Miracle-dz/UniFAR-FTUs huggingface dataset:
Cdc42 GEF Tuba regulates the junctional configuration of simple epithelial cells

Epithelial cells are typically arranged in a honeycomb-like pattern, minimizing their cell–cell contact areas, which suggests that some tension operates for shaping of the cell boundaries. However, the molecular mechanisms that generate such tension remain unknown. We found that Tuba, which is a Cdc42-specific GEF, was concentrated at the apical-most region of cell junctions in simple epithelia via its interaction with ZO-1. RNAi–mediated depletion of Tuba altered the geometrical configuration of cell junctions, resulting in a curved and slack appearance. At the subcellular level, Tuba inactivation modified the assembly pattern of junctional F-actin and E-cadherin. Tuba RNAi also retarded cell junction formation in calcium-switch experiments. Suppression of Cdc42 activity or depletion of N-WASP, which is an effector of Cdc42, mimicked the effects of Tuba depletion. Conversely, overexpression of dominant-active Cdc42 or N-WASP enhanced the junction formation of Tuba-depleted cells. These results suggest that Tuba controls the shaping of cell junctions through the local activation of Cdc42 and its effectors.
Feasibility Study: The Effect of Therapeutic Yoga on Quality of Life in Children Hospitalized With Cancer

Purpose: To describe the effect of therapeutic yoga on child and parental reports of quality of life in children hospitalized with oncological diagnoses. Methods: Six children participated in 5 yoga sessions over 2 months. The PedsQL 4.0 was administered to each child and participating parent/caregivers at baseline and after completion of the yoga intervention. The Wilcoxon nonparametric rank test measured individual differences over time. Results: Statistically significant differences (P < .05) were found in child perception of gross motor function. Conclusion: These feasibility study data suggest that therapeutic yoga positively affected child perception of gross motor function measured on the PedsQL 4.0. Further studies are needed, including a randomized control trial and with a larger number of participants, to clarify and confirm the effect of therapeutic yoga.
Human Papillomavirus Type Distribution in Cervical Cancer in Delhi, India

This hospital-based study in New Delhi, North India was performed to evaluate the prevalence of human papillomavirus (HPV) in cases of invasive cervical carcinoma (ICC). A total of 10 cases presenting with an obvious cervical growth were included in this study. 108 cases that was shown to be ICC on histology (101 squamous cell carcinomas, 4 adenocarcinomas, and one neuroendocrine carcinoma) were included in the analysis. DNA was extracted from tumor tissue and HPV genotype was determined by a consensus PCR assay using a reverse line blot hybridization assay. Of 106 evaluable cases, 104 (98.1%) were positive for HPV infection. Twelve different high-risk HPV types were found. There were 125 infections, 119 of which were high risk. Six cases had associated low risk infections. HPV 16 was the commonest type, seen in 73.6% cases followed by HPV 18 (14.2%) and 45 (11.3%). A vaccine with 100% efficacy in prevention of HPV 16 and 18 infections would theoretically reduce the total cancer burden in New Delhi by more than 75% (assuming 100% coverage). Increasing the genotype spectrum (e.g. valency) if the existing vaccines would be expected to have only a modest impact on the potential for cervical protection.
The magnetic field around late-type stars revealed by the circumstellar H2O masers

Through polarization observations, circumstellar masers are excellent probes of the magnetic field in the envelopes of late-type stars. Whereas observations of the polarization of the SiO masers close to the star and on the OH masers much further out were fairly commonplace, observations of the magnetic field strength in the intermediate density and temperature region where the 22 GHz H2O masers occur have only recently become possible. Here we present the analysis of the circular polarization, due to Zeeman splitting, of the H2O masers around the Mira variable stars U Her and U Ori and the supergiant VX Sgr. We present an upper limit of the field around U Her that is lower but consistent with previous measurements, reflecting possible changes in the circumstellar envelope. The field strengths around U Ori and VX Sgr are shown to be of the order of several Gauss. Moreover, we show for the first time that large scale magnetic fields permeate the circumstellar envelopes of an evolved star; the polarization of the H2O masers around VX Sgr reveals a dipole field structure. We discuss the coupling of the magnetic field with the stellar outflow, as such fields could possibly be the cause of distinctly aspherical mass-loss.
Inflammatory Bowel Disease in Hispanics: The University of Puerto Rico IBD Registry

A registry of patients with inflammatory bowel diseases, ulcerative colitis (UC) and Crohn's disease (CD), was created at the University of Puerto Rico in 1995. Subjects with a documented diagnosis of IBD by clinical, radiologic, endoscopic, and/or pathologic criteria were recruited from the IBD clinics, support groups, and community practices, and demographic and medical data was collected. All entries from 1995 to 2009 were analyzed for demographics, family history, disease extent, extraintestinal manifestations, surgery, and smoking history. Results were described using summary statistics. 635 Hispanics living in Puerto Rico, 299 with UC and 336 with CD, were included. Mean ages were 40.3 for UC and 30.9 for CD. Over half (56%) of UC and 41% of CD were females. Family history was present in 19.3% of UC and 17.5% of CD. Surgery for IBD had been performed in 31.9% of UC and 51.2% of the CD patients. Over one-fourth of the patients reported extraintestinal manifestations, most frequently arthropathies. Our findings contribute to the limited epidemiologic and clinical data on Hispanics with IBD.
In Vivo Microdialysis To Determine Subcutaneous Interstitial Fluid Penetration and Pharmacokinetics of Fluconazole in Intensive Care Unit Patients with Sepsis

ABSTRACT The objective of the study was to describe the subcutaneous interstitial fluid (ISF) pharmacokinetics of fluconazole in critically ill patients with sepsis. This prospective observational study was conducted at two tertiary intensive care units in Australia. Serial fluconazole concentrations were measured over 24 h in plasma and subcutaneous ISF using microdialysis. The concentrations in plasma and microdialysate were measured using a validated high-performance liquid chromatography system with electrospray mass spectrometer detector method. Noncompartmental pharmacokinetic analysis was performed. Twelve critically ill patients with sepsis were enrolled. The mean in vivo fluconazole recovery rates ± standard deviation (SD) for microdialysis were 51.4% ± 16.1% with a mean (±SD) fluconazole ISF penetration ratio of 0.52 ± 0.30 (coefficient of variation, 58%). The median free plasma area under the concentration-time curve from 0 to 24 h (AUC0–24) was significantly higher than the median ISF AUC0–24 (340.4 versus 141.1 mg · h/liter; P = 0.004). There was no statistical difference in median fluconazole ISF penetration between patients receiving and not receiving vasopressors (median, 0.28 versus 0.78; P = 0.106). Both minimum and the maximum concentrations of drug in serum (Cmax and Cmin) showed a significant correlation with the fluconazole plasma exposure (Cmax, R2 = 0.86, P < 0.0001; Cmin, R2 = 0.75, P < 0.001). Our data suggest that fluconazole was distributed variably, but incompletely, from plasma into subcutaneous interstitial fluid in this cohort of critically ill patients with sepsis. Given the variability of fluconazole interstitial fluid exposures and lack of clinically identifiable factors by which to recognize patients with reduced distribution/exposure, we suggest higher than standard doses to ensure that drug exposure is adequate at the site of infection.
A structural basis for the mechanism of aspartate‐β‐semialdehyde dehydrogenase from Vibrio cholerae

L‐Aspartate‐β‐semialdehyde dehydrogenase (ASADH) catalyzes the reductive dephosphorylation of β‐aspartyl phosphate to L‐aspartate‐β‐semialdehyde in the aspartate biosynthetic pathway of plants and micro‐organisms. The aspartate pathway produces fully one‐quarter of the naturally occurring amino acids, but is not found in humans or other eukaryotic organisms, making ASADH an attractive target for the development of new antibacterial, fungicidal, or herbicidal compounds. We have determined the structure of ASADH from Vibrio cholerae in two states; the apoenzyme and a complex with NADP, and a covalently bound active site inhibitor, S‐methyl‐L‐cysteine sulfoxide. Upon binding the inhibitor undergoes an enzyme‐catalyzed reductive demethylation leading to a covalently bound cysteine that is observed in the complex structure. The enzyme is a functional homodimer, with extensive intersubunit contacts and a symmetrical 4‐amino acid bridge linking the active site residues in adjacent subunits that could serve as a communication channel. The active site is essentially preformed, with minimal differences in active site conformation in the apoenzyme relative to the ternary inhibitor complex. The conformational changes that do occur result primarily from NADP binding, and are localized to the repositioning of two surface loops located on the rim at opposite sides of the NADP cleft.
Obesity-induced Insulin Resistance and Hyperglycemia: Etiologic Factors and Molecular Mechanisms

Obesity is a major cause of type 2 diabetes, clinically evidenced as hyperglycemia. The altered glucose homeostasis is caused by faulty signal transduction via the insulin signaling proteins, which results in decreased glucose uptake by the muscle, altered lipogenesis, and increased glucose output by the liver. The etiology of this derangement in insulin signaling is related to a chronic inflammatory state, leading to the induction of inducible nitric oxide synthase and release of high levels of nitric oxide and reactive nitrogen species, which together cause posttranslational modifications in the signaling proteins. There are substantial differences in the molecular mechanisms of insulin resistance in muscle versus liver. Hormones and cytokines from adipocytes can enhance or inhibit both glycemic sensing and insulin signaling. The role of the central nervous system in glucose homeostasis also has been established. Multipronged therapies aimed at rectifying obesity-induced anomalies in both central nervous system and peripheral tissues may prove to be beneficial.
Two-bit transform for binary block motion estimation

One-bit transforms (1BTs) have been proposed for low-complexity block-based motion estimation by reducing the representation order to a single bit, and employing binary matching criteria. However, as a single bit is used in the representation of image frames, bad motion vectors are likely to be resolved in 1BT-based motion estimation algorithms particularly for small block sizes. It is proposed in this paper to utilize a two-bit transform (2BT) for block-based motion estimation. Image frames are converted into two-bit representations by a simple block-by-block two bit transform based on multithresholding with mean and linearly approximated standard deviation values. In order to avoid blocking effects at block boundaries during the block-by-block transformation while enabling the two-bit representation to be constructed according to local detail, threshold values are computed within a larger window surrounding the transforming block. The 2BT makes use of lower bit-depth and binary matching criteria properties of 1BTs to achieve low-complexity block motion estimation. The 2BT improves motion estimation accuracy and seriously reduces the amount of bad motion vectors compared to 1BTs, particularly for small block sizes. It is shown that the proposed 2BT-based motion estimation technique improves motion estimation accuracy in terms of peak signal-to-noise ratio of reconstructed frames and also results in visually more accurate frames subsequent to motion compensation compared to the 1BT-based motion estimation approach.
Pairwise Decomposition of Image Sequences for Active Multi-view Recognition

A multi-view image sequence provides a much richer capacity for object recognition than from a single image. However, most existing solutions to multi-view recognition typically adopt hand-crafted, model-based geometric methods, which do not readily embrace recent trends in deep learning. We propose to bring Convolutional Neural Networks to generic multi-view recognition, by decomposing an image sequence into a set of image pairs, classifying each pair independently, and then learning an object classifier by weighting the contribution of each pair. This allows for recognition over arbitrary camera trajectories, without requiring explicit training over the potentially infinite number of camera paths and lengths. Building these pairwise relationships then naturally extends to the next-best-view problem in an active recognition framework. To achieve this, we train a second Convolutional Neural Network to map directly from an observed image to next viewpoint. Finally, we incorporate this into a trajectory optimisation task, whereby the best recognition confidence is sought for a given trajectory length. We present state-of-the-art results in both guided and unguided multi-view recognition on the ModelNet dataset, and show how our method can be used with depth images, greyscale images, or both.
The Neural Basis of Perceptual Hypothesis Generation and Testing

Four-dot masking is a new form of visual masking that does not involve local contour interactions or spatial superimposition of the target stimulus and the mask (as, e.g., in pattern or metacontrast masking). Rather, the effective masking mechanism is based on object substitution. Object substitution masking occurs when low-level visual information representations are altered before target identification through iterative interaction with high-level visual processing stages has been completed. Interestingly, object substitution interacts with attention processes: Strong masking effects are observed when attentional orientation toward the target location is delayed. In contrast, no masking occurs when attention can be rapidly shifted to and engaged onto the target location. We investigated the neural basis of object substitution masking by studying the interaction of spatial attention and masking processes using functional magnetic resonance imaging. Behavioral data indicated a two-way interaction between the factors Spatial Attention (valid vs. invalid cueing) and Masking (four-dot vs. pattern masking). As expected, spatial attention improved performance more strongly during object substitution masking. Functional correlates of this interaction were found in the primary visual cortex, higher visual areas, and left intraparietal sulcus. A region-of-interest analysis in these areas revealed that the largest blood oxygenation level-dependent signal changes occurred during effective four-dot masking. In contrast, the weakest signal changes in these areas were observed when target visibility was highest. The data suggest that these areas represent an object substitution network dedicated to the generation and testing of a perceptual hypotheses as described by the object substitution theory of masking of Di-Lollo et al. Competition for consciousness among visual events: The psychophysics of reentrant visual processes. Journal of Experimental Psychology: General, 129, 481507, 2000.
Jugendkriminalität und Geschlecht. Eine empirische Analyse im Bezugsrahmen der Power-Control Theory

There is plenty of evidence that boys commit more crime than girls. A prominent theory that seeks to explain the gender gap in juvenile delinquency is John Hagan’s Power-Control Theory. It posits that work-related power differentials between parents determine levels of control levied over sons and daughters. Gender-specific differences in parental control are linked to higher risk preferences and lower risk perceptions of boys compared to girls, which result in boys being more delinquent than girls. In this study, a test of the Power-Control Theory is performed, based on a student survey conducted in Upper Austria. The results support both the power and the control related elements of the theory.
TGF-Beta Negatively Regulates the BMP2-Dependent Early Commitment of Periodontal Ligament Cells into Hard Tissue Forming Cells

Transforming growth factor beta (TGF-β) is a multi-functional growth factor expressed in many tissues and organs. Genetic animal models have revealed the critical functions of TGF-β in craniofacial development, including the teeth and periodontal tissue. However, the physiological function of TGF-β in the periodontal ligament (PDL) has not been fully elucidated. In this study, we examined the roles of TGF-β in the cytodifferentiation of PDL cells using a TGF-β receptor kinase inhibitor, SB431542. Mouse PDL cell clones (MPDL22) were cultured in calcification-inducing medium with or without SB431542 in the presence or absence of various growth factors, such as bone morphogenetic protein (BMP)-2, TGF-β and fibroblast growth factor (FGF)-2. SB431542 dramatically enhanced the BMP-2-dependent calcification of MPDL22 cells and accelerated the expression of ossification genes alkaline phosphatase (ALPase) and Runt-related transcription factor (Runx) 2 during early osteoblastic differentiation. SB431542 did not promote MPDL22 calcification without BMP-2 stimulation. The cell growth rate and collagen synthesis during the late stage of MPDL22 culture were retarded by SB431542. Quantitative reverse transcription polymerase chain reaction analysis revealed that the expressions of Smurf1 and Smad6, which are negative feedback components in the TGF-β/BMP signaling pathway, were downregulated in MPDL22 cells with SB431542 treatment. These results suggest that an endogenous signal from TGF-β negatively regulates the early commitment and cytodifferentiation of PDL cells into hard tissue-forming cells. A synthetic drug that regulates endogenous TGF-β signals may be efficacious for developing periodontal regenerative therapies.
EFFECTS OF RESTING STATE ON PERCEPTUAL LEARNING

DEDICATION ~~~ This work is dedicated to my brother Stephen Alwin (1986-2010) who lives on in reactivations of networks in my brain. ~~~ iv ACKNOWLEDGEMENTS I would like to acknowledge the following people for their support and influence over the years: A doctoral program requires patient family members and for that I'm very thankful for the patience and support of my husband David Eagleman. I'm also thankful for the support and encouragement from my mother, Susan Alwin-Popp, my stepfather, Thomas Popp, my father, Steven Alwin, my stepmother Shelley Alwin, and the rest of my large family. I'm very fortunate to be surrounded by loving, encouraging people. It is doubtful that I would be able to do half of what I do without them. I'd also like to thank my son Ari, for being the kind of baby content to listen to science papers as bedtime stories. I'm grateful for the people I've shared lab space with for these past 7 years. I'd like to thank Diego Gutnisky for the long lectures and drawings of mathematics equations during my first few years. Thank you also for continuing to be a close friend and mentor. Thank you Bryan Hansen for spending time teaching me how to work with all of the equipment in the lab and for having to rerun your own experiments to make up for things I'd break. I'd also like to thank Marcello Mulas for the incredible collaboration we had collecting and analyzing data for the resting state projects. Thank you to Jose Fernandez-Leon for the collaboration with the analysis and discussion of the extended reactivation project presented in this thesis. Having someone push me to defend what I do, has helped me become a better scientist and thinker. Thank you to Mircea Chelaru for thoughtful discussions on much of the work that is presented here. I'd also like to thank everyone Ming Hu for their thoughtful input and for making the lab a pleasant place to come day in and day out. Thank you to my current supervisory committee members: Drs. also like to thank previous faculty members who have served on my committees in the past: Drs. Neal Waxham, Ruth Heidelberger, and Pramod Dash. I'd like to thank Drs. Anthony Wright and Daniel Felleman for guiding me through rotation experiments early on in their laboratories before I joined Valentin's lab. I'd also like to thank my undergraduate …
The impact of LiPS instruction and teacher perception on beginning readers

The purpose of this study was two-fold. First the researcher set out to determine if phonemic awareness skills improved for first grade students of teachers who used the Lindamood Phoneme Sequencing Program (LiPS; Lindamood & Lindamood, 1998). Second, an attempt was made to determine if there was a relationship between reading improvement in decoding and teacher level variables (i.e., perception of their knowledge of the LiPS program (Lindamood & Lindamood, 1998), and relevant demographic variables). Students’ scores based on the Learning Disabilities Working Committee Kindergarten screening tool (LDWC, 2005) were compared to their respective scores on the Learning Disabilities Working Committee Grade One screening tool (LDWC, 2002). Comparison of progress for all students were evaluated as well as assessment of progress for students deemed at risk (below the 25 percentile) of reading failure compared to those not at risk (above the 25 percentile). Teachers’ perceptions of the critical elements of the LiPS program (Lindamood & Lindamood, 1998) and demographic information were collected. The teacher level variables gathered from this survey (i.e., teaching experience, formal training, knowledge, or skill level in program delivery) were correlated to students’ scores on the screening tools. Results revealed that teacher demographics, such as teaching experience, specialized training, and intensity of instructional approach are related to student reading achievement in decoding; however, no clearly defined relationship was found between teachers’ perceptions of the LiPS program (Lindamood & Lindamood, 1998) and student achievement. Paired-sample t-tests were also used to determine if statistically significant