Miracle-dz/UniFAR-FTUs huggingface dataset:
genome annotation of Oryza sativa ssp . japonica and comparative genome analysis with Arabidopsis thaliana The Rice Annotation Project

Access the most recent version at doi: 2007 17: 175-183; originally published online Jan 8, 2007; Genome Res. Gojobori, Takuji Sasaki and for the Rice Annotation Project Yamamoto, Naoyuki Yamamoto, Yeisoo Yu, Hao Zhang, Qiang Zhao, Kenichi Higo, Benjamin Burr, Takashi Mika Tsugane, Akhilesh K. Tyagi, Apichart Vanavichit, Aihui Wang, Rod A. Wing, Kaori Yamaguchi, Mayu Smith-White, Jun-ichi Takeda, Motohiko Tanino, Tatiana Tatusova, Supat Thongjuea, Fusano Todokoro, Motoaki Seki, Michie Shibata, Yuji Shimizu, Kazuo Shinozaki, Yuji Shinso, Nagendra K. Singh, Brian Sakai, Yasumichi Sakai, Katsumi Sakata, Tetsuya Sakurai, Fumihiko Sato, Yoshiharu Sato, Heiko Schoof, Satoshi OOta, Naoki Osato, Lance E. Palmer, Francis Quetier, Saurabh Raghuvanshi, Naomi Saichi, Hiroaki Nobukazu Namiki, Hisataka Numa, Shin Nurimoto, Claire O’Donovan, Hajime Ohyanagi, Toshihisa Okido, Richard McCombie, Joachim Messing, Akio Miyao, Nicola Mulder, Yoshiaki Nagamura, Jongmin Nam, Kubooka, Damien Lieberherr, Yao-Cheng Lin, David Lonsdale, Takashi Matsumoto, Akihiro Matsuya, W. Hiroaki Kawashima, Jitendra P. Khurana, Shoshi Kikuchi, Setsuko Komatsu, Kanako O. Koyanagi, Hiromi Tadashi Imanishi, Yukiyo Ito, Pankaj Jaiswal, Masako Kanno, Yoshihiro Kawahara, Toshiyuki Kawamura, Hirohiko Hirochika, Douglas Hoen, Hiroki Hokari, Satomi Hosokawa, Yue Hsing, Hiroshi Ikawa, Kazuho Ikeo, Costa de Oliveira, Galina Fuks, Takuya Habara, Georg Haberer, Bin Han, Erimi Harada, Aiko T. Hiraki, Antonio Baltazar A. Antonio, Hideo Aono, Rolf Apweiler, Richard Bruskiewich, Thomas Bureau, Frances Burr, Takeshi Itoh, Tsuyoshi Tanaka, Roberto A. Barrero, Chisato Yamasaki, Yasuyuki Fujii, Phillip B. Hilton, Arabidopsis thaliana comparative genome analysis with and japonica ssp. Oryza sativa Curated genome annotation of
Pregnancy improves cognitive deficit and neuronal morphology atrophy in the prefrontal cortex and hippocampus of aging spontaneously hypertensive rats

It is well known that the survival is higher in women compared to men and women have a better survival prognosis than men in some pathologies such as vascular dementia (VD). Our previous reports showed that the spontaneously hypertensive (SH) rat, an animal model of VD, exhibited dendritic atrophy of pyramidal neurons of the dorsal hippocampus (DH) and the prefrontal cortex (PFC) at 8 months of age. Cerebrolysin (CBL), a neurotrophic peptide mixture, reduces dendritic atrophy and improves the memory process in aged rats. Here, we investigated whether one pregnancy or/and CBL was capable of improving cognitive behavior and neuronal alterations in old female SH rats. Diastolic and systolic blood pressure were assessed before pregnancy (3 months old) and CBL administration (6 months old), and after CBL administration (12 months old). Immediately after of 6 months of CBL treatment, locomotor activity in novel environments and memory and learning by the Morris Water Maze test were evaluated. By the Golgi‐Cox staining method, dendritic parameters were assessed in PFC and DH. Our results suggest that rats with one pregnancy showed better memory with an enhancement in dendritic length and dendritic spine density in the aforementioned regions.
Non-Intrusive Measurement of Workload in Real-Time

We present a new method to measure workload that offers several advantages. First, it uses non-intrusive means: cameras and a mouse. Second, the workload is measured in real-time. Third, the setup is comparably cheap: the cameras and sensors are off-the-shelf components. Fourth, we go beyond measuring performance and demonstrate that just using such measures does not suffice to measure workload. Fifth, by using a Bayesian Network to assess the workload from the various manifesting measures the model adapts itself to the individual user as well as to a particular task. Sixth, we use a cognitive computational model to explain the cognitive mechanisms that cause the differences in workload and performance.
Longitudinal analysis of the relationship of existential meaning with depression and hope

Longitudinal Analysis of the Relationship of Existential Meaning with Depression and Hope. (August 2006) Nathan Mascaro, B.S., Louisiana State University; M.S., Texas A&M University Co-Chairs of Advisory Committee: Dr. David H. Rosen Dr. Leslie C. Morey Although researchers are now able to assess reliably the variable of existential meaning, quality longitudinal investigations of meaning’s relationship with specific clinical variables are scarce. The author conceptualizes existential meaning as a composite of personal, spiritual, and implicit meaning. These latter three variables are, respectively, the experience of one’s particular life as having purpose and coherence, experiencing a transcendent or spiritual presence from which one derives a sense of unique purpose, and manifesting attitudes and behavior that are normatively valued. Utilizing a sample of 395 male and female undergraduates and employing the framework subscale of the Life Regard Index-Revised (LRI-R-framework), the Spiritual Meaning Scale (SMS), and the Personal Meaning Profile (PMP) to measure personal, spiritual, and implicit meaning, respectively, the author explored existential meaning’s relationship over time with depressive symptoms (as measured with the Beck Depression Inventory-II, depression scale of the Depression Anxiety Stress Scales, and depression scale of the Personality Assessment Inventory) and hope (as measured with the Herth Hope Scale, the Adult State Hope Scale, and the Beck Hopelessness Scale). A latent cross-lagged panel analysis of the relationship between meaning and depression over 2 one-month time periods indicated that meaning exerted unidirectional influence on depression, with decreases in meaning leading to increases in depressive symptoms. Additionally, hierarchical regression analysis showed that individuals
Digital Visions vs. Product Practices: Understanding Tensions in Incumbent Manufacturing Firms

Incumbent manufacturing firms face challenges when expanding their product focus with digital services. Such expansion creates tensions in organizations in the servitization process. While management visions and conceptualizes new service oriented businesses, the actual practice of implementing these service concepts is influenced by the product paradigmatic way of thinking in the organization. This dominant thinking creates tensions between business visions and business practice. We use the case of remote diagnostics services to provide insights into a manufacturing firm's attempt to transform the dominant oriented business models into a new networked environment. We suggest that such acts that may or may not lead to transition are lingered by dominant logics related to the product focus. This indicates that firms are required to embed new logics into their existing practice in order to exploit the full potential of digital technology.
Improving the Performance of GALS-Based NoCs in the Presence of Process Variation

Current integration scales allow designing chip multiprocessors (CMP) where cores are interconnected by means of a network-on-chip (NoC). Unfortunately, the small feature size of current integration scales cause some unpredictability in manufactured devices because of process variation. In NoCs,variability may affect links and routers causing that they do not match the parameters established at design time. In this paper we first analyze the way that manufacturing deviations affect the components of a NoC by applying a comprehensive and detailed variability model to 200 instances of an 8x8 mesh NoC synthesized using 45nm technology. A second contribution of this paper is showing that GALS-based NoCs present communication bottlenecks under process variation. To overcome this performance reduction we draft a novel approach, called performance domains, intended to reduce the negative impact of variability on application execution time. This mechanism is suitable when several applications are simultaneously running in the CMP chip.
Advances in nanotechnology-based carrier systems for targeted delivery of bioactive drug molecules with special emphasis on immunotherapy in drug resistant tuberculosis – a critical review

Abstract From the early sixteenth and seventeenth centuries to the present day of life, tuberculosis (TB) still is a global health threat with some new emergence of resistance. This type of emergence poses a vital challenge to control TB cases across the world. Mortality and morbidity rates are high due to this new face of TB. The newer nanotechnology-based drug-delivery approaches involving micro-metric and nano-metric carriers are much needed at this stage. These delivery systems would provide more advantages over conventional systems of treatment by producing enhanced therapeutic efficacy, uniform distribution of drug molecule to the target site, sustained and controlled release of drug molecules and lesser side effects. The main aim to develop these novel drug-delivery systems is to improve the patient compliance and reduce therapy time. This article reviews and elaborates the new concepts and drug-delivery approaches for the treatment of TB involving solid-lipid particulate drug-delivery systems (solid-lipid micro- and nanoparticles, nanostructured lipid carriers), vesicular drug-delivery systems (liposomes, niosomes and liposphere), emulsion-based drug-delivery systems (micro and nanoemulsion) and some other novel drug-delivery systems for the effective treatment of tuberculosis and role of immunomodulators as an adjuvant therapy for management of MDR-TB and XDR-TB.
A mini review on the design of interactive tool for medical image segmentation

Manual segmentation has been widely accepted in medical image analysis because the user will assume absolute control over final output. Nonetheless, the method is infamous for being time consuming and sensitive to inter-observer variability. Semi-automated methods incorporate user knowledge to initialize computerized segmentation and thus, is a versatile approach to tackle real time segmentation problem. Interactive tool or Graphic User Interface is the most critical medium of communication between user and computer but this element has always been neglected. Intuitively, the design of efficient interactive tool will impose significant effect on segmentation efficiency. In this work, we have presented a mini review on the design element of graphic user interface in medical image segmentation to highlight the importance of this tool in ensuring desirable segmentation output.
A user-friendly CAD tool for the Rigorous and Efficient Analysis of Finline Waveguiding Structures for Millimetre Applications

In this paper we present the computation of the finline parameters using the transverse resonance method and spectral domain analysis suitable for the design of microwave and millimeter-wave integrated circuits. However, this powerful method has one drawback when many hybrid modes are required because the above technique is used to yield a homogeneous system of equations to determine the propagation constants. In this work and in order to avoid this difficulty, once the equations are written in terms of the transverse components of the fields in the spectral domain, Galerkin's method is used to yield a homogeneous system of equations to determine the propagation constants, but due to the new approach formulation the equations can be rewritten as a linear matrix eigenvalue system for the propagation constant when the eigenvectors of an auxiliary problem are used to expand the modes of the original problem. The key issue of the present study is to use an expanding set of modes at cutoff as auxiliary eigenvectors First, we have obtained the hybrid and complex spectrum of various finlines configurations. This analysis includes the characteristic impedance, attenuation due to dielectric and conductor losses, and the effect of finite metallization thickness. Secondly, configurations of the field components were also studied. We also present a software package; all examples are developed for numerical computation using MATLAB. Comparison with previously accurate published data was performed to confirm the accuracy of our procedure.
Cognitive therapy versus medication in augmentation and switch strategies as second-step treatments: a STAR*D report.

OBJECTIVE The authors compared the effectiveness of cognitive therapy and pharmacotherapy as second-step strategies for outpatients with major depressive disorder who had received inadequate benefit from an initial trial of citalopram. Cognitive therapy was compared with medication augmentation and switch strategies. METHOD An equipoise-stratified randomization strategy was used to assign participants to either augmentation of citalopram with cognitive therapy (N=65) or medication (N=117; either sustained-release bupropion [N=56] or buspirone [N=61]) or switch to cognitive therapy (N=36) or another antidepressant (N=86; sertraline [N=27], sustained-release bupropion [N=28], or extended-release venlafaxine [N=31]). Treatment outcomes and the frequency of adverse events were compared. RESULTS Less than one-third of participants consented to randomization strata that permitted comparison of cognitive therapy and pharmacotherapy. Among participants who were assigned to second-step treatment, those who received cognitive therapy (either alone or in combination with citalopram) had similar response and remission rates to those assigned to medication strategies. For those who continued on citalopram, medication augmentation resulted in significantly more rapid remission than augmentation with cognitive therapy. Among those who discontinued citalopram, there were no significant differences in outcome, although those who switched to a different antidepressant reported significantly more side effects than those who received cognitive therapy alone. CONCLUSIONS After an unsatisfactory response to citalopram, patients who consented to random assignment to either cognitive therapy or alternative pharmacologic strategies had generally comparable outcomes. Pharmacologic augmentation was more rapidly effective than cognitive therapy augmentation of citalopram, whereas switching to cognitive therapy was better tolerated than switching to a different antidepressant.
Which Bond Matters More? Assessing the Differential Strengths of Parental Bonding Measures on Adolescent Delinquency Over Time

Although Hirschi’s social bonds theory, especially the attachment component, has received a large amount of empirical support in the literature, research has not clarified whether it matters if the juvenile is attached to his or her mother or his or her father. This study addresses this issue by analyzing the impact of three attachment measures—the juveniles’ perceived attachment to their mother, their father, and both parents combined—on self-reported delinquency using a nationally representative data source. Cross-sectional and longitudinal results reveal mixed results. A discussion of the results and directions for future research are presented.
Measurement of Insulin Sensitivity in Children

OBJECTIVE—In this study we compared fasting insulin and measures of insulin sensitivity (M) based on fasting insulin and glucose (i.e., homeostasis model assessment [HOMA], quantitative insulin sensitivity check index [QUICKI], and fasting glucose–to–insulin ratio [FGIR]) or triglycerides to the insulin clamp in a cohort of children/adolescents. RESEARCH DESIGN AND METHODS—The subjects were Minneapolis fifth- to eighth-grade students. Euglycemic-hyperinsulinemic clamps were performed on 323 adolescents at mean age 13 and were repeated on 300 of these subjects at mean age 15. Insulin sensitivity was determined by glucose uptake (milligrams per kilogram per minute) adjusted for lean body mass (MLBM) and steady-state insulin (MLBM/ln SSI). Comparisons were made for the whole cohort and by body size (BMI <85th percentile vs. BMI ≥85th percentile). Receiver operating characteristic (ROC) curves were used to test whether specific fasting insulin cut points separated true-positive from false-positive approximations of insulin resistance. RESULTS—Fasting insulin was significantly correlated with HOMA (r = 0.99), QUICKI (r = 0.79), FGIR (r = −0.62), and (ln fasting insulin + ln triglycerides) (r = 0.88). Correlations of the surrogates with MLBM were significantly lower than those with M for the total cohort and ≥85th percentile group. In general, correlations in the ≥85th percentile group were higher than those in the <85th percentile group. Correlations with MLBM and MLBM/ln SSI decreased in the total cohort and ≥85th percentile group from age 13 to 15. ROC curves showed only a modest capability to separate true- from false-positive values. CONCLUSIONS—Surrogate measures are only modestly correlated with the clamp measures of insulin sensitivity and do not offer any advantage over fasting insulin. In general, lower correlations are seen with MLBM than with M and with thinner than with heavier individuals.
Embryo donation: attitudes toward donation procedures and factors predicting willingness to donate.

BACKGROUND The aim of the study was to assess infertile couples' attitudes toward the procedures of embryo donation (ED) and to identify factors predicting interest in donation. METHODS Fifty-one couples who had received IVF treatment and had subsequently had embryos cryopreserved for >3 years were located and sent written information about the procedures for ED and possible implications of donation. A total of 49 couples agreed to participate in the study with 36 women and 31 men subsequently returning questionnaires describing their reasons for not claiming unused embryos and attitudes towards ED. RESULTS Patients were supportive of donor screening procedures, but less comfortable sharing non-identifying information. Comfort levels declined as information became increasingly personal. Support for unconditional (i.e. the donation of embryos without conditions attached) and conditional (i.e. where couples could limit the donation of their embryos to persons/couples according to their preferences) models of donation was highly polarized and a substantial minority expressed strong opposition to each model. Willingness to donate was associated with greater comfort about disclosing personal information, a desire to know the outcome of donation and willingness to have future contact with a child, but not with current family size. CONCLUSIONS Comfort in sharing information with a recipient couple is more important than acceptance of screening procedures, or attainment of family size goals in predicting willingness to donate embryos. Offering the option of conditional donation could increase the acceptability of ED for some patients.
One world, one psychology: ‘Relevance’ and ethnopsychology

Intellectual and political separatism have propagated two ideas deeply damaging to psychology in the developing countries, and in Africa in particular. One is that the working class of the developing countries — the poor, the ill-educated, and the rural — inhabit a third world that is at a lower evolutionary level than the glittering first world of psychologists and other professionals. The second is that until an indigenous third world (or African) psychology has been developed, psychology and its practitioners will remain irrelevant to the people and problems of the developing countries. In this article the author argues that both the world and psychology are unitary, and that this one psychology is indeed relevant to the developing countries, and that psychology's curriculum in these settings can be enriched not by ‘relevance’, but by human welfare applications derived from psychology as it now exists.
Primary focal dystonia: evidence for distinct neuropsychiatric and personality profiles

Background: Primary focal dystonia (PFD) is characterised by motor symptoms. Frequent co-occurrence of abnormal mental conditions has been mentioned for decades but is less well defined. In this study, prevalence rates of psychiatric disorders, personality disorders and traits in a large cohort of patients with PFD were evaluated. Methods: Prevalence rates of clinical psychiatric diagnoses in 86 PFD patients were compared with a population based sample (n = 3943) using a multiple regression approach. Furthermore, participants were evaluated for personality traits with the 5 Factor Personality Inventory. Results: Lifetime prevalence for any psychiatric or personality disorder was 70.9%. More specifically, axis I disorders occurred at a 4.5-fold increased chance. Highest odds ratios were found for social phobia (OR 21.6), agoraphobia (OR 16.7) and panic disorder (OR 11.5). Furthermore, an increased prevalence rate of 32.6% for anxious personality disorders comprising obsessive–compulsive (22.1%) and avoidant personality disorders (16.3%) were found. Except for social phobia, psychiatric disorders manifested prior to the occurrence of dystonia symptoms. In the self-rating of personality traits, PFD patients demonstrated pronounced agreeableness, conscientiousness and reduced openness. Conclusions: Patients with PFD show distinct neuropsychiatric and personality profiles of the anxiety spectrum. PFD should therefore be viewed as a neuropsychiatric disorder rather than a pure movement disorder.
Motion artifact suppression in MRI using k-Space overlap processing

Starting from the general assumption of rigid body motion, we consider the case when the acquisition of the k-space is in the form of bands of finite number of lines arranged in a rectilinear fashion to cover the k-space area of interest. We consider cases with an averaging factor of at least 2. Instead of acquiring a full k-space of each image and then average the result, we develop a new acquisition strategy based on acquiring the k-space in consecutive overlapped bands. In case of no motion, this overlap can be used as the second acquisition. On the other hand, when motion is encountered, such overlap can be used to substantially reduce motion artifacts in the resultant image. This is achieved by utilizing the overlap area to estimate the motion, which is then taken into consideration in image reconstruction. We demonstrate the success of this approach using both numerical simulations as well as real data acquired from a human volunteer. The new method has the potential for practical applications to make more efficient use of MRI scanners and making the scan time lower allowing for more comfort to the patient.
Fully Discrete Finite Element Approximations of the Navier-Stokes-Cahn-Hilliard Diffuse Interface Model for Two-Phase Fluid Flows

This paper develops and analyzes some fully discrete finite element methods for a parabolic system consisting of the Navier--Stokes equations and the Cahn--Hilliard equation, which arises as a diffuse interface model for the flow of two immiscible and incompressible fluids. In the model the two sets of equations are coupled through an extra phase induced stress term in the Navier--Stokes equations and a fluid induced transport term in the Cahn--Hilliard equation. Fully discrete mixed finite element methods are proposed for approximating the coupled system, it is shown that the proposed numerical methods satisfy a mass conservation law, and a discrete energy law which is analogous to the basic energy law for the phase field model. The convergence of the numerical solutions to the solutions of the phase field model and its sharp interface limit is established by utilizing the discrete energy law. As a by-product, the convergence result also provides a constructive proof of the existence of weak solutions to the Navier--Stokes-Cahn--Hilliard phase field model. Numerical experiments are also presented to validate the theory and to show the effectiveness of the combined phase field and finite element approach.