Miracle-dz/UniFAR-FTUs huggingface dataset:
Activated chemoreceptor arrays remain intact and hexagonally packed

Bacterial chemoreceptors cluster into exquisitively sensitive, tunable, highly ordered, polar arrays. While these arrays serve as paradigms of cell signalling in general, it remains unclear what conformational changes transduce signals from the periplasmic tips, where attractants and repellents bind, to the cytoplasmic signalling domains. Conflicting reports support and contest the hypothesis that activation causes large changes in the packing arrangement of the arrays, up to and including their complete disassembly. Using electron cryotomography, here we show that in Caulobacter crescentus, chemoreceptor arrays in cells grown in different media and immediately after exposure to the attractant galactose all exhibit the same 12 nm hexagonal packing arrangement, array size and other structural parameters. ΔcheB and ΔcheR mutants mimicking attractant‐ or repellent‐bound states prior to adaptation also show the same lattice structure. We conclude that signal transduction and amplification must be accomplished through only small, nanoscale conformational changes.
mmr, a Mycobacterium tuberculosis Gene Conferring Resistance to Small Cationic Dyes and Inhibitors

ABSTRACT The mmr gene, cloned from Mycobacterium tuberculosis, was shown to confer to Mycobacterium smegmatis resistance to tetraphenylphosphonium (TPP), erythromycin, ethidium bromide, acriflavine, safranin O, and pyronin Y. The gene appears to code for a protein containing four transmembrane domains. Studies of [3H]TPP intracellular accumulation strongly suggest that the resistance mediated by the Mmr protein involves active extrusion of TPP.
Testis-specific Fank1 gene in knockdown mice produces oligospermia via apoptosis

Fank1 is exclusively expressed in the testis from the meiosis phase to the haploid phase of spermatogenesis. In this study, we examined the function of Fank1 by establishing a Fank1-knockdown transgenic mouse model. The apoptotic statuses of the testes of the transgenic mice were tested using the terminal deoxynucleotidyl transferase dUTP nick end labeling (TUNEL) method. The FANK1 consensus DNA-binding sequence was identified using cyclic amplification of sequence target (CAST) analysis. Differentially expressed genes were examined using microarray analysis. A reduction in sperm number and an increase in apoptotic spermatocytes were observed in Fank1-knockdown mice, and the apoptotic cells were found to be primarily spermatogonia and spermatocytes. The CAST results demonstrated that the consensus DNA-binding sequence was AAAAAG, in which the percentage occurrence of each base at each position ranged from 55 to 86%. This sequence was present in the promoter regions of 10 differentially expressed genes that were examined using microarray analysis. In total, 17 genes were differentially expressed with changes in their expression levels greater than twofold. The abnormal expression of Fank1 target genes that were regulated directly or indirectly by Fank1 reduced the number of sperm in the knockdown mice. Thus, FANK1 may play a pivotal role in spermatogenesis as a transcription factor.
Deciding on Success Criteria for Predictability of Pharmacokinetic Parameters from In Vitro Studies: An Analysis Based on In Vivo Observations

Prediction accuracy of pharmacokinetic parameters is often assessed using prediction fold error, i.e., being within 2-, 3-, or n-fold of observed values. However, published studies disagree on which fold error represents an accurate prediction. In addition, "observed data" from only one clinical study are often used as the gold standard for in vitro to in vivo extrapolation (IVIVE) studies, despite data being subject to significant interstudy variability and subjective selection from various available reports. The current study involved analysis of published systemic clearance (CL) and volume of distribution at steady state (Vss) values taken from over 200 clinical studies. These parameters were obtained for 17 different drugs after intravenous administration. Data were analyzed with emphasis on the appropriateness to use a parameter value from one particular clinical study to judge the performance of IVIVE and the ability of CL and Vss values obtained from one clinical study to "predict" the same values obtained in a different clinical study using the n-fold criteria for prediction accuracy. The twofold criteria method was of interest because it is widely used in IVIVE predictions. The analysis shows that in some cases the twofold criteria method is an unreasonable expectation when the observed data are obtained from studies with small sample size. A more reasonable approach would allow prediction criteria to include clinical study information such as sample size and the variance of the parameter of interest. A method is proposed that allows the "success" criteria to be linked to the measure of variation in the observed value.
Height, Weight and Body Mass Index Percentiles of Children Aged 6-14 Years Living at Moderate Altitudes

Objective: Individuals living at high altitudes are reported to have lower stature and also a smaller chest size in relation to their stature. Altitude-related hypobaric hypoxia is considered to be the major cause of these alterations in growth, but adverse socioeconomic and/or other environmental conditions may also have a role in poor growth performance. This study was undertaken to provide growth data on children and adolescents living in a moderate-altitude area in Turkey. Methods: The dataset of an anthropometric study conducted among a population living in a city at an altitude of 2000 meters was analyzed. A total of 1638 children and adolescents (871 males and 767 females) aged between 6 and 14 years were included in this study. The LMS method was used in the analysis and percentile values corresponding to the 3rd, 5th, 10th, 15th, 25th, 50th, 75th, 85th, 90th, 95th and 97th percentiles for height, weight and body mass index (BMI) were estimated. The results were compared with the measurements of children and adolescents living in areas of lower altitude in Turkey. Results: Starting at ages 0-10 years, height, weight and BMI values of children and adolescents of both genders living at an altitude of 2000 meters were noticeably lower than those reported for their counterparts living in areas of lower altitude in Turkey. Conclusions: The higher values for height, weight and BMI in children living in low-altitude areas can be attributed to altitude effect, but socioeconomic and microclimate effects cannot be discarded and further studies are needed. Conflict of interest:None declared.
Learning affinities of exemplar videos for multi-view action recognition

approved: Sinisa Todorovic This thesis addresses a fundamental computer vision problem, that of action recognition. The goal of action recognition is to recognize a class of human actions in a given video. Action recognition has a wide range of applications, including automated surveillance, sports video analysis, internet-based searches etc. The main challenge is that actors move and change their pose while performing the action, and/or that the actors may be captured from different viewing angles. For example, certain viewpoints of a distinct action class may produce very similar appearance and motion features in the videos. This may cause confusion in recognizing the two action classes. Therefore, action recognition should be invariant to changes in camera viewpoints. While action recognition in videos captured from a fixed view has received significant interest in the past, multi-view action recognition is still an under-explored field. We have specified an exemplar based approach for multi-view action recognition. We propose a novel method for training the K Nearest Neighbor (K-NN) classifier. Specifically, the K-NN is learned within a large-margin framework with a set of suitable constraints specified over camera viewpoints and action classes. Our constraints enforce that affinity between videos belonging to the same class should be larger than that of the videos belonging to distinct classes. Moreover, within the same action class, affinity between videos captured from the same camera viewpoint should be larger than that of distinct viewpoints. We efficiently compute the affinity between any two videos based on many-to-many matching of their supervoxels. The correspondences of the supervoxels of two videos are treated as latent random variables. Thus, we formulate a novel latent large-margin learning of the K-NN, subject to a set of viewpoint and class constraints. Given a new video, we use K-NN classifier to identify K closest training exemplars to the video, and transfer their majority action class label as the class label of the new video. Our approach outperforms the state of art on benchmark datasets: INRIA IXMAS, a newer version of IXMAS (NIXMAS) and i3DPost. c ©Copyright by Anirban Roy August 30, 2013 All Rights Reserved Learning Affinities of Exemplar Videos for Multi-View Action Recognition
Network anomaly detection using artificial neural networks

This paper presents a method of identifying and classifying network anomalies using an artificial neural network for analyzing data gathered via Netflow protocol. Potential anomalies and their properties are described. We propose using a multilayer perceptron, trained with the backpropagation algorithm. We experiment both with datasets acquired from a real ISP monitoring system and with datasets modified to simulate the presence of anomalies; some Netflow records are modified to contain known patterns of several network attacks. We evaluate the viability of the approach by practical experimentation with various anomalies and iteration sizes.
Entropy-Based Dynamic Complexity Metrics for Service-Oriented Systems

The complexity analysis of service systems is mainly from the static aspect, and the dynamic complexity measurement has not attracted enough attention yet. In this paper, we attempt to provide some dynamic complexity metrics for service systems through measuring their execution behaviors. At first, two models, i.e., service unit vector and service pair matrix, are presented to represent the execution traces. Meanwhile, distance entropy is adapted in our work for analyzing execution traces. Based on the modeling representation of execution traces, the basic Shannon entropy and the adapted distance entropy are used to measure the dynamic complexity of a service system. In addition, the effectiveness of our proposed entropy-based metrics of dynamic complexity is validated by several examples of service systems and a real application. Particularly, the metric of combining the adapted distance entropy and service pair matrix has the strongest ability to depict the dynamic complexity.
Coincidence of P-Insertion Sites and Breakpoints of Deletions Induced by Activating P Elements in Drosophila

We isolated a set of seven deletions in the 67B region by activating a nearby P-element insertion. The structures of the deletions were characterized by cloning and sequencing. The results showed that the P-induced deletions occurred nonrandomly in the genomic sites. One breakpoint of the deletions was located precisely at the end of the starting element, i.e., at the end of the inverted terminal repeats. The other breakpoint was nearby the retained starting element and coincided with preferential P-element insertion sites that harbor transcription initiation activities. It is known that P elements induce male recombination near the starting elements, giving rise to deletions with one breakpoint precisely located at an inverted terminal repeat of the retained starting element. Database analyses further revealed that deletions generated in P-induced male recombination also contained the other breakpoint in genomic regions that coincided with preferential P-insertion sites. The results suggest that nonrandom distribution of the deletion breakpoints is characteristic of the mechanism by which P elements induce deletions near the starting elements.
Impacts of refresh interval parameters on M-OLSR performance for Wireless Mesh Networks

Modified Optimized Link State Routing (M-OLSR) has been developed for adaptability in Wireless Mesh Networking (WMNs) scenarios and exhibits a much better scalability of traffic load and mobility in sparse and dense network. The protocol uses some refresh timers for periodic updates of link information and for subsequent topology maintenance. In this paper, we investigate the impact of configuring refresh timer interval on protocol's performance under various networking scenarios. Simulation results demonstrate that, HELLO message timer interval has bigger impact than Topology control (TC) message timer on M-OLSR performance. And, as the network mobility increases, the impact of configuring refresh timer interval has greater effect than a relatively stable network.
Cardiac source localization by means of a single moving dipole solution during endocardial pacing in an animal model

The accuracy of localizing the initiation site of cardiac activation by noninvasively estimating a single moving dipole (SMD) was investigated in a swine model. Body surface potential mapping (BSPM) and intracavitary noncontact mapping (NCM) were performed simultaneously during acute left ventricular (LV) endocardial pacing. For each animal, the boundary element model was constructed from preoperative magnetic resonance images (MRI). In each pacing study, the initiation site was localized by inversely estimating the location of an SMD from BSPM data. The results were compared with the precise pacing sites recorded by the NCM system. In total, four pacing sites from two pigs were analyzed, and the averaged source localization error was 16.8 ± 2.3 mm. The present results indicate the potential of localizing focal cardiac events by estimating single moving dipole.
Update on Chlamydomonas Oxidative Phosphorylation Proteome The Mitochondrial Oxidative Phosphorylation Proteome of Chlamydomonas reinhardtii Deduced from the Genome Sequencing Project 1

Mitochondria originated from an endosymbiotic process that involved an a-proteobacterium (Martin and Muller, 1998; Gray et al., 1999). The evolution of the organelle has been associated with the massive migration of the endosymbiont genes to the nucleus of the host and with the acquisition of new proteins that were originally present in the host (Karlberg et al., 2000; Andersson et al., 2003; Richly et al., 2003). Mitochondrial proteomes are thus a mosaic of mitochondriaand nucleus-encoded proteins, the latter having a combined eubacterial/eukaryotic origin. The increasing number of complete genome sequences has naturally led to an attempt to establish a relationship between these genomes and their corresponding transcriptomes and proteomes. Of particular interest for bioenergeticists are the efforts performed toward establishing the proteomes of chloroplasts and mitochondria. Mitochondria are the site of oxidative phosphorylation (OXPHOS). This process comprises an electron-transfer chain that is driven by substrate oxidation and is coupled to the synthesis of ATP through an electrochemical transmembrane gradient. Therefore, the OXPHOS proteome (or more simply the OXPHOSome) will be the anatomical description of the protein components that participate in this process (complexes I–V and additional oxidoreductases). THE STANDARDS OF REFERENCE: THE BOVINE, YEAST, AND PLANT OXPHOSOMES
[Atherosclerosis and rheumatoid arthritis: relationships between intima-media thickness of the common carotid arteries and disease activity and disability].

OBJECTIVES To investigate the intima-media thickness of the common carotid arteries (IMT-CCA) in patients with Rheumatoid Arthritis (RA), and its relationships with classical atherosclerosis risk factors and disease features i.e. duration, activity and disability. METHODS 48 RA patients (35 F, 13 M; age ed 26-69 years median 55; disease duration 1-18 years, median 8), and 22 controls (16 F, 6 M; age 28-66, median 50) matched for classical atherosclerosis risk factors, i.e. age, sex, smoking, blood pressure, body mass index, diabetes, familiarity, and for postmenopausal status, were studied. IMT and plaques were measured in the left and right common carotid arteries. Serum total cholesterol, triglyceride, high-density lipoprotein cholesterol, low-density lipoprotein cholesterol, apoliporotein AI, apolipoprotein B, and rheumatoid factor were determined in patients and controls. The DAS28, the HAQ-DI and disease duration were considered as clinical parameters reflecting disease status. RESULTS The IMT-CCA (mean +/- SD) was significantly greater in the 48 RA patients than in the 22 controls subjects (1.00+/-0.25 vs. 0.78+/-0.21; p=0.0007). In the 70 subjects investigated CCA-IMT resulted to be significantly correlated with diastolic blood pressure, body mass index, triglyceride and RA status. In the 48 RA patients no correlation was detected with either disease duration or activity or disability. CONCLUSION our study confirms an increased IMT in RA patients without any clinically evident manifestation of cardiovascular disease. It supports the existence of subclinical atherosclerosis in RA.
Natural Reference to Objects in a Visual Domain

This paper discusses the basic structures necessary for the generation of reference to objects in a visual scene. We construct a study designed to elicit naturalistic referring expressions to relatively complex objects, and find aspects of reference that have not been accounted for in work on Referring Expression Generation (REG). This includes reference to object parts, size comparisons without crisp measurements, and the use of analogies. By drawing on research in cognitive science, neurophysiology, and psycholinguistics, we begin developing the input structure and background knowledge necessary for an algorithm capable of generating the kinds of reference we observe.
Central projections of sensory neurons in the Drosophila embryo correlate with sensory modality, soma position, and proneural gene function

The peripheral nervous system (PNS) of the Drosophila embryo is especially suited for investigating the specification of neuronal identity: the PNS consists of a relatively simple but diverse set of individually identified sensory neurons; mutants, including embryonic lethals, can be readily generated and analyzed; and axon growth can potentially be followed from the earliest stages. We have developed a staining method to reveal the central projections of the full set of sensory neurons in the preterminal abdominal segments of the embryo. The sensory neurons exhibit modality-specific axonal projections in the CNS. The axons of external sense (es) organ neurons, primarily tactile in function, are restricted to a particular region within each neuromere and exhibit a somatotopic mapping within the CNS. The axons of stretch-receptive chordotonal (ch) organs project into a discrete longitudinal fascicle. Sensory neurons with multiple-branched dendrites (md neurons) project into a separate fascicle. A small number of md neurons have distinctive dorsal-projecting axonal processes in the CNS. A classification of sensory neurons based on their axon morphology correlates closely with the identity of the proneural gene responsible for their generation, suggesting that proneural genes play a central role in determining neuronal identity in the PNS of the embryo.
A wavelet-based multiresolution approach to stereo matching of face images

Stereo matching is one of the most active research areas in computer vision. To find the corresponding point in a stereo pair of face images often consider intensity or color differences as a local matching metric, which is sensitive to contrast changes. We proposed a multiwavelet based algorithm for stereo matching, which depends on multiple spatial frequency channels for matching of a stereo pair of face image. The stereo test images of popular face database and middlebury database are used to generate experimental results. The results show that the proposed technique produces disparity maps with fewer mismatch errors.
A response to Grieve and Campbell's medieval experiments on child language

When we were preparing our paper ‘Language origin accounts: was the gesture in the beginning? ’ (Bonvillian, Garber & Dell 1997) we had three principal goals in mind. The first was to bring to the readers’ attention a relatively little-known investigation of language origins conducted by Akbar, the emperor of Hindustan, about 400 years ago. The second was to re-examine the findings of the well-known, but often derided, study of language origins allegedly conducted more than 2500 years ago by King Psammetichus of Egypt. Although the conclusion of this study that Phrygian was the world’s oldest language is clearly wrong, there are other aspects of Psammetichus’ investigation that lend credence to the accounts. Our third goal was to suggest that if some of the reports of the Akbar study were correct in indicating that the children learned to communicate gesturally,then this outcome might not be far removed from certain contemporary investigators’ thinking that gestures and manual signs played a substantial role in the emergence of human language. We sincerely regret not including Campbell & Grieve’s outstanding I982 paper ‘Royal investigations of the origin of language’ in our discussion of accounts of language origins. When we had prepared an early draft of our paper, we sent copies to more than a dozen colleagues in linguistics, psycholinguistics and Asian studies for feedback on content and style. From this group, one colleague remembered having read a paper about Akbar sometime during the previous decade. Although he remembered that paper favourably, he was unable to provide us with a citation. We then spent several days conducting computer . searches and scrutinizing reference sections, but failed to unearth the article. I f nothing else, we hope the current interest in
Vaginal transmission of chimeric simian/human immunodeficiency viruses in rhesus macaques

Chimeric simian/human immunodeficiency viruses (SHIVs) that express the env genes derived from distinct HIV type 1 (HIV-1) isolates were tested for the ability to infect rhesus macaques following intravaginal inoculation. SHIVs containing either the HIV-1 HXBc2 or the HIV-1 89.6 envelope glycoproteins were capable of replicating in intravenously inoculated rhesus macaques. However, intravaginal inoculation of animals with these two SHIVs resulted in infection only with the SHIV containing the HIV-1 89.6 glycoprotein. Thus, properties conferred by the envelope glycoproteins in the chimeric virus affect the ability of particular SHIVs to initiate a systemic infection following vaginal inoculation. These results provide indirect support for the hypothesis that the selection of specific viral variants occurs in the genital tracts of individuals exposed to HIV by sexual contact.