Miracle-dz/UniFAR-FTUs huggingface dataset:
Mining Protein Kinases Regulation Using Graphical Models

Abnormal kinase activity is a frequent cause of dis- eases, which makes kinases a promising pharmacological target. Thus, it is critical to identify the characteristics of protein kinases regulation by studying the activation and inhibition of kinase sub- units in response to varied stimuli. Bayesian network (BN) is a for- malism for probabilistic reasoning that has been widely used for learning dependency models. However, for high-dimensional dis- crete random vectors the set of plausible models becomes largeand a full comparison of all the posterior probabilities related to the competing models becomes infeasible. A solution to this problem is based on the Markov Chain Monte Carlo (MCMC) method. This paper proposes aBN-based frameworkto discoverthe dependency correlations of kinase regulation. Our approach is to apply the MCMC method to generate a sequence of samples from a prob- ability distribution, by which to approximate the distribution. The frequent connections (edges) are identified from the obtained sam- pling graphical models. Our results point to a number of novel candidate regulation patterns that are interesting in biology and include inferred associations that were unknown. Index Terms—Activation, AMPK, Bayesian network, depen- dency, inhibition, pathway, protein kinases, stimulus, subunit.
ANATOMICAL TRAUMA TO SPONGE·CORAL REEF FISHES CAPTURED BY TRAWLING AND ANGLING

External signs of trauma were examined in 15 sponge-coral reef fish species captured while trawling and angling at 37 m depth. Internal evidence of trauma was noted for all species and quantified for a sample of angling-caught black sea bass, Centropristis striata. Distinct differences were noted in the types and frequencies of trauma experienced among species, and between gear tYPes within species. Black sea bass; red snappers, Lutjanus ca1npecoonus; short bigeyes, Pristigli'tlys aUa; and Mycteroperca groupers exhibited high frequencies of oral protrusions. Planehead filefish, Motlacantkus kispidus; orange filefish, AleuterltB sclwepfi; and blue angelfish, HOUuunthusberm'lldensis, were particularly prone to cloacal protrusions. External signs of trauma were few in vermilion snappers, Rh.om1Joplites auroruhlitls; porgies (SteTl/,otO'lllus ckrgs(Jps, Calam.usleucosteU8, and Pagrus pagrus); tomtates, Haemuloll a.lt·rolineatu1n; and two trawl-caught serranids (Centropristis ocyurus and Diplectrum fO'rlll08um). Angling produced oral protrusions in black sea bass more frequently than trawling. Trawl-caught red snappers had a higher stomach eversion frequency when brought to the surface more quickly. Angling-caught black sea bass experienced high frequencies of tissue emphysema and swim-bladder rupture. These results should be considered in studies of feeding biology, released·fish survivorship, and fishery management.
Conservation Biogeography of the Sahara‐Sahel: additional protected areas are needed to secure unique biodiversity

Identification of priority conservation areas and evaluation of coverage of the current protected areas are urgently needed to halt the biodiversity loss. Identifying regions combining similar environmental traits (climate regions) and species assemblages (biogroups) is needed for conserving the biodiversity patterns and processes. We identify climate regions and biogroups and map species diversity across the Sahara‐Sahel, a large geographical area that exhibits wide environmental heterogeneity and multiple species groups with distinct biogeographical affinities, and evaluate the coverage level of current network of protected areas for biodiversity conservation.
Type designation for Cyclachaena xanthiifolia ( Euphrosyne xanthiifolia ) (Heliantheae, Asteraceae)

Cyclachaena xanthiifolia ( Iva xanthiifolia ) is a North American member of the Heliantheae-Ambrosiinae (Asteraceae), which is currently accepted in the genus Euphrosyne . It is a nitrophilous plant, usually growing in disturbed grounds related to human activities, and this fact has probably favoured its introduction and naturalization in Eurasia and New Zealand. As part of the taxonomical work on the Iberian Compositae, typification of the name Cyclachaena xanthiifolia is effected here by selection of a lectotype and an epitype from the material housed at FR (Frankfurt am Main, Germany). The protologue and original material are discussed, and pictures of the relevant material are presented. Some historical aspects are also discussed to justify typification.
Synthesis, Characterization, and Evaluation for Antibacterial and Antifungal Activities of N-Heteroaryl Substituted Benzene Sulphonamides

The synthesis and biological activity of N-heteroaryl substituted benzene sulphonamides (3a–h) were successful. Simple condensation reaction of benzene sulphonyl chloride (1) with substituted heteroaromatic compounds (2a–h) under dry pyridine and acetone gave the target molecules (3a–h) in good to excellent yield. The compounds were characterized using FTIR, 1HNMR, and 13CNMR. The compounds were screened for antibacterial activity against E. coli, Salmonella typhi, P. aeruginosa, B. cereus, K. pneumonia, and Sarcina lutea and antifungal activity against C. albicans and A. niger. The results of the antimicrobial activity showed improved biological activity against some tested organisms.
Missing kinaesthesia challenges precise naturalistic cortical prosthetic control

A major assumption of brain-machine interface (BMI) research is that patients with disconnected neural pathways can still volitionally recall precise motor commands that could be decoded for naturalistic prosthetic control. However, the disconnected condition of these patients also blocks kinaesthetic feedback from the periphery, which has been shown to regulate centrally generated output responsible for accurate motor control. Here we tested how well motor commands are generated in the absence of kinaesthetic feedback by decoding hand movements from human scalp electroencephalography (EEG) in three conditions: unimpaired movement, imagined movement, and movement attempted during temporary disconnection of peripheral afferent and efferent nerves by ischemic nerve block. Our results suggest that the recall of cortical motor commands is impoverished in absence of kinaesthetic feedback, challenging the possibility of precise naturalistic cortical prosthetic control.
Financial stability challenges in a low-growth, low-rate era

Chapter 1 finds that short-term risks to global financial stability have abated since April 2016, but that medium-term risks continue to build. Financial institutions in advanced economies face a number of cyclical and structural challenges and need to adapt to low growth and low interest rates, as well as to an evolving market and regulatory environment. Weak profitability could erode banks’ buffers over time and undermine their ability to support growth. A cyclical recovery will not resolve the problem of low profitability. More deep-rooted reforms and systemic management are needed, especially for European banks. The solvency of many life insurance companies and pension funds is threatened by a prolonged period of low interest rates. Corporate leverage in emerging market economies remains elevated in some countries, but the current favorable external environment presents an opportunity for overly indebted firms to restructure their balance sheets. The political climate is unsettled in many countries. A lack of income growth and a rise in inequality have opened the door for populist, inward-looking policies. These factors make it even harder to tackle legacy problems and further expose economies and markets to shocks. A potent and more balanced policy mix is needed to deliver a stronger path for growth and financial stability, and avoid slipping into a state of financial and economic stagnation.
Food Web Changes over Fourteen Years Following Introduction of Rainbow Smelt into a Colorado Reservoir

Abstract Rainbow smelt Osmerus mordax were introduced into Horsetooth Reservoir, Colorado, in 1983 to increase prey availability for walleyes Stizostedion vitreum. The introduction was highly successful. Rainbow smelt abundance reached at least 0.4 fish/m3 within 6 years, and walleye growth improved by 50%. Zooplankton sampling provided the first clues that the Horsetooth Reservoir food web was undergoing dramatic changes in response to the rainbow smelt introduction. During 1989–1994 the abundant rainbow smelt population apparently reduced April and May crustacean zooplankton concentrations from historical levels of 40–80 organisms/L to less than 1.0 organism/L, and a switch occurred in the cladoceran species composition. Standardized sampling with beach seines and gill nets indicated that after 1988 walleye recruitment ceased. Efforts to bolster walleye recruitment by fry stocking in 1992 and 1993 also failed. A recent decrease in rainbow smelt density allowed a resurgence of zooplankton and a shift in .
Strategies for mycorrhizal inoculation of six annual bedding plant species

We inoculated six common annual bedding plant species with the vesicular- arbuscular mycorrhizal fungus Glomus intraradices Schenck & Smith using two fertilizer P concentrations (3 or 15 μg·mL -1 ) and three inoculation timings (inoculation at sowing, at transplanting, or at both times). The plant species used were: Salvia splendens F. Sellow ex Roem. & Schult. cv. Firecracker Rose; Impatiens walleriana Hook. f. cv. Sun and Shade Royal Red; Tagetes patula L. cv. Girls Golden; Petunia ×hybrida Hort. Vilm. -Andr. cv. Freedom Blue; Coleus ×hybridus Voss. cv. Jazz Salmon; and Viola ×wittrockiana Gams. cv. Majestic Giant White. In general, Coleus, Petunia, and Viola were colonized more than were Impatiens, Tagetes, and Salvia. Inoculation at sowing required less inoculum than either of the other methods. Moreover, it was generally as effective in promoting coloni- zation as double inoculation, and was often more effective than inoculation at transplant- ing. Mycorrhizal colonization was significantly reduced by the higher P concentration. The use of Myconate®, a water-soluble form of the flavonoid formononetin, significantly stimulated colonization in Salvia.
SPACE VECTOR BASED VARIABLE SWITHCHING FREQUENCY PWM ALGORITHMS FOR INDUCTION MOTOR DRIVES WITH REDUCED COMPLEXITY

This paper presents a simple space vector based variable switching frequency PWM algorithm for induction motor drives. The classical space vector approach needs the calculation of angle, sector and reference voltage in each sampling period, which increases the complexity of the PWM algorithm. To reduce the complexity, this paper presents a simple space vector approach in which by using the phase voltages the switching times are calculated in a simple form. By using the proposed approach various switching sequences such as space vector PWM (SVPWM) basic bus-clamping PWM (BBCPWM) and advance busclamping PWM (ABCPWM) algorithms are derived. Then, the rms flux ripple which is a measure of current ripple characteristics were plotted for all the sequences. Based on the rms flux ripple characteristics, the zones of superior performance are identified. Then, in each sampling time period, the suitable sequence, which gives reduced flux ripple is applied to the. To validate the proposed algorithm simulation studies have been carried on v/f controlled induction motor drive at various modulation indices and the results are presented. The results show the effectiveness of the proposed work.
Carcass composition and skeletal muscle morphology of swine expressing an insulin-like growth factor I transgene §

Abstract. Research was conducted to determine if directing expression of insulin-like growth factor I (IGF1) specifically to striated muscle would enhance lean muscle growth in swine. At 120 kg BW, 25 transgenic (T) and 26 control (C) pigs were sacrificed to evaluate carcass composition. T-pigs had lower percentages of fat and higher percentages of lean tissues than C-pigs for the overall carcass and each carcass region (P ≤ 0.002 for each). Expression of the IGF1 transgene did not alter the percentages of the three fiber types in the five skeletal muscles, however, fiber areas of longissimus dorsi muscle (LM) and serratus ventralis were larger (P ≤ 0.031) in T- than in C-pigs. In Tpigs the relative abundance of IGF1 mRNA in gastrocnemius, gluteus medius, LM, and the average for all five skeletal muscles (ASM) was positively (P ≤ 0.011) correlated with percentage of carcass lean (r = +0.597 to 0.804), whereas the relative abundance of IGF1 mRNA in the LM and the ASM was negatively (P ≤ 0.047) correlated with average backfat (r = −0.546 and −0.488, respectively). Based on these results we conclude that expression of IGF1 specifically in skeletal muscle had a positive effect on carcass composition of swine.
A preliminary revision of the Synalpheus paraneptunus Coutière, 1909 species complex (Crustacea: Decapoda: Alpheidae)

The western Atlantic Synalpheus paraneptunus Coutière, 1909 species complex is revised based on the type material kept in the National Museum of Natural History, Smithsonian Institution, Washington DC (USNM), specimens from Dominica, Puerto Rico and some other Caribbean localities (USNM), and fresh material recently collected in Belize and Panama. The type material of S. paraneptunus, composed of three specimens, appears to include more than one species. Therefore, S. paraneptunus is restricted to the holotype from Morrosquillo, Colombia, dredged from 77 m. The identity of the two paratypes, one of them an abnormal female, could not be satisfyingly determined. Five species are described as new. Synalpheus duffyi n. sp. is described based on the recently collected material from Isla Grande, Panama. The colony structure of S. duffyi n. sp. , including the large number of sexually undeveloped individuals and one larger breeding female, suggests eusocial life style. A further presumably eusocial species, S. riosi n. sp. , significantly larger than S. duffyi n. sp. , is described based on 139 specimens from Dominica, all apparently forming a single colony. Furthermore, three pair-living species are recognized: S. brevidactylus n. sp. from Isla Grande and Bocas del Toro, Panama; S. bocas n. sp. from Bocas del Toro, Panama, S. belizensis n. sp. from Carrie Bow Cay, Belize. All reported species are contrasted to each other morphologically; occurrence (in large groups vs. pairwise) and colour patterns are also considered where data is available. A provisionary key to six known species of the S. paraneptunus complex is provided.
The Politics of Legislative Evaluations: Fire-Alarm and Police Patrol as Oversight Procedures

Oversight is the evaluative function of legislatures. During oversight, legislators monitor policy implementation to detect and remedy problems, or violations of legislative intent. Most oversight, like formative evaluation, is directed at producing information that can be used by legislators and administrators to improve policies during implementation. Indeed, legislators seldom use oversight to decide whether a policy should be discontinued. This article examines how state legislatures practice evaluation by analyzing oversight strategies used to monitor recent education reforms in six states (Arizona, California, Florida, Georgia, Minnesota and Pennsylvania). ’ The central theme of the article is the inextricable link between politics and oversight; the choice of oversight strategy, and, therefore, the methods legislatures use to evaluate policy implementation, are driven largely by politics. The study found that oversight of education reform in the six sample states was conducted in ways that minimized time commitments and maximized political benefits for legislators.
Diptera, Drosophilidae: historical occurrence in Brazil

This study presents a literature review of Drosophilidae (Diptera) species occurrence in Brazil. The number of species recorded is 304, with Drosophila being the genus with the greatest number of species, followed by Zygothrica , Hirtodrosophila and Diathoneura , which belong to the Drosophilinae subfamily. Drosophila was shown to be the most investigated taxon in the family, with the best resolved species distribution. The low number of records of species from other genera indicates the paucity of studies specifically designed to investigate these species. Records of species for some regions of the country like the north and northeast, as well as for some biomes like Caatinga, Pantanal and the Pampas, are likewise rare. Apart from the banana bait, different collection methods may be necessary, like the collection at other oviposition resources, the use of baits other than fermenting fruit, and the adoption of sampling approaches that do not use baits.
Resistance mechanisms to fenazaquin in Iranian populations of two-spotted spider mite, Tetranychus urticae Koch (Acari: Tetranychidae)

Resistance mechanisms to fenazaquin were surveyed in Iranian populations of the two-spotted spider mite, Tetranychus urticae Koch. The bioassay was carried out on four populations, collected from Isfahan, Yazd and Rasht using the leaf-dip method. The results showed that resistance ratios of Isfahan, Yazd and Rasht populations were 3109-, 439.5- and 10.53-fold, respectively, compared with the susceptible population. Enzyme assays revealed that esterase activities in the Isfahan, Yazd and Rasht populations were 3.9-, 1.8- and 1.5-fold higher than that in the susceptible population, respectively, when α-naphthyl acetate was used as the substrate. Glutathione S-transferase (GST) activity in the Isfahan, Yazd and Rasht populations was 2.3-, 2.4- and 1.4-fold higher, respectively, than that in the susceptible one. Zymogram analysis of esterase and GST showed that there was some difference in the pattern of bands between the populations. Also, the activity of lipase in Yazd, Isfahan and Rasht populations was 1.98, 1.68 and 2.84-fold more than that in the susceptible population. Furthermore, the results showed that the amount of cytochrome P450 was much higher in Isfahan and Yazd populations than in the susceptible compartment. The bioassay and biochemical results suggested the involvement of three detoxification enzymes, esterase, MFO and GST, in fenazaquin resistance but the role of these enzymes in Isfahan and Yazd populations was low. Due to high resistance ratio in the Isfahan and Yazd populations, in addition to metabolic resistance, it seems the main resistance mechanism to fenazaquin is the insensitivity of the target site.
Glc7-E101Q is a novel tool for integrated genomic and proteomic analysis of PP1Glc7 phosphatase functional networks in Saccharomyces cerevisiae

Reversible phosphorylation is a major mechanism for regulating the activity, localization and stability of proteins required for vital cellular processes such as glucose metabolism, gene expression, establishment of polarity, mitosis and cytokinesis. Phospho-regulation is driven by the activities of kinases and phosphatases. Together, these enzymes account for ∼3% of eukaryotic genomes and it is estimated that 30% of the eukaryotic proteome is composed of phospho-proteins. Protein kinases (PKs) have been studied extensively, however relatively little is known regarding the signaling networks of protein phosphatases (PPases). The identification of PPase functional networks has been slow due to the redundant nature of the majority of PPases, the complexity of their substrate recognition in vivo, and the lack of large-scale analyses that would facilitate network analysis. We hypothesized that large-scale analysis of genetic interactions using the Synthetic Genetic Array (SGA) and proteomic analyses using 2D-PAGE Difference Gel Electrophoresis (DiGE) could reveal PPase functional networks. Here, we apply this approach to the essential and conserved PP1 PPase Glc7 as it regulates numerous cellular processes in budding yeast. For this study, we created a glc7 hypomorphic mutant (glc7-E101Q) suited for both SGA and DiGE analyses. SGA analysis of glc7-E101Q revealed a broad network of 147 synthetic sick/lethal (SSL) and 178 synthetic rescue (SR) interactions. DiGE comparison of the glc7-E101Q proteome relative to wild-type at medium-resolution (∼1000 proteins) revealed alterations in 39 proteins that changed as a consequence of both the mutation and growth conditions. One of the proteins identified in this analysis was Eno1, a non-essential enolase that is mis-regulated in the presence of glucose and identified a SR mutation in the glc7-E101Q SGA. Subsequent phenotypic analysis suggests a novel, non-metabolic role for Eno1 in the Glc7 interaction network. Our results reveal that parallel analysis, using SGA and DIGE, can reveal novel functions and networks that a single analysis may not detect.
SEARCHING FOR GENETIC DETERMINANTS FOR SODIUM LITHIUM COUNTERTRANSPORT, AN INTERMEDIATE TRAIT FOR ESSENTIAL HYPERTENSION

Essential hypertension (EH) is a major risk factor for cardiovascular disorders, the leading cause of death in the United States. Given its great public health impact, it is crucial to understand the genetic basis of EH. EH is highly heterogeneous and to use an intermediate phenotype of EH, sodium lithium countertransport (SLC), will provide substantial advantage for disease genes discovery. We proposed two approaches to explore the genes for SLC.The first study examined the relationship between SLC and a positional candidate gene, SLC34A2, which is linked to SLC in baboon. We sequenced gene SLC34A2 in baboon and human. Strong homology was established in exonic organization and sequence between human and baboon SLC34A2 genes and extensive variation in both species was identified. Association studies between SLC and SLC34A2 were carried out in 1856 RFHS phase II individuals and 634 baboons. Significant association of SLC with human SNP rs3775909 (p=0.03) in SLC34A2 and haplotype block 2 (p<0.005) were observed. Strong evidence for association of SLC with SLC34A2 was found for baboon SNP Asn136Asn (p=0.0001). Consistent findings in two different species implied that SLC34A2 may be one of the genes involved in SLC. However, linkage analyses conditional on genotypes of baboon Asn136Asn suggest that Asn136Asn is not the primarily functional site for SLC. We conclude that SLC34A2 is associated with SLC, though it may not be the major effect gene.In second study, we integrated gene expression micrarray with linkage analysis to search for genes for SLC. Two independent microarrays (U133A and U133_plus_2.0) were used to identify the differentially expressed genes in high verse low SLC groups. Five genes, IER3, ARHGAP15, CD47, CDKAL1 and PRKRA, were among top 1% of differentially expressed genes in both arrays and also mapped to linkage region for SLC in RFHS Phase II population. A follow-up association study for IER3 shows that SNP rs8512 is significantly associated with SBP (p=0.002) and DBP (p=0.0008), and SNP rs2284174 has marginal association with SLC (p=0.055) and SBP (p=0.085). In conclusion, we identified some interesting susceptible genes for SLC by combining gene expression profiling and linkage study.
Bacterial protease activity, an indicator of bacterial pathogenicity in chronic wounds even in the absence of overt clinical signs

• Bacterial proteases are a type of virulence factor, which have been implicated in a range of medical conditions, including wound infections. • Clinical Signs of critical colonisation/infection may not be apparent in all chronic wounds. • Measuring CFU levels only in chronic wounds does not determine if bacteria are in a pathogenic state. • Testing wound fluid for bacterial protease activity may be a useful method for detecting the presence of pathogenic bacteria, at a clinically significant stage in the infection continuum. • On this basis, a new qualitative point of care test is under development to detect bacterial protease activity in chronic wounds, which may help identify the presence of pathogenic bacteria.