Miracle-dz/UniFAR-FTUs huggingface dataset:
Models of convergent extension during morphogenesis

Convergent extension (CE) is a fundamental and conserved collective cell movement that forms elongated tissues during embryonic development. Thus far, studies have demonstrated two different mechanistic models of collective cell movements during CE. The first, termed the crawling mode, was discovered in the process of notochord formation in Xenopus laevis embryos, and has been the established model of CE for decades. The second model, known as the contraction mode, was originally reported in studies of germband extension in Drosophila melanogaster embryos and was recently demonstrated to be a conserved mechanism of CE among tissues and stages of development across species. This review summarizes the two modes of CE by focusing on the differences in cytoskeletal behaviors and relative expression of cell adhesion molecules. The upstream molecules regulating these machineries are also discussed. There are abundant studies of notochord formation in X. laevis embryos, as this was one of the pioneering model systems in this field. Therefore, the present review discusses these findings as an approach to the fundamental biological question of collective cell regulation. WIREs Dev Biol 2018, 7:e293. doi: 10.1002/wdev.293
Constructive tool for orbital stabilization of underactuated nonlinear systems: virtual constraints approach

We present a constructive tool for generation and orbital stabilization of periodic solutions for underactuated nonlinear systems. Our method can be applied to any mechanical system with a number of independent actuators smaller than the number of degrees of freedom by one. The synthesized feedback control law is nonlinear and time-dependent. It is derived from a feedback structure that explicitly uses the general or full integral of the systems zero dynamics. The control law generates a periodic solution and makes it exponentially orbitally stable.
Modular compilers based on monad transformers

The monadic style of language specification has the advantages of modularity and extensibility: it is simple to add or change features in an interpreter to reflect modifications in the source language. It has proven difficult to extend the method to compilation. We demonstrate that by introducing machine-like stores (code and data) into the monadic semantics and then partially evaluating the resulting semantic expressions, we can achieve many of the same advantages for a compiler as for an interpreter. A number of language constructs and features are compiled: expressions, CBV and CBN evaluation of /spl lambda/ expressions, dynamic scoping, and various imperative features. The treatment of recursive procedures is outlined as well. The resulting method allows compilers to be constructed in a mix and match fashion just as in a monad structured interpreter.
A parallel algorithm for static slicing of concurrent programs

Slicing of concurrent programs is a compute‐intensive task. To speed up the slicing process, we have developed a parallel algorithm. For this purpose we used the concurrent control flow graph (CCFG) as the intermediate representation. We used a network of communicating processes to develop our parallel algorithm. We have implemented our parallel algorithm and the experimental results appear promising. Copyright © 2004 John Wiley & Sons, Ltd.
Ketoconazole-Associated Preferential Increase in Dopamine D2 Receptor Occupancy in Striatum Compared to Pituitary In Vivo: Role for Drug Transporters?

Abstract Membrane transporters such as P-glycoprotein (P-gp) and breast cancer resistance protein (BCRP) are efflux pumps that remove drugs from the brain back to the peripheral blood compartment, serving as a functional component of the blood-brain barrier (BBB). We report here that coadministration of the P-gp and BCRP inhibitor ketoconazole with risperidone may preferentially increase D2 receptor occupancy in the striatum compared to pituitary. Four male patients with schizophrenia or schizoaffective disorder who had received at least 4 prior injections of the long-acting risperidone at a stable dose of 25 to 50 mg participated in this positron emission tomography study. Multiple-dose ketoconazole coadministration reduced the P-gp activity as shown by fexofenadine oral challenge. Importantly, we found a strong statistical trend in this sample of 4 subjects who consistently showed a decrease in striatal fluorine 18 (18F)-fallypride binding (an indication of increased D2 receptor occupancy) after ketoconazole coadministration (P = 0.057), whereas the pituitary (a region that lies outside the BBB) 18F-fallypride binding did not change (P = 0.99). These observations warrant further research with selective drug transporter inhibitors. We suggest that in neuroimaging studies, the pituitary drug occupancy can serve as a useful new “positive control” to evaluate whether drug occupancy is preferentially increased in brain regions that fall inside the BBB after cotreatment with P-gp and BCRP inhibitors. This is a noteworthy study design consideration regarding the future clinical testing of novel adjunct interventions aimed at modulating membrane transporter function at the BBB, with the goal of augmenting drug access into the brain compartment, particularly in treatment-resistant psychiatric illness.
Serum gastrin in patients with cirrhosis of the liver.

Serum gastrin concentrations were examined following atropinization in 30 patients with liver cirrhosis and in 30 control subjects either basally or after oral glycine load. Basal gastrinaemia and post-glycine serum increases above basal levels were found to be significantly greater in the cirrhotic group (48.56 ± 9.97 and 72.85 ± 10.88 pg/ml, respectively) than in the control group (32.36 ± 6.67 and 53.43 ± 9.67 pg/ml, respectively) (ρ
Prognostic Significance of Exercise-induced Right Ventricular Dysfunction in Asymptomatic Degenerative Mitral Regurgitation

Background— The role of exercise-induced pulmonary hypertension in decision making regarding surgical timing for asymptomatic chronic mitral regurgitation is controversial. We reasoned that the exercise-induced pulmonary hypertension response could not be interpreted without knowledge of right ventricular (RV) function. The aim of this study was to assess the role of RV measures at rest and during exercise as predictors of prognosis in asymptomatic mitral regurgitation. Methods and Results— Comprehensive resting and exercise echocardiography was performed in 196 consecutive patients (56±13 years; 64% male) with isolated moderate to severe mitral regurgitation (effective regurgitant orifice area, 38±18 mm2) and preserved left ventricular function in whom initial management was expectant. Left ventricular and RV longitudinal strain were analyzed at rest using velocity vector imaging. Tricuspid annular plane systolic excursion and systolic pulmonary arterial pressure were measured at rest and during exercise. Valve surgery was performed in 88 patients (45%) over 27±15 months. After adjustment for age and sex in a Cox proportional-hazards model, exercise tricuspid annular plane systolic excursion (hazard ratio, 0.26; P<0.001), was associated with valve surgery-free survival, independent of resting left ventricular strain (hazard ratio, 1.09; P=0.027), exercise systolic pulmonary arterial pressure (hazard ratio, 1.03; P<0.001), and resting RV strain (hazard ratio, 1.10; P=0.004). In sequential Cox models, a model based on clinical data and left ventricular strain (&khgr;2, 15.9) was improved by RV strain and RV chamber size (&khgr;2, 28.8; P=0.003) and exercise systolic pulmonary arterial pressure (&khgr;2, 40.1; P=0.002) and further increased by exercise tricuspid annular plane systolic excursion (&khgr;2, 52.2; P=0.002). Conclusions— Exercise-induced RV dysfunction provides important incremental prognostic value in the management of asymptomatic mitral regurgitation.
Intelligent Local Face Recognition

Our faces are complex objects with features that can vary over time. However, we humans have a natural ability to recognize faces and identify persons in a glance. Of course, our natural recognition ability extends beyond face recognition, where we are equally able to quickly recognize patterns, sounds or smells. Unfortunately, this natural ability does not exist in machines, thus the need to simulate recognition artificially in our attempts to create intelligent autonomous machines. Intelligent systems are being increasingly developed aiming to simulate our perception of various inputs (patterns) such as images, sounds.etc. Biometrics, in general, and facial recognition in particular are examples of popular applications for artificial intelligent systems. Face recognition by machines can be invaluable and has various important applications in real life, such as, electronic and physical access control, national defence and international security. Simulating our face recognition natural ability in machines is a difficult task, but not impossible. Throughout our life time, many faces are seen and stored naturally in our memories forming a kind of database. Machine recognition of faces requires also a database which is usually built using facial images, where sometimes different face images of a one person are included to account for variations in facial features. The development of an intelligent face recognition system requires providing sufficient information and meaningful data during machine learning of a face. This chapter presents a brief review of known face recognition methods such as Principal Component Analysis (PCA) (Turk & Pentland, 1991), Linear Discriminant Analysis (LDA) (Belhumeur et al., 1997) and Locality Preserving Projections (LPP) (He et al., 2005), in addition to intelligent face recognition systems that use neural networks such as (Khashman, 2006) and (Khashman, 2007). There are many works emerging every year suggesting different methods for face recognition (Delac & Grgic, 2007); these methods are mostly appearance-based or feature-based methods that search for certain global or local representation of a face. The chapter will also provide a detailed case study on intelligent local face recognition, where a neural network is used to identify a person upon presenting his/her face image. Local pattern averaging is used for face image preprocessing prior to training or testing the neural network. Averaging is a simple but efficient method that creates "fuzzy" patterns as compared to multiple "crisp" patterns, which provides the neural network with meaningful learning while reducing computational expense. In previous work (Khashman, 2007) an intelligent global face recognition system which considers a person’s face and its background was presented, and suggestions were made O pe n A cc es s D at ab as e w w w . in te ch w eb . o rg
Secular change in muscular strength of indigenous rural youth 6–17 years in Oaxaca, southern Mexico: 1968–2000

Abstract Objective: The study compared the grip strength of indigenous school youth 6–17 years of age in Oaxaca, southern Mexico, who were surveyed in 1968, 1978 and 2000. Methods: Grip strength (Smedley/Stoelting) was measured to 0.5 kg in 1280 children and adolescent, 621 males and 659 females, in the three surveys. Height and weight were also measured. Strength of the right and left hands was summed to provide a general estimate of muscular strength. Summed grip strength was also expressed per unit body mass (kg/kg) and height (kg/m). Subjects were classified into four age groups: 6–8 years (childhood), 9–11 years (transition in adolescence), 12–14 years (early adolescence) and 15–17 years (later adolescence). Children 6–14 years were surveyed in 1968, 1978 and 2000 while adolescents 15–17 years were surveyed in 1978 and 2000. Sex-specific MANCOVAs were used for comparisons among years within age groups. Results: Changes in grip strength between 1968 and 1978 among children 6–14 years were small and significant only in girls. Grip strength increased, on average, between 1978 and 2000 in boys 6–17 years but only in girls 6–14 years; adolescent girls 15–17 years in 1978 were stronger than those in 2000. Secular gains in muscular strength were generally proportional to secular gains in body weight and height. Conclusion: The data demonstrate secular changes in muscular strength in indigenous rural youth in a community in the process of transition from subsistence level agriculture to an economy is less dependent upon agriculture.
Increasing Sucrose Uptake Capacity of Wheat Grains Stimulates Storage Protein Synthesis1[W]

Increasing grain sink strength by improving assimilate uptake capacity could be a promising approach toward getting higher yield. The barley (Hordeum vulgare) sucrose transporter HvSUT1 (SUT) was expressed under control of the endosperm-specific Hordein B1 promoter (HO). Compared with the wild type, transgenic HOSUT grains take up more sucrose (Suc) in vitro, showing that the transgene is functional. Grain Suc levels are not altered, indicating that Suc fluxes are influenced rather than steady-state levels. HOSUT grains have increased percentages of total nitrogen and prolamins, which is reflected in increased levels of phenylalanine, tyrosine, tryptophan, isoleucine, and leucine at late grain development. Transcript profiling indicates specific stimulation of prolamin gene expression at the onset of storage phase. Changes in gene expression and metabolite levels related to carbon metabolism and amino acid biosynthesis suggest deregulated carbon-nitrogen balance, which together indicate carbon sufficiency and relative depletion of nitrogen. Genes, deregulated together with prolamin genes, might represent candidates, which respond positively to assimilate supply and are related to sugar-starch metabolism, cytokinin and brassinosteroid functions, cell proliferation, and sugar/abscisic acid signaling. Genes showing inverse expression patterns represent potential negative regulators. It is concluded that HvSUT1 overexpression increases grain protein content but also deregulates the metabolic status of wheat (Triticum aestivum) grains, accompanied by up-regulated gene expression of positive and negative regulators related to sugar signaling and assimilate supply. In HOSUT grains, alternating stimulation of positive and negative regulators causes oscillatory patterns of gene expression and highlights the capacity and great flexibility to adjust wheat grain storage metabolism in response to metabolic alterations.
Abnormal collagen fibrils in tendons of biglycan/fibromodulin‐deficient mice lead to gait impairment, ectopic ossification, and osteoarthritis

Small leucine‐rich proteoglycans (SLRPs) regulate extracellular matrix organization, a process essential in development, tissue repair, and metastasis. In vivo interactions of biglycan and fibromodulin, two SLRPs highly expressed in tendons and bones, were investigated by generating biglycan/fibromodulin double‐deficient mice. Here we show that collagen fibrils in tendons from mice deficient in biglycan and/or fibromodulin are structurally and mechanically altered resulting in unstable joints. As a result, the mice develop successively and progressively 1) gait impairment, 2) ectopic tendon ossification, and 3) severe premature osteoarthritis. Forced use of the joints increases ectopic ossification and osteoarthritis in the double‐deficient mice, further indicating that structurally weak tendons cause the phenotype. The study shows that mutations in SLRPs may predispose to osteoarthritis and offers a valuable and unique animal model for spontaneous osteoarthritis characterized by early onset and a rapid progression of the disease
Economic Incentives and the Fertility-Sex Ratio Trade-off S Anukriti

Demographic change in several Asian countries has displayed two key trends in the recent decades: fertility decline and an increase in the male-female sex ratio at birth. Figure 1 plots these trends for India and China, the two most populous countries in the world. While their total fertility rates have decreased from close to 6 births per woman in 1960 to 2.6 and 1.6 births in 2011, the sex ratios at birth in India (2006-08) and China (2010) have risen to 1.11 and 1.18, respectively. Relative to the “natural” sex ratio at birth (≈ 1.05), these numbers reflect a substantial demographic imbalance.
Dopamine agonist‐induced antecollis in Parkinson's disease

Few cases of dopamine agonist‐induced antecollis in Parkinson's disease (PD) have been reported. Literature review of 16 PD patients including our 3 cases with dopamine agonist‐induced antecollis showed predominance of (1) Japanese, (2) women, and (3) Hoehn‐Yahr stage of ≥3. We experienced three Japanese PD patients who subacutely exhibited antecollis following increased dopamine agonist dose that improved just after withdrawal of the agonist. One patient developed antecollis during increasing pramipexole dose in combination with cabergoline. Antecollis in another patient appeared during increasing pramipexole dose; it worsened after substituting pergolide for pramipexole, but improved after withdrawal of pergolide. Our cases indicate that there is no specific dopamine agonist causing antecollis, and it is possibly caused by a number of single dopamine agonists or a combination of them. Dopamine agonist‐induced antecollis should be considered when encountering antecollis in PD patients being treated with dopamine agonists and withdrawal of the agonist can improve symptoms. © 2009 Movement Disorder Society
Should companies bid on their own brand in sponsored search?

Sponsored Search allows companies to place text advertisements for selected keywords on Search Engine Results Pages (SERPs). The objective of the present research is to determine whether and under what circumstances it makes sense, in economic terms, for brand owners to pay for sponsored search ads for their brand keywords. This issue is the subject of a heated debate in business practice, especially when the company is already placed prominently in the organic search results. In this paper we describe and apply a non-reactive method that is based on an A/B-test. It was employed in a case study of a European Internet pharmacy. The results of this study indicate that the use of sponsored search advertising for the own brand name enables advertisers to generate more visitors (>10%)s, resulting in higher sales volumes at relatively low advertising costs even when the company is already listed in first position in the organic part of the respective SERP.
The apolipoprotein E ε4 allele selectively increases the risk of frontotemporal lobar degeneration in males

Objective: To determine whether polymorphic variations in the apolipoprotein E gene (APOE) are associated with increased risk of frontotemporal lobar degeneration (FTLD) when mutation in tau gene is absent. Methods: The APOE gene was genotyped by polymerase chain reaction from DNA routinely extracted from blood or brain tissues. The APOE ε4 allele frequency in 198 patients with FTLD not associated with mutations in tau gene was compared with that of a control group of 756 normal individuals drawn from the same geographical region. Analyses were done according to clinical subtype or sex. Results: The APOE ε4 allele frequency (19.4%) was increased (p = 0.01) in FTLD v the whole control group (14.1%), while the APOE ε2 allele frequency in FTLD (6.5%) was slightly lower than in controls (8.0%) (NS). The APOE ε4 allele frequency in men with FTLD (22.3%) was greater (p = 0.002) than in male controls (12.3%); the frequency in women (16.3%) was similar to that in female controls (14.8%) (NS). The APOE ε2 allele frequency in men with FTLD was 4.9% while in male controls it was 9.5% (p = 0.06), but there was no difference in women (7.5% v 7.9%, NS). Neither the APOE ε2 nor APOE ε4 allele frequency varied significantly between any of the clinical subtypes. Conclusions: In FTLD not associated with mutations in tau gene, possession of APOE ε4 allele in men roughly doubles the chances of developing disease, whereas this has no impact upon disease risk in women.
Isolation of Mutants of the Nitrogen-Fixing Actinomycete Frankia

Frankia is a nitrogen (N)-fixing multicellular actinomycete which establishes root-nodule symbiosis with actinorhizal plants. Several aspects of Frankia N fixation and symbiosis are distinct, but genes involved in the specific features are largely unknown because of the lack of an efficient mutant screening method. In this study, we isolated mutants of Frankia sp. strain CcI3 using hyphae fragments mutagenized by chemical mutagens. Firstly, we isolated uracil auxotrophs as gain-of-function mutants resistant to 5-fluoroorotic acid (5-FOA). We obtained seven 5-FOA resistant mutants, all of which required uracil for growth. Five strains carried a frame shift mutation in orotidine-5′-phosphate decarboxylase gene and two carried an amino acid substitution in the orotate phosphoribosyltransferase gene. Secondly, we isolated mutants showing loss-of-function phenotypes. Mutagenized hyphae were fragmented by ultrasound and allowed to multiply at their tips. Hyphae were fragmented again and short fragments were enriched by filtration through 5 μm pores filters. Next-generation and Sanger sequencing revealed that colonies formed from the short hyphae fragments consisted of cells with an identical genotype. From the mutagenized colony population, we isolated three pigmentation mutants and a mutant with reduced N-fixation activity. These results indicate that our procedure is useful for the isolation of loss-of-function mutants using hyphae of Frankia.
Measurement of fault latency in a digital avionic mini processor, part 2

The results of fault injection experiments utilizing a gate-level emulation of the central processor unit of the Bendix BDX-930 digital computer are described. Several earlier programs were reprogrammed, expanding the instruction set to capitalize on the full power of the BDX-930 computer. As a final demonstration of fault coverage an extensive, 3-axis, high performance flght control computation was added. The stages in the development of a CPU self-test program emphasizing the relationship between fault coverage, speed, and quantity of instructions were demonstrated.
Reliability of renal length measurements made with ultrasound compared with measurements from helical CT multiplanar reformat images.

OBJECTIVE The purpose of this article is to determine the reliability of sonographic renal length measurements compared with measurements obtained from helical CT multiplanar reformat images and compared with standard renal growth curves. MATERIALS AND METHODS A retrospective review was performed of 76 subjects who underwent both renal ultrasound and abdominal CT within 2 weeks of one another. Renal lengths were measured using oblique coronal reformat images of helically acquired CT data by two observers on two occasions. Intraobserver and interobserver error for these measurements were calculated. Ultrasound renal length measurements were compared with CT measurements. Measurement variation was compared with standard renal growth curves. RESULTS The mean (± SD) of the absolute value of interobserver error of CT measurements was 0.9 ± 0.8 mm. Compared with CT, individual ultrasound measurements underestimated renal length by 1.5 ± 5.6 mm on average, with a 95% CI of -12.5 to 9.5 mm. When the maximum of three ultrasound renal length measurements was used, the SD was 4.7 mm, with a 95% CI of -8.2 to 10.1 mm of the reported renal length. This corresponds to greater or less than 3.3 years of normal renal growth. CONCLUSION Lack of renal growth can be asserted only when renal length falls below the growth curve, taking into account the corresponding measurement error limits, which we found to be greater or less than 9.3 mm. If the follow-up measurement falls within these limits, one should not infer lack of appropriate renal growth, even if the renal length measurement decreases or remains unchanged for up to 3 years.