Miracle-dz/UniFAR-FTUs huggingface dataset:
Ectopic Expression of miR 160 Results in Auxin Hypersensitivity , Cytokinin Hyposensitivity , and Inhibition of Symbiotic Nodule Development in Soybean 1 [ W ] [ OPEN ]

Symbiotic root nodules in leguminous plants result from interaction between the plant and nitrogen-fixing rhizobia bacteria. There are two major types of legume nodules, determinate and indeterminate. Determinate nodules do not have a persistent meristem, while indeterminate nodules have a persistent meristem. Auxin is thought to play a role in the development of both these types of nodules. However, inhibition of rootward auxin transport at the site of nodule initiation is crucial for the development of indeterminate nodules but not determinate nodules. Using the synthetic auxin-responsive DR5 promoter in soybean (Glycine max), we show that there is relatively low auxin activity during determinate nodule initiation and that it is restricted to the nodule periphery subsequently during development. To examine if and what role auxin plays in determinate nodule development, we generated soybean composite plants with altered sensitivity to auxin. We overexpressed microRNA393 to silence the auxin receptor gene family, and these roots were hyposensitive to auxin. These roots nodulated normally, suggesting that only minimal/reduced auxin signaling is required for determinate nodule development. We overexpressed microRNA160 to silence a set of repressor auxin response factor transcription factors, and these roots were hypersensitive to auxin. These roots were not impaired in epidermal responses to rhizobia but had significantly reduced nodule primordium formation, suggesting that auxin hypersensitivity inhibits nodule development. These roots were also hyposensitive to cytokinin and had attenuated expression of key nodulation-associated transcription factors known to be regulated by cytokinin. We propose a regulatory feedback loop involving auxin and cytokinin during nodulation.
Mutation trend of hemagglutinin of influenza A virus: a review from a computational mutation viewpoint

AbstractSince 1999 we have developed two computational mutation approaches to analyze the protein primary structure whose methodology and implications were reviewed in 2002. Our first approach is the calculation of predictable and unpredictable portions of amino-acid pairs in a protein, and the second is the calculation of amino-acid distribution rank in a protein. Both approaches provide quantitative measures to present a protein, which we have used to study a number of proteins with numerous mutations such as p53 proteins. More recently, we focussed our efforts on analyzing the proteins mutating frequently over time such as hemagglutinins of influenza A viruses. In this review we summarise our findings and their implications for hemagglutinin mutations in combination with some newly available data. Our approaches throw light on the true nature of genetic heterogeneity of influenza virus hemagglutinins; that is, the protein variability is highly relevant to its amino-acid construction. Using these approaches, we can monitor new mutations from influenza virus hemagglutinins and may predict their mutations in the future.
Determinants of quaternary association in legume lectins

It is well known that the sequence of amino acids in proteins code for its tertiary structure. It is also known that there exists a relationship between sequence and the quaternary structure of proteins. The question addressed here is whether the nature of quaternary association can be predicted from the sequence, similar to the three‐dimensional structure prediction from the sequence. The class of proteins called legume lectins is an interesting model system to investigate this problem, because they have very high sequence and tertiary structure homology, with diverse forms of quaternary association. Hence, we have used legume lectins as a probe in this paper to (1) gain novel insights about the relationship between sequence and quaternary structure; (2) identify the sequence motifs that are characteristic of a given type of quaternary association; and (3) predict the quaternary association from the sequence motif.
Concentration of Energy in Corn and 10 sources of Corn DDGS Fed to Growing Pigs 1 Corn

Plant carbohydrates can be classified into three categories: 1) simple sugars and their conjugates (glucose, fructose, etc.); 2) storage reserve compounds (starch); and 3) structural carbohydrates (cellulose, hemicellulose, etc.). Simple sugars and storage compounds are primarily digested in the upper gastrointestinal tract, although not completely, while structural carbohydrates are only partially degraded by the microflora in the cecum and large intestine (Slominski, 1991). Because most of the starch is removed from corn during ethanol production, the resultant co-product, dried distillers grains with solubles (DDGS), contains concentrated levels of protein, minerals, and fiber (Spiehs et al., 2002; Pedersen et al., 2007; Anderson, 2009). With pigs being able to utilize moderate, but not high levels of fiber in the nursery (Whitney and Shurson, 2004; Weber et al., 2008) and finisher (Whitney et al., 2006) period, there is a need to increase the ability of the pig to utilize the energy associated with the structural carbohydrates contained in cornderived co-products (Muley et al., 2007). With the large amount of corn being utilized for ethanol production in the U.S., the amount of high fiber corn co-products available for animal feeds continues to increase. In order to minimize the cost associated with dietary energy and amino acids, it is essential that we develop and evaluate technologies that increase digestibility of energy and other nutrients. Use of exogenous enzymes is one of these technologies that offer promise for improving the nutritional value of high fiber corn co-products, particularly DDGS.
Conformal Infinity

The notion of conformal infinity has a long history within the research in Einstein’s theory of gravity. Today, “conformal infinity” is related with almost all other branches of research in general relativity, from quantisation procedures to abstract mathematical issues to numerical applications. This review article attempts to show how this concept gradually and inevitably evolved out of physical issues, namely the need to understand gravitational radiation and isolated systems within the theory of gravitation and how it lends itself very naturally to solve radiation problems in numerical relativity. The fundamental concept of null-infinity is introduced. Friedrich’s regular conformal field equations are presented and various initial value problems for them are discussed. Finally, it is shown that the conformal field equations provide a very powerful method within numerical relativity to study global problems such as gravitational wave propagation and detection.
Effects of Urinary and Recombinant Gonadotropins on In Vitro Maturation Outcomes of Mouse Preantral Follicles

Gonadotropins including follicle-stimulating hormone (FSH) and luteinizing hormone (LH) play a crucial role in human-assisted reproduction techniques. Despite wide use of recombinant gonadotropins in clinical practice, the efficacy of urinary gonadotropins and the dosage of LH component have not yet been elucidated. This study was designed to investigate the difference of follicle culture outcomes according to various compositions of gonadotropins during in vitro culture of mouse preantral follicles. Ovaries were obtained from the 14-day-old C57BL/6 mice, and preantral follicles were isolated and cultured in culture media supplemented with human menopausal gonadotropin (hMG) 200 mIU/mL (group 1), recombinant FSH and LH (rFSH + rLH) 200 mIU/mL each (group 2), rFSH 200 mIU/mL + rLH 100 mIU/mL (group 3), or rFSH 200 mIU/mL + rLH 20 mIU/mL (group 4). Follicle survival rate was significantly lower in group 4. Antral follicles in lower doses of LH (groups 3, 4) showed a statistically significant larger diameter and tended to have a higher antral formation rate. However, follicles in group 1 tended to have a higher oocyte maturation rate. Estradiol concentration from conditioned media from 2:1 FSH/LH (group 3) was significantly higher than those from 1:1 FSH/LH (group 2) or 10:1 FSH/LH (group 4). Half dose of rLH to rFSH facilitated upregulation of growth differentiation factor 9 (Gdf9) expression in granulosa cells when compared to 1:1 FSH/LH or 10:1 FSH/LH. Conclusively, recombinant gonadotropins provided a comparable condition to hMG, and half dose of rLH to rFSH seems to be more suitable for follicular development during in vitro culture.
Hypertrophy causes delayed conduction in human and guinea pig myocardium: accentuation during ischaemic perfusion.

OBJECTIVE The aim was to investigate why cardiac hypertrophy causes increased vulnerability to arrhythmias during myocardial ischaemia. METHODS The electrophysiological basis for this increased vulnerability was studied in isolated perfused guinea pig hearts obtained 50 and 150 d after aortic constriction, and in sham operated controls. Cellular electrophysiology, conduction, and refractory periods were examined during control perfusion and during low flow (coronary flow reduced to 10% of control) and zero flow ischaemia. ECGs in patients with left ventricular hypertrophy and in controls matched for age and heart rate were also studied. RESULTS Aortic constriction increased heart weight:body weight ratio by 33% at 50 d and by 69% at 150 d. Action potentials were unchanged in hypertrophied hearts. Significant conduction delay occurred in 150 d hypertrophied hearts [conduction time index 23(SEM 4) ms v 18(3) ms, p < 0.001; QRS width 40(1) ms v 35(1) ms, p < 0.01], but not in 50 d hypertrophied hearts. Conduction delay was also present in humans with left ventricular hypertrophy [QRS width 96(13) ms v 87(8) ms, p < 0.01]. Although the QTc interval was increased in humans, at 422(23) ms v 411(17) ms in controls, p < 0.05, this could be explained by the increased QRS duration. During ischaemia, ventricular arrhythmias tended to occur earlier in hypertrophied hearts. Hypertrophy was also associated with a greater increase in conduction delay. Ischaemia reduced action potential duration and refractory periods; the reduction in action potential duration was attenuated by hypertrophy (p < 0.01), although the reverse was apparent during low flow ischaemia at 50 d. CONCLUSIONS Delayed conduction is an important feature of severe cardiac hypertrophy in guinea pigs and man. Hypertrophy is associated with accentuated conduction delay and altered repolarisation during ischaemia.
Clinical Study Subclinical Cardiovascular System Changes in Obese Patients with Juvenile Idiopathic Arthritis

1 Department of Pediatrics, Endocrinology, Diabetology with Cardiology Division, Medical University of Bialystok, Waszyngtona 17 Street, 15-274 Białystok, Poland 2Department of Pediatrics and Developmental Disorders, Medical University of Bialystok, Waszyngtona 17 Street, 15-274 Białystok, Poland 3Department of Statistics and Medical Informatics, Medical University of Bialystok, Szpitalna 37 Street, 15-295 Białystok, Poland 4Department of Rheumatology and Internal Medicine, Medical University of Bialystok, M. Skłodowskiej-Curie 24A Street, 15-276 Białystok, Poland
Punding prevalence in Parkinson's disease

The purpose of this study was to determine punding prevalence in an ambulatory Parkinson's disease (PD) population. We conducted a patient‐and‐caregiver–completed punding survey in 373 consecutive patients in an academic ambulatory center. Completion rate was 78%. Only four patients were identified as punding. Patients did not retain insight to their behavior. Forty patients with high‐dose levodopa monotherapy or levodopa and dopamine agonist treatment had physician‐administered interview. None had punding. Punding incidence was low in this patient group (1.4%) in contrast with previous reports of 14%. Despite the low incidence, this behavior is disruptive and should be carefully elicited by physicians caring for Parkinson's disease patients. © 2006 Movement Disorder Society
CLIP Tool Kit (CTK): a flexible and robust pipeline to analyze CLIP sequencing data

Summary: UV cross‐linking and immunoprecipitation (CLIP), followed by high‐throughput sequencing, is a powerful biochemical assay that maps in vivo protein‐RNA interactions on a genome‐wide scale. The CLIP Tool Kit (CTK) aims at providing a set of tools for flexible, streamlined and comprehensive CLIP data analysis. This software package extends the scope of our original CIMS package. Availability and Implementation: The software is implemented in Perl. The source code and detailed documentation are available at http://zhanglab.c2b2. columbia.edu/index.php/CTK. Contact: cz2294@columbia.edu
SLTP: A Fast Descriptor for People Detection in Depth Images

This paper presents a new feature descriptor for real-time people detection in depth images. The shape cue in depth images can reduce negative impacts of variations of clothing, lighting conditions and the complexity of backgrounds. The proposed Simplified Local Ternary Patterns (SLTP) can take advantage of depth images to describe human body shape with low computational cost. To evaluate the SLTP feature, we establish a dataset with 7260 positive samples. A series of experiments are carried out on this dataset, and the results show that the SLTP feature can achieve a high detection rate with a low false positive rate. Besides, SLTP is easy to implement, and performs fast (over 80 frames per second) on a standard desktop computer.
Impact of Intermittent Apnea on Myocardial Tissue Oxygenation—A Study Using Oxygenation-Sensitive Cardiovascular Magnetic Resonance

Background Carbon dioxide (CO2) is a recognized vasodilator of myocardial blood vessels that leads to changes in myocardial oxygenation through the recruitment of the coronary flow reserve. Yet, it is unknown whether changes of carbon dioxide induced by breathing maneuvers can be used to modify coronary blood flow and thus myocardial oxygenation. Oxygenation-sensitive cardiovascular magnetic resonance (CMR) using the blood oxygen level-dependent (BOLD) effect allows for non-invasive monitoring of changes of myocardial tissue oxygenation. We hypothesized that mild hypercapnia induced by long breath-holds leads to changes in myocardial oxygenation that can be detected by oxygenation-sensitive CMR. Methods and Results In nine anaesthetized and ventilated pigs, 60s breath-holds were induced. Left ventricular myocardial and blood pool oxygenation changes, as monitored by oxygenation-sensitive CMR using a T2*-weighted steady-state-free-precession (SSFP) sequence at 1.5T, were compared to changes of blood gas levels obtained immediately prior to and after the breath-hold. Long breath-holds resulted in an increase of paCO2, accompanied by a decrease of paO2 and pH. There was a significant decrease of blood pressure, while heart rate did not change. A decrease in the left ventricular blood pool oxygenation was observed, which was similar to drop in SaO2. Oxygenation in the myocardial tissue however, was maintained throughout the period. Changes in myocardial oxygenation were strongly correlated with the change in paCO2 during the breath-hold (r = 0.90, p = 0.010). Conclusion Despite a drop in blood oxygen levels, myocardial oxygenation is maintained throughout long breath-holds and is linearly correlated with the parallel increase of arterial CO2, a known coronary vasodilator. Breathing maneuvers in combination with oxygenation-sensitive CMR may be useful as a diagnostic test for coronary artery function.
The differential representation of number and gender in Spanish

Abstract This paper investigates the geometry of phi-features, with a special emphasis on number and gender in Spanish. We address two sets of questions: (i) are number and gender bundled together or do they constitute separate categories, and (ii) does the internal feature composition of number and gender follow a single- or a multi-valued system? Given the lack of consensus on these issues based on primary data, we approach these questions experimentally, using the phenomenon of agreement attraction: a situation in which ungrammatical sequences are perceived as grammatical when one of the NPs is erroneously identified as determining agreement. Our results offer novel support in favor of an agreement model in which number and gender are in separte projections and are valued independently. In addition, our results indicate that number but not gender in Spanish is multi-valued.
Seroprevalence of Human Immunodeficiency Virus, Hepatitis B, Hepatitis C, Syphilis, and Co-infections among Antenatal Women in a Tertiary Institution in South East, Nigeria

Background: Sexually transmitted infections and human immunodeficiency virus (HIV)/AIDS are a major public health concern owing to both their prevalence and propensity to affect offspring through vertical transmission. Aim: The aim was to determine the seroprevalence of HIV, hepatitis B virus (HBV), hepatitis C virus (HCV), syphilis, and co-infections among antenatal women in Enugu, South-East Nigeria. Materials and Methods: A retrospective study of antenatal women at the University of Nigeria Teaching Hospital, Enugu, South-East Nigeria from 1 st May 2006 to 30 th April 2008. A pretested data extraction form was used to obtain data on sociodemographic variables and screening test results from the antenatal records. The analysis was done with SPSS version 17 (Chicago, IL, USA). Results: A total of 1239 antenatal records was used for the study. The seroprevalence of HIV, HBV, HCV, and syphilis among the antenatal women were 12.4% (154/1239), 3.4% (42/1239) 2.6 (32/1239) 0.08% (1/1239), respectively. The HIV/HBV and HIV/HCV co-infection prevalence rates were 0.24% (3/1239), 0.16% (2/1239), respectively. There was no HBC and HCV co-infection among both HIV positive and negative antenatal women. There was no statistically significant difference in HBV and HCV infection between the HIV positive and negative antenatal women. The only woman that was seropositive for syphilis was also positive to HIV. Conclusion: The seroprevalence of HIV, HBV, HCV, and syphilis is still a challenge in Enugu. Community health education is necessary to reduce the prevalence of this infection among the most productive and economically viable age bracket.
The Impact of Lymphovascular Space Invasion on Recurrence and Survival in Iranian Patients With Early Stage Endometrial Cancer

Background The aim of this study was to assess the impact of lymphovascular space involvement (LVSI) on recurrence and survival in early stage of endometrial cancer (EC). Methods Patients with EC referred to Imam Khomeini Hospital in Tehran were examined and enrolled over a 10-year period (2004 - 2015). The effect of LVSI on recurrence and overall survival was analyzed using the Kaplan-Meier and log-rank test methods. Results A total of 160 patients with early stage EC were identified. Out of 160 women with EC, 135 (84.4%) underwent primary surgery. One hundred and twenty-one (76.2%) patients were not found to have LVSI, whereas 38 (23.8%) were found to have LVSI. Of the 38 patients with LVSI, 21 (55.3%) had endometrioid cell type tumor, 10 (26.3%) had serous, one (2.6%) had clear cell and six (15.8%) had adeno-squamous cell type tumor. Conclusion The presence of LVSI represents a factor strongly associated with high risk of recurrence and poor survival in early stage EC. Patients with lower International Federation of Obstetrics and Gynecology (FIGO) stages may be at increased risk of recurrence and a poor overall survival if the pathological findings confirm the presence of LVSI. Thus, LVSI should be added to the traditional factors used to decide whether patients with early stage EC are at high risk of recurrence and adjuvant therapy planning.
Perceptions and Practices of Replication by Social and Behavioral Scientists: Making Replications a Mandatory Element of Curricula Would Be Useful

We live in a time of increasing publication rates and specialization of scientific disciplines. More and more, the research community is facing the challenge of assuring the quality of research and maintaining trust in the scientific enterprise. Replication studies are necessary to detect erroneous research. Thus, the replicability of research is considered a hallmark of good scientific practice and it has lately become a key concern for research communities and science policy makers alike. In this case study we analyze perceptions and practices regarding replication studies in the social and behavioral sciences. Our analyses are based on a survey of almost 300 researchers that use data from the German Socio-Economic Panel Study (SOEP), a multidisciplinary longitudinal multi-cohort study. We find that more than two thirds of respondents disagree with the statement that replications are not worthwhile, because major mistakes will be found at some point anyway. Nevertheless, most respondents are not willing to spend their time to conduct replication studies. This situation can be characterized as a "tragedy of the commons": everybody knows that replications are useful, but almost everybody counts on others to conduct them. Our most important finding concerning practical consequences is that among the few replications that are reported, a large majority is conducted in the context of teaching. In our view, this is a promising detail: in order to foster replicability, one avenue may be to make replication studies a mandatory part of curricula as well as of doctoral theses. Furthermore, we argue that replication studies need to be more attractive for researchers. For example, successful replications could be listed in the publication lists of replicated authors. Vice versa, data sharing needs to receive more recognition, for example by considering data production and subsequent data sharing as scientific output.
Blue light is ess nt al for high light acclimation and photoprotection in the diatom Phaeodactylum tricornutum

In mammals, cadmium is widely considered as a non-genotoxic carcinogen acting through a methylation-dependent epigenetic mechanism. Here, the effects of Cd treatment on the DNA methylation patten are examined together with its effect on chromatin reconfiguration in Posidonia oceanica. DNA methylation level and pattern were analysed in actively growing organs, under short(6 h) and long(2 d or 4 d) term and low (10 mM) and high (50 mM) doses of Cd, through a Methylation-Sensitive Amplification Polymorphism technique and an immunocytological approach, respectively. The expression of one member of the CHROMOMETHYLASE (CMT) family, a DNA methyltransferase, was also assessed by qRT-PCR. Nuclear chromatin ultrastructure was investigated by transmission electron microscopy. Cd treatment induced a DNA hypermethylation, as well as an up-regulation of CMT, indicating that de novo methylation did indeed occur. Moreover, a high dose of Cd led to a progressive heterochromatinization of interphase nuclei and apoptotic figures were also observed after long-term treatment. The data demonstrate that Cd perturbs the DNA methylation status through the involvement of a specific methyltransferase. Such changes are linked to nuclear chromatin reconfiguration likely to establish a new balance of expressed/repressed chromatin. Overall, the data show an epigenetic basis to the mechanism underlying Cd toxicity in plants.