Miracle-dz/UniFAR-FTUs huggingface dataset:
Fast Bayesian Shape Matching Using Geometric Algorithms

Summary We present a Bayesian approach to comparison of geometric shapes with applications to classication of the molecular structures of proteins. Our approach involves the use of distributions dened on transformation invariant shape spaces and the specication of prior distributions on bipartite matchings. Here we emphasize the computational aspects of posterior inference arising from such models, and explore computationally ecien t approximation algorithms based on a geometric hashing algorithm which is suitable for fully Bayesian shape matching against large databases. We demonstrate this approach on the problems of protein structure alignment, structural database searching, and structure classication. We discuss extensions to exible shape spaces developed in previous work.
The αvβ3 Integrin Regulates α5β1-mediated Cell Migration toward Fibronectin*

This study examines the interactions of αvβ3 and α5β1 in the regulation of cell migration. Human embryonic kidney (HEK) 293 cells that express α5β1 endogenously were transfected with αvβ3 and β3 mutants, and their attachment and migration to fibronectin (Fn) and vitronectin (Vn) were measured. An αvβ3 blocking antibody and the αvβ3 ligand cyclic G-Pen-GRGDSPC-A inhibited α5β1-mediated migration toward Fn, but not attachment to Fn. This function was αvβ3-specific since αvβ5 transfection and αvβ5 blocking antibody did not produce this effect. Mutations introduced into the β3 integrin subunit to dissect this phenomenon revealed the following. Disruption of the ligand binding domain by the Glanzmann thrombasthenia mutation β3-D119Y constitutively abolished migration toward both Vn and Fn, and attachment to Vn but not to Fn. Insertion of the Glanzmann mutation β3-S752P into the cytoplasmic domain or its truncation (β3-Δ717) abolished binding to Vn but not to Fn. Inhibition of migration toward Fn was inhibited in these cells by αvβ3 blocking antibody. αvβ3-mediated inhibition was, however, abolished by truncation of the transmembrane domain (β3-Δ693). These findings demonstrate αvβ3 regulation of α5β1-mediated cell migration and suggest that the β3 transmembrane domain is essential for this function.
Structure of fibrous cellulose acetate: X‐ray diffraction, positron annihilation and electron microscopy investigations

X-ray diffraction, positron annihilation, electron microscopy and bulk density measurements are reported as a function of the degree of acetylation for a linters cotton. Heterogeneous reaction proceeds with a retention of ordered structure in the fibers. Substitution does increase the extent of disorder but is not sufficiently extensive to disrupt completely order at the fiber, fibril, micro fibril, and crystallite levels. The generation of disorder is associated with an increase in the interfibrillar distance, a breakup of the microfibrillar structure without a total disruption of the microcrystalline structure.
Cross-linking of Human Multidrug Resistance P-glycoprotein by the Substrate, Tris-(2-maleimidoethyl)amine, Is Altered by ATP Hydrolysis

We identified a thiol-reactive substrate, Tris-(2-maleimidoethyl)amine (TMEA), to explore the contribution of the TM segments 6 and 12 of the human multidrug resistance P-glycoprotein (P-gp) during transport. TMEA is a trifunctional maleimide and stimulated the ATPase activity of Cys-less P-gp about 7-fold. Cysteine-scanning mutagenesis of TM12 showed that the activity of mutant V982C was inhibited by TMEA. P-gp mutants containing V982C (TM12) and another cysteine in TM6 were constructed and tested for cross-linking with TMEA. A cross-linked product was observed in SDS-polyacrylamide gel electrophoresis for mutant L339C(TM6)/V982C(TM12). Cross-linking by TMEA also inhibited the ATPase activity of the mutant protein. Substrates such as cyclosporin A, vinblastine, colchicine, or verapamil inhibited cross-linking by TMEA. In the presence of ATP at 37 °C, cross-linking of mutant L339C/V982C was decreased. In contrast, there was enhanced cross-linking of mutant F343C(TM6)/V982C(TM12) in the presence of ATP. These results show that cross-linking must be within the drug-binding domain, that residues L339C(TM6)/V982C(TM12) must be at least 10 Å apart, and that ATP hydrolysis promotes rotation of one or both TM helices.
Diastolic Viscous Properties of the Intact Canine Left Ventricle

The diastolic viscous properties of the intact heart were studied in seven conscious dogs and in four right heart bypass preparations. The passive elastic properties were first determined by fitting a linear relation between the natural logarithm (hi) of the left ventricular pressure and the diameter or between In of the diastolic wall stress and the strain (r - 0.93-0.99). When the velocity of lengthening was less than 1 diam/sec, the pressure and stress data fell within the 95% confidence interval of the static elastic curve, both at low and high strain. At velocities of lengthening greater than 1 diam/sec, the pressure and stress values always deviated from the passive elastic relationship, but the magnitude of this deviation was not linearly related to the velocity of lengthening. When pressure and stress data at high velocities of lengthening were compared, the pressure or stress deviation from the passive elastic curve was always greater at high diameter than at low diameter. Moreover, the pressure and stress data at the time of minimum left ventricular pressure after systole showed greater deviation from the passive curve than expected from the diameter and the velocity of lengthening alone (+8 mm Hg in conscious dogs, P < 0.002; +2.4 mm Hg in open-chest dogs, P < 0.05), suggesting incomplete ventricular relaxation at that time. We conclude that the viscous properties of the left ventricle, like those of isolated cardiac muscle, are not linear but increase with length. These observations, together with the influence of incomplete ventricular relaxation in early diastole, preclude the determination of diastolic properties from only one diastolic cycle. Ore Res 45: 410-419, 1979
Iron elevations in the aging Parkinsonian brain: a consequence of impaired iron homeostasis?

The contribution of iron dysregulation to the etiology of a variety of neuronal diseases comes as no surprise given its necessity in numerous general cellular and neuron‐specific functions, its abundance, and its highly reactive nature. Homeostatic mechanisms such as the iron regulatory protein and hypoxia‐inducible factor pathways are firmly evolutionarily set in place to prevent ‘free’ iron from participating in chemical Fenton and Haber‐Weiss reactions which can result in subsequent generation of toxic hydroxyl radicals. However, given the multiple layers of complexity in cellular iron regulation, disruption of any number of genetic and environmental components can disturb the delicate balance between the various molecular players involved in maintaining an appropriate metabolic iron homeostasis. In this review, we will primarily focus on: (i) the impact of aging and gender on iron dysfunction as these are important criteria in the determination of iron‐related disorders such as Parkinson’s disease (PD), (ii) how iron mismanagement via disruption of cellular entry and exit pathways may contribute to these disorders, and (iii) how the availability of non‐invasive measurement of brain iron may aid in PD diagnosis.
The transcription factor Sox5 modulates Sox10 function during melanocyte development

The transcription factor Sox5 has previously been shown in chicken to be expressed in early neural crest cells and neural crest-derived peripheral glia. Here, we show in mouse that Sox5 expression also continues after neural crest specification in the melanocyte lineage. Despite its continued expression, Sox5 has little impact on melanocyte development on its own as generation of melanoblasts and melanocytes is unaltered in Sox5-deficient mice. Loss of Sox5, however, partially rescued the strongly reduced melanoblast generation and marker gene expression in Sox10 heterozygous mice arguing that Sox5 functions in the melanocyte lineage by modulating Sox10 activity. This modulatory activity involved Sox5 binding and recruitment of CtBP2 and HDAC1 to the regulatory regions of melanocytic Sox10 target genes and direct inhibition of Sox10-dependent promoter activation. Both binding site competition and recruitment of corepressors thus help Sox5 to modulate the activity of Sox10 in the melanocyte lineage.
Learning and Optimizing the Features with Genetic Algorithms

The quality of the data being analyzed is a critical factor that affects the accuracy of data mining algorithms. There are two important aspects of the data quality, one is relevance and the other is data redundancy. The inclusion of irrelevant and redundant features in the data mining model results in poor predictions and high computational overhead. Feature extraction aims to reduce the computational cost of feature measurement, increase classifier efficiency, and allow greater classification accuracy based on the process of deriving new features from the original features. This paper represents an approach for classifying students in order to predict their final grades based on features extracted from logged data in an educational web-based system. A combination of multiple classifiers leads to a significant improvement in classification performance. By weighing feature vectors representing feature importance using a Genetic Algorithm (GA), we can optimize the prediction accuracy and obtain a marked improvement over raw classification. We further show that when the number of features is few, feature weighting and transformation into a new space works efficiently compared to the feature subset selection. This approach is easily adaptable to different types of courses, different population sizes, and allows for different features to be analyzed.
Assembly of Gold Nanoparticles in a Rod‐Like Fashion Using Proteins as Templates

An area of considerable current interest is the development of a practical approach for assembling inorganic nanoparticles into well‐defined arrays because such a technique would offer immense opportunities leading to applications in microimaging, optoelectronics, therapeutics, etc. This paper illustrates a new, simple one‐step process in which proteins act as templates to assemble gold nanoparticles in a shape‐selective fashion. We show, for the first time, that antibodies to vascular endothelial growth factor 165 isoform, 2C3, and epidermal growth factor receptor can act as templates when present in solution during the synthesis of gold nanoparticles. These proteins direct the assembly of the gold nanoparticles into rod‐like shapes when cooled to –20 °C followed by thawing at room temperature. Immunoglobulin G and bovine serum albumin can also direct the assembly process in a similar fashion; however, small molecules, such as poly(L‐lysine) and lysine, cannot. The formation of a self‐assembled structure in the form of a continuous rod, or the assembly of discrete nanoparticles in a rod‐like fashion, can be tailored by controlling the ratio of the precursor gold salt, HAuCl4, to the antibody/protein used as the template. The nanoconjugates are characterized using UV‐vis spectroscopy, transmission electron microscopy, and infrared spectroscopy. The nano‐bioconjugates obtained via this process may find wide application in areas ranging from optoelectronics and biosensors to therapeutics in neoplastic disorders.
Deductive and intuitive approaches to solving geometrical problems

Approaches to the teaching and learning of a chosen topic in geometry can be located somewhere between what is characterised as the “intuitive” and the “formal”. There seems to be a number of ways of looking at the relationship between these two positions. Utilising an analysis of data from a study of students tackling problems using dynamic geometry software, this paper illustrates how a deductive and an intuitive approach can prove to be mutually reinforcing when solving geometrical problems.
Human papillomavirus type 16 oropharyngeal cancers in lymph nodes as a marker of metastases.

BACKGROUND Oropharyngeal squamous cell carcinomas (OSCCs) are associated with high-grade human papillomavirus (HPV) infection in 20% to 30% of cases. HPV-16 DNA has been detected in cervical lymph node metastases of HPV-16(+) OSCC. However, the meaning of HPV-16 DNA detection in lymph nodes remains controversial. Does the presence of HPV-16 DNA in lymph nodes correlate with their metastatic involvement, or is it just a consequence of the filter function of lymph nodes? METHODS Viral load quantification using reverse transcriptase-polymerase chain reaction was retrospectively performed in primary tumors and in cervical lymph nodes, originating from levels IIa, IIb, and III, in 11 patients with HPV-16(+) OSCC and in 3 control patients with HPV-16(-) OSCC. RESULTS A total of 45 lymph node levels were analyzed. HPV-16 DNA was not detected in HPV-16(-) OSCC lymph nodes. No statistically significant difference was found between primary tumors and metastatic lymph nodes viral load (P > .01). The viral load value was significantly higher in metastatic lymph nodes than in tumor-free lymph nodes (P < .01). Among 27 tumor-free lymph node levels, the viral load value was undetectable in 16, low or medium (<10(5) copies per million cells) in 8, and high (>10(5) copies per million cells) in 3. CONCLUSIONS HPV-16 DNA detection in lymph nodes of patients affected with HPV-16(+) oropharyngeal cancer is indicative of metastatic involvement. Tumor-free lymph nodes with a high viral load value would suggest the presence of occult lymph nodes metastasis and the opportunity to use HPV-16 DNA as a metastatic marker. Further investigations are needed.
Research Review: altered reward function in adolescent depression: what, when and how?

BACKGROUND Conceptual models and recent evidence indicate that neural response to reward is altered in depression. Taking a developmental approach to investigating reward function in adolescent depression can elucidate the etiology, pathophysiology and course of depression, a disorder that typically begins during adolescence and has high rates of recurrence. METHODS This conceptual review describes the what, when and how of altered reward function in adolescent depression. With the goal of generating new, testable hypotheses within a developmental affective neuroscience framework, we critically review findings and suggest future directions. Peer-reviewed empirical papers for inclusion in this critical review were obtained by searching PubMed, PsycInfo and ScienceDirect for the years 1990-2010. RESULTS A pattern of low striatal response and high medial prefrontal response to reward is evident in adolescents and adults with depression. Given the salience of social stimuli for positive affect and depression, reward function might be especially disrupted in response to social rewards. Because of changes in the dopamine system and reward function with aging, altered reward function in depression might be more evident during adolescence than later in life; however, low reward function may also be a stable characteristic of people who experience depression. Mechanisms of altered reward function in depression could include disrupted balance of corticostriatal circuit function, with disruption occurring as aberrant adolescent brain development. CONCLUSIONS Future studies should examine responses to social rewards; employ longitudinal and prospective designs; and investigate patterns of functional connectivity in reward circuits. Understanding altered reward function in depression has potential implications for treatment development. A more rigorous approach to investigating anhedonia, threat-reward interactions and comorbid anxiety will be valuable to future progress in describing the role of reward function in the pathophysiology of depression.
The Politics of Government Investment

This paper investigates the relation between corporate political connections and government investment. We study various forms of political influence, ranging from passive connections between firms and politicians, such as those based on politicians’ voting districts, to active forms, such as lobbying, campaign contributions, and employment of connected directors. Using hand-collected data on firm applications for capital under the Troubled Asset Relief Program (TARP), we find that politically connected firms are more likely to be funded, controlling for other characteristics. Yet investments in politically connected firms underperform those in unconnected firms. Overall, we show that connections between firms and regulators are associated with distortions in investment efficiency.
Acute Abdominal Compartment Syndrome following Extraperitoneal Bladder Perforation

Extraperitoneal bladder perforation is a known complication of a commonly performed rigid cystoscopy. If unrecognized, this complication can lead to continuous intra-abdominal fluid leakage with consequent organ function impairment and symptoms. This is the first case report in literature of a transurethral bladder perforation causing an acute abdominal compartment syndrome, which was subsequently managed conservatively with supportive management only. Case Presentation. We describe a clinical course of a 73-year-old Caucasian female whose initial acute presentation involved urinary symptoms. Surgery and general anaesthesia during rigid cystoscopy were complicated by an initially unrecognized extraperitoneal bladder perforation, resulting in fluid extravasation. This extravasation resulted in transurethral bladder resection syndrome with acute intra-abdominal free fluid accumulation. This complication caused acute abdominal compartment syndrome resulting in respiratory end-organ compromise and immediate postextubation respiratory failure. Patient required an emergency reintubation. During the management, diagnosis was considered through the use of the point of care abdominal ultrasound. Postoperatively, patient was managed conservatively in intensive care. Postoperative course included an approximate nine liters of urinary diuresis and supportive ventilation for four days. Conclusion. There is equipoise in the clinical management of abdominal compartment syndrome with regard to supportive medical management alone or invasive surgical treatment.
Effect of hematopoietic growth factors on MR images of bone marrow in children undergoing chemotherapy.

PURPOSE To evaluate the effects of hematopoietic growth factors on magnetic resonance (MR) image signal intensity (SI) of bone marrow in children undergoing neoadjuvant chemotherapy for musculoskeletal malignancies. MATERIALS AND METHODS Blinded evaluations were performed of T1-weighted and short inversion time inversion recovery images of the pelvis and/or lower extremities of 15 patients undergoing chemotherapy, with or without granulocyte or granulocyte-macrophage colony-stimulating factor. RESULTS Four of the 11 patients who received growth factors initially had hematopoietic marrow SI that did not change during therapy. All seven with initially fatty marrow had SI changes consistent with reconversion to hematopoietic marrow that coincided temporally with increases in absolute neutrophil counts from minimums of 0-2,580/mm3 to maximums of 10,858-45,880/mm3. The four patients who did not receive growth factors had no MR imaging changes in initially hematopoietic (n = 1) or fatty (n = 3) marrow. CONCLUSION Hematopoietic activity induced by growth factors can produce changes in bone marrow SI that may simulate bone marrow involvement by musculoskeletal tumors.
A worksite programme significantly alters nutrient intakes

Abstract Objective To examine whether a worksite nutrition programme using a low-fat vegan diet could significantly improve nutritional intake. Design At two corporate sites of the Government Employees Insurance Company, employees who were either overweight (BMI ≥ 25 kg/m2) and/or had type 2 diabetes participated in a 22-week worksite-based dietary intervention study. Setting At the intervention site, participants were asked to follow a low-fat vegan diet and participate in weekly group meetings that included instruction and group support (intervention group). At the control site, participants received no instruction (control group). At weeks 0 and 22, participants completed 3 d dietary records to assess energy and nutrient intake. Subjects A total of 109 participants (sixty-five intervention and forty-four control). Results In the intervention group, reported intake of total fat, trans fat, saturated fat and cholesterol decreased significantly (P ≤ 0·001), as did energy and protein (P = 0·01), and vitamin B12 (P = 0·002), compared with the control group. Intake (exclusive of any use of nutritional supplements) of carbohydrate, fibre, vitamin C, magnesium and potassium increased significantly (P ≤ 0·0001), as did that for β-carotene (P = 0·0004), total vitamin A activity (P = 0·004), vitamin K (P = 0·01) and sodium (P = 0·04) in the intervention group, compared with the control group. Conclusions The present study suggests that a worksite vegan nutrition programme increases intakes of protective nutrients, such as fibre, folate and vitamin C, and decreases intakes of total fat, saturated fat and cholesterol.
Genome-Wide Characterization and Expression Profiles of the Superoxide Dismutase Gene Family in Gossypium

Superoxide dismutase (SOD) as a group of significant and ubiquitous enzymes plays a critical function in plant growth and development. Previously this gene family has been investigated in Arabidopsis and rice; it has not yet been characterized in cotton. In our study, it was the first time for us to perform a genome-wide analysis of SOD gene family in cotton. Our results showed that 10 genes of SOD gene family were identified in Gossypium arboreum and Gossypium raimondii, including 6 Cu-Zn-SODs, 2 Fe-SODs, and 2 Mn-SODs. The chromosomal distribution analysis revealed that SOD genes are distributed across 7 chromosomes in Gossypium arboreum and 8 chromosomes in Gossypium raimondii. Segmental duplication is predominant duplication event and major contributor for expansion of SOD gene family. Gene structure and protein structure analysis showed that SOD genes have conserved exon/intron arrangement and motif composition. Microarray-based expression analysis revealed that SOD genes have important function in abiotic stress. Moreover, the tissue-specific expression profile reveals the functional divergence of SOD genes in different organs development of cotton. Taken together, this study has imparted new insights into the putative functions of SOD gene family in cotton. Findings of the present investigation could help in understanding the role of SOD gene family in various aspects of the life cycle of cotton.
Effects of coordinate system rotation on two novel closed-from localization estimators using azimuth/elevation

In this paper two novel solutions are developed for the 3D localization problem using azimuth/elevation angles by reformulating the nonlinear azimuth and elevation measurements in a linear way. The proposed solutions provide computationally non-demanding approaches for this problem and can be used for initializing iterative algorithms e.g., maximum likelihood estimator. This paper studies the effect of the xy-coordinate system rotation on the performance of these two estimators. It has been shown that the xy-coordinate system rotation can significantly change the performance of one of the estimators, while having no effect on the performance of the other one. This paper establishes this observation and provides a closed-form solution for finding the rotation angle that can effectively reduce the bias. The residual error criteria is used to compare the performance of the proposed estimators and select the one with better performance for different scenarios.