Miracle-dz/UniFAR-FTUs huggingface dataset:
A Protein Conjugation System in Yeast with Homology to Biosynthetic Enzyme Reaction of Prokaryotes*

Protein conjugation, such as ubiquitination, is the process by which the C-terminal glycine of a small modifier protein is covalently attached to target protein(s) through sequential reactions with an activating enzyme and conjugating enzymes. Here we report on a novel protein conjugation system in yeast. A newly identified ubiquitin relatedmodifier, Urm1 is a 99-amino acid protein terminated with glycine-glycine. Urm1 is conjugated to target proteins, which requires the C-terminal glycine of Urm1. At the first step of this reaction, Urm1 forms a thioester with a novel E1-like protein, Uba4. Δurm1 and Δuba4 cells showed a temperature-sensitive growth phenotype. Urm1 and Uba4 show similarity to prokaryotic proteins essential for molybdopterin and thiamin biosynthesis, although the Urm1 system is not involved in these pathways. This is the fifth conjugation system in yeast, following ubiquitin, Smt3, Rub1, and Apg12, but it is unique in respect to relation to prokaryotic enzyme systems. This fact may provide an important clue regarding evolution of protein conjugation systems in eukaryotic cells.
Reinforcement learning in partially observable mobile robot domains using unsupervised event extraction

This paper describes how learning tasks in partially observable mobile robot domains can be solved by combining reinforcement learning with an unsupervised learning "event extraction" mechanism, called ARAVQ. ARAVQ transforms the robot's continuous, noisy, high-dimensional sensory input stream into a compact sequence of high-level events. The resulting hierarchical control system uses an LSTM recurrent neural network as the reinforcement learning component, which learns high-level actions in response to the history of high-level events. The high-level actions select low-level behaviors which take care of the real-time motor control. Illustrative experiments based on the Khepera mobile robot simulator are presented.
Egg Production Pattern of Japanese Quail (Coturnix Coturnix Japonica) in Northern Guinea Savannah Zone of Nigeria

The technology drive from egg production in relationship with genetic selection makes today’s egg production quails quite different from those of a decade ago. For instance age at 5 percent production is now earlier and total egg number has increased. The quail eggs are renowned for their high biological value (George, 2002). Although it was first considered mainly as a model animal for commercial poultry (Wilson et al., 1961), the modern Japanese quail is a good egg layer in its own right (Baumgartner, 1994), and it is farmed intensively for egg production, especially in Japan and South East Asia (Minvielle, 1998). The female Japanese quail may start laying eggs as early as 35 days (Varghense, 2002) of age under proper conditions. Piano et al. (2004) stated that under high intensive care, female Japanese quails start laying at an age of 42 days and reach peak production by 10 – 12 weeks of age. Randall, Abstract: A study was carried out with 48 Japanese quails (Coturnix coturnix japonica) at the poultry unit Department of Animal Science, Ahmadu Bello University, Zaria. The birds were individually caged and intensively reared for a period of 165 days to study the egg production pattern of the birds in terms of egg number, number of clutches, clutch size, number of pause, days pause and paused length; and also the association of each with egg number. It was observed that the 165 days egg production pattern characteristic of the birds were egg number 103 + 15, number of clutches 38 + 6, clutch size 3 + 1, number of pause 38 + 4, days pause 54 + 14 and pause length 2 + 1. The level of variation for the measured characteristic over the period was in the range of CV values of 15 to 33% with the highest level of variability exhibited by clutch size. There was a significant (P = 0.05) positive relationship between egg number and clutch size (r = 0.85) but negatively related with number of clutches, number of pauses, days paused and pause length (r = -0.46 to -0.72). While number of clutches was negatively correlated with clutch size (P = 0.01; r = 0.84) it was positively correlated with the number of pauses and days paused (r = 0.82 and 0.51). The clutch size was positively correlated with number of pauses (r = 0.75) and negatively with days paused and pause length r = 0.75 and -0.27). The number of pauses was positively correlated with days paused and paused (r = 0.35). This study has shown that Japanese quails commence egg production at 71%, attained a peak production of 86% which gradually decline to 57% by 165 days of age. Egg number was favoured by clutch size but negated by number of clutches, number of pauses, days paused and pause length. The age at peak production was 12 weeks (84 days) of age.
Memorializing the Past: Everyday Life in South Africa after the Truth and Reconciliation Commission

This work is mediation on the shaping of time and its impact on living with and understanding atrocity in South Africa in the wake of the Truth and Reconciliation Commission (TRC). It is an examination of the ways that the institutionalization of memory has managed perceptions of time and "transition," of events and happenings, of sense and emotion, of violence and recovery, of the "past" and the "new. " Through this process a public language of "memory" has been carved into collective modes of meaning. It is a language that seems deprived of the hopes, dreams, and possibilities for the promise of a just and redemptive future it once nurtured. Truth commission are profoundly implicated in the social politics of memorialisation. Memory, as a conceptual, historical, and experiential discourse about "the past," relates to the ways in which cruelty is integrated into societal understandings, which include cognitive and philosophic frameworks and constructions of social meaning. The politics of historical truth, of memory and of justice, play out in unintended ways. There is not only the ongoing struggle for survivors of state terror, but also the ways that the everyday shapings of silences, the emptiness of reconciliation and the fracturing of hope remain embedded in political life.
A high-efficiency power amplifier using GaN HEMTs

This paper reports a high efficiency power amplifier using a gallium nitride high electron mobility transistor(GaN HEMT), which is designed at the L band of 1.5GHz. To improve output power and efficiency by suppressing harmonic powers, input and output matching network using transmission lines are designed. For the center frequency 1.5GHz, the added efficiency (PAE) of 67.43% with a power gain of 13.37dB is achieved at an output power of 46.17dBm. The broadband performance with a power gain over 12dB and PAE over 60% is maintained through 20MHz.
Hurricane tangential wind profile from synthetic aperture radar observations

Over the last several years, considerable efforts have been devoted to investigate hurricane surface winds using SAR observations [1]-[6]. Compared to optical satellite sensors, synthetic aperture radar (SAR) has advantages for observation of ocean surface winds, with high resolution and large spatial coverage, in almost all-weather conditions. Measurements of the inner-core intensities and tangential wind profiles are generally provided by NOAA aircraft flying though the hurricanes [7]. However, aircraft only can provide single point observations along the flight track. Thus, there can be some variance in the aircraft-measured tangential wind profiles, particularly for those hurricanes with asymmetric wind structures. For example, for a non-symmetric hurricane with an elliptic eye, we can assume that the true maximum wind speed exists somewhere on the major axis direction. Therefore, if the aircraft flies along the minor axis of this hurricane, instead of the major axis, the maximum wind and the radius of maximum wind (RMW) observations are probably not accurate. In this study, we determine the hurricane eye center and its extent, and propose a model to estimate hurricane intensity and structure parameters. A specific objective is to describe the tangential wind profile corresponding to the reintensification phase in the hurricane eyewall replacement cycle (ERC).
Cardiac-specific Activation of Signal Transducer and Activator of Transcription 3 Promotes Vascular Formation in the Heart*

Signal transducer and activator of transcription 3 (STAT3) functions in cell proliferation, differentiation, and cell survival. Previously, we have demonstrated that the activation of STAT3 is required for glycoprotein 130-mediated induction of VEGF in cardiac myocytes, but the functional importance of STAT3 as an angiogenic mediator remains to be determined. To address this issue, we first generated the adenoviral vector expressing constitutively active STAT3 (caSTAT3). Adenoviral gene transfer of caSTAT3 induced an increase in the expression of VEGF in cultured cardiomyocytes. The conditioned medium from caSTAT3-transfected cardiomyocyte culture promoted endothelial tubule formation, which was inhibited by anti-VEGF antibody. Next, we generated the transgenic (TG) mice with cardiac-specific overexpression of caSTAT3 and demonstrated that caSTAT3 TG mice showed evidence of VEGF induction in the hearts. The caSTAT3 TG hearts also demonstrated increased capillary density accompanied by an increase in the expression of VE-cadherin, an endothelial-specific component. These data indicate that caSTAT3 TG hearts exhibit an enriched vascular structure compared with non-transgenic hearts. The study presented here provides the first evidence that activation of STAT3 controls vessel growth in vivo and suggests that STAT3 contributes to cardiac adaptation by regulating vascular function under the conditions of stress.
Assessing the Evolutionary Impact of Amino Acid Mutations in the Human Genome

Quantifying the distribution of fitness effects among newly arising mutations in the human genome is key to resolving important debates in medical and evolutionary genetics. Here, we present a method for inferring this distribution using Single Nucleotide Polymorphism (SNP) data from a population with non-stationary demographic history (such as that of modern humans). Application of our method to 47,576 coding SNPs found by direct resequencing of 11,404 protein coding-genes in 35 individuals (20 European Americans and 15 African Americans) allows us to assess the relative contribution of demographic and selective effects to patterning amino acid variation in the human genome. We find evidence of an ancient population expansion in the sample with African ancestry and a relatively recent bottleneck in the sample with European ancestry. After accounting for these demographic effects, we find strong evidence for great variability in the selective effects of new amino acid replacing mutations. In both populations, the patterns of variation are consistent with a leptokurtic distribution of selection coefficients (e.g., gamma or log-normal) peaked near neutrality. Specifically, we predict 27–29% of amino acid changing (nonsynonymous) mutations are neutral or nearly neutral (|s|<0.01%), 30–42% are moderately deleterious (0.01%<|s|<1%), and nearly all the remainder are highly deleterious or lethal (|s|>1%). Our results are consistent with 10–20% of amino acid differences between humans and chimpanzees having been fixed by positive selection with the remainder of differences being neutral or nearly neutral. Our analysis also predicts that many of the alleles identified via whole-genome association mapping may be selectively neutral or (formerly) positively selected, implying that deleterious genetic variation affecting disease phenotype may be missed by this widely used approach for mapping genes underlying complex traits.
Job satisfaction of nurses and identifying factors of job satisfaction in Slovenian Hospitals

Aim To determine the level of job satisfaction of nursing professionals in Slovenian hospitals and factors influencing job satisfaction in nursing. Methods The study included 4 hospitals selected from the hospital list comprising 26 hospitals in Slovenia. The employees of these hospitals represent 29.8% and 509 employees included in the study represent 6% of all employees in nursing in Slovenian hospitals. One structured survey questionnaire was administered to the leaders and the other to employees, both consisting 154 items evaluated on a 5 point Likert-type scale. We examined the correlation between independent variables (age, number of years of employment, behavior of leaders, personal characteristics of leaders, and managerial competencies of leaders) and the dependent variable (job satisfaction – satisfaction with the work, coworkers, management, pay, etc) by applying correlation analysis and multivariate regression analysis. In addition, factor analysis was used to establish characteristic components of the variables measured. Results We found a medium level of job satisfaction in both leaders (3.49 ± 0.5) and employees (3.19 ± 0.6), however, there was a significant difference between their estimates (t = 3.237; P = <0.001). Job satisfaction was explained by age (P < 0.05; β = 0.091), years of employment (P < 0.05; β = 0.193), personal characteristics of leaders (P < 0.001; β = 0.158), and managerial competencies of leaders (P < 0.000; β = 0.634) in 46% of cases. The factor analysis yielded four factors explaining 64% of the total job satisfaction variance. Conclusion Satisfied employees play a crucial role in an organization’s success, so health care organizations must be aware of the importance of employees’ job satisfaction. It is recommended to monitor employees’ job satisfaction levels on an annual basis.
Penerapan Strategi SQ3R dan peta Konsep dalam Pembelajaran Fisika Ditinjau dari Kemampuan Memori Siswa

ABSTRACT The purposes of this research are to find out 1) the effect of the SQ3R and Concept Mapping learning strategies toward student’s achievement, 2) the effect of high and low memory toward student’s achievement, 3) interaction between the SQ3R and Concept Mapping learning strategies and the student’s memory toward student’s achievement. The reseach was conducted in January 2009 – Mei 2010 and used experimental method. Population in this research was all of students in grade VIII state Junior High School Kediri year 2009/2010. Sample of this research consisted of two classes which was taken using cluster random sampling. The classes treated using SQ3R learning strategies was class VIIIA and the classes treated using Concept Mapping of learning was class VIIIB. The data was collected using test method for student’s achievement, student’s memory. The research hypothesis were tested using ANOVA with 2x2x2 factorial design and calculated using Minitab 15. The date analysis show that : 1) there is an effect of the SQ3R and Concept Mapping learning strategies toward student’s achievement (p-value = 0,046 > 0,050), 2) there is an effect of the high and low memory toward student’s achievement (p-value = 0,028 > 0,050), 3) there is an interaction the SQ3R and Concept Mapping learning strategies and the student’s memory toward student’s achievement (p-value = 0,018 < 0,050). ABSTRAK Penelitian ini bertujuan untuk mendeskripsikan adanya : 1) pengaruh strategi pembelajaran SQ3R dan Peta konsep terhadap prestasi belajar fisika, 2) pengaruh kemampuan memori tinggi dan rendah terhadap prestasi belajar fisika, 3) interaksi strategi pembelajaran SQ3R dan Peta konsep dengan kemampuan memori terhadap prestasi belajar fisika. Penelitian ini dilaksanakan pada bulan Januari 2009 – Mei 2010 menggunakan metode eksperimen. Populasi adalah semua siswa kelas VIII MTs.Miftahul’Ulum Kediri tahun pelajaran 2009/2010. Sampel adalah dua kelas yang diambil secara acak (cluster random sampling). Kelas yang menggunakan strategi pembelajaran SQ3R terpilih kelas VIIIA dan kelas yang menggunakan strategi pembelajaran peta konsep kelas VIIIB. Pengumpulan data prestasi belajar fisika, dilakukan dengan tes. Tingkat kreativitas siswa diperoleh dengan angket kreativitas. Uji hipotesis penelitian menggunakan ANAVA dan dihitung dengan bantuan software Minitab 15. Hasil analisis data penelitian adalah 1) terdapat pengaruh strategi pembelajaran SQ3R dan peta konsep terhadap prestasi belajar fisika (p-value = 0,046 < 0,050), 2) terdapat pengaruh kemampuan memori tinggi dan rendah terhadap prestasi belajar fisika (p-value = 0,028 < 0,050), 3) terdapat interaksi antara strategi pembelajaran SQ3R dan peta konsep dengan kemampuan memori siswa terhadap prestasi belajar fisika (p-value = 0,018 < 0,050).
Certificate Revocation List (CRL)

Beim praktischen Einsatz von Schlüsselzertifikaten kann es erforderlich sein, dass das Zertifikat eines Teilnehmers in einer Public Key-Infrastruktur vorzeitig, d.h. noch innerhalb des Gültigkeitszeitraums für ungültig erklärt werden muss. Dieser Vorgang wird Zertifikats-Rückruf oder -Sperrung genannt. Da der Rückruf sich nicht auf den Schlüssel, sondern auf die Bestätigungsaussage des Zertifikats bezieht, muss er von der Zertifizierungsstelle vorgenommen werden. Der Rückruf eines Schlüsselzertifikats wird vom Schlüsselinhaber (bzw. einem im Zertifikat explizit ermächtigten Vertreter) oder – im Fall der Kompromittierung des CA-Schlüssels – direkt von der Zertifizierungsinstanz eingeleitet. Dafür sind organisatorische Abläufe erforderlich, die eine Authentisierung des Schlüsselinhabers (bzw. des Vertreters) bei der Rückrufannahme erlauben.
Logical Coupling Based on Fine-Grained Change Information

Logical coupling reveals implicit dependencies between program entities, by measuring how often they changed together during development. Current approaches use coarse-grained change information extracted from the version control history of the software system under study. Entities that are registered as having changed during a commit transaction have their coupling increased by the same amount, regardless of how and how much they actually changed. We present several new logical coupling measures taking into account fine-grained semantic changes. We evaluate their respective accuracy compared to the classical logical coupling measure on two case studies; in particular, we evaluate how well the new measures can estimate logical coupling with less data. Results show that our approach based on fine-grained information greatly ameliorates the state-of-the-art of logical coupling detection.
14-3-3 proteins associate with phosphorylated simple epithelial keratins during cell cycle progression and act as a solubility cofactor

14-3-3 is a ubiquitous protein family that interacts with several signal transduction kinases. We show that 14-3-3 proteins associate with keratin intermediate filament polypeptides 8 and 18 (K8/18) that are expressed in simple-type epithelia. The association is stoichiometrically significant (> or = one 14-3-3 molecule/keratin tetramer), occurs preferentially with K18, and is phosphorylation- and cell cycle-dependent in that it occurs during S/G2/M phases of the cell cycle when keratins become hyperphosphorylated. Binding of phospho- K8/18 to 14-3-3 can be reconstituted in vitro using recombinant 14-3-3 or using total cellular cytosol. Phosphatase treatment results in dissociation of 14-3-3, and dephosphorylation of phospho-K8/18 prevents reconstitution of the binding. Three cellular keratin subpopulations were analyzed that showed parallel gradients of keratin phosphorylation and 14-3-3 binding. Incubation of 14-3-3 with keratins during or after in vitro filament assembly results in sequestering of additional soluble keratin, only in cases when the keratins were hyperphosphorylated. Our results demonstrate a stoichiometrically significant cell cycle- and phosphorylation-regulated binding of 14-3-3 proteins to K18 and in vitro evidence of a simple epithelial keratin sequestering role for 14-3-3 proteins.
Signaling strategies for dual-function radar communications: an overview

The last decade witnessed a growing demand on radio frequency that is driven by technological advances benefiting the end consumer but requiring new allocations of frequency bandwidths. Further, higher data rates for faster communications and wireless connections have called for an expanded share of existing frequency allocations. Concerns for spectrum congestion and frequency unavailability have spurred extensive research efforts on spectrum management and efficiency within the same type of service and have led to cognitive radio and cognitive radar. On the other hand, devising schemes for coexistence among different services have eased the competition for spectrum resources, especially for radar and wireless communication systems. Both systems have been recently given a common portion of the spectrum by the Federal Communications Commission.
[Influence of spectral interferences on the results of quartz determination by infrared spectrometry].

BACKGROUND Determination of quartz by Fourier transform infrared spectrometry (FTIR) is not specific: the obtained results are influenced by matrix components, some of which cause spectral interference. The aim of the study was to evaluate the effect of dust components responsible for spectral interference with quartz on the results of its determinations, and to develop methods to minimize the effects of interferences. MATERIAL AND METHODS Investigation of interferent effects were conducted using respirable dusts: quartz SRM 1878a, cristobalite SRM 1879a, synthetic amorphous silica (Zeosil) and feldspar, albite and kaolinite. For the study 17 mixtures with quartz and interferents at concentrations from 10 to 90% were prepared. Determinations of quartz were carried out by the KBr disc method. RESULTS In mixtures of quartz with interferents, the results based on bands 798-779 cm-1 were overestimated by 10-55%, while those based on band 695 cm-1 were closer to the true content of quartz. It was found that the best methods able to decrease the impact of spectral interference are: scaled subtraction of IR spectra of feldspar or kaolinite analysed in nonashed samples, correction curve for kaolinite also investigated in nonashed samples with quartz-content calculation based on band 695 cm-1 in mixtures with cristobalite, amorphous silica or kaolinite in ashed samples. CONCLUSIONS The study indicates the need to identify spectral interferences in dust when determining crystalline silica by FT-IR and to take actions to minimize their impact on the obtained results.
Geometric De-noising of Protein-Protein Interaction Networks

Understanding complex networks of protein-protein interactions (PPIs) is one of the foremost challenges of the post-genomic era. Due to the recent advances in experimental bio-technology, including yeast-2-hybrid (Y2H), tandem affinity purification (TAP) and other high-throughput methods for protein-protein interaction (PPI) detection, huge amounts of PPI network data are becoming available. Of major concern, however, are the levels of noise and incompleteness. For example, for Y2H screens, it is thought that the false positive rate could be as high as 64%, and the false negative rate may range from 43% to 71%. TAP experiments are believed to have comparable levels of noise. We present a novel technique to assess the confidence levels of interactions in PPI networks obtained from experimental studies. We use it for predicting new interactions and thus for guiding future biological experiments. This technique is the first to utilize currently the best fitting network model for PPI networks, geometric graphs. Our approach achieves specificity of 85% and sensitivity of 90%. We use it to assign confidence scores to physical protein-protein interactions in the human PPI network downloaded from BioGRID. Using our approach, we predict 251 interactions in the human PPI network, a statistically significant fraction of which correspond to protein pairs sharing common GO terms. Moreover, we validate a statistically significant portion of our predicted interactions in the HPRD database and the newer release of BioGRID. The data and Matlab code implementing the methods are freely available from the web site: http://www.kuchaev. com/Denoising.