

Background This research aimed to test whether positive, negative, or conflicting appraisals about activated mood states (e.g., energetic and high states) predicted bipolar disorder. Methods A sample of individuals from clinical and control groups (171 with bipolar disorder, 42 with unipolar depression, and 64 controls) completed a measure of appraisals of internal states. Results High negative appraisals related to a higher likelihood of bipolar disorder irrespective of positive appraisals. High positive appraisals related to a higher likelihood of bipolar disorder only when negative appraisals were also high. Individuals were most likely to have bipolar disorder, as opposed to unipolar depression or no diagnosis, when they endorsed both extremely positive and extremely negative appraisals of the same, activated states. Limitations Appraisals of internal states were based on self-report. Conclusions The results indicate that individuals with bipolar disorder tend to appraise activated, energetic internal states in opposing or conflicting ways, interpreting these states as both extremely positive and extremely negative. This may lead to contradictory attempts to regulate these states, which may in turn contribute to mood swing symptoms. Psychological therapy for mood swings and bipolar disorder should address extreme and conflicting appraisals of mood states.
Coxiella burnetii, the Agent of Q Fever, Replicates within Trophoblasts and Induces a Unique Transcriptional Response

Q fever is a zoonosis caused by Coxiella burnetii, an obligate intracellular bacterium typically found in myeloid cells. The infection is a source of severe obstetrical complications in humans and cattle and can undergo chronic evolution in a minority of pregnant women. Because C. burnetii is found in the placentas of aborted fetuses, we investigated the possibility that it could infect trophoblasts. Here, we show that C. burnetii infected and replicated in BeWo trophoblasts within phagolysosomes. Using pangenomic microarrays, we found that C. burnetii induced a specific transcriptomic program. This program was associated with the modulation of inflammatory responses that were shared with inflammatory agonists, such as TNF, and more specific responses involving genes related to pregnancy development, including EGR-1 and NDGR1. In addition, C. burnetii stimulated gene networks organized around the IL-6 and IL-13 pathways, which both modulate STAT3. Taken together, these results revealed that trophoblasts represent a protective niche for C. burnetii. The activation program induced by C. burnetii in trophoblasts may allow bacterial replication but seems unable to interfere with the development of normal pregnancy. Such pathophysiologocal processes should require the activation of immune placental cells associated with trophoblasts.
Cooperative Inter-vehicle Communication Protocol With Low Cost Differential GPS

This paper describes a cooperative MANET protocol dedicated to intelligent transport systems, named CIVIC (Communication Inter Vehicule Intelligente et Cooperative). The CIVIC protocol is an auto-configuration inter-vehicle communication protocol, which supports adhoc and infrastructure networks, contains reactive and proactive routing components, and adapts different wireless standards. It is a context-aware protocol reacting to vehicle status, road traffic, and geographic environment. It supports location-based communication. To improve the accuracy of GPS, it integrates a localization solution called LCD-GPS (Low Cost Differential GPS). It has been implemented and experimented on the LiveNode sensor developed by our lab. At the end of this paper, an application project MobiPlus is introduced.
3D Model Generation by Morphing

This paper proposes a 3D model generation system that outputs intermediate 3D shape models between two already existing 3D models by morphing. Although there have been a lot of computer animation software, it takes a long time to create a 3D shape model even using such computer animation software. Morphing is one of the techniques used to easily create 3D models. If we have two different 3D shape models, it is possible to generate intermediate 3D shape models between them by morphing. However, there are two main problems in the morphing of polygonal models. Those are vertex mismatch and semantic topology mismatch. In this paper, the authors propose an algorithm that is free from the vertex mismatch problem and that automatically determines the semantic topology match. The proposed system based on the algorithm decomposes both two polygonal models, makes decomposed element pairs between them, and then generates intermediate 3D shape models by morphing as for the decomposed element pairs automatically
$p$-Laplacian Regularized Sparse Coding for Human Activity Recognition

Human activity analysis in videos has increasingly attracted attention in computer vision research with the massive number of videos now accessible online. Although many recognition algorithms have been reported recently, activity representation is challenging. Recently, manifold regularized sparse coding has obtained promising performance in action recognition, because it simultaneously learns the sparse representation and preserves the manifold structure. In this paper, we propose a generalized version of Laplacian regularized sparse coding for human activity recognition called p-Laplacian regularized sparse coding (pLSC). The proposed method exploits p-Laplacian regularization to preserve the local geometry. The p-Laplacian is a nonlinear generalization of standard graph Laplacian and has tighter isoperimetric inequality. As a result, pLSC provides superior theoretical evidence than standard Laplacian regularized sparse coding with a proper p. We also provide a fast iterative shrinkage-thresholding algorithm for the optimization of pLSC. Finally, we input the sparse codes learned by the pLSC algorithm into support vector machines and conduct extensive experiments on the unstructured social activity attribute dataset and human motion database (HMDB51) for human activity recognition. The experimental results demonstrate that the proposed pLSC algorithm outperforms the manifold regularized sparse coding algorithms including the standard Laplacian regularized sparse coding algorithm with a proper p.
The Emergent Role of Virtual Reality in the Treatment of Neuropsychiatric Disease

The development of outstanding computer science technologies such as virtual reality (VR) and augmented reality (AR) has provided new avenues in order to challenge the functional connectivity disruption seen in neurodegenerative diseases. Virtually simulating the outside world with high realism, close-to-total immersion and easiness of interaction presents an interesting way to decipher new therapeutic perspectives as a noninvasive and non-pharmacological neuromodulation tool. As of recently, these cutting-edge techniques already appear to be used in the treatment of some neuropsychiatric disorders, cognitive and behavioral impairments since the patient is placed in an environment virtually yet specifically adapted to his needs. Specific use of VR and AR becomes interesting for both social and functional rehabilitation whether it originates from traumatic situations and injuries or from pathologies known to show from neuromuscular disturbances to decay. Virtual reality is already used in research in combination to rehabilitation adapted treadmills in order to help treat children with cerebral palsy (coordination impairment, stiff andweakmuscles, tremors, etc.) that appear in early childhood (Sloot et al., 2015; Cho et al., 2016). However, there is still some work to be done to improve the actual research setups and the reproducibility of results. Therefore, we will review here the innovative and emergent role of cybertherapies and focus on the possibilities to extend its use as far as rehabilitation centers to everyday well-being.
Optimal all-to-some personalized communication on hypercubes

In a hypercube multiprocessor with distributed memory, each data element has a street address and an apartment number (i.e. a hypercube node address and a local memory address). We describe an optimal algorithm for performing the all-to-some personalized communication (ASPC) on Boolean n-cubes, defined as (i|j)/spl rarr/(i/spl plusmn/2/sup j/|j), i/spl isin/[0,2/sup n/-1], j/spl isin/[0,n-1], where (i|j) denote the data element on node i and location j. The algorithm also gives an optimal schedule for emulating PM2I networks on hypercubes under the binary-reflected Gray code encoding. We also study an important class of parallel algorithms, called /spl plusmn/2/sup b/-descend, which perform log M iterations on an M-element input a[O:M-1]. For b=log M-1,. ,0, iteration b computes new values of each a[i] as a function of a[i], a[i+2/sup b/], a[i-2/sup b/]. For large applications, the problem size M is typically much larger than the number of nodes N. We show that on hypercubes, the optimal ASPC algorithm devised in this paper can be used in combination with pipelining communication and computation in /spl plusmn/2/sup b/-descend computations to reduce the communication steps from 2.log N.M/N to 4(log M+M/N-1). At one communication step, a hypercube node can send n elements along its n links, one per link.
Draft Genome Sequence of the Vaginal Isolate Corynebacterium amycolatum ICIS 9

ABSTRACT Corynebacterium amycolatum ICIS 9 was isolated from a vaginal smear of a healthy woman. Here, we report the draft genome sequence of C. amycolatum ICIS 9, which will be useful for further studies of specific genetic features of this strain and for understanding its probiotic properties.
Applied Microbial and Cell Physiology

The growth kinetics and metabolic and antioxidant activities of the functional synbiotic combination of Lactobacillus gasseri 505 and Cudrania tricuspidata leaf extract Abstract In a previous study, the synbiotic combination of selected Lactobacillus gasseri strains and Cudrania tricuspidata leaf extract (CT) was shown to significantly improve the functionality of fermented milk, and the greatest synbiotic effect was exhibited with L. gasseri 505. The aim of the present study was to investigate the growth kinetics and fermentation metabolism of this specific synbiotic combination. Fermentation was carried out in synthetic media and milk with or without CT supplementation using L. gasseri 505. Whole genome sequencing and comparative genomics analyses were conducted to verify the novelty of strain. Titratable acidity, pH, microbial population, and organic acid production were measured during the fermentation period. The addition of CT accelerated the acidification rate, supporting the growth of L. gasseri 505, and the production of fermentation metab-olites such as lactic acid and pyruvic acid also significantly increased during fermentation of both of CT-supplemented synthetic media and milk. In particular, the formic acid and propionic acid in CT were significantly utilized during fermentation of milk by L. gasseri 505. Moreover, the antioxi-dant capacity of CT-supplemented fermented milk increased due to the release of bioactive compounds until the exponential growth phase, after which the antioxidant activity declined due to degradation and loss of potency. Therefore, this study established that L. gasseri 505 efficiently utilized the CT-related nutrients during fermentation producing resulting me-tabolites with health-promoting effects, although it is necessary to control the fermentation time to obtain dairy products with optimum functionality.
Simulations of the Role of the Muscarinic-Activated Calcium-Sensitive Nonspecific Cation CurrentINCM in Entorhinal Neuronal Activity during Delayed Matching Tasks

Entorhinal lesions impair performance in delayed matching tasks, and blockade of muscarinic cholinergic receptors also impairs performance in these tasks. Physiological data demonstrate that muscarinic cholinergic receptor stimulation activates intrinsic cellular currents in entorhinal neurons that could underlie the role of entorhinal cortex in performance of these tasks. Here we use a network biophysical simulation of the entorhinal cortex to demonstrate the potential role of this cellular mechanism in the behavioral tasks. Simulations demonstrate how the muscarinic-activated calcium-sensitive nonspecific cation current INCM could provide a cellular mechanism for features of the neuronal activity observed during performance of delayed matching tasks. In particular, INCM could underlie (1) the maintenance of sustained spiking activity during the delay period, (2) the enhancement of spiking activity during the matching period relative to the sample period, and (3) the resistance of sustained activity to distractors. Simulation of a larger entorhinal network with connectivity chosen randomly within constraints on number, distribution, and weight demonstrates appearance of other phenomena observed in unit recordings from awake animals, including match suppression, non-match enhancement, and non-match suppression.
Connection, Technology, Positionality: An Inside Look at Women Faculty's Positionality toward "Connection" and "Technology"

Connection, Technology, Positionality: An Inside Look at Women Faculty‟s Positionality Toward “Connection” and “Technology” by Wei Zhai, Doctor of Philosophy Utah State University, 2010 Major Professors: Dr. J. Nicholls Eastmond and Dr. Ronda Callister Department: Instructional Technology and Learning Sciences Women faculty members have been reported rating their level of knowledge and experience in using technologies lower than male faculty members. A closer examination revealed that women faculty members were likely to use technologies that fit into their pedagogy, met students‟ learning styles and needs, and facilitated their interactions with colleagues and students. So women faculty‟s choices of particular technologies can be assumed to reflect their particular instructional beliefs and perspectives, represented as a connected approach to learning and teaching. Gender alone is inadequate to explain women faculty‟s use of technology. The purpose of this study was to explore women faculty‟s understanding of teacher-student, student-student, and student learning-life connections and how technology affects these connections. A theoretical framework called positionality is used, which approaches women not solely from their biological or psychological attributes but also from the contexts in which they are situated. The results of the study suggested that women faculty members exhibited a positional understanding of the teacher-student,
Dynamic Properties of the Alkaline Vesicle Population at Hippocampal Synapses

In compensatory endocytosis, scission of vesicles from the plasma membrane to the cytoplasm is a prerequisite for intravesicular reacidification and accumulation of neurotransmitter molecules. Here, we provide time-resolved measurements of the dynamics of the alkaline vesicle population which appears upon endocytic retrieval. Using fast perfusion pH-cycling in live-cell microscopy, synapto-pHluorin expressing rat hippocampal neurons were electrically stimulated. We found that the relative size of the alkaline vesicle population depended significantly on the electrical stimulus size: With increasing number of action potentials the relative size of the alkaline vesicle population expanded. In contrast to that, increasing the stimulus frequency reduced the relative size of the population of alkaline vesicles. Measurement of the time constant for reacification and calculation of the time constant for endocytosis revealed that both time constants were variable with regard to the stimulus condition. Furthermore, we show that the dynamics of the alkaline vesicle population can be predicted by a simple mathematical model. In conclusion, here a novel methodical approach to analyze dynamic properties of alkaline vesicles is presented and validated as a convenient method for the detection of intracellular events. Using this method we show that the population of alkaline vesicles is highly dynamic and depends both on stimulus strength and frequency. Our results implicate that determination of the alkaline vesicle population size may provide new insights into the kinetics of endocytic retrieval.