Miracle-dz/UniFAR-FTUs huggingface dataset:
CPG16, a Novel Protein Serine/Threonine Kinase Downstream of cAMP-dependent Protein Kinase*

Gene expression is necessary for the formation and consolidation of long term memory in both invertebrates and vertebrates. Here, we describe the expression and characterization of candidate plasticity gene 16 (cpg16), a protein serine/threonine kinase that was previously isolated from rat hippocampus as a plasticity-related gene. CPG16, when expressed in and purified from bacteria and COS7 cells, was only capable of autophosphorylation and phosphorylation of myelin basic protein but failed to phosphorylate many other peptides and proteins in in vitro phosphorylation assays. Recombinant CPG16, when overexpressed and purified from COS7 cells, had a relatively low level of autophosphorylation activity. This activity was significantly stimulated when cAMP-elevating agents (forskolin, 8-bromo-cAMP) were added to the cells but not by any other extracellular stimuli tested,e.g. serum, phorbol esters, and a calcium ionophore. Although the stimulation of CPG16 activity was inhibited by the cAMP-dependent protein kinase inhibitor H-89, it did not serve as a direct substrate for this kinase. This suggests that CPG16 may be activated by a cAMP-stimulated protein kinase cascade. Immunolocalization studies in COS7 and NIH-3T3 cells showed mostly cytoplasmic localization of CPG16 that turned partially nuclear upon stimulation with 8-bromo-cAMP. Moreover, overexpression of CPG16 seems to partially inhibit cAMP-stimulated activity of the transcription factor CREB (cAMP response element-binding protein), suggesting its involvement in the down-regulation of cAMP-induced transcription. Thus, CPG16 is a protein serine/threonine kinase that may be involved in a novel signaling pathway downstream of cAMP-dependent protein kinase.
Integrated stratigraphy of the Priabonian (upper Eocene) Urtsadzor section, Armenia

The transition from the Bartonian to the Priabonian, as traditionally understood, has long been associated with a series of extinctions and originations in several microfossil groups. The planktonic foraminifer genus Morozovelloides and large species of Acarinina suffered a rapid global extinction, as did many radiolarians. Calcareous nannofossils show several assemblage changes including the acme beginning of Cribrocentrum erbae and the lowest and highest occurrences of Chiasmolithus oamaruensis and C. grandis respectively. In shallow water environments, larger foraminifera also show an extinction among large species of Nummulites, as well as the first occurrences of the stratigraphically important genus Spiroclypeus. However, the correlation between shallow and deep water records remains uncertain, as do the mechanisms driving these biotic events. Here we present the results of a new integrated stratigraphical study (calcareous nannofossils, planktonic foraminifera, larger benthic foraminifera, and low-resolution magnetostratigraphy) of the Urtsadzor section in south-western Armenia which appears to be continuous through this interval. The Urtsadzor section consists of calcareous siltstones rich in micro- and nannofossils, with interbedded limestones containing abundant larger benthic foraminifera. Our new data enable us to correlate larger foraminiferal events with global plankton biostratigraphy, in a section outside of southwest Europe where most previous correlations have been based. At Urtsadzor, the large Nummulites species of N. millecaput-group are present throughout the whole section but decrease in abundance toward the top. The first occurrence of Spiroclypeus, also occurs in the upper part of the section, marking the SBZ 18/19 boundary. These events are associated with the phylogenetic development of the Nummulites fabianii and Heterostegina reticulata lineages. However, the calcareous plankton biostratigraphy indicates the section is well within the Priabonian; within planktonic foraminiferal Zones E14 and E15 and calcareous nannoplankton Zones CNE 18 and CNE 19. These results indicate larger foraminiferal events occur well above the planktonic foraminiferal extinction level and nannofossil assemblage changes indicating the events are not synchronous across groups, with implications for biostratigraphy and recognition of the basal Priabonian in different depositional settings and regions.
Input Synthesis for Sampled Data Systems by Program Logic

Inspired by a concrete industry problem we consider the input synthesis problem for hybrid systems: given a hybrid system that is subject to input from outside (also called disturbance or noise), find an input sequence that steers the system to the desired postcondition. In this paper we focus on sampled data systems--systems in which a digital controller interrupts a physical plant in a periodic manner, a class commonly known in control theory--and furthermore assume that a controller is given in the form of an imperative program. We develop a structural approach to input synthesis that features forward and backward reasoning in program logic for the purpose of reducing a search space. Although the examples we cover are limited both in size and in structure, experiments with a prototype implementation suggest potential of our program logic based approach.
High Blood Glucose Levels Correlate with Tumor Malignancy in Colorectal Cancer Patients

Background Research shows that type 2 diabetes mellitus (T2DM) affects the risk and prognosis of colorectal cancer (CRC). Here, we conducted a retrospective study to investigate whether the clinicopathological features of CRC patients correlate with their blood glucose levels. Material/Methods We enrolled 391 CRC patients hospitalized in our center between 2008 and 2013. Data of their first fasting plasma glucose (FPG) and 2-h postprandial glucose (2hPPG) level after admission, their clinicopathological features, and survival were collected. The correlations between blood glucose level and clinicopathological features were analyzed by Pearson chi-square analysis. Patient survival was analyzed by Kaplan-Meier and Cox-regression analysis. Results There were 116 out of the 391 CRC patients who had high blood glucose level (H-G group, 29.67%), among which 58 (14.83%), 18 (4.60%), and 40 (10.23%) were diabetes mellitus (DM), impaired glucose tolerance (IGT), and impaired fasting glucose (IFG), respectively, while 275 (70.33%) patients had normal glucose level (N-G group). Compared with the N-G group, patients in the H-G group had larger tumor diameters and lower tumor differentiation (p<0.05). A higher ratio of patients in the H-G group also had more advanced TNM staging and more ulcerative CRC gross type (p<0.05). No significant difference was observed in patient overall survival among different glucose groups. No effect of insulin therapy on CRC development and patient survival was observed. Conclusions Blood glucose level in CRC patients correlates significantly with local tumor malignancy, but no significant effect on distant metastasis and patient overall survival was observed.
Sequence capture by hybridization to explore modern and ancient genomic diversity in model and nonmodel organisms

Abstract The recent expansion of next-generation sequencing has significantly improved biological research. Nevertheless, deep exploration of genomes or metagenomic samples remains difficult because of the sequencing depth and the associated costs required. Therefore, different partitioning strategies have been developed to sequence informative subsets of studied genomes. Among these strategies, hybridization capture has proven to be an innovative and efficient tool for targeting and enriching specific biomarkers in complex DNA mixtures. It has been successfully applied in numerous areas of biology, such as exome resequencing for the identification of mutations underlying Mendelian or complex diseases and cancers, and its usefulness has been demonstrated in the agronomic field through the linking of genetic variants to agricultural phenotypic traits of interest. Moreover, hybridization capture has provided access to underexplored, but relevant fractions of genomes through its ability to enrich defined targets and their flanking regions. Finally, on the basis of restricted genomic information, this method has also allowed the expansion of knowledge of nonreference species and ancient genomes and provided a better understanding of metagenomic samples. In this review, we present the major advances and discoveries permitted by hybridization capture and highlight the potency of this approach in all areas of biology.
The changes in morphology and morphometrical indices of endometrium of ovariectomized mice in response to exogenous ovarian hormones

Background: The preparation of endometrium for embryo reception and implantation are controlled by ovarian hormones. These hormones have distinct cyclical changes during estrus cycle. Objective: The aim of this study was to evaluate the changes in morphology and morphometrical indices of endometrium by daily injections of estrogen and progesterone in ovariectomized mouse. Materials and Methods: In total 60 adult NMRI female mice were ovariectomized and after two weeks, they were randomly divided into five groups: control, sham group, estrogen treated mice (which received daily dosage of 0.5 ml/mouse of hormone for five days), progesterone treated mice (which received daily dosage of 0.2 ml/mouse of progesterone hormone for five days) and estrogen-progesterone treated mice (they received 0.5 ml/mouse estrogen on the first day and 0.2 ml/mouse progesterone injections from the second day to the fifth day of treatment). The mice were sacrificed in every day (n=5) up to five days after treatment and their uterine horns were obtained and processed for morphological and morphometrical studies. Results: On the second day of treatment, the diameter of glands was observed to be more in the progesterone group (53.75±6.32μ) than this in the estrogen (45.13±7.78 μ) and estrogen-progesterone treated groups (48.17±13.58 μ). While, the number of glands (76.25±17.37) and thickness of endometrium (39.58±3.37 μ) were observed to be more in the estrogen treated group (p=0.01). Conclusion: Progesterone had effect on the gland whereas estrogen caused increased in height of surface epithelium of endometrium. Overall, the day 2 after treatment (in all experimental groups) is suitable day for sampling for further studies.
SPARSE APPROXIMATION AND RECOVERY BY GREEDY ALGORITHMS IN BANACH SPACES

Abstract We study sparse approximation by greedy algorithms. We prove the Lebesgue-type inequalities for the weak Chebyshev greedy algorithm (WCGA), a generalization of the weak orthogonal matching pursuit to the case of a Banach space. The main novelty of these results is a Banach space setting instead of a Hilbert space setting. The results are proved for redundant dictionaries satisfying certain conditions. Then we apply these general results to the case of bases. In particular, we prove that the WCGA provides almost optimal sparse approximation for the trigonometric system in $L_p$ , $2\le p<\infty $ .
Coronal properties of the EQ Pegasi binary system

Context. The activity indicators of M dwarfs are distinctly different for early and late types. The coronae of early M dwarfs display high X-ray luminosities and temperatures, a pronounced inverse FIP effect, and frequent flaring to the extent that no quiescent leve l can be defined in many cases. For late M dwarfs, fewer but more v iolent flares have been observed, and the quiescent X-ray lum inosity is much lower. Aims. To probe the relationship between coronal properties with spectral type of active M dwarfs, we analyze the M3.5 and M4.5 components of the EQ Peg binary system in comparison with other active M dwarfs of spectral types M0.5 to M5.5. Methods. We investigate the timing behavior of both components of the EQ Peg system, reconstruct their differential emission measure, and investigate the coronal abundance ratios based on emission-measure independent line ratios from their Chandra HETGS spectra. Finally we test for density variations in different states of activity. Results. The X-ray luminosity of EQ Peg A (M3.5) is by a factor of 6‐10 brighter than that of EQ Peg B (M4.5). Like most other active M dwarfs, the EQ Peg system shows an inverse FIP effect. The abundances of both components are consistent within the errors; however, there seems to be a tendency toward the inverse FIP effect being less pronounced in the less active EQ Peg B when comparing the quiescent state of the two stars. This trend is supported by our comparison with other M dwarfs. Conclusions. As the X-ray luminosity decreases with later spectral type, so do coronal temperatures and flare rate. The amplitude of the observed abundance anomalies, i. e. the inverse FIP effect, declines; however, clear deviations from solar abundances remain.
Impact of retrograde flexible ureteroscopy and intracorporeal lithotripsy on kidney functional outcomes

ABSTRACT Objective: The aim of the study was to evaluate renal function and to identify factors associated with renal function deterioration after retrograde intrarenal surgery (RIRS) for kidney stones. Materials and Methods: We retrospectively analyzed patients with renal stones treated by RIRS between January 2010 and June 2013 at a single institute. We used the National Kidney Foundation classification of chronic kidney disease (CKD) to classify Glomerular Filtration Rate (GFR) in 5 groups. The baseline creatinine level was systematically pre-operatively and post-operatively evaluated. All patients had a creatinine blood measurement in June 2013. A change toward a less or a more favorable GFR group following RIRS was considered significant. Results: We included 163 patients. There were 86 males (52.8%) and 77 females (47.3%) with a mean age of 52.8±17 years. After a mean follow-up of 15.5±11.5 months, median GFR was not significantly changed from 84.3±26.2 to 84.9±24.5 mL/min (p=0.675). Significant renal function deterioration occurred in 8 cases (4.9%) and significant renal function amelioration occurred in 23 cases (14.1%). In univariate analysis, multiple procedures (p=0.023; HR: 5.4) and preoperative CKD (p=0.011; HR: 6.8) were associated with decreased renal function. In multivariate analysis these factors did not remain as predictive factors. Conclusion: Stone management with RIRS seems to have favorable outcomes on kidney function; however, special attention should be given to patients with multiple procedures and preoperative chronic kidney disease.
A Study on the Use of Songs to Improve Students’ Pronunciation and Listening Skill

The aims of this research are to describe how is the process of teaching listening and pronunciation by using songs and to find out if the use of songs can help improve students’ pronunciation and listening skill at English education department. This study is a classroom action research. The population of this research was students of the second semester at English Education Department. The sample of this research was class B in Intermediate Listening subject and the total students involved in this research were of 23 students. The instruments of this research were tests, in the form of oral test and written test, observation sheetsand documents. The implementation of this research was conducted in two cycles, every cycle consisted with the steps of planning, acting, observing, and reflecting. The findings in the analysis show that the action research was successfull, because the results of quantitative data obtained for the first cycle was 39.3 % of the total number of students declared not succeeded and the second cycle 86.9 % of the total number of students declared successful and the results of qualitative data through observation sheets and documents showed that the use of songs can improve students’ pronunciation and listening skill. There is an increase in student learning outcomes of intermediate listening subjects after using the songs in teaching and learning activities. Based on the findings it is concluded that the use of songs could improve students’ pronunciation and listening skill. Furthermore the use of songs is effective as a media to improve students’ pronunciation and listening skill. Thus this research may suggest that the use of songs should be used routinely in each learning activity because in the activity the students would be able to comprehend what they learn. It is recommended, the use of songs which are simple, enjoyable, pleasurable, comfortable, and easy to learn may help students’ learning. Key Words: Songs, English Foreign Language , Pronunciation, and Listening
Not4‐dependent translational repression is important for cellular protein homeostasis in yeast

Translation of aberrant or problematic mRNAs can cause ribosome stalling which leads to the production of truncated or defective proteins. Therefore, cells evolved cotranslational quality control mechanisms that eliminate these transcripts and target arrested nascent polypeptides for proteasomal degradation. Here we show that Not4, which is part of the multifunctional Ccr4–Not complex in yeast, associates with polysomes and contributes to the negative regulation of protein synthesis. Not4 is involved in translational repression of transcripts that cause transient ribosome stalling. The absence of Not4 affected global translational repression upon nutrient withdrawal, enhanced the expression of arrested nascent polypeptides and caused constitutive protein folding stress and aggregation. Similar defects were observed in cells with impaired mRNA decapping protein function and in cells lacking the mRNA decapping activator and translational repressor Dhh1. The results suggest a role for Not4 together with components of the decapping machinery in the regulation of protein expression on the mRNA level and emphasize the importance of translational repression for the maintenance of proteome integrity.
Networks of Order Independent Queues with Signals

We study the steady-state distribution of networks of order independent queues with negative signals which delete customers. An Order Independent queue is defined by a service rate which is independent on the order of the customers in the queue. Such an abstract discipline may be used to model complex blocking mechanism (for instance the Multiserver Station with Concurrent Classes of Customers). Order independent queues are in general neither symmetric nor reversible. We prove that, under usual assumptions on the arrivals, the services and the routing of customers, such a network of queues with signals has a steady-state distribution with product form solution. The proof is based on the quasi-reversibility of the queues. We also present some examples of application for this new analytical result.
Control of Pollen Tube Tip Growth by a Rop GTPase–Dependent Pathway That Leads to Tip-Localized Calcium Influx

We have shown that Rop1At, a pollen-specific Rop GTPase that is a member of the Rho family of small GTP binding proteins, acts as a key molecular switch controlling tip growth in Arabidopsis pollen tubes. Pollen-specific expression of constitutively active rop1at mutants induced isotropic growth of pollen tubes. Overexpression of wild-type Arabidopsis Rop1At led to ectopic accumulation of Rop1At in the plasma membrane at the tip and caused depolarization of pollen tube growth, which was less severe than that induced by the constitutively active rop1at. These results indicate that both Rop1At signaling and polar localization are critical for controlling the site of tip growth. Dominant negative rop1at mutants or antisense rop1at RNA inhibited tube growth at 0.5 mM extracellular Ca2+, but growth inhibition was reversed by higher extracellular Ca2+. Injection of anti-Rop antibodies disrupted the tip-focused intracellular Ca2+ gradient known to be crucial for tip growth. These studies provide strong evidence for a Rop GTPase–dependent tip growth pathway that couples the control of growth sites with the rate of tip growth through the regulation of tip-localized extracellular Ca2+ influxes and formation of the tip-high intracellular Ca2+ gradient in pollen tubes.
Bayesian Document Generative Model with Explicit Multiple Topics

In this paper, we proposed a novel probabilistic generative model to deal with explicit multiple-topic documents: Parametric Dirichlet Mixture Model(PDMM). PDMM is an expansion of an existing probabilistic generative model: Parametric Mixture Model(PMM) by hierarchical Bayes model. PMM models multiple-topic documents by mixing model parameters of each single topic with an equal mixture ratio. PDMM models multiple-topic documents by mixing model parameters of each single topic with mixture ratio following Dirichlet distribution. We evaluate PDMM and PMM by comparing F-measures using MEDLINE corpus. The evaluation showed that PDMM is more effective than PMM.
miR-107 Activates ATR/Chk1 Pathway and Suppress Cervical Cancer Invasion by Targeting MCL1

MicroRNAs (miRNAs) are a class of single-stranded, non-coding RNAs of about 22 nucleotides in length. Increasing evidence implicates miRNAs may function as oncogenes or tumor suppressors. Here we showed that miR-107 directly targeted MCL1 and activated ATR/Chk1 pathway to inhibit proliferation, migration and invasiveness of cervical cancer cells. Moreover, we found that MCL1 was frequently up-regulated in cervical cancer, and knockdown of MCL1 markedly inhibited cancer cell proliferation, migration and invasion, whereas ectopic expression of MCL1 significantly enhances these properties. The restoration of MCL1 expression can counteract the effect of miR-107 on the cancer cells. Together, miR-107 is a new regulator of MCL1, and both miR-107 and MCL1 play important roles in the pathogenesis of cervical cancer. We have therefore identified a mechanism for ATR/Chk1 pathway which involves an increase in miR-107 leading to a decrease in MCL1. Correspondingly, our results revealed that miR-107 affected ATR/Chk1 signalling and gene expression, and implicated miR-107 as a therapeutic target in human cervical cancer. We also demonstrated that taxol attenuated migration and invasion in cervical cancer cells by activating the miR-107, in which miR-107 play an important role in regulating the expression of MCL1. Elucidation of this discovered MCL1 was directly regulated by miR-107 will greatly enhance our understanding of the mechanisms responsible for cervical cancer and will provide an additional arm for the development of anticancer therapies.
VLA Observations of Carbon 91α Recombination Line Emission in W49 North

We have detected C91α (8.5891 GHz) emission toward four ultracompact H II regions (UCHs; W49G, J, L, and C) in the W49 North massive star-forming region with the Very Large Array (VLA) at 3'' resolution. No carbon line emission was detected toward UCHs W49F, A, O, S, and Q at this frequency to a 3 σ level of 2 mJy. We also observed the same region in the C75α line (15.3 GHz) with no detection at a 3 σ level of 6 mJy with a 1. ″7 beam. Detection of line emission toward these sources add supporting data to the 2005 result of Roshi et al. that many UCHs have an associated photodissociation region (PDR). The similarity of the LSR velocities of carbon recombination lines and H2CO absorption toward UCHs in W49 North suggests that the PDRs reside in the dense interface zone surrounding these H II regions. Combining the observed carbon line parameters at 8.6 GHz with the upper limits on line emission at 15.3 GHz, we obtain constraints on the physical properties of the PDRs associated with W49G and J. The upper limit on the number density of hydrogen molecule obtained from carbon line models is ~5 × 106 cm-3.