Miracle-dz/UniFAR-FTUs huggingface dataset:
Maize endosperm-specific transcription factors O2 and PBF network the regulation of protein and starch synthesis

Significance Nutritional quality and yield are equally important considerations in crop breeding, although they sometimes appear at odds. In this work we made the discovery that these traits are linked through regulation by two transcription factors. Mutations that affect the expression of these transcription factors can improve the nutritional quality of the seed but also can reduce kernel yield and hardness. Therefore future corn-breeding programs should silence zein genes directly, not by blocking transcription factors. The maize endosperm-specific transcription factors opaque2 (O2) and prolamine-box binding factor (PBF) regulate storage protein zein genes. We show that they also control starch synthesis. The starch content in the PbfRNAi and o2 mutants was reduced by ∼5% and 11%, respectively, compared with normal genotypes. In the double-mutant PbfRNAi;o2, starch was decreased by 25%. Transcriptome analysis reveals that >1,000 genes were affected in each of the two mutants and in the double mutant; these genes were mainly enriched in sugar and protein metabolism. Pyruvate orthophosphate dikinase 1 and 2 (PPDKs) and starch synthase III (SSIII) are critical components in the starch biosynthetic enzyme complex. The expression of PPDK1, PPDK2, and SSIII and their protein levels are further reduced in the double mutants as compared with the single mutants. When the promoters of these genes were analyzed, we found a prolamine box and an O2 box that can be additively transactivated by PBF and O2. Starch synthase IIa (SSIIa, encoding another starch synthase for amylopectin) and starch branching enzyme 1 (SBEI, encoding one of the two main starch branching enzymes) are not directly regulated by PBF and O2, but their protein levels are significantly decreased in the o2 mutant and are further decreased in the double mutant, indicating that o2 and PbfRNAi may affect the levels of some other transcription factor(s) or mRNA regulatory factor(s) that in turn would affect the transcript and protein levels of SSIIa and SBEI. These findings show that three important traits—nutritional quality, calories, and yield—are linked through the same transcription factors.
Association of Sociodemographic and Perceived Environmental Factors with Public Bicycle Use among Taiwanese Urban Adults

Background: This study examined the sociodemographic and perceived environmental factors associated with public bicycle use among Taiwanese urban adults. Methods: A random-digit-dialing telephone-based cross-sectional survey was administered to Taiwanese urban adults aged 20–64 years in 2015. Data on sociodemographic variables, perceived environmental factors (for attributes identified in the International Physical Activity Questionnaire-Environmental Module), and public bicycle use were obtained from 1002 adults in three cities. Adjusted logistic regression was used. Results: After adjustment for potential confounders, the results showed that adults aged 20–29 years (odds ratio (OR) = 4.42) with a university degree or higher (OR = 2.03) were more likely to use public bicycles. In addition, adults living in Kaohsiung City were less likely to use public bicycles (OR = 0.24). Adults who saw people being active (OR = 1.76; 95% CI: 1.05–2.86) and had positive aesthetic experiences of their environment (OR = 1.69) were more likely to use public bicycles. Conclusions: Our findings suggest that seeing physically active people and positive aesthetic perceptions of the environment are key factors for developing transportation policies and intervention strategies for promoting public bicycle use among Taiwanese urban adults.
Volatile Anesthetic Action in a Computational Model of the Thalamic Reticular Nucleus

Background:Although volatile anesthetics (VAs) modulate the activity of multiple ion channels, the process whereby one or more of these effects are integrated to produce components of the general anesthetic state remains enigmatic. Computer models offer the opportunity to examine systems level effects of VA action at one or more sites. Motivated by the role of the thalamus in consciousness and sensory processing, a computational model of the thalamic reticular nucleus was used to determine the collective impact on model behavior of VA action at multiple sites. Methods:A computational model of the thalamic reticular nucleus was modified to permit VA modulation of its ion channels. Isobolographic analysis was used to determine how multiple sites interact. Results:VA modulation of either T-type Ca2+ channels or γ-aminobutyric acid type A receptors led to increased network synchrony. VA modulation of both further increased network synchronization. VA-induced decrements in Ca2+ current permitted greater impact of inhibitory currents on membrane potential, but at higher VA concentrations the decrease in Ca2+ current led to a decreased number of spikes in the burst generating the inhibitory signal. MAC-awake (the minimum alveolar concentration at which 50% of subjects will recover consciousness) concentrations of both isoflurane and halothane led to similar levels of network synchrony in the model. Conclusions:Relatively modest VA effects at both T-type Ca2+ channels and γ-aminobutyric acid type A receptors can substantially alter network behavior in a computational model of a thalamic nucleus. The similarity of network behavior at MAC-awake concentrations of different VAs is consistent with a contribution of the thalamus to VA-induced unconsciousness through action at these channels.
Polymorphisms and variants in the prion protein sequence of European moose (Alces alces), reindeer (Rangifer tarandus), roe deer (Capreolus capreolus) and fallow deer (Dama dama) in Scandinavia

The prion protein (PrP) sequence of European moose, reindeer, roe deer and fallow deer in Scandinavia has high homology to the PrP sequence of North American cervids. Variants in the European moose PrP sequence were found at amino acid position 109 as K or Q. The 109Q variant is unique in the PrP sequence of vertebrates. During the 1980s a wasting syndrome in Swedish moose, Moose Wasting Syndrome (MWS), was described. SNP analysis demonstrated a difference in the observed genotype proportions of the heterozygous Q/K and homozygous Q/Q variants in the MWS animals compared with the healthy animals. In MWS moose the allele frequencies for 109K and 109Q were 0.73 and 0.27, respectively, and for healthy animals 0.69 and 0.31. Both alleles were seen as heterozygotes and homozygotes. In reindeer, PrP sequence variation was demonstrated at codon 176 as D or N and codon 225 as S or Y. The PrP sequences in roe deer and fallow deer were identical with published GenBank sequences.
Tunable fiber Bragg gratings modeling and simulation

Thermally tunable fiber Bragg gratings (FBGs) have been widely used in optical communication systems for wavelength tuning and dispersion compensation. To simulate the FBG thermal tuning process, a mathematical thermal tuning model has been developed, a stored heat energy Bragg wavelength mathematical relationship has been defined and the thermal tuning response time calculated.
Construction of batik heritage ontology through automated mapping

The wave of ontology has spread drastically in the cultural heritage domain.The impact can be seen from the growing number of cultural heritage web information systems, available textile ontology and harmonization works with the core ontology, CIDOC CRM.The aim of this study is to provide a base for common views in automating the process of mapping between revised TMT Knowledge Model and CIDOC CRM. In this study, manual mapping was conducted to find similar or overlapping concepts which are aligned to each other in order to achieve ontology similarity.Although there are several problems encountered during mapping process, the result shows an instant view of the classes which are found to be easily mapped between both models.
Scanning Enhanced Low-Profile Broadband Phased Array With Radiator-Sharing Approach and Defected Ground Structures

In this paper, a scanning enhanced low-profile broadband phased array is presented. This array is based on the radiator-sharing approach and the defected ground structures (DGSs). In this phased array, the radiator-sharing approach has been implemented by using metasurface antenna, and the scanning range has been remarkably enhanced by reducing element spacing. An attractive behavior in broadband impedance matching has still been obtained, in spite that closely spaced feedings are adopted. Moreover, the scanning performance is considerably improved by applying meander-line slots cut from the ground plane, forming DGS. In order to validate this proposed design, a nine-element linear phased array with DGSs has been fabricated and measured. Based on the uniform magnitude and the progressive phase, the capability of wide-angle scanning can be achieved over the measured bandwidth of 23.1% (4.6–5.8 GHz). At the center frequency of 5.2 GHz, this array scans up to 50° and the realized gain varies from 14.76 to 11.85 dBi.
Frequency synthesis for high precision wideband millimeter wave radar systems using a SiGe bipolar chip

The performance of frequency synthesizers with respect to bandwidth and phase noise limits the overall performance of high precision FMCW radar systems. An essential challenge of fractional-N ramp synthesizers is to combine high reference frequency and low division ratio in the loop to minimize phase noise. For an 80GHz radar system with ultra high bandwidth of 24.5 GHz we meet this challenge with a programmable frequency divider with unrivaled high input frequency. These building blocks have been implemented on a single SiGe integrated circuit. The developed phase-locked loop (PLL) includes a reverse phase downconversion mixer driven by a fixed frequency PLL to attain constant loop gain. The phase noise of the fixed frequency PLL has been measured to be -104 dBc/Hz at 20kHz offset from the center frequency of 48 GHz, which enables a phase noise of the 80GHz radar output of -93 dBc/Hz at 20 kHz offset frequency.
Reusing OCL in a Programming Language

The Object Constraint Language (OCL) is a well-accepted ingredient in model-driven engineering and accompanying modeling languages such as UML (Unified Modeling Language) and EMF (Eclipse Modeling Framework) which support object-oriented software development. Among various possibilities, OCL offers the formulation of class invariants and operation contracts in form of preand postconditions, and side effect-free query operations. Much research has been done on OCL and various mature implementations are available for it. OCL is also used as the foundation for several modeling-specific programming and transformation languages. However, an intrusive way of embedding OCL into these language hampers us when we want to benefit from the existing achievements for OCL. In response to this shortcoming, we propose the language SOIL (Simple OCL-like Imperative Language), which we implemented in the UML and OCL modeling tool USE to amend its declarative model validation features. The expression sub-language of SOIL is identical to OCL. SOIL adds imperative constructs for programming in the domain of models. Thus by employing OCL and SOIL, it is possible to describe any operation in a declarative way and in an operational way on the modeling level without going into the details of a conventional programming language. In contrast to other similar approaches, the embedding of OCL into SOIL is done in a careful, non-intrusive way so that purity of OCL is preserved.
A SCHEME FOR NESTINGALGORITHMIC SKELETONSMohammad Hamdan ?

A scheme for arbitrary nesting of algorithmic skeletons is explained which is based on the idea of groups in MPI. The scheme is part of a semi-automatic compilation system which generates parallel code for nested HOFs. Two skeletons were developed which run in a nested mode: a binary divide and conquer and a process farm for a parallel implementation of fold and map HOFs respectively. Examples showing various cases for nesting the two skeletons are presented. The experiments were conducted on the Fujitsu AP1000 parallel machine.
3D reconstruction of the proximal femur with low-dose digital stereoradiography

Objective: Accurate three-dimensional (3D) geometry of the proximal femur may be helpful for fracture risk evaluation, as well as for planning and assisting surgical procedures. The purpose of this study was to apply and validate a stereoradiographic 3D reconstruction method on the proximal femur from radiographic contours identified on bi-planar radiographs. Materials and Methods: Twenty-five excised non-pathologic proximal femurs were investigated using a low-dose digital radiographic device. Three-dimensional personalized models were reconstructed using the Non-Stereo Corresponding Contours (NSCC) algorithm. Three-dimensional CT-scan reconstructions were defined as geometric references for the comparison protocol, in order to assess the accuracy and reproducibility of the personalized 3D stereoradiographic reconstructions. In addition, the reliability of a set of 3D parameters obtained from stereoradiographic models was evaluated. Results: This study demonstrated the validity of the NSCC method when applied to the proximal femur, with good results for accuracy (mean error = 0.7 mm) and reproducibility (Wilcoxon test: p > 0.28). Moreover, a precision study for the set of 3D parameters yielded a coefficient of variation lower than 5%. Conclusions: Once this approach has been validated in vivo, it should find multiple applications in therapeutic fields (e.g., for surgical planning, computer assisted surgery, etc.), as well as in diagnostic contexts (e.g., equilibrium studies or osteoporosis fracture risk assessment).
Wherefore heart thou? Embryonic origins of cardiogenic mesoderm

The developing heart in avian embryos has been examined extensively over the past several decades using classic embryologic and, more recently, molecular and genetic approaches. Still, conflicting reports arise as to the location and regulation of early heart progenitors in the embryo. In addition, a new source of cardiomyocytes has been identified recently that contributes to the outflow tract after the heart initially forms. The focus of this review is the examination of the tissue interactions, signaling molecules, and gene regulatory mechanisms that, together, control heart formation from primary and secondary heart forming fields of the embryo. Early studies of the induction and regulation of the secondary heart field indicate that at least some of the events of primary cardiomyogenesis are recapitulated when the conotruncal myocardium is recruited into the heart. The consideration of classic embryologic studies of the heart forming fields in terms of modern molecular and genetic tools provides reinforcing evidence for the location of cardiac progenitors in the embryo. The accurate definition of early cardiac regulatory events provides a necessary foundation for the generation of new therapeutic sources of cardiomyocytes. © 2002 Wiley‐Liss, Inc.
Prolactinoma as the first manifestation of Gardner's syndrome

Familial adenomatous polyposis (FAP) is an inherited condition causing numerous adenomatous colorectal polyps and a markedly elevated risk of colon cancer. FAP may be associated with various extracolonic manifestations such as desmoid fibromatosis and osteomas (termed Gardner's syndrome) and brain tumors, usually medulloblastoma or glioma [termed Brain Tumor Polyposis (BTP) syndrome type 2]. We describe a pediatric patient who initially presented with prolactinoma and later was found to have Gardner's syndrome. A germline mutation of the APC (adenomatous polyposis coli) gene was identified. Our case illustrates the association between prolactinoma and FAP, which may represent a rare subtype of Gardner's and BTP syndromes. Pediatr Blood Cancer 2008;50:409–412. © 2006 Wiley‐Liss, Inc.
'Langsam begannen sich meine Zweifel aufzuweichen...': Mechanismen der Neutralisation von Unrechtsbewusstsein in korruptiven Beziehungen

„Gradually my Doubts Began to Disappear. “ – Mechanisms of Neutralization in Corruptive Relationships Prosecutors agree that corruptive offenders are only weakly aware of wrongdoing, although their social and occupational status would lead one to expect a sufficient familiarity concerning the relevant legal norms. How should we interpret these findings? How can 24 Soziale Probleme, 11. Jg. , 2000 we explain the reduced awareness of wrongdoing with regard to corruptive action? To answer this question, I analyse the examination records of accused corruptors in light of the theory of neutralization originally formulated by Sykes and Matza. However, the search for justifications that „precede deviant behaviour and make deviant behaviour possible“ (Sykes/Matza) turns out to be problematic. Obviously, the statements of the ‘respondents’ are strongly motivated by the wish to exonerate themselves and to escape punishment. For this reason, I first determine the prevailing justification patterns of corruptive actors. In a second step, throughout this veil of subsequent rationalization, I identify some conditions and mechanisms that might explain the reduced awareness of wrongdoing in cases of corruption.
The Human H2A and H2B Histone Gene Complement

Abstract Sequences and expression patterns of newly isolated human histone H2A and H2B genes and the respective proteins were compared with previously isolated human H2A and H2B genes and proteins. Altogether, 15 human H2A genes and 17 human H2B genes have been identified. 14 of these are organized as H2A/H2B gene pairs, while one H2A gene and three H2B genes are solitary genes. Two H2A genes and two H2B genes turned out to be pseudogenes. The 13 H2A genes code for at least 6 different amino acid sequences, and the 15 H2B genes encode 11 different H2B isoforms. Each H2A/H2B gene pair is controlled by a divergent promoter spanning 300 to 330 nucleotides between the coding regions of the two genes. The highly conserved divergent H2A/H2B promoters can be classified in two groups based on the patterns of consensus sequence elements. Group I promoters contain a TATA box for each gene, two Oct-1 factor binding sites, and three CCAAT boxes. Group II promoters contain the same elements as group I promoters and an additional CCAAT box, a binding motif for E2F and adjacent a highly conserved octanucleotide (CACAGCTT) that has not been described so far. Five of the 6 gene pairs and 4 solitary genes with group I promoters are localized in the large histone gene cluster at 6p21.3–6p22, and one gene pair is located at 1q21. All group II promoter associated genes are contained within the histone gene subcluster at D6S105, which is located at a distance of about 2 Mb from the major subcluster at 6p21.3–6p22 containing histone genes with group I promoters. Almost all group II H2A genes encode identical amino acid sequences, whereas group I H2A gene products vary at several positions. Using human cell lines, we have analyzed the expression patterns of functional human H2A/H2B gene pairs organized within the two histone gene clusters on the short arm of chromosome 6. The genes show varying expression patterns in different tumor cell lines.
Therapeutic relevance of the protein phosphatase 2A in cancer

Chromosomal Instability (CIN) is regarded as a unifying feature of heterogeneous tumor populations, driving intratumoral heterogeneity. Polo-Like Kinase 1 (PLK1), a serine-threonine kinase that is often overexpressed across multiple tumor types, is one of the key regulators of CIN and is considered as a potential therapeutic target. However, targeting PLK1 has remained a challenge due to the off-target effects caused by the inhibition of other members of the polo-like family. Here we use synthetic dosage lethality (SDL), where the overexpression of PLK1 is lethal only when another, normally non-lethal, mutation or deletion is present. Rather than directly inhibiting PLK1, we found that inhibition of PP2A causes selective lethality to PLK1-overexpressing breast, pancreatic, ovarian, glioblastoma, and prostate cancer cells. As PP2A is widely regarded as a tumor suppressor, we resorted to gene expression datasets from cancer patients to functionally dissect its therapeutic relevance. We identified two major classes of PP2A subunits that negatively correlated with each other. Interestingly, most mitotic regulators, including PLK1, exhibited SDL interactions with only one class of PP2A subunits (PPP2R1A, PPP2R2D, PPP2R3B, PPP2R5B and PPP2R5D). Validation studies and other functional cell-based assays showed that inhibition of PPP2R5D affects both levels of phospho-Rb as well as sister chromatid cohesion in PLK1-overexpressing cells. Finally, analysis of clinical data revealed that patients with high expression of mitotic regulators and low expression of Class I subunits of PP2A improved survival. Overall, these observations point to a context-dependent role of PP2A that warrants further exploration for therapeutic benefits.
Integrating complementary therapies into community mental health practice: an exploration.

OBJECTIVES To (1) describe the integration of massage and energy-based therapies with psychotherapy in a community mental health center, (2) to present qualitative feedback on the service, and (3) to present pilot data from a sample of long-term clients with persistent mental health concerns. DESIGN A noncontrolled pilot study was conducted using interview data before and self-report instruments after completing a brief program of complementary therapy accompanying ongoing psychotherapy. SETTINGS/LOCATION The program took place at a comprehensive community mental health center in southern Maine and in the private offices of massage therapists and energy healing practitioners who contracted with the program. SUBJECTS Subjects were 20 women and 5 men, with mean age of 42 years and a mean history of 7.4 years of mental health treatment. All had histories that included trauma, 10 of which involved sexual abuse. The Diagnostic and Statistical Manual of Mental Disorders IV Axis I diagnoses were PTSD (10), major depression (nine), anxiety disorder (three), and dual diagnosis (three). INTERVENTIONS Clients receiving ongoing psychotherapy were assigned to one modality of complementary therapy based on clinical judgment, availability of practitioners, and client interest. Modalities used were massage, acupuncture, Reiki, and Healing Touch. The mean number of sessions was five. OUTCOME MEASURES Clients completed an investigator-generated instrument with Likert-scaled ratings of satisfaction and perceived changes in four dimensions of trauma recovery: perceived interpersonal safety, interpersonal boundary setting, bodily sensation, and bodily shame. RESULTS Clients reported high levels of satisfaction with the service and significant levels of perceived (self-rated) change on each outcome measure. Qualitative results included enhanced psychotherapeutic outcomes reported by mental health clinicians. CONCLUSIONS The integration of complementary therapies into community mental health practice may hold promise of enhancing mental health outcomes and improving quality of life for long-term users of mental health services.