Miracle-dz/UniFAR-FTUs huggingface dataset:
Development of the cone photoreceptor mosaic in the mouse retina revealed by fluorescent cones in transgenic mice.

PURPOSE Normal function of the retina relies on the orderly stereotyped organization of different neurons and their synaptic connections. How such neural organization is patterned during development remains poorly understood due to the paucity of adequate developmental markers. This study was to examine the spatial organization and development of cone photoreceptors quantitatively in the mouse retina. METHODS A transgenic approach was used to generate a living cone cell marker by driving GFP expression in mouse cones with the human red/green opsin gene 5' sequences. The spatial organization and development of the cones in the mouse retinas were examined quantitatively with epifluorescence and scanning laser confocal microscopy. Cone specific GFP expression in the developing retinas was verified with peanut agglutinin (PNA) staining. Developmental expression of mouse cone opsin genes was determined with RT-PCR. RESULTS The fluorescent retinal cells expressing GFP can be visualized as early as on embryonic day E15. Following up morphological differentiation of these cells revealed features that were consistent with the typical morphology of the mouse cones. Double labeling with cone specific PNA showed that these cells were co-labeled starting from postnatal day P1, and that a subpopulation of PNA positive cones expressed the GFP. The fluorescent cell densities had a similar ventral and dorsal distribution from E15 to P2, increased dramatically in the ventral by P6, and in the dorsal from P7. Nearest neighbor distance analysis demonstrated that this subpopulation of cones was organized into a regular mosaic pattern with a regularity index of 4.82 in the central and 3.55 in the peripheral retina. Quantitative pattern assessment of the developing cones revealed that the fluorescent cells appeared to be distributed in a non-random array before birth. The regularity of the cone array began to rise on P7, in parallel with the onset of mouse green opsin gene expression and the development of cone pedicles. The regular pattern of cone mosaic organization was basically formed by P10, coinciding with the timing of the cone pedicle maturation. CONCLUSIONS The cones in the mouse retina are organized in a regular mosaic pattern. Patterning the cone mosaic appears to follow a two phase developmental process involving regulated opsin gene expression and cone pedicle maturation: an early phase where a non-random array emerges during cone differentiation, and a late phase where the regular mosaic pattern is mature at the time when cone synaptic contacts are being formed.
Structural Basis for Differential Neutralization of Ebolaviruses

There are five antigenically distinct ebolaviruses that cause hemorrhagic fever in humans or non-human primates (Ebola virus, Sudan virus, Reston virus, Taï Forest virus, and Bundibugyo virus). The small handful of antibodies known to neutralize the ebolaviruses bind to the surface glycoprotein termed GP1,2. Curiously, some antibodies against them are known to neutralize in vitro but not protect in vivo, whereas other antibodies are known to protect animal models in vivo, but not neutralize in vitro. A detailed understanding of what constitutes a neutralizing and/or protective antibody response is critical for development of novel therapeutic strategies. Here, we show that paradoxically, a lower affinity antibody with restricted access to its epitope confers better neutralization than a higher affinity antibody against a similar epitope, suggesting that either subtle differences in epitope, or different characteristics of the GP1,2 molecules themselves, confer differential neutralization susceptibility. Here, we also report the crystal structure of trimeric, prefusion GP1,2 from the original 1976 Boniface variant of Sudan virus complexed with 16F6, the first antibody known to neutralize Sudan virus, and compare the structure to that of Sudan virus, variant Gulu. We discuss new structural details of the GP1-GP2 clamp, thermal motion of various regions in GP1,2 across the two viruses visualized, details of differential interaction of the crystallized neutralizing antibodies, and their relevance for virus neutralization.
New theory in wavelet equation and its applications in astronomy

Methods based on hypothesis tests (HTs) in the Haar domain are widely used to denoise Poisson count data. Facing large datasets or real-time applications, Haar-based denoisers have to use the decimated transform to meet limited-memory or computation-time constraints. Unfortunately, for regular underlying intensities, decimation yields discontinuous estimates and strong staircase artifacts. In this paper, we propose to combine the HT framework with the decimated biorthogonal Haar (Bi-Haar) transform instead of the classical Haar, The Bi-Haar filter bank is normalized such that the p-values of Bi-Haar coefficients (PBH) provide good approximation to those of Haar (PH) for high-intensity settings or large scales; for low-intensity settings and small scales, we show that PBH are essentially upper-bounded by PH. Thus. we may apply the Haar-based HTs to Bi-Haar coefficients to control a prefixed false positive rate. By doing so, we benefit from the regular Bi-Haar filter bank to gain a smooth estimate while always maintaining a low computational complexity, A Fisher-approximation-based threshold implementing the HTs is also established. The efficiency of this method is illustrated on an example of hyperspectral-source-flux estimation.
Sundar Iyer 1 / 3 RESEARCH STATEMENT

My research interests span the areas of network algorithms, system architecture and component design. A common thread in my research is in understanding the theory and design of scalable architectures and parallel systems. I have resorted to mathematical methods of proof which are borrowed from the areas of Algorithms, Architecture, Combinatorics, Probability, & Queueing Theory. Broadly speaking, my research belongs to the area of Network Architecture (which deals with the fundamental principles of network design), an upcoming field which is still in its infancy and whose theoretical foundations are just being laid.
Evaluation of two devices for self-measurement of blood pressure according to the international protocol: the Omron M5-I and the Omron 705IT

BackgroundTwo devices for self-measurement of blood pressure at the brachial artery—the Omron M5-I and the Omron 705IT—were evaluated according to the international protocol of the European Society of Hypertension. DesignThe international validation protocol is divided into two phases: the first phase is performed on 15 selected subjects and if the device passes this phase, 18 supplementary subjects are included making a total number of 33 subjects on which the final validation is performed. MethodsFor each subject, four blood pressure (BP) measurements were performed simultaneously by two trained observers using mercury sphygmomanometers alternately with three measurements by the tested device. The difference between the BP value given by the device and that obtained by the two observers (mean of the two observers) was calculated for each measure. The 99 differences were classified into categories (≤5, ≤10, ≤15 mmHg). The number of differences in each category was compared to the number required by the international protocol. An individual analysis was then done to determine for each subject the number of comparisons ≤5 mmHg. At least 22 of the 33 subjects should have two of their three comparisons ≤5 mmHg. ResultsThe two tested devices passed the first phase of the validation process. For the second phase, the average differences between the device and mercury sphygmomanometer readings were −0.9±5.8 and −0.8±4.8 mmHg for systolic blood pressure (SBP) and diastolic blood pressure (DBP) respectively for the Omron M5-I device and −0.2±4.5 and −2.0±4.8 mmHg for the Omron 705IT device. Readings for the two devices differing by less than 5, 10 and 15 mmHg for systolic and diastolic values fulfil the recommendation criteria of the international protocol as well as the individual analysis. ConclusionsThe Omron M-5I and the Omron 705IT devices pass the validation recommendations of the international protocol.
EMOT – Evolutionary Approach to 3D Computer Animation

Key-framing and Inverse Kinematics are popular animation methods, but new approaches are still developed. We propose a new evolutionary method of animation creation – system EMOT (Evolutionary MOTion). It allows for automation of motion of animated characters. It uses new evolutionary approach – Gene Expression Programming (GEP). Characters are controlled by computer programs, an animator has to provide the way of motion evaluation. GEP works with a randomly selected initial population, uses directed but random selection. Experiments show that the proposed method can develop robust controllers.
Real-time three-dimensional flexible needle tracking using two-dimensional ultrasound

Needle insertion is one of the most commonly performed minimally invasive procedures. Visualization of the needle during insertion is key for either successful diagnosis or therapy. This work presents the real-time three-dimensional tracking of flexible needles during insertion into a soft-tissue simulant using a two-dimensional (2D) ultrasound transducer. The transducer is placed perpendicular to the needle tip to measure its position. During insertion the transducer is robotically repositioned to track the needle tip. Positioning of the transducer is accomplished by a compensator, that uses the needle insertion velocity corrected by needle tip velocities to determine out-of-plane motion. Experiments are performed to validate the needle tip pose during tracking. The maximum mean errors in needle tip position along the x-, y- and z-axes are 0.64 mm, 0.25 mm and 0.27 mm, respectively. The error in tip orientations (θ-about the y-axis and φ-about the z-axis) are 2.68° and 2.83°, respectively. This study demonstrates the ability to compute the needle tip pose using a 2D ultrasound transducer. The tip pose can be used to robotically steer needles, and thereby improve accuracy of medical procedures.
Pressure-Induced Vasoconstriction of Renal Microvessels in Normotensive and Hypertensive Rats: Studies in the Isolated Perfused Hydronephrotic Kidney

The capacity of small arteries to respond to increased intravascular pressure may be altered in hypertension. In the kidney, hypertension is associated with a compensatory shift in the autoregulatory response to pressure. To directly determine the effects of established hypertension on the renal mkrovascular response to changes of perfusion pressure, we evaluated pressure-induced vasoconstriction in hydronephrotic kidneys isolated from normotensive Wistar-Kyoto (WKY) and spontaneously hypertensive rats (SHR). Vessel diameters of interlobular arteries (ILAs) and afferent and efferent arterioles were determined by computerassisted videomicroscopy daring alterations in renal arterial pressure (RAP) from 80 to 180 mm Hg. Increased RAP induced a pressure-dependent vasoconstriction in preglomerular vessels (afferent arterioles and ILAs), but not in postglomerular vessels (efferent arterioles). The calcium antagonist nifedipine prevented pressure-induced afferent arteriolar vasoconstriction with a similar half-maximal inhibitory concentration (IC50) (WKY, 63 ± 27 vs. SHR, 60 ± 32 nM). The pressure-activation curves for ILAs in SHR and WKY were similar. In contrast, the pressure-activation curve for afferent arterioles in SHR kidneys exhibited a rightward shift, which was observed at every segment of the afferent arteriole (i.e., near ILA, at midportion, and near glomerulus). These findings demonstrate that the HA and the afferent arteriole both possess the ability to constrict in response to increased pressure, whereas this property is lacking in the efferent arteriole. Hypertension was associated with a compensatory shift in the pressure response of the afferent arteriole, such that higher RAPs were required to elicit vasoconstriction in this vessel.
Family Strategies for Living with Rare Disease: The Experience of Cystinosis

Objective: Medical advances have transformed the rare disease cystinosis from fatal in childhood to chronic and manageable well into adulthood, creating new challenges for patients, families, and providers. In response, families are adapting strategies to meet the demands of the illness and its treatments during a developmentally dense stage of life. Method: The study uses a classic grounded theory approach to understand the experience of adults and emerging adults living with cystinosis. Data were collected through focus groups and/or semi-structured interviews with 46 individuals (22 patients and 24 parents) recruited through national cystinosis advocacy/support organizations. Constant comparative analysis guided data collection and analysis. Results: In the context of much uncertainty, these patients and families described interconnected strategies to negotiate childhood and adolescence, enter into adulthood with self-care skills, and integrate normative developmental tasks with adequate management of illness. Strategies included educating, regimenting, pushing/protecting, connecting, coming to terms, and finding a fit. Conclusions: As both the understanding of and treatment options for rare and genetic childhood diseases expand, health care providers and multidisciplinary teams should consider regularly assessing the strategies used by families to manage illness. Families and individuals adapt as treatment protocols evolve and as children survive into adulthood, facing new, and perhaps unexpected, developmental tasks. The strategies described by participants can help frame the expectations of families across rare disease groups and suggest new avenues for resources and support.
ON PREDICTING SOFTWARE DEVELOPMENT EFFORT USING MACHINE LEARNING TECHNIQUES AND LOCAL DATA

This paper analyses the accuracy of predictions for software development effort using various machine learning techniques. The main aim is to investigate the stability of these predictions by analyzing if particular techniques achieve a similar level of accuracy for different datasets. Two key assumptions are that (1) predictions are performed using local empirical data and (2) very little expert input is required. The study involves using 23 machine learning techniques with four publicly available datasets: COCOMO, Desharnais, Maxwell and QQDefects. The results show that the accuracy of predictions for each technique varies depending on the dataset used. With feature selection most techniques provide higher predictive accuracy and this accuracy is more stable across different datasets. The highest positive impact of feature selection on the accuracy has been observed for the K* technique, which has generated the most accurate predictions across all datasets.
Utilizing Descriptive Statements from the Biodiversity Heritage Library to Expand the Hymenoptera Anatomy Ontology

Hymenoptera, the insect order that includes sawflies, bees, wasps, and ants, exhibits an incredible diversity of phenotypes, with over 145,000 species described in a corpus of textual knowledge since Carolus Linnaeus. In the absence of specialized training, often spanning decades, however, these articles can be challenging to decipher. Much of the vocabulary is domain-specific (e.g., Hymenoptera biology), historically without a comprehensive glossary, and contains much homonymous and synonymous terminology. The Hymenoptera Anatomy Ontology was developed to surmount this challenge and to aid future communication related to hymenopteran anatomy, as well as provide support for domain experts so they may actively benefit from the anatomy ontology development. As part of HAO development, an active learning, dictionary-based, natural language recognition tool was implemented to facilitate Hymenoptera anatomy term discovery in literature. We present this tool, referred to as the ‘Proofer’, as part of an iterative approach to growing phenotype-relevant ontologies, regardless of domain. The process of ontology development results in a critical mass of terms that is applied as a filter to the source collection of articles in order to reveal term occurrence and biases in natural language species descriptions. Our results indicate that taxonomists use domain-specific terminology that follows taxonomic specialization, particularly at superfamily and family level groupings and that the developed Proofer tool is effective for term discovery, facilitating ontology construction.
Inria's Participation at ImageCLEF 2013 Plant Identification Task

This paper describes the participation of Inria within the Pl@ntNet project at ImageCLEF2013 plant identification task. For the SheetAsBackground category (scans or photographs of leaves with a uniform background), the submitted runs used a multiscale triangle-based approaches, either alone or combined with other shape-based descriptors. For the NaturalBackground category (unconstrained photographs of leaves, flowers, fruits, stems,.), the four submitted runs used local features extracted using different geometric constraints. Three of them were based on large scale matching of individual local feature, while the last one used a Fisher vector representation. Metadata like the flowering date or/and plant identifier were successfully combined to the visual content. Overall the proposed methods performed very well for all categories and sub-categories.
Static behavior analysis of silicon carbide power MOSFET for temperature variations

This paper proposes an analysis of the static behavior of a SiC-MOSFET power transistor for temperature variations. The commercial transistor model (CMF10120D Cree 1200V/24A) is used. The approach consists to exploit the Spice electrical model provided by the constructor and to set its limits. Two main parameters: the threshold voltage and mobility are investigated to meet the needs of the static study and refine the temperature behavior of the Spice model. The obtained simulation results are compared to experimental measurements achieved in a static athermal mode.
Thai Word Segmentation Verification Tool

Since Thai has no explicit word boundary, word segmentation is the first thing to do before developing any Thai NLP applications. In order to create large Thai word-segmented corpora to train a word segmentation model, an efficient verification tool is needed to help linguists work more conveniently to check the accuracy and consistency of the corpora. This paper proposes Thai Word Segmentation Verification Tool Version 2.0, which has significantly been improved from the version 1.0 in many aspects. By using hash table in its data structures, the new version works more rapidly and stably. In addition, the new user interfaces have been ameliorated to be more user-friendly too. The description on the new data structures is explained, while the modification of the new user interfaces is described. An experimental evaluation, in comparing with the previous version, shows the improvement in every aspect.
Event detection for video surveillance using an expert system

Video Surveillance is in the center of research due to high importance of safety and security issues. Usually, humans have to monitor an area and often they have to do this for 24 hours a day. Thus, it would be desirable to have automatic surveillance systems that support this job automatically. The system described in this paper is such an automatic surveillance system that has been developed to detect several dangerous situations in a subway station. This paper discusses the high-level module of the system. Herein, an expert system is used to detect events.
Passive and accurate torque control of series elastic actuators

The principle of series elastic actuation offers considerable advantages for haptic displays compared to stiff actuators. The interaction force between motor and load is directly proportional to their relative position, which corresponds to the elongation of the elastic element. This way, the torque control task is transformed to a position control task, which comes natural to traditional DC motors. In this paper, several existing control strategies are analyzed and compared with respect to passivity concerns. Cascaded control with a fast inner velocity loop results to be the best option. Based on the analysis, boundaries for the parameters are presented, such that the force controller may contain integral action without jeopardizing passivity.
Elementary excitations in magnetically ordered systems with orbital degeneracy

The generalized Holstein-Primakoff transformation is used to develop a quantum flavor wave theory for spin systems with orbital degeneracy. Elementary excitations of ordered ground states consist of spin, orbital, and spin-orbital waves. Spin and spin-orbital waves couple to each other due to orbital anisotropy and Hund[close quote]s rule, resulting in modes observable by inelastic neutron scattering. In the SU(4) limit, flavor waves are dispersionless along one or more directions, and give rise to quantum fluctuations of reduced dimensionality. [copyright] [ital 1999] [ital The American Physical Society]
The Prediction of Terminal Intelligence from Infant and Preschool Tests

Wellman (19, 20, 21, 22) and Skeels (12, 13, 14, 15) have called some of the assumptions of modern intelligence-test theory into question. Their results, based upon infant or preschool tests as origins, are interpreted to show that a favorable environment produces great changes upward, and an unfavorable environment great changes downward, in true intelligence. This contribution to the Year book is not concerned with the results of these studies in detail, but is concerned with the reliance that is to be placed upon infant and preschool tests as measures of what is later known as intelligence, even if we accept the published :findings as correct. Because of the use of the criterion of age progression in the standardization of inf ant and preschool tests and the neglect of the criteria of ratings, of measures of scholastic achievement, and of internal consistency that are used with older age levels, inf ant scales consist very largely of motor items. Infant-scale scores show zero or very low positive correlations with intelligence scores at later ages (2, 6). Recently Richards and Nelson (8, 9, 10), and others, have found that the items in inf ant scales correlate in different degrees with intelligencetest scores at later ages and suggest that by item analysis and weighting through partial correlation, the correlations of infant tests as a whole with later measures may be raised. In this chapter, I propose the use of test performance at later age levels as a criterion and am concerned with the implications involved in its use. The proposal as-