Miracle-dz/UniFAR-FTUs huggingface dataset:
The Construction of the Knowledge Base of Immune System

The paradigm shift from experimentals to bioinformatics is apparent in many areas of biology. There are immediate demands to construct databases that are designed for computer analysis of biological phenomena. Speci cally, the immune system has been researched very intensely in experimentals because it is essential to protect our bodies against viruses, bacteria, and other foreign things. The immune system is made up of cell-cell interactions and cytoplasmic signal transductions. In recent years many molecules have been identi ed and characterized, as well as many interactions among them. Thus, we focus on the immune system and investigate most speci ed and embodied cell-cell interactions. Among multicellular organisms, only vertebrates can have immune system in their bodies, and various events would occur by complicated interactions between speci ed cells, T-cells, B-cells, macrophages, etc. In addition, cell di erentiation is deeply crosslinked to the immune system in terms of cells' roles, because cells are changing their characters through di erentiation by ligand stimulation. Therefore when we try to understand the immune system, we must refer to cell di erentiation in terms of signal transductions and analyze the pathways that result from many interactions. However, there is virtually no database for the immune system that refers to signal transductions and cell-cell interactions. Our database is designed in a similar way as BRITE [1] database which contains cell cycles and early developing stages, and we can analyze systematically the immune system, for example, by using the information of the whole genomes sequences.
Georegistration of Landsat data via robust matching of multiresolution features

The goal of the project described in this paper is to build a prototype of an operational system, which will provide registration within subpixel accuracy of multitemporal Landsat data, acquired by either Landsat-5 or Landsat-7 Thematic Mapper instruments. Integrated within an automated mass processing system for Landsat data, the input to our registration system consists of scenes that have been geometrically and radiometrically corrected, as well as preprocessed for detection of clouds and cloud shadows. Such preprocessed scenes are then georegistered relative to a database of Landsat chips. This paper describes the entire registration process, including the use of landmark chips, feature extraction performed by an overcomplete wavelet representation, and feature matching using statistically robust techniques. Knowing the approximate longitudes and latitudes or the UTM coordinates of the four corners of each incoming scene, a subset of the chips that represent landmarks included in the scene are selected to perform the registration. For each of these selected landmark chips, a corresponding window is extracted from the incoming scene, and each chip-window pair is registered using a robust wavelet feature-matching methodology. Based on the transformations from the chip-window pairs, a global transformation is then computed for the entire scene using a variant of a robust least median of squares estimator. Empirical results of this registration process, which provided subpixel accuracy for several multitemporal scenes from different study areas, are presented and discussed.
Utilization of lignins in rubber compounding

Lignin in the form of lignosulfonate containing about 33% moisture was found to be dispersible in natural rubber by dry mixing. Properties such as tear resistance, abrasion resistance, flex crack resistance, and crack growth resistance improved upon addition of lignin, irrespective of the nature of filler added. This lignin was found to have negative effects on modulus, tensile strenght, resilience, heat buildup, and compression set, which showed, however, remarkable improvement upon aging.
The initial U3 snoRNA:pre-rRNA base pairing interaction required for pre-18S rRNA folding revealed by in vivo chemical probing

The synthesis of ribosomal subunits in the eukaryotic nucleolus is a conserved, essential process that results in cytoplasmic ribosomes with precisely processed and folded rRNAs assembled with ribosomal proteins. It has been proposed, but never directly demonstrated, that the U3 small nucleolar RNA (snoRNA) is a chaperone for pre‐18S rRNA folding. To test this, we used in vivo chemical probing with dimethyl sulfate to detect changes in pre‐rRNA structure upon genetic manipulation of the yeast, S. cerevisiae. Based on changes in nucleotide reactivity, we found that the U3 snoRNA is indeed required for folding of the pre‐18S rRNA. Furthermore, we detected a new essential base‐pairing interaction that is likely the initial anchor that recruits the U3 snoRNA to the pre‐rRNA, is a prerequisite for the subsequent interactions, and is required for the small subunit (SSU) processome formation. Thus, the U3 snoRNP, via base‐pairing, orchestrates the pre‐rRNA folding that results in the assembly of the small ribosomal subunit. This work was supported by NIH GM52581.
Severing and end-to-end annealing of neurofilaments in neurons

Significance Neurofilaments, which are the intermediate filaments of neurons, are major components of nerve cells, but their assembly dynamics have not been determined. Here we demonstrate efficient end-to-end annealing of neurofilaments in nerve cells, and we show that there also is a mechanism that severs these polymers. Our efforts thus identify severing of neuronal intermediate filaments in vivo and suggest a mechanism for regulating intermediate filament length involving a dynamic cycle of severing and end-to-end annealing. We have shown previously that neurofilaments and vimentin filaments expressed in nonneuronal cell lines can lengthen by joining ends in a process known as “end-to-end annealing. ” To test if this also occurs for neurofilaments in neurons, we transfected cultured rat cortical neurons with fluorescent neurofilament fusion proteins and then used photoconversion or photoactivation strategies to create distinct populations of red and green fluorescent filaments. Within several hours we observed the appearance of chimeric filaments consisting of alternating red and green segments, which is indicative of end-to-end annealing of red and green filaments. However, the appearance of these chimeric filaments was accompanied by a gradual fragmentation of the red and green filament segments, which is indicative of severing. Over time we observed a progressive increase in the number of red–green junctions along the filaments accompanied by a progressive decrease in the average length of the alternating red and green fluorescent segments that comprised those filaments, suggesting a dynamic cycle of severing and end-to-end-annealing. Time-lapse imaging of the axonal transport of chimeric filaments demonstrated that the red and green segments moved together, confirming that they were indeed part of the same filament. Moreover, in several instances, we also were able to capture annealing and severing events live in time-lapse movies. We propose that the length of intermediate filaments in cells is regulated by the opposing actions of severing and end-to-end annealing, and we speculate that this regulatory mechanism may influence neurofilament transport within axons.
Is ʔ an Element? Towards a Non-segmental Phonology

This paper argues that the element calculus of Government Phonology is overburdened. In particular it shows that the simple act of supposing extra elements to explain consonantal phenomena leads to far reaching and undesirable empirical consequences. An alternative approach is proposed which leaves the elemental inventory containing only those elements attested in both nuclei and non-nuclei. The phonetic impression of consonantism is attributed to the direct interpretation of supra-skeletal structure. Some typical textbook problems involving consonant ‘mutations’ are explored in light of this simple shift of perspective, with attractive solutions. The metatheoretical benefits of this approach are highlighted and particular areas of existing supra-skeletal theory are singled out as likely to require ‘tweaking’.
Structure in scientific networks: towards predictions of research dynamism

Certain areas of scientific research flourish while others lose advocates and attention. We are interested in whether structural patterns within citation networks correspond to the growth or decline of the research areas to which those networks belong. We focus on three topic areas within optical physics as a set of cases; those areas have developed along different trajectories: one continues to expand rapidly; another is on the wane after an earlier peak; the final area has re-emerged after a short waning period. These three areas have substantial overlaps in the types of equipment they use and general methodology; at the same time, their citation networks are largely independent of each other. For each of our three areas, we map the citation networks of the top-100 most-cited papers, published pre-1999. In order to quantify the structures of the selected articles' citation networks, we use a modified version of weak tie theory in tandem with entropy measures. Although the fortunes of a given research area are most obviously the result of accumulated innovations and impasses, our preliminary study provides evidence that these citation networks' emergent structures reflect those developments and may shape evolving conversations in the scholarly literature.
Brain regions and molecular pathways responding to food reward type and value in honey bees

The ability of honey bees to evaluate differences in food type and value is crucial for colony success, but these assessments are made by individuals who bring food to the hive, eating little, if any, of it themselves. We tested the hypothesis that responses to food type (pollen or nectar) and value involve different subsets of brain regions, and genes responsive to food. mRNA in situ hybridization of c‐jun revealed that brain regions responsive to differences in food type were mostly different from regions responsive to differences in food value, except those dorsal and lateral to the mushroom body calyces, which responded to all three. Transcriptomic profiles of the mushroom bodies generated by RNA sequencing gave the following results: (1) responses to differences in food type or value included a subset of molecular pathways involved in the response to food reward; (2) genes responsive to food reward, food type and food value were enriched for (the Gene Ontology categories) mitochondrial and endoplasmic reticulum activity; (3) genes responsive to only food and food type were enriched for regulation of transcription and translation; and (4) genes responsive to only food and food value were enriched for regulation of neuronal signaling. These results reveal how activities necessary for colony survival are channeled through the reward system of individual honey bees.
Auditors’ Personal Values and Ethical Judgement at Different Levels of Ethical Climate: A Conceptual Link

The purpose of this paper is come up with theoretical model through understanding the causes and motives behind the auditor judgements. The finding of this study that there are several ethical theories a models provide a significant understanding of ethical issues and suggested factors that may affect ethical judgement decision. The suggestion model proposes that ethical judgements are influenced by personal values via ethical sensitivity. Nonetheless, the influence of personal values on ethical sensitivity is expected to be stronger at higher level of ethical climate.
Assessment of biological effects of chlorinated hydrocarbons in osprey chicks

Osprey(Pandion haliaetus) eggs were collected during 1995 and 1996 at seven sites along the Fraser and Columbia River systems of British Columbia, Canada, and Washington and Oregon, USA. Fifty‐four eggs were placed into a laboratory incubator. Thirty‐eight of the hatched chicks were sacrificed within 24 h. Hatching success did not differ among sites and therefore between treatment and reference areas. Residual yolk sacs of eggs collected downstream of the large bleached‐kraft pulp mill at Castlegar contained greater mean concentrations of 2,3,7,8‐tetrachlorodibenzo‐p‐dioxin (TCDD, 2,930 ng/kg lipid) compared with reference sites such as the Nechako River, an upper tributary of the Fraser system (33.7 ng/kg). Total polychlorinated biphenyls (PCBs) in yolk sacs were also higher at Castlegar and in samples from the Columbia River downstream of Portland, Oregon, compared with those from the Nechako River. Concentrations of measured chemicals, including TCDD toxic equivalents (TEQs), total PCBs, p, p′‐dichlorodiphenylethylene (p, p′‐DDE), and other organochlorines were not different in eggs that failed to hatch compared with calculated whole‐egg values for hatched eggs. There were significant biochemical responses; a hepatic cytochrome P4501A (CYP1A) cross‐reactive protein was detected in all samples tested and correlated positively with ethoxyresorufin o‐deethylase (EROD) activity and yolk sac concentrations of TEQs and total PCBs. Tissue concentrations of vitamin A compounds varied among sites and correlated positively with yolk sac concentrations of TEQs and PCBs. Morphological, histological, and other physiological parameters, including chick growth, edema, deformities, and hepatic and renal porphyrin concentrations, neither varied among sites nor showed concentration‐related effects.
Dissecting the in vivo assembly of the 30S ribosomal subunit reveals the role of RimM and general features of the assembly process

Ribosome biogenesis is a tightly regulated, multi-stepped process. The assembly of ribosomal subunits is a central step of the complex biogenesis process, involving nearly 30 protein factors in vivo in bacteria. Although the assembly process has been extensively studied in vitro for over 40 years, very limited information is known for the in vivo process and specific roles of assembly factors. Such an example is ribosome maturation factor M (RimM), a factor involved in the late-stage assembly of the 30S subunit. Here, we combined quantitative mass spectrometry and cryo-electron microscopy to characterize the in vivo 30S assembly intermediates isolated from mutant Escherichia coli strains with genes for assembly factors deleted. Our compositional and structural data show that the assembly of the 3′-domain of the 30S subunit is severely delayed in these intermediates, featured with highly underrepresented 3′-domain proteins and large conformational difference compared with the mature 30S subunit. Further analysis indicates that RimM functions not only to promote the assembly of a few 3′-domain proteins but also to stabilize the rRNA tertiary structure. More importantly, this study reveals intriguing similarities and dissimilarities between the in vitro and the in vivo assembly pathways, suggesting that they are in general similar but with subtle differences.
Origins of strabismus and loss of binocular vision

Strabismus is a frequent ocular disorder that develops early in life in humans. As a general rule, it is characterized by a misalignment of the visual axes which most often appears during the critical period of visual development. However other characteristics of strabismus may vary greatly among subjects, for example, being convergent or divergent, horizontal or vertical, with variable angles of deviation. Binocular vision may also vary greatly. Our main goal here is to develop the idea that such “polymorphy” reflects a wide variety in the possible origins of strabismus. We propose that strabismus must be considered as possibly resulting from abnormal genetic and/or acquired factors, anatomical and/or functional abnormalities, in the sensory and/or the motor systems, both peripherally and/or in the brain itself. We shall particularly develop the possible “central” origins of strabismus. Indeed, we are convinced that it is time now to open this “black box” in order to move forward. All of this will be developed on the basis of both presently available data in literature (including most recent data) and our own experience. Both data in biology and medicine will be referred to. Our conclusions will hopefully help ophthalmologists to better understand strabismus and to develop new therapeutic strategies in the future. Presently, physicians eliminate or limit the negative effects of such pathology both on the development of the visual system and visual perception through the use of optical correction and, in some cases, extraocular muscle surgery. To better circumscribe the problem of the origins of strabismus, including at a cerebral level, may improve its management, in particular with respect to binocular vision, through innovating tools by treating the pathology at the source.
Cytotoxin Genes of Helicobacter pylori in Chronic Gastritis, Gastroduodenal Ulcer and Gastric Cancer: An Age and Gender Matched Case‐Control Study

Helicobacter pylori (H. pylori) infection is involved in many gastrointestinal diseases, such as chronic gastritis (CAG), peptic ulcer and gastric cancer (GCA). Both host factors and H. pylori strain differences may contribute to differences in the diseases. Thus, we conducted an age and gender matched case‐control study of 35 patients each with CAG, gastric ulcer (GUL), duodenal ulcer (DUL) and gastric cancer (GCA) to examine the role of strain differences of the H, pylori cytotoxin genes cagA and vacA in these diseases. We employed polymerase chain reaction to examine the gastric juice for H. pylori DNA. The test was positive for 26 (74.3%) CAG, 29 (82.9%) GUL, 28 (80.0%) DUL and 27 (77.1%) GCA patients, showing no statistically significant difference among the diseases (P= 0.84). cagA and vacA genes (picked up by using a vacAl+vacA2 primer pair which detected nonvariable regions of the vacA gene) were detected by PCR in the H. pylori DNA‐positive cases as follows: CAG, 92.3% and 76.9%; GUL, 100% and 86.2%; DUL, 89.3% and 89.3%; GCA, 92.6% and 85.2%, respectively. No statistically significant differences were found in the frequencies of these cytotoxin genes in H. pylori ‐positive cases among the various gastric diseases (P=0.39 for cagA and P=0.64 for vacA).
Effect of code coverage on software reliability measurement

Existing software reliability-growth models often over-estimate the reliability of a given program. Empirical studies suggest that the over-estimations exist because the models do not account for the nature of the testing. Every testing technique has a limit to its ability to reveal faults in a given system. Thus, as testing continues in its region of saturation, no more faults are discovered and inaccurate reliability-growth phenomena are predicted from the models. This paper presents a technique intended to solve this problem, using both time and code coverage measures for the prediction of software failures in operation. Coverage information collected during testing is used only to consider the effective portion of the test data. Execution time between test cases, which neither increases code coverage nor causes a failure, is reduced by a parameterized factor. Experiments were conducted to evaluate this technique, on a program created in a simulated environment with simulated faults, and on two industrial systems that contained tenths of ordinary faults. Two well-known reliability models, Goel-Okumoto and Musa-Okumoto, were applied to both the raw data and to the data adjusted using this technique. Results show that over-estimation of reliability is properly corrected in the cases studied. This new approach has potential, not only to achieve more accurate applications of software reliability models, but to reveal effective ways of conducting software testing.
Thermographic analysis of temperature rise in the pulp chamber with LED and QTH light curing units: An in vitro investigation

Aims: To compare the temperature rise in the pulp chamber with light-emitting diode (LED) and Quartz-Tungsten-Halogen (QTH) light curing units by infrared thermography. Materials and Methods: Class V cavity was prepared in 20 freshly extracted maxillary first premolars measuring 2 mm depth, 4 mm width, and 1 mm above the cement enamel junction. The samples were divided into two groups ( n = 10). Cavity was etched with 37% phosphoric acid, rinsed and bonding agent was applied over the etched cavity surface on both the groups. In group I the samples were cured with LED curing unit, whereas group II were cured with QTH unit, which was followed by two incremental curing of composite. Thermal emission for QTH and LED (fast mode) light curing units were noted by Fluke Ti32 infrared thermography after 20 s bonding agent curing and first and second increment composite curing for 40 s each. Statistical Analysis: Data were analyzed with Student t -test and Friedman test using SPSS version 11.5 software. Results: The statistical analysis revealed that the temperature rise was significantly minimal with LED fast mode (Group I) in all stages of curing compared with QTH unit (Group II). There is significant rise of temperature during first incremental curing of composite, whereas insignificant increase of temperature during curing of second increment of composite ( P Conclusions: Temperature rise caused due to both QTH and LED light curing units does not result in irreversible pulpal damage and thermography is a viable means of quantifying the temperature changes during photo polymerization.
Realization of realistic and rich facial expressions by face robot

Facial expression is the most import factor for communication in terms of non-verbal information. We have been developing face robot which can express facial expressions like human being for 10 years to realize emotional communication between human and robot. Because face skin is made by silicone rubber, durability of connector mounted on the backside of skin for pulling was issues to be solved. We find the solution and realize the receptionist system for practical use. The basic working principle is applied for the patent soon. The expected market with business model is shown in this paper.
Discrete-Valued Control by Sum-of-Absolute-Values Optimization

In this paper, we propose a new design method of discrete-valued control for continuous-time linear time-invariant systems based on sum-of-absolute-values (SOAV) optimization. We first formulate the discrete-valued control design as a finite-horizon SOAV optimal control, which is an extended version of L1 optimal control. We then give simple conditions that guarantee the existence, discreteness, and uniqueness of the SOAV optimal control. Also, we give the continuity property of the value function, by which we prove the stability of infinite-horizon model predictive SOAV control systems. We provide a fast algorithm for the SOAV optimization based on the alternating direction method of multipliers (ADMM), which has an important advantage in real-time control computation. A simulation result shows the effectiveness of the proposed method.
Merging Pose Estimates Across Space and Time

Numerous ‘non-maximum suppression’ (NMS) post-processing schemes have been proposed for merging multiple independent object detections. We propose a generalization of NMS beyond bounding boxes to merge multiple pose estimates in a single frame. The final estimates are centroids rather than medoids as in standard NMS, thus being more accurate than any of the individual candidates. Using the same mathematical framework, we extend our approach to the multi-frame setting, merging multiple independent pose estimates across space and time and outputting both the number and pose of the objects present in a scene. Our approach sidesteps many of the inherent challenges associated with full tracking (e.g. objects entering/leaving a scene, extended periods of occlusion, etc.). We show its versatility by applying it to two distinct state-of-the-art pose estimation algorithms in three domains: human bodies, faces and mice. Our approach improves both detection accuracy (by helping disambiguate correspondences) as well as pose estimation quality and is computationally efficient.