Miracle-dz/UniFAR-FTUs huggingface dataset:
Positive regulation of the pts operon of Escherichia coli: genetic evidence for a signal transduction mechanism

The pts operon of Escherichia coli is composed of the genes ptsH, ptsI, and crr, which code for three proteins of the phosphoenolpyruvate-dependent phosphotransferase system (PTS): the HPr, enzyme I (EI), and EIIIGlc proteins, respectively. These three genes are organized in a complex operon in which the major part of expression of the distal gene, crr, is initiated from a promoter region within ptsI. Expression from the promoter region of the ptsH and ptsI genes has been studied in vivo by using gene fusions with lacZ. Transcription from this promoter region is under the positive control of catabolite activator protein (CAP)-cyclic AMP (cAMP) and is also enhanced during growth in the presence of glucose (a PTS substrate). This report describes a genetic characterization of the mechanism by which growth on glucose causes transcriptional stimulation of the pts operon. This regulation is dependent on transport through the glucose-specific permease of the PTS, EIIGlc. Our results strongly suggest that transcriptional regulation of the pts operon is the consequence of an increase in the level of unphosphorylated EIIGlc which is produced during glucose transport. Furthermore, overproduction of EIIGlc in the absence of transport was found to stimulate expression of the pts operon. We also observed that CAP-cAMP could cause stimulation independently of the EIIGlc and that glucose could activate in the absence of cAMP in a strain overproducing EIIGlc. Our results indicate that glucose acts like an environmental signal through a mechanism of signal transduction. A sequence similarity between the C terminus of EIIGlc and the consensus of transmitter modules of the sensor proteins defined by E. C. Kofoid and J. S. Parkinson (Proc. Natl. Acad. Sci. USA 85:4981-4985, 1988) suggests that EIIGlc might have properties in common with the sensors of the two-component systems.
Microscopic Anatomy of the Ringed Seal (Phoca hispida) Lower Respiratory Tract

The microscopic anatomy of the ringed seal lung exhibits unique features and many features similar to those described in other seal species. Unique features include: Trachealis muscle predominately oriented longitudinally; Large veins within the tracheal wall supported by elastic fibers; Goblet cells and pseudostratified epithelium lining the duct system of bronchial glands of the segmental bronchi; Lamina propria of the segmental bronchus heavily invested with elastic fibers clustered into dense longitudinal bundles; and Capillaries and venules covered with squamous epithelium protruding into bronchiolar lumina. Common features include: Cartilage support of the bronchial tree extending distally into respiratory bronchioles; Smooth muscle enhancements in the distal airways producing sphincter like formations; and Lungs extensively supported with interstitial tissue, which divide lungs into lobules.
The Potential for Green Fluorescent Protein as a Screening Tool in the Production of Haploid Potato

___________________________________________________________________ ii Acknowledgements ___________________________________________________________ iii List of Tables and Figures _____________________________________________________ vi Chapter 1: Introduction ______________________________________________________ 1 Haploids __________________________________________________________________ 1 Haploid Inducing Pollinators _________________________________________________ 1 Transformations ____________________________________________________________ 3 Green Fluorescent Protein____________________________________________________ 3 Purpose ___________________________________________________________________ 4 Chapter 2: Materials and Methods _____________________________________________ 6 Plant Material ______________________________________________________________ 6 Transformation_____________________________________________________________ 7 Agrobacteria preparation ___________________________________________________ 8 Agrobacteria transformation _________________________________________________ 8 Agrobacteria elimination ____________________________________________________ 8 Media ___________________________________________________________________ 9 Flow Cytometry_____________________________________________________________ 9 Primary Transformant GFP Testing ___________________________________________ 10 Self pollinations ___________________________________________________________ 13 Anther culture_____________________________________________________________ 15 Procedure_______________________________________________________________ 15 Media __________________________________________________________________ 16 Phenotypic selections _______________________________________________________ 16 Seedling GFP Testing_______________________________________________________ 17 Initial screening __________________________________________________________ 17 High, Medium, Low Replicated Study _________________________________________ 17 Low, None Replicated Study_________________________________________________ 17 Pollen screening ___________________________________________________________ 18 Field Tests ________________________________________________________________ 18 Visual Screening of GFP Expression __________________________________________ 20 Haploid Induction__________________________________________________________ 20 Chapter 3: Results __________________________________________________________ 22 Transformation Results _____________________________________________________ 22 GFP Seedling Selection Results_______________________________________________ 23 High, Medium, Low Replicated Study _________________________________________ 30 Low, None Replicated Study_________________________________________________ 30 Initial GFP Selections _____________________________________________________ 34 Phenotypic Selections______________________________________________________ 41 Mature Plant GFP and Vigor________________________________________________ 44
Multi-input sliding mode control of nonlinear systems with uncertain affine dependence on the control

In the extension to multi-input non linear uncertain systems of the sliding mode methodology a crucial role is played by the matrix pre multiplying the control in the dynamic equation of the sliding output. If this matrix is perfectly known and invertible it is possible to transform a multi-input sliding mode control problem in an almost decoupled set of single input problems. If this matrix is uncertain nothing can be done in general, and the investigation is oriented to find condition ensuring the feasibility of control strategies in a progressively increasing set of uncertain matrices. In the case of uncertain but constant matrices it is possible, in principle, to manage the case in which the matrix in question is invertible. The corresponding adaptive or switching strategy suffer of the curse of dimensionality of the so called Unmixing Set. In this paper the case of time and state varying uncertain matrix is dealt with. The more general class of such a matrices for which there is, at least locally, a solution of the problem is found. The introduction of artificial integrators in the output channel (the integral sliding mode control methodology) allows the practical implementation of the control law without requiring the a priori knowledge of parameters featured by the solution of a relevant nonlinear Lyapunov equation.
Differentials in mortality.

Changes and differences in mortality rates are analyzed for three adult age groups and by sex for Scotland and compared with data for selected developed countries including England and Wales for the period 1973-1975 to 1981-1983. For five out of the six age-sex groups Scotland had the highest mortality for all causes of death. Furthermore in many cases the differentials between Scotland and the other countries considered have increased over time. The author suggests that both physical and social environmental factors as well as differences in life-styles may be associated with these differentials.
Using Deep Reinforcement Learning to Improve Sensor Selection in the Internet of Things

We study the problem of handling timeliness and criticality trade-off when gathering data from multiple resources in complex environments. In IoT environments, where several sensors transmitting data packets - with various criticality and timeliness, the rate of data collection could be limited due to associated costs (e.g., bandwidth limitations and energy considerations). Besides, environment complexity regarding data generation could impose additional challenges to balance criticality and timeliness when gathering data. For instance, when data packets (either regarding criticality or timeliness) of two or more sensors are correlated, or there exists temporal dependency among sensors, incorporating such patterns can expose challenges to trivial policies for data gathering. Motivated by the success of the Asynchronous Advantage Actor-Critic (A3C) approach, we first mapped vanilla A3C into our problem to compare its performance in terms of criticality-weighted deadline miss ratio to the considered baselines in multiple scenarios. We observed degradation of the A3C performance in complex scenarios. Therefore, we modified the A3C network by embedding long short term memory (LSTM) to improve performance in cases that vanilla A3C could not capture repeating patterns in data streams. Simulation results show that the modified A3C reduces the criticality-weighted deadline miss ratio from 0.3 to 0.19.
Vegetable and fruit consumption, education and plasma vitamin C concentration in Russian and Finnish Karelia, 1992–2002

Abstract Objective To examine (i) whether the consumption of fresh vegetables, fruit and berries is associated with plasma vitamin C concentration and (ii) educational differences in plasma vitamin C concentration in two neighbouring areas in Russia and Finland. Design Cross-sectional risk factor surveys in 1992, 1997 and 2002. Logistic regression analysis was applied to examine the associations of consumption of selected foods and education with plasma vitamin C concentration. Setting District of Pitkäranta in the Republic of Karelia, Russia and North Karelia, Finland. Subjects Adults aged 25–64 years: 579 men and 612 women in Pitkäranta; 974 men and 642 women in North Karelia. Results The plasma vitamin C concentration was strikingly low in Pitkäranta, Russia across the study years. During the 10 years of monitoring, the mean plasma vitamin C concentration among men ranged from 2·5 to 8·0 μmol/l in Pitkäranta, Russia and from 27·1 to 53·9 μmol/l in North Karelia, Finland. In both areas, daily consumption of fruit was most strongly associated with plasma vitamin C, while the association of fresh vegetable consumption with plasma vitamin C was less consistent. Consumption of berries was less important in explaining plasma vitamin C. In Pitkäranta, the plasma vitamin C concentration was lower among respondents in the lowest education group. Conclusions Differences in the consumption of fresh vegetables and fruit resulted in notable differences in vitamin C status between Pitkäranta and North Karelia in spring. In comparative settings, knowledge of local food culture and validation pilots are important before conducting large population surveys.
Biomarker Validation of Recent Unprotected Sexual Intercourse in a Prospective Study of Young Women Engaged in Sex Work in Phnom Penh, Cambodia

Background Accurate measurement of unprotected sex is essential in HIV prevention research. Since 2001, the 100% Condom Use Program targeting female sex workers (FSWs) has been a central element of the Cambodian National HIV/AIDS Strategy. We sought to assess the validity of self-reported condom use using the rapid prostate-specific antigen (PSA) test among Cambodian FSWs. Methods From 2009 to 2010, we enrolled 183 FSWs in Phnom Penh in a prospective study of HIV risk behavior. Prostate-specific antigen test results from the OneStep ABAcard were compared with self-reported condom use in the past 48 hours at quarterly follow-up visits. Results Among women positive for seminal fluid at the first follow-up visit, 42% reported only protected sex or no sex in the detection period. Discordant results were more likely among brothel and street-based FSW versus entertainment (56% vs. 17%), recent (last 3 months) amphetamine-type stimulant (ATS) users (53% vs. 20%), and those with 5 or more partners in the past month (58% vs. 13%). In multivariable regression models, positive PSA results were associated with recent ATS use (adjusted risk ratio [ARR], 1.5; 95% confidence interval [CI], 1.1–2.2), having a nonpaying last sex partner (ARR, 1.7; CI, 1.2–2.5), and sex work venue (ARR, 3.0; CI, 1.4–6.5). Correspondingly, women with a nonpaying last sex partner were more likely to report unprotected sex (ARR, 1.5; CI, 1.1–2.2), but no associations were found with sex work venue or ATS use. Conclusions Results confirm the questionable validity of self-reported condom use among FSW. The PSA biomarker assay is an important monitoring tool in HIV/sexually transmitted infection research including prevention trials.
New Algorithms for Large-Scale Support Vector Machines. (Nouveaux Algorithmes pour l'Apprentissage de Machines à Vecteurs Supports sur de Grandes Masses de Données)

Internet as well as all the modern media of communication, information and entertainment entails a massive increase of digital data quantities. In various domains ranging from network security, information retrieval, to online advertisement, or computational linguistics automatic methods are needed to organize, classify or transform terabytes of numerical items. Machine learning research concerns the design and development of algorithms that allow computers to learn based on data. A large number of accurate and eﬃcient learning algorithms now exist and it seems rewarding to use them to automate more and more complex tasks, especially when humans have diﬃculties to handle large amounts of data. Unfortunately, most learning algorithms performs well on small databases but cannot be trained on large data quantities. Hence, there is a deep need for machine learning methods able to learn with millions of training instances so that they could enjoy the huge available data sources. We develop these issues in our introduction, in Chapter 1. In this thesis, we propose solutions to reduce training time and memory requirements of learning algorithms while keeping strong performances in accuracy. In particular, among all the machine learning models, we focus on Support Vector Machines (SVMs) that are standard methods mostly used for automatic classiﬁcation. We extensively describe them in Chapter 2 Throughout this dissertation, we propose diﬀerent original algorithms for learning SVMs, depending on the ﬁnal task they are destined to. First, in Chapter 3, we study the learning process of Stochastic Gradient Descent for the particular case of linear SVMs. This leads us to deﬁne and validate the new SGD-QN algorithm. Then we introduce a brand new learning principle: the Process/Reprocess strategy. We present three algorithms implementing it. The Huller and LaSVM are discussed in Chapter 4. They are designed towards training SVMs for binary classiﬁcation. For the more complex task of structured output prediction, we reﬁne intensively LaSVM: this results in the LaRank algorithm which is detailed in Chapter 5. Finally, in Chapter 6 is introduced the original framework of learning under ambiguous supervision which we apply to the task of semantic parsing of natural language. Each algorithm introduced in this thesis achieves state-of-the-art performances, especially in terms of training speed. Almost all of them have been published in international peer-reviewed journals or conference proceedings. Corresponding implementations have also been released. As much as possible, we always keep the description of our innovative methods as generic as possible because we want to ease the design of any further derivation. Indeed, many directions can be followed to carry on with what we present in this dissertation. We list some of them in Chapter 7.
The 1.65 Å resolution structure of the complex of AZD4547 with the kinase domain of FGFR1 displays exquisite molecular recognition.

The fibroblast growth factor receptor (FGFR) family are expressed widely in normal tissues and play a role in tissue repair, inflammation, angiogenesis and development. However, aberrant signalling through this family can lead to cellular proliferation, evasion of apoptosis and induction of angiogenesis, which is implicated in the development of many cancers and also in drug resistance. The high frequency of FGFR amplification or mutation in multiple cancer types is such that this family has been targeted for the discovery of novel, selective drug compounds, with one of the most recently discovered being AZD4547, a subnanomolar (IC50) FGFR1 inhibitor developed by AstraZeneca and currently in clinical trials. The 1.65 Å resolution crystal structure of AZD4547 bound to the kinase domain of FGFR1 has been determined and reveals extensive drug-protein interactions, an integral network of water molecules and the tight closure of the FGFR1 P-loop to form a long, narrow crevice in which the AZD4547 molecule binds.
Comparative diagnosis of Mycobacterium bovis by Polymerase chain reaction and Ziel- Neilson staining technique using Milk and nasal washing

The present study elucidated the status of Bovine tuberculosis (BTB) diagnosis by acid-fast staining and polymerase chain reaction using milk and nasal washing samples to compare their efficacy in the diagnosis of bovine tuberculosis. The study was carried out in unorganized dairy sector and cows attending Madras Veterinary College LAC (OP) hospital. Ninety two nasal washings and eighty two milk samples were collected and subjected to acid fast staining and polymerase chain reaction (PCR). Of the 92 smears examined, 2 (2.17 percent) were found positive for acid-fast mycobacteria. Milk sample smears from 82 animals were subjected to acid-fast staining of which, 2(2.44 percent) were positive for acid-fast mycobacteria. DNA was extracted from 92 nasal washing and 82 milk samples were subjected to Polymerase chain reaction (PCR). Nine (9.8 per cent) animals were positive for nasal washing PCR and 10 animals (12.2) were positive for milk PCR. Seven animals positive for nasal washing are also positive for milk PCR. Two animals positive for nasal washing were dry animals and three pleuriparous animals positive for milk PCR were not positive for nasal washing. PCR have high sensitivity (100 per cent) and specificity (97.6 per cent) of detecting M.bovis in nasal washings. Similarly for milk PCR have high sensitivity (100 per cent) and specificity (87.6 per cent).
Morphological Aspects of the Larval Instars of Chrysomya albiceps (Diptera, Calliphoridae) Reared in the Laboratory

In order to study the morphology of young Chrysomya albiceps forms, newly hatched larvae were collected at 2 hr intervals, during the first 56 hr; after this time the collection was made at 12 hr intervals. For identification and drawing, larvae were placed between a slide and a coverslip. The cephalopharyngeal skeletons along with the first and last segments were cut off for observation of their structures and spiracles. The larvae present microspines, which are distributed randomly throughout the 12 segments of the body surface; the cephalopharyngeal skeleton varies in shape and extent of sclerotization according to larval instar; the second and third instars have relatively long processes (tubercles) on the dorsal, lateral and ventral surfaces, with microspine circles on the terminal portion. Guimaraes et al. (1978) were the first researchers who recorded the presence of Chrysomya albiceps (Wiedemann, 1819), Chrysomya megacephala (Fabricius, 1974) and Chrysomya putoria (Wiedemann, 1818) in Brazil. According to them, these species were probably introduced in the southern region of Brazil by ships coming from Angola, Africa. These Diptera are considered important from the sanitary standpoint, since they may be mechanical vector of enteropathogens for humans as well as cause facultative myiasis. Today, they are widely distributed throughout the neotropical region (Prado & Guimaraes 1982, Baumgartner 1988), and have drawn the attention of several researchers. However, only the last two species have been well studied in terms of biology and taxonomy of the adults. The taxonomy of C. albiceps is still quite unknown since it was long thought to be indistinguishable from those of C. rufifacies (Macquart, 1842) (Patton 1922, Zumpt 1965, Kurahashi 1981, Richard & Gerrish 1983), a species that has not yet been recorded in Brazil. However, more accurate observations have shown some morphological aspects of the third instar of both species that allow their differentiation (Erzinclioglu 1987, Tantawi & Greenberg 1993). During the 70’s the two species were geographically isolated, C. albiceps being restricted to Africa and C. rufifacies to regions of Eastern Asia and Australia, although occupying the same biological niches in their respective natural biotopes
Wnt / ß-catenin activation by epigenetically aberrant stroma drives myelodysplastic syndrome

Tushar D. Bhagat, Si Chen, Matthias Bartenstein, A. ,Trevor Barlowe, Dagny Von Ahrens, Gaurav S. Choudhary, Patrick Tivnan, Elianna Amin, Mario Marcondes, Mathijs A. Sanders, Remco M. Hoogenboezem, Suman Kambhampati, Nandini Ramachandra, , Iaonnis Mantzaris, Vineeth Sukrithan, Remi Laurence, Robert Lopez, Prafullla Bhagat, Orsi Giricz, Davendra Sohal, Amittha Wickrema, Cecilia Yeung, Kira Gritsman, Peter Aplan, Konrad Hochedlinger, Yiting Yu, Kith Pradhan, Jinghang Zhang, John M. Greally, Siddhartha Mukherjee, Andrea Pellagatti, Jacqueline Boultwood, Britta Will, Ulrich Steidl, Marc H.G. P. Raaijmakers, H. Joachim Deeg, Michael G. Kharas*, Amit Verma
The role of Ar III in quantitative spectroscopy on hot argon plasmas

We perform quantitative optical emission spectroscopy on the hot core of the cathode region of a free-burning arc in argon under atmospheric pressure. As the peak temperatures in the centre of the discharge exceed 22 000K we are able to observe three spectra of argon (Ar I, Ar II and Ar III) and the continuum emission. We report on some inconsistencies concerning the evaluation of Ar III radiation in both line and continuum emission. These are caused by erroneous data in the literature and common misconceptions about the influence of Ar III on the plasma emission. We discuss the impact of this fact on published data. r 2006 Elsevier Ltd. All rights reserved. PACS: 52.25. b; 52.25. Jm; 52.70. m; 52.80. Mg