Miracle-dz/UniFAR-FTUs huggingface dataset:
The Zebrafish Thrombospondin 3 and 4 Genes ( thbs3 and thbs4 ): cDNA and Protein Structure

The cDNA sequences of the zebrafish thrombospondin 3 gene ( thbs3 ) and thrombospondin 4 gene ( thbs4 ) have been determined, and the encoded amino acid sequences (Thbs3 and Thbs4) have been analyzed. Thbs3 cDNA specifies a protein of 962 amino acid residues (MW 105,787), while Thbs4 cDNA specifies a protein of 949 residues (MW 103,989). Both proteins are highly acidic with Asp + Glu contents of 15.8% (Thbs3) and 16.9% (Thbs4). The acidic amino acids are clustered in the region of the Type III repeats and part of the C-terminal domain. The presence of signal peptides indicates that Thbs3 and Thbs4 function as secreted, extracellular proteins. The two polypeptides contain homologous sequences with two cysteines that are likely to form interchain disulfide bonds. Potential glycosylation sites were identified, five for Thbs3 and three for Thbs4. The polypeptides share the domain structure characteristic of the thrombospondin 3/thrombospondin 4/COMP subgroup of thrombospondin proteins. This domain structure consists of an amino-terminal thrombospondin N-terminal-like domain (TSPN domain), four Type II (EGF-like) repeats, seven Type III (calcium-binding) repeats, and a carboxyl terminal region. In aligning the Thbs3 and Thbs4 domain sequences with those of other thrombospondins, a gradient of sequence homology is observed that increases from N-terminus to C-terminus.
Assessing the Net Effects of Specific Claims Settlements in First Nations Communities in the Context of Community Well-being

The historical relationship between the Crown and First Nations people in Canada is one of the most fundamental in Canada society; indeed, it has framed the context in which First Nations have developed across a broad spectrum of dimensions, including cultural, social, economic, and political. In certain instances, the legal obligations of Canada to First Nations people, rooted in historic treaties, the Indian Act, and other formal agreements, have failed to be met, with adverse consequences that are sometimes difficult to fully grasp and quantify. The specific claims process is one mechanism that has been designed to address outstanding grievances of First Nations people. Each specific claim addresses the unique historical relationship between the Crown and a specific First Nation (Butt and Hurley, 2006; Indian Affairs Canada, 2006). The scope of the claim can vary from improper management of First Nations funds, to failing to provide sufficient reserve land, to surrendering reserve lands in the absence of consent from a First Nation. Specific claims serve a few key purposes: improving the socio-economic well-being of communities and addressing historic injustices to build trust and foster cohesion between Aboriginal and non-Aboriginal Canadians.
Expression Analysis of an R3-Type MYB Transcription Factor CPC-LIKE MYB4 (TRICHOMELESS2) and CPL4-Related Transcripts in Arabidopsis

The CAPRICE (CPC)-like MYB gene family encodes R3-type MYB transcription factors in Arabidopsis. There are six additional CPC-like MYB sequences in the Arabidopsis genome, including TRYPTICHON (TRY), ENHANCER OF TRY AND CPC1 and 2 (ETC1 and ETC2), ENHANCER OF TRY AND CPC3/CPC-LIKE MYB3 (ETC3/CPL3), and TRICHOMELESS1 and 2 (TCL1 and TCL2). We independently identified CPC-LIKE MYB4 (CPL4), which was found to be identical to TCL2. RT-PCR analysis showed that CPL4 is strongly expressed in shoots, including true leaves, but not in roots. Promoter-GUS analyses indicated that CPL4 is specifically expressed in leaf blades. Although CPC expression was repressed in 35S::ETC1, 35S::ETC2 and 35S::CPL3 backgrounds, CPL4 expression was not affected by ETC1, ETC2 or CPL3 over-expression. Notably, several chimeric transcripts may result from inter-genic alternative splicing of CPL4 and ETC2, two tandemly repeated genes on chromosome II. At least two chimeric transcripts named CPL4-α and CPL4-β are expected to encode complete CPC-like MYB proteins.
Input Information Complexity and Information Processing in Electronic Discussions: An Experimental Investigation

The findings of a laboratory experiment of electronic collaboration among the members of work groups reveal that both input information load and diversity have curvilinear (∩) relationships with the output information complexity generated by the groups and negative relationships with group interaction behaviors manifested through group members’ communication and participation activities. Also, output information complexity and group interaction behavior have positive relationships with group members’ satisfaction with the electronic meeting process.
Evidence That Light Modulates Protein Nitration in Rat Retina *

As part of ongoing efforts to better understand the role of protein oxidative modifications in retinal pathology, protein nitration in retina has been compared between rats exposed to damaging light or maintained in the dark. In the course of the research, Western methodology for detecting nitrotyrosine-containing proteins has been improved by incorporating chemical reduction of nitrotyrosine to aminotyrosine, allowing specific and nonspecific nitrotyrosine immunoreactivity to be distinguished. A liquid chromatography MS/MS detection strategy was used that selects all possible nitrotyrosine peptides for MS/MS based on knowing the protein identity. Quantitative liquid chromatography MS/MS analyses with tetranitromethane-modified albumin demonstrated the approach capable of identifying sites of tyrosine nitration with detection limits of 4–33 fmol. Using two-dimensional gel electrophoresis, Western detection, and mass spectrometric analyses, several different nitrotyrosine-immunoreactive proteins were identified in light-exposed rat retina compared with those maintained in the dark. Immunocytochemical analyses of retina revealed that rats reared in darkness exhibited more nitrotyrosine immunoreactivity in the photoreceptor outer segments. After intense light exposure, immunoreactivity decreased in the outer segments and increased in the photoreceptor inner segments and retinal pigment epithelium. These results suggest that light modulates retinal protein nitration in vivo and that nitration may participate in the biochemical sequela leading to light-induced photoreceptor cell death. Furthermore, the identification of nitrotyrosine-containing proteins from rats maintained in the dark, under non-pathological conditions, provides the first evidence of a possible role for protein nitration in normal retinal physiology.
Acute- and chronic-phase chronic myelogenous leukemia colony-forming units are highly sensitive to the growth inhibitory effects of c-myb antisense oligodeoxynucleotides.

We have previously demonstrated that malignant hematopoietic colony-forming units (CFUs) may be purged from normal CFU by exposure to c-myb antisense oligodeoxynucleotides (oligomers). This novel strategy appeared particularly promising for patients with chronic myelogenous leukemia (CML) in blast crisis, since in some cases complete elimination of bcr-abl-expressing cells was accomplished. We have examined 11 additional patients, including seven in chronic phase, in order to extend these initial observations. We sought in particular to determine if elimination of bcr-abl-expressing clones was a usual event. Exposure of CML cells to c-myb antisense oligomers resulted in inhibition of CFU-granulocyte, macrophage (CFU-GM)-derived colony formation in eight of 11 (73%) cases evaluated. Inhibition was antisense sequence-specific, dose-dependent, ranged between 58% and 93%, and was statistically significant (P less than or equal to .03) in seven of the eight cases. In two cases, CFU-granulocyte, erythrocyte, monocyte, megakaryocyte (CFU-GEMM)-derived colony formation was also examined and found to be inhibited by the c-myb antisense oligomers in a sequence-specific manner. To determine whether CML CFU had been reduced or eliminated after exposure to the antisense oligomers, we examined cells in the residual colonies for bcr-abl mRNA expression using a reverse transcription-polymerase chain reaction detection technique (RT-PCR). Eight cases were evaluated and in each case where antisense myb inhibited growth, bcr-abl expression as detected by RT-PCR was either greatly decreased or nondetectable. No residual leukemic CFU were demonstrable on replating of treated cells. These results suggest that c-myb antisense oligomers substantially inhibit the growth and survival of CML CFU in both chronic and blast phase of disease. They may therefore prove useful for both ex vivo and in vivo treatment of CML.
A “Globally” Convergent Controller for Multi-Machine Power Systems Using Structure-Preserving Models

The design of excitation controllers to improve transient stabilization of power systems is a topic of renewed interest in the control community. Existence of a state-feedback stabilizing law for multi-machine aggregated reduced network models has recently been established. In this paper we extend this result in two directions: first, in contrast with aggregated models, we consider the more natural and widely popular structure-preserving models that preserve the identity of the network components (generators, loads and lines) and allow for a more realistic treatment of the loads. Second, we explicitly compute a control law that, under a detectability assumption, ensures that all trajectories converge to the desired equilibrium point, provided that they start and remain in the region where the model makes physical sense.
Sensitivity to change of mobility measures in musculoskeletal conditions on lower extremities in outpatient rehabilitation settings

Abstract Study design: Prospective longitudinal study. Objective: To examine the sensitivity of the Mobility Activities Measure for lower extremities and to compare it to the sensitivity of the Physical Functioning Scale (PF-10) and the Patient-Specific Functional Scale (PSFS) at week 4 and week 8 post-hospitalization in outpatient rehabilitation settings. Background: Mobility Activities Measure is a set of short mobility measures to track outpatient rehabilitation progress: its scales have shown good properties but its sensitivity to change has not been reported. Methods: Patients with musculoskeletal conditions were recruited at admission in three outpatient rehabilitation settings in Spain. Data were collected at admission, week 4 and week 8 from an initial sample of 236 patients (mean age ± SD = 36.7 ± 11.1). Main outcome measures: Mobility Activities Measure scales for lower extremity; PF-10; and PSFS. Results: All the Mobility Activities Measure scales were sensitive to both positive and negative changes (the Standardized Response Means (SRMs) ranged between 1.05 and 1.53 at week 4, and between 0.63 and 1.47 at week 8). The summary measure encompassing the three Mobility Activities Measure scales detected a higher proportion of participants who had improved beyond the minimal detectable change (MDC) than detected by the PSFS and the PF-10 both at week 4 (86.64% vs. 69.81% and 42.23%, respectively) and week 8 (71.14% vs. 55.65% and 60.81%, respectively). Conclusions: The three Mobility Activities Measure scales assessing the lower extremity can be used across outpatient rehabilitation settings to provide consistent and sensitive measures of changes in patients’ mobility. Implications for rehabilitation All the scales of the Mobility Activities Measure for the lower extremity were sensitive to both positive and negative change across the follow-up periods. Overall, the summary measure encompassing the three Mobility Activities Measure scales for the lower extremity appeared more sensitive to positive changes than the Physical Functioning Scale, especially during the first four weeks of treatment. The summary measure also detected a higher percentage of participants with positive change that exceeded the minimal detectable change than the Patient-Specific Functional Scale and the Physical Functioning Scale at the first follow-up period. By demonstrating their consistency and sensitivity to change, the three Mobility Activities Measures scales can now be considered in order to track patients’ functional progress. Mobility Activities Measure can be therefore used in patients with musculoskeletal conditions across outpatient rehabilitation settings to provide estimates of change in mobility activities focusing on the lower extremity.
Learning from Mutants: Using Code Mutation to Learn and Monitor Invariants of a Cyber-Physical System

Cyber-physical systems (CPS) consist of sensors, actuators, and controllers all communicating over a network; if any subset becomes compromised, an attacker could cause significant damage. With access to data logs and a model of the CPS, the physical effects of an attack could potentially be detected before any damage is done. Manually building a model that is accurate enough in practice, however, is extremely difficult. In this paper, we propose a novel approach for constructing models of CPS automatically, by applying supervised machine learning to data traces obtained after systematically seeding their software components with faults ("mutants"). We demonstrate the efficacy of this approach on the simulator of a real-world water purification plant, presenting a framework that automatically generates mutants, collects data traces, and learns an SVM-based model. Using cross-validation and statistical model checking, we show that the learnt model characterises an invariant physical property of the system. Furthermore, we demonstrate the usefulness of the invariant by subjecting the system to 55 network and code-modification attacks, and showing that it can detect 85% of them from the data logs generated at runtime.
Rotation-Invariant Object Detection in High-Resolution Satellite Imagery Using Superpixel-Based Deep Hough Forests

This letter presents a rotation-invariant method for detecting geospatial objects from high-resolution satellite images. First, a superpixel segmentation strategy is proposed to generate meaningful and nonredundant patches. Second, a multilayer deep feature generation model is developed to generate high-level feature representations of patches using deep learning techniques. Third, a set of multiscale Hough forests with embedded patch orientations is constructed to cast rotation-invariant votes for estimating object centroids. Quantitative evaluations on the images collected from Google Earth service show that an average completeness, correctness, quality, and F1- measure values of 0.958, 0.969, 0.929, and 0.963, respectively, are obtained. Comparative studies with three existing methods demonstrate the superior performance of the proposed method in accurately and correctly detecting objects that are arbitrarily oriented and of varying sizes.
Role of monocytes in polyclonal immunoglobulin production stimulated by sonicates of periodontally associated bacteria

These studies were initiated to investigate monocyte regulation of polyclonal antibody responses of human peripheral blood lymphocytes stimulated by sonicates of periodontally associated bacteria. With pokeweed mitogen (PWM) as a positive reference, the role of monocytes in the peripheral blood lymphocyte response to Streptococcus sanguis and Wolinella HVS was examined by manipulating the number of monocytes and lymphocytes in culture. In comparison to PWM, optimal responses to the bacterial sonicates required very few monocytes (0.3% of the total cultured cells). Restoration of monocytes to physiological levels resulted in suppression of the response. PWM-stimulated responses were optimal at 5 to 15% monocyte content and were abolished after monocyte depletion. Individuals who were low responders or nonresponders to bacterial sonicates responded at normal levels after manipulation of monocyte concentration. Nonresponders produced normal levels of antibody when the monocyte concentration was reduced to 0.3% but were inhibited after monocyte reconstitution. The effects of monocyte concentration were tested over a wide dose range of bacterial sonicate and found to conform to the observed pattern throughout the dose range tested (10 to 1,000 micrograms/ml). The contrasting monocyte requirement of peripheral blood lymphocytes stimulated with PWM versus bacterial sonicates may reflect a quantitative difference in optimal macrophage concentration or may be due to a qualitative difference in lymphocyte-monocyte interactions in response to these activators.
Microbial Targets for the Development of Functional Foods Accordingly with Nutritional and Immune Parameters Altered in the Elderly

Objective: The development of functional foods for microbiota modulation in the elderly constitutes an interesting strategy. However, for such development, specific targets, not just in terms of microbiota but also considering immune and nutritional parameters, should be identified in this population. Methods: We analyzed the intestinal microbiota and immune parameters in 38 institutionalized elderly (mean 84 years old) and a group of 38 elderly adults (mean 62 years old). Nutritional assessments were also carried out. Results: The elderly people in this study presented reduced levels of Faecalibacterium genus and Bacteroides and Blautia coccoides groups and increased Lactobacillus group, as well as reduced levels of fecal short-chain fatty acids (SCFA) when compared to younger adults. Moreover, they showed higher levels of the proinflammatory cytokines tumor necrosis factor (TNF)-α and interleukin (IL)-12 as well as the chemokine IL-8. Significant nutritional deficiencies were also observed in the elderly group. Conclusion: The results obtained in this study suggest potential targets for the development of functional foods for the elderly population.
NS4B Self-Interaction through Conserved C-Terminal Elements Is Required for the Establishment of Functional Hepatitis C Virus Replication Complexes

ABSTRACT Hepatitis C virus (HCV) is an important human pathogen, persistently infecting more than 170 million individuals worldwide. Studies of the HCV life cycle have become possible with the development of cell culture systems supporting the replication of viral RNA and the production of infectious virus. However, the exact functions of individual proteins, especially of nonstructural protein 4B (NS4B), remain poorly understood. NS4B triggers the formation of specific, vesicular membrane rearrangements, referred to as membranous webs, which have been reported to represent sites of HCV RNA replication. However, the mechanism of vesicle induction is not known. In this study, a panel of 15 mutants carrying substitutions in the highly conserved NS4B C-terminal domain was generated. Five mutations had only a minor effect on replication, but two of them enhanced assembly and release of infectious virus. Ten mutants were replication defective and used for selection of pseudoreversions. Most of the pseudoreversions also localized to the highly conserved NS4B C-terminal domain and were found to restore replication competence upon insertion into the corresponding primary mutant. Importantly, pseudoreversions restoring replication competence also restored heterotypic NS4B self-interaction, which was disrupted by the primary mutation. Finally, electron microscopy analyses of membrane alterations induced by NS4B mutants revealed striking morphological abnormalities, which were restored to wild-type morphology by the corresponding pseudoreversion. These findings demonstrate the important role of the C-terminal domain in NS4B self-interaction and the formation of functional HCV replication complexes.
Kännsch-Updates and Improvements to the Swiss German Keyboard Bachelor Thesis

In the German speaking parts of Switzerland, it is common among young people to write in their dialect when communicating in a non-formal setting. As there are masses of Swiss German dialects, it is very difficult to build a mobile keyboard application that can suggest Swiss German words taylored to the user’s typing style. One project which attempts to fill this gap is Kännsch, a mobile keyboard for Android smartphones, developed over two master thesis at the ETH. In this project we refine some of the application’s internal mechanisms to provide more accurate word suggestions, and we update the application to a newer, more visually appealing and feature-rich version. Finally, we build a framework that uses the accumulated usage data to estimate the effectiveness of the different variants of the new algorithms.
Transcriptional and post‐translational regulation of neutral trehalase in Schizosaccharomyces pombe during thermal stress

In the fission yeast Schizosaccharomyces pombe, a heat shock enhances transcription of the ntp1+ gene, encoding the hydrolytic enzyme neutral trehalase. As compared to wild‐type cells, cells devoid of the MAP kinase Sty1p showed a strong decrease in ntp1+ expression induced by the temperature upshift, indicating that the stress‐activated protein kinase (SAPK) pathway regulates the expression of this gene during heat shock. The transcription factor Atf1p, which is the main downstream target for Sty1p in the SAPK pathway, appears to be involved in such control, since ntp1+ expression under heat shock proved to be significantly blocked in atf1+‐disrupted cells. Serial deletion and point mutation analyses of the ntp1+ promoter, as well as electrophoretic mobility shift assays, revealed the existence of a CRE‐like element as the target for Atf1p‐mediated expression under thermal stress. The relevance of two putative HSE elements located in the ntp1+ promoter was also investigated for their potential role in regulating ntp1+ transcription during heat shock. The results support a model in which heat‐induced Atf1p binding to the CRE‐like element favours the subsequent interaction of the heat shock factor (HSF) with HSE elements in the ntp1+ promoter. Unlike what happens under osmostress or oxidative treatments, Sty1p has no role in the post‐translational activation of neutral trehalase induced by heat shock in the fission yeast. Copyright © 2004 John Wiley & Sons, Ltd.
Experiment on slow-moving mobile video signal transmission in SRD band

This contribution presents experimental results and conclusions of an experiment focused on the video signal transmission in the frequency bands allocated for the Short Range Devices (SRD). We restrict ourselves only to slow — moving mobile application. Additional condition is to employ low cost simple devices based on ordinary and affordable third party transmission modules. Frequency modulation is used as the best candidate for the video signal transmission under such conditions. The results for two representative reception and/or movement scenarios are presented.