Crystal structure of a CAP-DNA complex: the DNA is bent by 90 degrees

The 3 angstrom resolution crystal structure of the Escherichia coli catabolite gene activator protein (CAP) complexed with a 30-base pair DNA sequence shows that the DNA is bent by 900. This bend results almost entirely from two 400 kinks that occur between TG/CA base pairs at positions 5 and 6 on each side of the dyad axis of the complex. DNA sequence discrimination by CAP derives both from sequence-dependent distortion of the DNA helix and from direct hydrogen-bonding interactions between three protein side chains and the exposed edges of three base pairs in the major groove of the DNA. The structure of this transcription factor-DNA complex provides insights into possible mechanisms of transcription activation

Total Variation Blind Deconvolution: The Devil Is in the Details

In this paper we study the problem of blind deconvolution. Our analysis is based on the algorithm of Chan and Wong [2] which popularized the use of sparse gradient priors via total variation. We use this algorithm because many methods in the literature are essentially adaptations of this framework. Such algorithm is an iterative alternating energy minimization where at each step either the sharp image or the blur function are reconstructed. Recent work of Levin et al. [14] showed that any algorithm that tries to minimize that same energy would fail, as the desired solution has a higher energy than the no-blur solution, where the sharp image is the blurry input and the blur is a Dirac delta. However, experimentally one can observe that Chan and Wong's algorithm converges to the desired solution even when initialized with the no-blur one. We provide both analysis and experiments to resolve this paradoxical conundrum. We find that both claims are right. The key to understanding how this is possible lies in the details of Chan and Wong's implementation and in how seemingly harmless choices result in dramatic effects. Our analysis reveals that the delayed scaling (normalization) in the iterative step of the blur kernel is fundamental to the convergence of the algorithm. This then results in a procedure that eludes the no-blur solution, despite it being a global minimum of the original energy. We introduce an adaptation of this algorithm and show that, in spite of its extreme simplicity, it is very robust and achieves a performance comparable to the state of the art.

Intrinsic pH-Sensitivity of Cells in the Retrotrapezoid Nucleus: Possible Role of Glia in Respiratory Drive

An increase in carbon dioxide (CO2) and protons (H+) are the primary signals for breathing. Cells that sense changes in CO2/H+ levels and increase breathing accordingly are located in a region of the caudal medulla oblongata called the retrotrapezoid nucleus (RTN). Specifically, select RTN neurons are intrinsically pH sensitive and send excitatory projections to the respiratory rhythm generator to drive breathing. Glial cells in the RTN are thought to contribute to this respiratory drive, possibly by releasing ATP in response to increases in CO2/H+ levels. However, pH sensitivity of RTN glial cells has yet to be determined. Therefore, the goal of my thesis is to determine if acutely dissociated RTN cells can respond to changes in pH in isolation. To make this determination I used ratiometric fluorescent microscopy to measure intracellular calcium in dissociated RTN cells during changes in bath pH. I found that a small percentage of RTN cells (16%) respond to bath acidification from pH 7.3 to pH 6.9 with an increase in fluorescence indicating an increase in intracellular calcium. Preliminary electrophysiological findings suggest that responsive cells are unable to make action potentials, thus suggesting their identity to be glia. These results indicate that a subset of pH sensitive cells in the RTN are intrinsically pH sensitive and that glia cells may possibly play a role in central chemoreception.

The Analysis of Airline Business Models in the Development of Possible Future Business Options

Innovations in the current interconnected world of organizations have lead to a focus on business models as a fundamental statement of direction and identity. Although industry transformations generally emanate from technological changes, recent examples suggest they may also be due to the introduction of new business models. In the past, different types of airline business models could be clearly separated from each other. However, this has changed in recent years partly due to the concentration process and partly to reaction caused by competitive pressure. At least it can be concluded that in future the distinction of different business models will remain less clear. To advance the use of business models as a concept, it is essential to be able to compare and perform analyses to identify the business models that may have the highest potential. This can essentially contribute to understanding the synergies and incompatibilities in the case of two airlines that are going in for a merger. This is illustrated by the example of Swiss Air-Lufthansa merger analysis. The idea is to develop quantitative methods and tools for comparing and analyzing Aeronautical/Airline business models. The paper identifies available methods of comparing airline business models and lays the ground work for a quantitative model of comparing airline business models. This can be a useful tool for business model analysis when two airlines are merged

Multiple proportion case-basing driven CBRE and its application in the evaluation of possible failure of firms

Case-based reasoning (CBR) is a unique tool for the evaluation of possible failure of firms (EOPFOF) for its eases of interpretation and implementation. Ensemble computing, a variation of group decision in society, provides a potential means of improving predictive performance of CBR-based EOPFOF. This research aims to integrate bagging and proportion case-basing with CBR to generate a method of proportion bagging CBR for EOPFOF. Diverse multiple case bases are first produced by multiple case-basing, in which a volume parameter is introduced to control the size of each case base. Then, the classic case retrieval algorithm is implemented to generate diverse member CBR predictors. Majority voting, the most frequently used mechanism in ensemble computing, is finally used to aggregate outputs of member CBR predictors in order to produce final prediction of the CBR ensemble. In an empirical experiment, we statistically validated the results of the CBR ensemble from multiple case bases by comparing them with those of multivariate discriminant analysis, logistic regression, classic CBR, the best member CBR predictor and bagging CBR ensemble. The results from Chinese EOPFOF prior to 3 years indicate that the new CBR ensemble, which significantly improved CBRs predictive ability, outperformed all the comparative methods.

Association of RNase mitochondrial RNA processing enzyme with ribonuclease P in higher ordered structures in the nucleolus: a possible coordinate role in ribosome biogenesis.

RNase mitochondrial RNA processing enzyme (MRP) is a nucleolar ribonucleoprotein particle that participates in 5.8S ribosomal RNA maturation in eukaryotes. This enzyme shares a polypeptide and an RNA structural motif with ribonuclease P (RNase P), a nuclear endoribonuclease originally described in the nucleus that processes RNA transcripts to generate their mature 5' termini. Both enzymes are also located in mitochondria. This report further characterizes the relationship between RNase MRP and RNase P. Antisense affinity selection with biotinylated 2'-O-methyl oligoribonucleotides and glycerol gradient fractionation experiments demonstrated that small subpopulations of RNase MRP and RNase P associate with each other in vivo in macromolecular complex, possibly 60-80S preribosomes. This latter notion was supported by fluorescence in situ hybridization experiments with antisense oligonucleotides that localized that RNA components of RNase MRP and RNase P to the nucleolus and to discrete cytoplasmic structures. These findings suggest that small subpopulations of RNase MRP and RNase P are physically associated, and that both may function in ribosomal RNA maturation or ribosome assembly.

Flashlight Europe N°7–09 July 2015. Greece After the Referendum: Three Possible Scenarios for the Euro Area

About ten days ago Alexis Tsipras, the Greek prime minister, announced that there was going to be a referendum, and thus terminated the negotiations on a new rescue package unilaterally. Since then the euro area has been plunged into a wholly unprecedented political crisis. Whether or not Greece can re-main in the monetary union is more uncertain than ever, and decisions that can give a new twist to the political and financial situation are being made almost every day. The Greek banks have been closed for over a week. The economic data are deteriorating rapidly. And yet a solution is nowhere to be seen. The No vote in the Greek referendum has not exactly improved the chances of reaching an agree-ment. For the time being the positions seem to have become uncompromising. At the summit of the heads of state and government on 7 July the Greek government was given five days and a “final deadline” in order to come up with viable proposals for reform. Thus the next few days are of crucial im-portance. At the weekend the heads of state and government of all 28 EU member states are going to meet in order to decide the future of Greece. This flashlight europe provides an overview of the events of the last few days, outlines possible scenarios for what may happen in the near future, and identifies factors which may exert an influence in the short term. We are not trying to give an exact forecast or to formulate action recommendations. But we are trying to shed some light on a confusing situation by identifying important patterns and some of the salient factors.

Az európai gazdasági kormányzás előtt álló kihívások. A hármas tagadás lehetetlensége (Challenges of European economic governance. The impossible trinity of denial.)

Az európai gazdasági integráció folyamata olyan kényszerhelyzetekben formálódott a múltban, amelyek a közgazdaságtudományban jól ismert lehetetlen háromság alapján is leírhatók. Az Európai Monetáris Rendszer a rögzített árfolyam-mechanizmusra és önálló jegybanki politikára épített, korlátozva a tőkemozgásokat. A Gazdasági és Monetáris Unió ugyanakkor a tőke szabad áramlásával és az árfolyamok visszavonhatatlan rögzítésével felszámolta a tagállami szintű jegybanki autonómiát. Az euróövezet működése egyszersmind arra a háromszoros tagadásra épül(t), hogy 1. nem lehetséges az euróövezetből való kilépés, 2. nem engedélyezett a kimentés és 3. nem kerülhet sor államcsődre. A 2008-ban Európát is elérő pénzügyi és gazdasági válság azonban elemi erővel mutatott rá e hármas tiltás tarthatatlanságára. A gazdasági kormányzás körül kibontakozott viták így jól közelíthetők a három tiltó szabály egyidejű érvényesülése lehetetlenségének bemutatásával, számba véve az egyes opciók költségeit és lehetséges hasznait. / === / The process of economic integration in the EU has been shaped by the well-known theorem of the impossible trinity. Accordingly, the European Monetary System was built upon a mix of a fixed exchange-rate regime and an autonomous monetary policy, thereby constraining capital mobility. In launching the EMU project, the EU countries decided to fix national currencies irrevocably and maintain full capital mobility, in exchange for delegating their monetary policy upwards to a supranational level. The introduction of the Euro zone, however, has simultaneously meant denial of the following three elements: (1) exit, (2) bail-out, and (3) default. Nevertheless, the 2008–9 financial and economic crisis has demonstrated mercilessly that these three pillars are incompatible with each other. So the current debates on reshaping economic governance in the EU can be modelled by introducing the “impossible trinity of denial”, concentrating on the benefits and the costs of each option.

The impossible anamesis. Memory versus history in Hubert Aquin’s « Blackout »

Soon after joining the Canadian Confederation in 1867, the province of Quebec adopted the phrase « Je me souviens » ("As I recall") as its "national" motto, although many Québécois do not remember today what they were supposed to memorize, as collective subject, when their government voted this motion. My thesis is that contrary to other countries which have a strong sense of history based on a secular tradition, this process was more complicated in Quebec — as if a collective memory loss lied at the heart of it's history. Through a rereading of Hubert Aquin's cult novel, Trou de mémoire (in its English translation Blackout), first published in 1968, I try to illustrate this paradox and to emphasize the heuristic functions of memory blanks, gaps and lapses in certain postmodern narratives, after the historical breakdown of "the great narratives" (Lyotard). In this perspective, the example of Quebec, through the voice of one of its more gifted yet controversial novelist, can be seen as emblematic of what happens when the mnemonic impossibility of rewriting history opens up new possibilities for writing fiction.

The impossible anamesis. Memory versus history in Hubert Aquin’s « Blackout »

Soon after joining the Canadian Confederation in 1867, the province of Quebec adopted the phrase « Je me souviens » ("As I recall") as its "national" motto, although many Québécois do not remember today what they were supposed to memorize, as collective subject, when their government voted this motion. My thesis is that contrary to other countries which have a strong sense of history based on a secular tradition, this process was more complicated in Quebec — as if a collective memory loss lied at the heart of it's history. Through a rereading of Hubert Aquin's cult novel, Trou de mémoire (in its English translation Blackout), first published in 1968, I try to illustrate this paradox and to emphasize the heuristic functions of memory blanks, gaps and lapses in certain postmodern narratives, after the historical breakdown of "the great narratives" (Lyotard). In this perspective, the example of Quebec, through the voice of one of its more gifted yet controversial novelist, can be seen as emblematic of what happens when the mnemonic impossibility of rewriting history opens up new possibilities for writing fiction.

Nutrition and health: the issue is not food, nor nutrients, so much as processing [Invited commentary]

Orthodox teaching and practice on nutrition and health almost always focuses on nutrients, or else on foods and drinks. Thus, diets that are high in folate and in green leafy vegetables are recommended, whereas diets high in saturated fat and in full-fat milk and other dairy products are not recommended. Food guides such as the US Food Guide Pyramid are designed to encourage consumption of healthier foods, by which is usually meant those higher in vitamins, minerals and other nutrients seen as desirable.What is generally overlooked in such approaches, which currently dominate official and other authoritative information and education programmes, and also food and nutrition public health policies, is food processing. It is now generally acknowledged that the current pandemic of obesity and related chronic diseases has as one of its important causes increased consumption of convenience including pre-prepared foods(1,2). However, the issue of food processing is largely ignored or minimised in education and information about food, nutrition and health, and also in public health policies.A short commentary cannot be comprehensive, and a general proposal such as that made here is bound to have some problems and exceptions. Also, the social, cultural, economic and environmental consequences of food processing are not discussed here. Readers comments and queries are invited

The queen is dead-long live the workers: intraspecific parasitism by workers in the stingless bee Melipona scutellaris

Insect societies are well known for their high degree of cooperation, but their colonies can potentially be exploited by reproductive workers who lay unfertilized, male eggs, rather than work for the good of the colony. Recently, it has also been discovered that workers in bumblebees and Asian honeybees can succeed in entering and parasitizing unrelated colonies to produce their own male offspring. The aim of this study was to investigate whether such intraspecific worker parasitism might also occur in stingless bees, another group of highly social bees. Based on a large-scale genetic study of the species Melipona scutellaris, and the genotyping of nearly 600 males from 45 colonies, we show that similar to 20% of all males are workers` sons, but that around 80% of these had genotypes that were incompatible with them being the sons of workers of the resident queen. By tracking colonies over multiple generations, we show that these males were not produced by drifted workers, but rather by workers that were the offspring of a previous, superseded queen. This means that uniquely, workers reproductively parasitize the next-generation workforce. Our results are surprising given that most colonies were sampled many months after the previous queen had died and that workers normally only have a life expectancy of similar to 30 days. It also implies that reproductive workers greatly outlive all other workers. We explain our results in the context of kin selection theory, and the fact that it pays workers more from exploiting the colony if costs are carried by less related individuals.

Attributions for the performance of self and other: It matters who the "other" is

This study tested hypotheses that locus of causality attributions for the academic performance of others are influenced by whether the other is a specific individual, or a typical other, and whether the other is similar or dissimilar to self. The research was carried out in two studies. Study 1 entailed development of two scales to measure perceptions of interpersonal similarity: 254 Australian undergraduates rated their similarity to either a specific other or to typical other students. In Study 2, 332 subjects completed one of the 16-item scales developed in Study 1, along with Rosenberg's self-esteem scale, and self-attribution and other-attribution versions of the Multidimensional Multi-attribution Causation Scale (MMCS). Results showed that attributions for the academic performance of others were strongly affected by whether the other was perceived to be similar or dissimilar to self, especially when the other was a specific individual. In particular, causal attributions for similar specific others were more favourable than attributions for self.

Postural activity of the diaphragm is reduced in humans when respiratory demand increases

1. Respiratory activity of the diaphragm and other respiratory muscles is normally co-ordinated with their other functions, such as for postural control of the trunk when the limbs move. The integration may occur by summation of two inputs at the respiratory motoneurons. The present study investigated whether postural activity of the diaphragm changed when respiratory drive increased with hypercapnoea. 2. Electromyographic (EMG) recordings of the diaphragm and other trunk muscles were made with intramuscular electrodes in 13 healthy volunteers. Under control conditions and while breathing through increased dead-space,subjects made rapid repetitive arm movements to disturb the stability of the spine for four periods each lasting 10 s, separated by 50 s. 3. End-tidal CO2, and ventilation increased for the first 60-120 s of the trial then reached a plateau. During rapid arm movement at the start of dead-space breathing, diaphragm EMG became tonic with superimposed modulation at the frequencies of respiration and arm movement. However, when the arm was moved after 60 s of hypercapnoea, the tonic diaphragm EMG during expiration and the phasic activity with arm movement were reduced or absent. Similar changes occurred for the expiratory muscle transversus abdominis, but not for the erector spinae. The mean amplitude of intra-abdominal pressure and the phasic changes with arm movement were reduced after 60 s of hypercapnoea. 4. The present data suggest that increased central respiratory drive may attenuate the postural commands reaching motoneurons. This attenuation can affect the key inspiratory and expiratory muscles and is likely to be co-ordinated at a pre-motoneuronal site.