Miracle-dz/UniFAR-FTUs huggingface dataset:
Structural Analysis of the Domain Interface in DrrB, a Response Regulator of the OmpR/PhoB Subfamily

ABSTRACT The N-terminal regulatory domains of bacterial response regulator proteins catalyze phosphoryl transfer and function as phosphorylation-dependent regulatory switches to control the output activities of C-terminal effector domains. Structures of numerous isolated regulatory and effector domains have been determined. However, a detailed understanding of regulatory interactions among these domains has been limited by the relative paucity of structural data for intact multidomain response regulator proteins. The first multidomain structures determined, those of transcription factor NarL and methylesterase CheB, both revealed extensive interdomain interfaces. The regulatory domains obstruct access to the functional sites of the effector domains, indicating a regulatory mechanism based on inhibition. In contrast, the recently determined structure of the OmpR/PhoB homologue DrrD revealed no significant interdomain interface, suggesting that the domains are tethered by a flexible linker and lack a fixed orientation relative to each other. To address the generality of this feature, we have determined the 1.8-Å resolution crystal structure of Thermotoga maritima DrrB, providing a second structure of a multidomain response regulator of the OmpR/PhoB subfamily. The structure reveals an extensive domain interface of 751 Å2 and therefore differs greatly from that observed in DrrD. Residues that are crucial players in defining the activation state of the regulatory domain contribute to this interface, implying that conformational changes associated with phosphorylation will influence these intramolecular contacts. The DrrB and DrrD structures are suggestive of different signaling mechanisms, with intramolecular communication between N- and C-terminal domains making substantially different contributions to effector domain regulation in individual members of the OmpR/PhoB family.
Sensorimotor Behavior of Baganda and Samia Infants

Previous research has demonstrated that Baganda infants of Uganda are comparatively advanced in their rate of sensorimotor development. This finding of precocity has been replicated in a number of African societies, giving rise to the "African precocity" issue. The present study reports data on smiling, sitting, and crawling skills for the Samia of Kenya. These data are compared with Baganda and U.S. norms to show that an understanding of the African precocity issue is enhanced by taking into account the adult sociocultural order, societal values, and specific childcare practices conceptualized as an interrelated system. The present data are also considered in terms of a biocultural, ecological perspective which represents an alternate interpretation of precocious infant development.
Mechanical analysis of controls on strain partitioning in the Himalayas of central Nepal

We present a mechanical analysis of the problem of slip partitioning between the major thrust systems in a collisional range. We focus on two structures in the Himalayas of central Nepal: the Main Himalayan Thrust (MHT) and the Main Central Thrust (MCT). We use finite element modeling to test the influence of various parameters, such as friction coefficients and surface processes, and we investigate how they affect the distribution of deformation between these two faults. We observe that reproduction of the late Quaternary kinematic pattern across the range with our model requires strict conditions on the friction coefficients, such that the MHT is very weak, whereas the MCT is significantly stronger. The most important parameter that controls slip partitioning appears to be the dip angle of the MCT, with a gentler or steeper MCT promoting or inhibiting slip, respectively. We also show that transient loading and unloading through focused glacial erosion in the higher part of the range can unclamp the MCT and allow a significant increase in slip rates. The results of this mechanical sensitivity investigation have important implications for the dynamics of the Himalayan wedge and point toward along-strike structural variations as a first-order control on slip partitioning.
Evaluating a dual-process model of risk: affect and cognition as determinants of risky choice

In three studies we addressed the impact of perceived risk and negative affect on risky choice. In Study 1, we tested a model that included both perceived risk and negative affect as predictors of risky choice. Study 2 and Study 3 replicated these findings and examined the impact of affective versus cognitive processing modes. In all the three studies, both perceived risk and negative affect were shown to be significant predictors of risky choice. Furthermore, Study 2 and Study 3 showed that an affective processing mode strengthened the relation between negative affect and risky choice and that a cognitive processing mode strengthened the relation between perceived risk and risky choice. Together, these findings show support for the idea of a dual-process model of risky choice. Copyright © 2008 John Wiley & Sons, Ltd.
The Asymptotic Performance of Linear Echo State Neural Networks

In this article, a study of the mean-square error (MSE) performance of linear echo-state neural networks is performed, both for training and testing tasks. Considering the realistic setting of noise present at the network nodes, we derive deterministic equivalents for the aforementioned MSE in the limit where the number of input data $T$ and network size $n$ both grow large. Specializing then the network connectivity matrix to specific random settings, we further obtain simple formulas that provide new insights on the performance of such networks.
The attachment, proliferation, and wound healing of endothelial and smooth muscle cells on nitinol thin film in vitro

Nitinol (TiNi) thin film is a potentially useful material for various clinical applications, e.g., vascular stents. In this study we examined the biological functions of bovine endothelial cell (BAEC) and bovine smooth muscle cells (BSMC) on 1-/spl mu/m thick amorphous TiNi films. BAEC and BSMC both attached on TiNi film, and exhibited increased cell spreading in the presence of serum containing media. Both cell types had decreased cell proliferation on TiNi as compared to glass control; however, BAEC had significantly greater proliferation rate than BSMC on TiNi. In an in vitro wound model, BSMC migrated faster than BAEC, resulting in a quicker closure of the monolayer. These results provide important insights into the interactions of vascular cells and TiNi thin film, and will help us to optimize the surface properties of TiNi film for applications in the vascular system.
Prenatal Exposure to Ethanol Causes Differential Effects in Nerve Growth Factor and its Receptor in the Basal Forebrain of Preweaning and Adult Rats

In this study we investigated nerve growth factor (NGF) levels in the cortex and hippocampus of the offspring of pregnant female Sprague-Dawley rats receiving a single intragastric administration of acute ethanol on the 15th day of gestation and compared them with a control group of rats that received an injection of sucrose. We also examined the distribution of the low-affinity NGF receptor, p75NGFR, on NGF-responsive neurons that are localized in the septum and the nucleus of Meynert, which receive the respective trophic support from the hippocampus and the cortex. In the ethanol-treated group, the results show that at post-natal age 15 days, the NGF septohippocampal pathways were markedly affected. At day 15, the NGF level was significantly higher in the offspring of ethanol-treated rats. By day 40, NGF values in both groups decreased to similar levels. At day 60, however, the NGF level in the ethanol-treated animals decreased to a significantly lower value than that of the control group, which remained essentially unchanged. In parallel, at day 60 the numbers of septal cholinergic neurons expressing p75NGFR were also significantly lower in ethanol-treated rats than in control animals. Because ethanol is known to induce neurological disorders, as well as deficits in cell proliferation and differentiation, the results suggest that one cause of the deleterious effects induced by ethanol is the low availability of NGF during certain stages of postnatal brain development.
Linguistic Distance: A Quantitative Measure of the Distance Between English and Other Languages

This paper develops a scalar or quantitative measure of the ‘distance’ between English and a myriad of other (non-native American) languages. This measure is based on the difficulty Americans have learning other languages. The linguistic distance measure is then used in an analysis of the determinants of English language proficiency among adult immigrants in the USA and Canada. It is shown that, when other determinants of English language proficiency are the same, the greater the measure of linguistic distance, the poorer is the respondent's English language proficiency. This measure can be used in research, evaluation and practitioner analyses, and for diagnostic purposes regarding linguistic minorities in English-speaking countries. The methodology can also be applied to develop linguistic distance measures for other languages.
Direct activation of forkhead box O3 by tumor suppressors p53 and p73 is disrupted during liver regeneration in mice

The p53 family of proteins regulates the expression of target genes that promote cell cycle arrest and apoptosis, which may be linked to cellular growth control as well as tumor suppression. Within the p53 family, p53 and the transactivating p73 isoform (TA‐p73) have hepatic‐specific functions in development and tumor suppression. Here, we determined TA‐p73 interactions with chromatin in the adult mouse liver and found forkhead box O3 (Foxo3) to be one of 158 gene targets. Global profiling of hepatic gene expression in the regenerating liver versus the quiescent liver revealed specific, functional categories of genes regulated over the time of regeneration. Foxo3 is the most responsive gene among transcription factors with altered expression during regenerative cellular proliferation. p53 and TA‐p73 bind a Foxo3 p53 response element (p53RE) and maintain active expression in the quiescent liver. During regeneration of the liver, the binding of p53 and TA‐p73, the recruitment of acetyltransferase p300, and the active chromatin structure of Foxo3 are disrupted along with a loss of Foxo3 expression. In agreement with the loss of Foxo3 transcriptional activation, a decrease in histone activation marks (dimethylated histone H3 at lysine 4, acetylated histone H3 at lysine 14, and acetylated H4) at the Foxo3 p53RE was detected after partial hepatectomy in mice. These parameters of Foxo3 regulation are reestablished with the completion of liver growth and regeneration and support a temporary suspension of p53 and TA‐p73 regulatory functions in normal cells during tissue regeneration. p53‐dependent and TA‐p73–dependent activation of Foxo3 was also observed in mouse embryonic fibroblasts and in mouse hepatoma cells overexpressing p53, TA‐p73α, and TA‐p73β isoforms. Conclusion: p53 and p73 directly bind and activate the expression of the Foxo3 gene in the adult mouse liver and murine cell lines. p53, TA‐p73, and p300 binding and Foxo3 expression decrease during liver regeneration, and this suggests a critical growth control mechanism mediated by these transcription factors in vivo. (HEPATOLOGY 2010;)
Low-Power Hybrid Memory Cubes With Link Power Management and Two-Level Prefetching

The hybrid memory cube (HMC) is a 3-D-stacked DRAM architecture designed for substantially improved memory bandwidth. In particular, its I/O interface achieves up to 320 GB/s of external bandwidth through high-speed serial links. However, it comes at the cost of large static power of off-chip links, which dominates total power consumption of HMCs. In this paper, we propose an adaptive mechanism to partially disable off-chip links of HMCs to reduce the energy consumption of the off-chip links. In order to determine the number of the links to be disabled upon application loads, we develop a simple hardware module called link delay monitor to simulate all different link configurations at the same time and find the largest number of the links to be disabled while satisfying the given performance constraint. We also present two-level prefetching with in-HMC prefetch buffers to further improve the efficiency of our link power management scheme in the presence of prefetching. Evaluations show that our scheme reduces the energy consumption of HMCs by 52% on average with a negligible performance degradation.
Conventional in vivo irradiation procedures are insufficient to accurately determine tumor responses to non-uniform radiation fields

Abstract Purpose: To determine differences in overall tumor responses measured by volumetric assessment and bioluminescence imaging (BLI) following exposure to uniform and non-uniform radiation fields in an ectopic prostate tumor model. Materials and methods: Bioluminescent human prostate tumor xenografts were established by subcutaneous implantation into male mice. Tumors were irradiated with uniform or non-uniform field configurations using conventional in vivo irradiation procedures performed using a 225 kVp generator with custom lead shielding. Tumor responses were measured using Vernier calipers and by BLI using an in vivo imaging system. Survival was defined as the time to quadroupling of pre-treatment tumor volume. Results: The correlation between BLI and tumor volume measurements was found to be different for un-irradiated (R = 0.61), uniformly irradiated (R = 0.34) and partially irradiated (R = 0.30) tumors. Uniformly irradiated tumors resulted in an average tumor growth delay of 60 days with median survival of 75 days, compared to partially irradiated tumors which showed an average growth delay of 24 days and median survival of 38 days. Conclusions: Correlation between BLI and tumor volume measurements is lower for partially irradiated tumors than those exposed to uniform dose distributions. The response of partially irradiated tumors suggests non-uniformity in response beyond physical dose distribution within the target volume. Dosimetric uncertainty associated with conventional in vivo irradiation procedures prohibits their ability to accurately determine tumor response to non-uniform radiation fields and stresses the need for image guided small animal radiation research platforms.
Associations between handedness and executive function in upper-middle-aged people

ABSTRACT Many studies have investigated the relationship between handedness and executive functioning using behavioural measures, although the exact nature of this relationship remains unclear. In this study, the relationship between handedness and executive function was examined using the D-CAT (Digit Cancellation Test) performances of 76 left-handed (42 men and 34 women) and 76 age-matched right-handed (42 men and 34 women) healthy community dwellers. The mean age of the participants was 62.7 years (SD = 10.3). In addition, the visuospatial performance was also examined using the Money Road Test. Left-handed people of both sexes showed a poor performance on both tests than right-handed people. Right-handed people showed typical laterality with regard to the relationship between the sex and facets of cognition, whereas left-handed people showed no clear laterality difference. Men showed no handedness difference in the executive function and women showed no handedness difference in the case of the visuospatial function test. The possible contributions of the three different executive functioning components, information updating, shifting, and inhibition, to this handedness difference in the upper-middle-aged people, are discussed.
Predicting Role Conflict, Overload and Contagion in Adult Women University Students with Families and Jobs

Many adult women studying at universities face difficulties related to their multiple roles, yet little is known about vulnerable groups or supportive responses. This study of 443 women with jobs and families enrolled in adult education, social work, or nursing identified to what extent life situations, institutional supports, and perceived demands and support systems predict role conflict, overload, and contagion. Multiple regression analysis was used to identify predictors. Income was the only life situation predictor, with lower income increasing vulnerability to role conflict. Perceived intensity of student demands was the strongest predictor of conflict, overload and contagion, with family and job demands next. Use of distance education eased conflict and contagion but some other university adaptations may increase vulnerability. Adult educators should press for increased access to adequate financial support and distance education, while continuing to evaluate the usefulness of other institutional supports for different nontraditional students.
Mothers' Perceptions of the Benefits and Drawbacks of Early Childhood Mainstreaming

The possible benefits and drawbacks of early childhood mainstreaming were evaluated by mothers of both special-needs and non-special-needs children representing a large community-based sample. Separate groups were recruited to establish comparisons related to children with cognitive delays, communication disorders, physical disabilities, and those at risk. A sample of typically developing children was also included. Results revealed widespread support for the benefits of mainstreaming, particularly promoting the acceptance of children with disabilities in the community, preparing the child for the real world, encouraging learning to a greater extent, and providing opportunities for more interesting and creative activities. However, a substantial number of perceived drawbacks was also noted, especially in connection with the availability of special help, special services, and qualified personnel as well as concerns regarding rejection by peers. Findings related to drawbacks suggest parental views that might counteract perceived benefits and reduced confidence in mainstreamed programs. In general, mothers' perceptions of mainstreaming were similar across family demographics, child characteristics, and type of program placement. A major exception was children's behavior problems, in which mainstreaming was perceived to be associated with more drawbacks.
Understanding and Improving Treatment Adherence in Patients with Psychotic Disorders: A Review and a Proposed Intervention

Non-adherence to treatment of patients with psychotic disorders is related to higher rates of relapse, hospitalization, and suicide. Important predictors of non-adherence include poor social structure, cognitive deficits, negative medication attitude, side effects, depression, a sealing-over recovery style, feelings of stigmatization, denial of treatment need, and lack of insight. Attempts to improve adherence have shown that psychoeducation alone is not fully effective, and that motivational interviewing, behavioral strategies, and linking a patient s personal goals to treatment may increase adherence. Based on the empirical data reviewed, we formed four clusters of possible causes of non-adherence, each of which can be targeted by a specific module of our developed Treatment Adherence Therapy (TAT). These four modules are: self-enhancement, motivational interviewing, medication dosage trials, and behavioral training. An individual patient may benefit from one or more of these modules; and thus the contents of TAT vary in accordance with individual causes of non-adherence. Basically, TAT aims to help patients work out what they want regarding treatment and then support them in following this through. TAT will be investigated in a multicenter randomized clinical trial in the Netherlands, starting March 2006.
Leaving Home and Family Relations in France

Youngsters in France tend to leave the parental home increasingly later. Unemployment is one main reason for this new behavior. Unemployment, taken alone, does not have a uniform effect on the intensity of generational relations. The impact of unemployment varies according to the young person's sex and residential situation. Although the influence of unemployment on rates of discussion with parents is uniformly weak among young men, rates of discussion vary among young women according to whether they live in the parental home: Young unemployed women living in the family household have a more intense relationship with their parents than young women on average. The intensification of family relations is found on the mother's side rather than on the father's.
Antidepressant drug‐induced stimulation of mouse hippocampal neurogenesis is age‐dependent and altered by early life stress

The continuous generation of new neurons in the adult hippocampus exhibits remarkable plasticity. Decreased neurogenesis is thought to underlie depression‐like behaviors, and increased neurogenesis is thought to occur following antidepressant drug treatment. Studies on different strains of mice, however, yielded contrasting results with regard to the link between behavioral modifications induced by antidepressant drugs or environmental enrichment and changes in adult hippocampal neurogenesis. Therefore, we conducted a comparative study on the inbred strains Balb/c and C57Bl/6 that differ substantially in emotionality, stress reactivity, and behavioral responses to chronic antidepressant drugs. Quantitative assessments of progenitor cell proliferation and immature neuronal differentiation in the dentate gyrus revealed that, despite significantly different basal proliferation rates between both strains, neither strain exhibited changes in adult neurogenesis after exposure to early life stress or adult chronic fluoxetine treatment. A stimulatory effect of fluoxetine on adult hippocampal neurogenesis was only detected when treatment was initiated during adolescence, and this effect was abolished in mice exposed to early life stress, a prominent risk factor for developing adult‐onset depression‐like behaviors. Thus, in both strains of mice neither adult fluoxetine treatment nor adolescent fluoxetine treatment following early life stress exposure increased the proliferation and early differentiation of adult neural progenitor cells. J. Comp. Neurol. 509:372–381, 2008. © 2008 Wiley‐Liss, Inc.
Using Achievement Goals and Interest to Predict Learning in Physical Education

On the basis of an integrated theoretical approach to achievement motivation, the authors designed this study to investigate the potential influence of mastery goal, performance-approach and avoidance-approach goals, individual interest, and situational interest on students' learning in a physical education softball unit. The authors collected and analyzed data from 6th graders (N = 177), using correlation and multiple regression analyses. The results revealed that the mastery goal was a significant predictor for the recognition of situational interest, although individual interest directly contributed to acquisition of knowledge and skill. The findings suggest a need for researchers to adopt an integrated theoretical framework to explore the complicated connection between achievement motivation and learning in physical education.