Miracle-dz/UniFAR-FTUs huggingface dataset:
Structure of the Cellulose Synthase Complex of Gluconacetobacter hansenii at 23.4 Å Resolution

Bacterial crystalline cellulose is used in biomedical and industrial applications, but the molecular mechanisms of synthesis are unclear. Unlike most bacteria, which make non-crystalline cellulose, Gluconacetobacter hansenii extrudes profuse amounts of crystalline cellulose. Its cellulose synthase (AcsA) exists as a complex with accessory protein AcsB, forming a 'terminal complex' (TC) that has been visualized by freeze-fracture TEM at the base of ribbons of crystalline cellulose. The catalytic AcsAB complex is embedded in the cytoplasmic membrane. The C-terminal portion of AcsC is predicted to form a translocation channel in the outer membrane, with the rest of AcsC possibly interacting with AcsD in the periplasm. It is thus believed that synthesis from an organized array of TCs coordinated with extrusion by AcsC and AcsD enable this bacterium to make crystalline cellulose. The only structural data that exist for this system are the above mentioned freeze-fracture TEM images, fluorescence microscopy images revealing that TCs align in a row, a crystal structure of AcsD bound to cellopentaose, and a crystal structure of PilZ domain of AcsA. Here we advance our understanding of the structural basis for crystalline cellulose production by bacterial cellulose synthase by determining a negative stain structure resolved to 23.4 Å for highly purified AcsAB complex that catalyzed incorporation of UDP-glucose into β-1,4-glucan chains, and responded to the presence of allosteric activator cyclic diguanylate. Although the AcsAB complex was functional in vitro, the synthesized cellulose was not visible in TEM. The negative stain structure revealed that AcsAB is very similar to that of the BcsAB synthase of Rhodobacter sphaeroides, a non-crystalline cellulose producing bacterium. The results indicate that the crystalline cellulose producing and non-crystalline cellulose producing bacteria share conserved catalytic and membrane translocation components, and support the hypothesis that it is the extrusion mechanism and order in linearly arrayed TCs that enables production of crystalline cellulose.
Are Flunkers Social Outcasts? A Multilevel Study of Grade Retention Effects on Same-Grade Friendships

We examine the association between grade retention and the number of same-grade friendships. Moreover, we investigate the effect of a school’s proportion of retained students on these friendships and the moderating effect of this school characteristic on the relationship between retention and the number of same-grade friendships. Multilevel analyses on data from 11,759 students in 83 Flemish secondary schools show that secondary school retention is related to a lower number of friendships. Primary school retention is unrelated to friendship quantity in secondary education. Furthermore, students attending schools with a higher percentage of retained students have fewer same-grade friendships. The retention composition also moderates the effect of individual grade retention on the number of same-grade friendships. The implications are discussed.
Strychnine blocks binaural inhibition in lateral superior olivary neurons

The present study seeks to identify neurotransmitters mediating binaural inhibition in lateral superior olivary nucleus neurons. Neurons in this auditory structure receive inputs from both ears and are thought to code for localization of sound in space. Iontophoretic application of glycine during monaural stimulation was found to mimic the inhibition observed with binaural stimulation. Binaural inhibition was blocked by application of the glycine receptor antagonist, strychnine, as were the effects of iontophoretic application of glycine. The post-strychnine recovery time course for return of synaptically mediated binaural inhibition and recovery of the effects of iontophoretic glycine application were identical. Although the superior olivary complex (SOC) neurons displaying binaural inhibition could in some cases be inhibited by GABA, the binaural inhibition rarely was blocked by iontophoretic application of the GABA receptor antagonist, bicuculline. These findings suggest that glycine may be a neurotransmitter mediating binaural inhibition in certain SOC neurons and that the projection to the lateral superior olivary nucleus from the medial nucleus of the trapezoid body may be glycinergic.
Think big, from voice to limb movement therapy

We will test the efficacy of an innovative physical therapy treatment technique based upon the Lee Silverman Voice Treatment (LSVT ® ). Thus, people with PD will undergo intensive practice of high effort/large amplitude arm movements while focusing on the sensory awareness of “movement bigness. ” As LSVT ® uses extensive practice and feedback/knowledge of results to teach patients the amount of effort needed to consistently perform “louder” voice, we will use similar motor learning techniques to teach patients the amount of effort needed to consistently perform “bigger” movements. Speech studies have shown that a treatment with a simple focus (think loud) may generalize to affect motor output in other systems (e.g., articulation, speaking rate, swallowing, respiratory mechanics). Thus, we predict that learning to perform bigger arm movements will not only improve arm function during everyday activities, but the effects will generalize to lower limb function and speech motor control.
DroidVault: A Trusted Data Vault for Android Devices

Mobile OSes and applications form a large, complex and vulnerability-prone software stack. In such an environment, security techniques to strongly protect sensitive data in mobile devices are important and challenging. To address such challenges, we introduce the concept of the trusted data vault, a small trusted engine that securely manages the storage and usage of sensitive data in an untrusted mobile device. In this paper, we design and build Droid Vault - the first realization of a trusted data vault on the Android platform. Droid Vault establishes a secure channel between data owners and data users while allowing data owners to enforce strong control over the sensitive data with a minimal trusted computing base (TCB). We prototype Droid Vault via the novel use of hardware security features of ARM processors, i.e., Trust Zone. Our evaluation demonstrates its functionality for processing sensitive data and its practicality for adoption in the real world.
Learning user's preferences by analyzing Web-browsing behaviors

This paper describes a method for an information filtering agent to learn user's preferences. The proposed method observes user's reactions to the filtered documents and learns from them the profiles for the individual users. Reinforcement learning is used to adapt the most significant terms that best represent user's interests. In contrast to conventional relevance feedback methods which require explicit user feedbacks, our approach learns user preferences implicitly from direct observations of browsing behaviors during interaction. Field tests have been made which involved 10 users reading a total of 18,750 HTML documents during 45 days. The proposed method showed superior performance in personalized information filtering compared to the existing relevance feedback methods.
Near-Maximum Entropy Models for Binary Neural Representations of Natural Images

Maximum entropy analysis of binary variables provides an elegant way for studying the role of pairwise correlations in neural populations. Unfortunately, these approaches suffer from their poor scalability to high dimensions. In sensory coding, however, high-dimensional data is ubiquitous. Here, we introduce a new approach using a near-maximum entropy model, that makes this type of analysis feasible for very high-dimensional data—the model parameters can be derived in closed form and sampling is easy. Therefore, our NearMaxEnt approach can serve as a tool for testing predictions from a pairwise maximum entropy model not only for low-dimensional marginals, but also for high dimensional measurements of more than thousand units. We demonstrate its usefulness by studying natural images with dichotomized pixel intensities. Our results indicate that the statistics of such higher-dimensional measurements exhibit additional structure that are not predicted by pairwise correlations, despite the fact that pairwise correlations explain the lower-dimensional marginal statistics surprisingly well up to the limit of dimensionality where estimation of the full joint distribution is feasible.
Prevalence of Zoonotic Intestinal Helminths of Canids in Moghan Plain, Northwestern Iran

Background The present study was aimed to elucidate the status of intestinal helminth infections in canids of Moghan Plain, northwestern Iran. Methods Eighty-five intestine samples from dead or shot wild canids, 59 fecal samples from sheepdogs and 5 from red foxes were collected from 2006 to 2008 and examined in Parasitology department of Pasteur Institute of Iran. Results Generally, adult worms, larvae, and eggs of 13 species of various parasitic helminths were recovered. Necropsy examinations showed that 96.47% animals harbored at least one helminth species. The prevalence of different species in necropsy were Mesocestoides sp. 84.7%, Rictolaria spp. 55.3%, Macranthorhynchus hirudinaceus 45.9%, Toxocara canis 43.5%, Toxascaris spp. 35.3%, Joyeuxiella sp. 34.1%; hookworms; 22.4%, Taenia spp. 11.8%, Alaria spp. 2.4% and Dipylidium caninum 1.2%. Besides, eggs belonging to 10 species of parasitic helminths were identified in 46 fecal samples and generally, 30.9% of samples harbored eggs of at least one helminth species. Conclusion The high prevalence of various helminth infections among canids in Moghan plain and contamination of environment by helminths eggs may increase the risk of infection for native people.
Particle optical backscattering along a chlorophyll gradient in the upper layer of the eastern South Pacific Ocean

Abstract. The particulate scattering, bp, and backscattering, bbp, coefficients are determined by the concentration and physical properties of suspended particles in the ocean. They provide a simple description of the influence of these particles on the scattering of light within the water column. For the remote observation of ocean color, bbp along with the total absorption coefficient govern the amount and spectral qualities of light leaving the sea surface. However, for the construction and validation of ocean color models measurements of bbp are still lacking, especially at low chlorophyll a concentrations ([Chl]). Here, we examine the relationships between spectral bbp and bp vs. [Chl] along an 8000 km transect crossing the Case 1 waters of the eastern South Pacific Gyre. In these waters, over the entire range of [Chl] encountered (~0.02–2 mg m3), both bbp and bp can be related to [Chl] by power functions (i.e. bp or bbp=α[Chl]β). Regression analyses are carried out to provide the parameters α and β for several wavelengths throughout the visible for both bbp and bp. When applied to the data, these functions retrieve the same fraction of variability in bbp and bp (coefficients of determination between 0.82 and 0.88). The bbp coefficient fall within the bounds of previous measurements at intermediate and high [Chl] recently published. Its dependence on [Chl] below ~0.1 mg m−3 is described for the first time with in situ data. The backscattering ratio (i.e. bbp/bp) with values near 0.01 for all stations appears to be spectrally neutral and not significantly dependent on [Chl]. These results should foster the development of improved forward models of the mean optical properties for oceanic Case 1 waters as well as inverse models based upon them.
LIMNOLOGICAL CHARACTERISTICS OF JANNAPURA TANK IN BHADRAVATHI TALUK OF KARNATAKA, INDIA

A detailed study was carried out in Jannapura tank near Bhadravathi town of Shimoga district on physico-chemical parameters, fish diversity, aquatic macrophytes and Plankton composition during January to December 2008. The results of physico-chemical parameters were compared with Bureau of India Standards (BIS) and World Health Organization (WHO) standards. The study revealed that, tank water is under eutrophic category as it possesses high BOD, phosphate and nitrate. Among fish diversity a total of 24 species belonging to 19 genera in 10 families of five orders were recorded. Majority of t h e s p e c i e s (2 1) w e r e n a t i v e. T h r e e s p e c i e s , viz.,Ctenopharyngodon idellus (Valenciennes), Cyprinus carpio(Linnaeus) and Oreochromis mossambica (Peters) were exotic species. Among aquatic plants, a total of 13 species belonging to 11 families were recorded. Pistia stratiotes and Alternanthera philoxeroides were regarded as pollution tolerant aquatic macrophytes and be used as a biological indicator for eutrophication. A total of 75 species of phytoplankton were recorded, of which Bacillariophyceae (22 species) and chlorophyceae (27 species) were dominant. 26 zooplankton species were also recorded. In the present study as per water quality recommended by WHO and BIS standards, the tank water is not suitable for drinking and cooking purposes. The present findings revealed that the surface quality of the tank is productive and eutrophic.
Developmental trajectories of brain volume abnormalities in children and adolescents with attention-deficit/hyperactivity disorder.

CONTEXT Various anatomic brain abnormalities have been reported for attention-deficit/hyperactivity disorder (ADHD), with varying methods, small samples, cross-sectional designs, and without accounting for stimulant drug exposure. OBJECTIVE To compare regional brain volumes at initial scan and their change over time in medicated and previously unmedicated male and female patients with ADHD and healthy controls. DESIGN, SETTING, AND PARTICIPANTS Case-control study conducted from 1991-2001 at the National Institute of Mental Health, Bethesda, Md, of 152 children and adolescents with ADHD (age range, 5-18 years) and 139 age- and sex-matched controls (age range, 4.5-19 years) recruited from the local community, who contributed 544 anatomic magnetic resonance images. MAIN OUTCOME MEASURES Using completely automated methods, initial volumes and prospective age-related changes of total cerebrum, cerebellum, gray and white matter for the 4 major lobes, and caudate nucleus of the brain were compared in patients and controls. RESULTS On initial scan, patients with ADHD had significantly smaller brain volumes in all regions, even after adjustment for significant covariates. This global difference was reflected in smaller total cerebral volumes (-3.2%, adjusted F(1,280) = 8.30, P =. 004) and in significantly smaller cerebellar volumes (-3.5%, adjusted F(1,280) = 12.29, P =. 001). Compared with controls, previously unmedicated children with ADHD demonstrated significantly smaller total cerebral volumes (overall F(2,288) = 6.65; all pairwise comparisons Bonferroni corrected, -5.8%; P =. 002) and cerebellar volumes (-6.2%, F( 2,288) = 8.97, P<. 001). Unmedicated children with ADHD also exhibited strikingly smaller total white matter volumes (F(2,288) = 11.65) compared with controls (-10.7%, P<.001) and with medicated children with ADHD (-8.9%, P<.001). Volumetric abnormalities persisted with age in total and regional cerebral measures (P =.002) and in the cerebellum (P =.003). Caudate nucleus volumes were initially abnormal for patients with ADHD (P =.05), but diagnostic differences disappeared as caudate volumes decreased for patients and controls during adolescence. Results were comparable for male and female patients on all measures. Frontal and temporal gray matter, caudate, and cerebellar volumes correlated significantly with parent- and clinician-rated severity measures within the ADHD sample (Pearson coefficients between -0.16 and -0.26; all P values were <.05). CONCLUSIONS Developmental trajectories for all structures, except caudate, remain roughly parallel for patients and controls during childhood and adolescence, suggesting that genetic and/or early environmental influences on brain development in ADHD are fixed, nonprogressive, and unrelated to stimulant treatment.
The Connection between Galaxies and Intergalactic Absorption Lines at Redshift 2 ≲ z ≲ 3

Absorption-line spectroscopy of 23 background QSOs and numerous background galaxies has let us measure the spatial distribution of metals and neutral hydrogen around 1044 UV-selected galaxies at redshifts 1.8 ≲ z ≲ 3.3. The typical galaxy is surrounded to radii r ~ 40 proper kpc by gas that has a large velocity spread (Δv > 260 km s-1) and produces very strong absorption lines (N ≫ 1014 cm-2) in the spectra of background objects. These absorption lines are almost as strong as those produced by a typical galaxy's own interstellar gas. Absorption with an average column density of N ≃ 1014 cm-2 extends out to ~80 kpc, a radius large enough to imply that most strong intergalactic C IV absorption is associated with star-forming galaxies like those in our sample. Our measurement of the galaxy-C IV spatial correlation function shows that even the weakest detectable C IV systems are found in the same regions as galaxies; we find that the cross-correlation length increases with C IV column density and is similar to the galaxy autocorrelation length (r0 ~ 4 h-1 Mpc) for N ≳ 1012.5 cm-2. Distortions in the redshift-space galaxy-C IV correlation function on small scales may imply that some of the C IV systems have large peculiar velocities. Four of the five detected O VI absorption systems in our sample lie within 400 proper kpc of a known galaxy. Strong Lyα absorption is produced by the intergalactic gas within 1 h-1 comoving Mpc of most galaxies, but for a significant minority (~) the absorption is weak or absent. This is not observed in smooth-particle hydrodynamic simulations that omit the effects of "feedback" from galaxy formation. We were unable to identify any statistically significant differences in age, dust reddening, environment, or kinematics between galaxies with weak nearby H I absorption and the rest, although galaxies with weak absorption may have higher star formation rates. Galaxies near intergalactic C IV systems appear to reside in relatively dense environments and to have distinctive spectral energy distributions that are characterized by blue colors and young ages.
Evaluating high school students anxiety and self-efficacy towards biology

Anxiety and self-efficacy are among the factors that impact students’ performance in biology. The current study aims to investigate high school students’ perception of biology anxiety and self-efficacy, in relation to gender, grade level, interest in biology, negative experience associated with biology classes, and teachers’ approaches in the class. The research was designed as a survey model. The study group consisted of 160 students in 9th, 10th, and 11th grades at 4 different high schools in Ankara during 2014 Spring Semester. Biology Anxiety Scale and Biology Self-Efficacy Perception Scale, both developed by the researchers, were used as data collection tools. Data were analyzed through t test, ANOVA, and Pearson Correlation in SPSS software package. The research results show that interest in biology and negative past experience were significant predictors of students’ biology anxiety and that students’ biology self-efficacy percepts significantly differed on gender, grade level, interest in biology, past experiences, and teachers’ approaches in the classes. Considering the relationship between anxiety and self-efficacy, activities must be organized at schools in order to reduce students’ biology anxieties. Key words: High school students, biology subject, perception, anxiety, self-efficacy.
Neuropharmacological effects of standardized aqueous stem bark extract of Parkia biglobossa in Wistar rats

Objective: Parkia biglobossa stem bark decoction is a popular medicinal plant preparation used as calming agent for tensed patients in traditional medicine. The aim of this study was to evaluate the effects of aqueous stem bark extract of Parkia biglobossa (AEPB) and its active fraction AEPBF3 on anxiety, spontaneous alternation behavior, and locomotor activity. The open field apparatus was used to evaluate effects of AEPB and AEPBF3 on locomotion. The APBE and the active fraction AEPBF3 were standardized using reverse phase high performance liquid chromatography to establish finger print to ascertain identity and stability of the extracts over time. Materials and Methods: The oral median lethal doses (LD50) of AEPB and AEPBF3 were evaluated using modified Lorke’s method in rats. The effect of APBE (50-200 mg/kg p.o.), APBEF3 (25 and 50 mg/kg p.o.), diazepam (2.5 mg/kg, i.p.), and 10 ml normal saline/kg on anxiety-like behavior, spontaneous alternation behavior, and locomotion activity were evaluated in rats on elevated plus maze (EPM), Zero-maze, Y-maze, and open field apparatus, respectively. The oral LD50 values of AEPB and AEPBF3 were estimated to be 5000 mg/kg and 3800 mg/kg body weight in rats, respectively. Results: AEPB and AEPBF3 significantly (F6, 41=2342, p<0.0001) increased time spent in the open arm of EPM and significantly (F6, 41=2323, p<0.0001) increased time spent in open arms of the Zero maze. The AEPB and AEPBF3 administration produced significant increase (F5, 35=154, p<0.0001) in spontaneous alternation behavior in rats. The AEPB extract and its fraction AEPBF3 significantly increased total locomotor activity (F6, 41=413, p<0.0001) and rearing (F6, 41=150, p<0.0001) in the open field apparatus. Conclusion: The results of the present study provided evidence for anxiolytic and nootropic effects of the AEPB and AEPBF3, thus providing scientific basis for its continuous use in the management of neuropsychiatric disorders characterized by apprehension and amnesia.
A Case of Successful Colonoscopic Treatment of Colonic Obstruction Caused by Phytobezoar

A phytobezoar is the most common type of bezoar, which is a gastrointestinal mass composed of vegetable. A persimmon is a common cause of a phytobezoar. The majority of bezoars are found in the stomach, with the small intestine being the next most commonly involved site. The colon is a rare site for a bezoar. Recently, we experienced a colonic bezoar that caused colonic obstruction in a 66-year-old female patient who took persimmons regularly. The patient came to the hospital because of abdominal pain and distension. To differentiate a tumor or other problems that can cause intestinal obstruction, we performed an abdominal computed tomography scan and found an ovoid intraluminal mass with a mottled gas pattern in the distal descending colon. A large impacted bezoar was seen in the sigmoid colon, which was completely obstructed, and it was successfully removed by using colonoscopy.