Passive smoking and lung cancer: a publication bias?

To assess the likelihood of publication bias in a recent review of the effect of passive smoking on lung cancer the evidence from the reviewed papers was visualised on a “funnel” plot. In such a plot if the relative risks from various studies are plotted according to sample size they should scatter round some underlying true value, the scatter being greatest where the studies have the lowest statistical power—thus showing a “funnel” pattern. If there is publication bias and studies with non-significant results are not being published there should be a “gap” in the plot. The logarithm of the relative risks was plotted against the standard error of the logarithm of the relative risk (which was used instead of sample size as a measure of statistical uncertainty). The resulting plot was compatible with a publication bias but only in studies on men.Further studies of passive smoking and lung cancer in men seem to be warranted.     

Why the need for qPCR publication guidelines?—The case for MIQE

The polymerase chain reaction (PCR) has matured from a labour- and time-intensive, low throughput qualitative gel-based technique to an easily automated, rapid, high throughput quantitative technology. Real-time quantitative PCR (qPCR) has become the benchmark technology for the detection and quantification of nucleic acids in a research, diagnostic, forensic and biotechnology setting. However, ill-assorted pre-assay conditions, poor assay design and inappropriate data analysis methodologies have resulted in the recurrent publication of data that are at best inconsistent and at worst irrelevant and even misleading. Furthermore, there is a lamentable lack of transparency of reporting, with the “Materials and Methods” sections of many publications, especially those with high impact factors, not fit for the purpose of evaluating the quality of any reported qPCR data. This poses a challenge to the integrity of the scientific literature, with serious consequences not just for basic research, but potentially calamitous implications for drug development and disease monitoring. These issues are being addressed by a set of guidelines that propose a minimum standard for the provision of information for qPCR experiments (“MIQE”). MIQE aims to restructure to-day’s free-for-all qPCR methods into a more consistent format that will encourage detailed auditing of experimental detail, data analysis and reporting principles. General implementation of these guidelines is an important requisite for the maturing of qPCR into a robust, accurate and reliable nucleic acid quantification technology.     

Use Open Access to promote JIPB and to have higher impact for your publication

<正>From 2015,JIPB starts to offer Open Access option that allows authors to have their online articles available for free to all users in the world.Open Access is a scholarly communication exchange that makes knowledge available to public without the barrier of affordability.Benefits of Open Access:1.Authors own the copyright,enabling you to have unrestricted use of your own publications     

Australopithecus afarensis : bipédie stricte ou associée à une composante arboricole ? Critiques et révision du matériel fémoral

Although much research has been carried out on Australopithecus afarensis locomotion, no consensus has yet been reached. Our new critic study on femoral material brings to the fore a strictly bipedal behaviour within this taxon. Our results are based on the pertinence of human anatomical characteristics among A. afarensis and on the absence of characteristics revealing arboreal displacement. These results have emerged from our different observation and interpretation of some preceding authors concerning the anatomy of these fossil hominids. It is important to underline that apomorphic characteristics of this species are difficult to interpret. They must not however be used to support the idea of arboreal displacement simply based on the fact of a no totally human morphe. We believe that present day humans do not necessarily reflect the earliest strict bipedal anatomic model. An the other hand, it appears that the disagreement between the two locomotor hypothesis for A. afarensis that are bipedalism and arboreal displacement, facing the possibility of bipedalism associated with negligible arboreal displacement, results more from an evolutionary fact than from a real scientific conflict.     

&#183;遗传咨询&#183;

1．多囊肾的遗传 问：我有家族多囊肾遗传史,自己双肾有囊肿,现在怀孕29周,胎儿彩超双肾大,有回声,医生判定为多囊肾,我如果不要这胎,再怀孕,有不遗传的可能吗？     

Chronic Atmospheric NO<Stack><Subscript>3</Subscript><Superscript>−</Superscript></Stack> Deposition Does Not Induce NO<Stack><Subscript>3</Subscript><Superscript>−</Superscript></Stack> Use by <Emphasis Type="Italic">Acer saccharum</Emphasis> Marsh.

The ability of an ecosystem to retain anthropogenic nitrogen (N) deposition is dependent upon plant and soil sinks for N, the strengths of which may be altered by chronic atmospheric N deposition. Sugar maple (Acer saccharum Marsh.), the dominant overstory tree in northern hardwood forests of the Lake States region, has a limited capacity to take up and assimilate NO₃⁻. However, it is uncertain whether long-term exposure to NO₃⁻ deposition might induce NO₃⁻ uptake by this ecologically important overstory tree. Here, we investigate whether 10 years of experimental NO₃⁻ deposition (30 kg N ha⁻¹ y⁻¹) could induce NO₃⁻ uptake and assimilation in overstory sugar maple (approximately 90 years old), which would enable this species to function as a direct sink for atmospheric NO₃⁻ deposition. Kinetic parameters for NH₄⁺ and NO₃⁻ uptake in fine roots, as well as leaf and root NO₃⁻ reductase activity, were measured under conditions of ambient and experimental NO₃⁻ deposition in four sugar maple-dominated stands spanning the geographic distribution of northern hardwood forests in the Upper Lake States. Chronic NO₃⁻ deposition did not alter the V _max or K _m for NO₃⁻ and NH₄⁺ uptake nor did it influence NO₃⁻ reductase activity in leaves and fine roots. Moreover, the mean V _max for NH₄⁺ uptake (5.15 μmol ¹⁵N g⁻¹ h⁻¹) was eight times greater than the V _max for NO₃⁻ uptake (0.63 μmol ¹⁵N g⁻¹ h⁻¹), indicating a much greater physiological capacity for NH₄⁺ uptake in this species. Additionally, NO₃⁻ reductase activity was lower than most values for woody plants previously reported in the literature, further indicating a low physiological potential for NO₃⁻ assimilation in sugar maple. Our results demonstrate that chronic NO₃⁻ deposition has not induced the physiological capacity for NO₃⁻ uptake and assimilation by sugar maple, making this dominant species an unlikely direct sink for anthropogenic NO₃⁻ deposition.     

Open access: A revolution in scientific publication? Or just a minor amendment of accessibility?

Scientific communication is a misnomer. The process of scientific publication is much less a forum where information is exchanged for information than a market where information is exchanged for attention. Nevertheless, the exchange of information for attention is a somewhat peculiar market, since it seems much more natural to sell the information one has produced laboriously for money. Why publish a discovery, why share it with other researchers when knowledge is power?In antiquity and in the middle ages, scientists were not preoccupied with publishing their findings. Up to the 17^th century, scholars, even in mathematics and astronomy, were pre-eminently concerned with protecting their claims to priority through secretiveness and mystification (Cf. ^{ref. 1}; on priority conflicts, see ^{ref. 2}). It was only through the emergence of new means of information sharing, such as academies and learned societies with their meetings and published proceedings, that the temptation to monopolize knowledge could be overcome. Ironically, these novel means of information sharing started as a novel branch of entertainment. The purpose of the academies and learned societies mushrooming in early modernity was the entertainment of noblemen bored of the habitual kinds of pastimes. Aristocrats were supposed to observe a code of conduct different from that of researchers and businessmen. The scholar, accordingly, did not risk his right of authorship and priority being stolen when presenting his findings to an audience of noblemen. As long as there were reliable witnesses around, this risk was minimal even when other scholars were in the audience. Testimony of a noble audience, rather, became the first step to what later came to be called intellectual property (^{ref. 3} and literature cited therein).As soon as scientists work for publication, they work for the “wage of fame,” i.e., for being paid attention.⁴ Publication puts intellectual property at the disposal of the general public under the sole condition that its processing into the user''s intellectual property is credited by citation. In terms of attention, citation is not free of cost. It means, rather, transfer of a part of the attention that the citing author earns for her or his work to the cited author. Citation, thus, tests the preparedness to pay on the part of the scientist looking for pre-processed information as a means of production. Since the account of the citations a theory or a theorem earns is a measure of its productivity (i.e., of the times it was used as a means of production), the process of citation amounts to a measuring process of the pragmatic value of scientific information.⁵Maximizing the pragmatic value of output is the best thing that the individual scientist can do for the collective advancement of knowledge. This means that scientists, as long as observing the pertinent rules of conduct, are doing exactly what they are supposed to do if they maximize citations in the way businessmen maximize profits.⁵ They are themselves entrepreneurs, who are supposed to maximize their income of expertise attention. This means that they have to have a professional interest in their products being marketed professionally. Marketing is the professional service publishers have to offer to scientists. At the same time, publishers can offer the service of pre-selection to those looking for pre-processed information as a means of production. Blind publication would have the disadvantage of a substantial waste of attention in looking for useful information. Since publishers are commercial enterprises, these services are not offered for free, but sold to the buyer or to the producer of the marketed product (or to both parties).Since its beginnings with the published proceedings of the learned societies’ meetings, the business of scientific publication has been a regular part of scientific communication by and large. As long as dissemination had to rely on analog media, it was only natural to package scientific information together with those services of pre-selection and marketing into the books and journals sold on commercial markets. Since the advent of digital media and, in particular, the Internet, a new business model has become popular that leaves the selling of information for money behind. Where what counts is just the attention a piece of information earns, offer it for free and advertise with the download figures! Where there are costs of providing to be covered, try to sell the service of attraction to the advertising industry! At any rate, don’t charge those demanding the information, since that might shoo them. With this business model, Google, for example has successfully entered the field of scientific communication. Google Scholar not only competes with traditional publishers, but was even invited to do so by the price policies some publishers of high-impact media were adopting. Since the advent of the Internet, complaints have been growing about publishers that use their market position to plunder library budgets.Google and the like, however, are no full-fledged competitors to Elsevier and the like. They just recycle material already published. In order to compete in full extent, another business idea was launched: open access. Open access means that the information is offered for free, whereas the production costs of the marketing and pre-selection services are borne by the author. It will be understood that this solution is hailed on the demand side. In a community where expecting that information is something one can download for free has become a general attitude, this solution may seem even mandatory. Open access, however, has an appeal for authors as well. Offering one’s product in free access media raises, other things being equal, the probability of being read and, accordingly, of being cited. In a sense, thus, paying for an open access publication amounts to buying into the probability of being cited. As long as the prices charged for the publication just compensate for the outlays incurred by the publisher, this possibility may be considered harmless. As soon, however, as the prices become negotiable, conflicts of objectives are imminent. The higher the impact factor of the medium, the higher its price expectations will be. With price expectations, the probability of discrimination between producers according to ability to pay will rise, as well as of interference between the requirement of objective selection and the commercial interest on the part of the publisher.Already we are warned of allowing the hopes raised by open access to fly too high. Open access is to be welcomed as an enrichment of business models competing in the market of scientific publication. Intensifying competition is the best-proven means to fight monopoly power. Open access, however, is suited to foster competition on the commercial market only. It is neutral with regards to competition in the market where information is exchanged for attention. It is neutral, accordingly, with regard to the monopoly power played off by the owners of high-impact media. The impact a medium calls its own is a function of its renown, which, in turn, is wealth of attention activated as an asset. The probability of a paper being cited depends, among other things, on the renown of the medium it is published in. The higher the renown of the medium, the more attractive it is for authors as well as for readers, and thus, for the libraries serving the readers’ needs. This is what the power of publishers owning high-impact media to plunder library budgets relies on. It is hopeless to fight this kind of monopoly power by fostering competition on the commercial market.Publishers are entrepreneurs in the commercial economy as well as in the economy of attention. In the attention economy, the interests of publishers largely coincide with those of authors. The attention a publication earns is shared between author and publisher. The higher the earnings, the higher the gain of reputation on both parts. The author is as interested in the reputation of the publisher as is the publisher in the reputation of the author. For the author, the reputation of the publisher is what the expected value of the publication heavily depends on. For the publisher, the reputation of the author is what the attractiveness of the organ for other reputed authors depends on. For him, the reputations of his authors are like bank deposits that he can turn into credits to newcomers who seem promising to him. By way of this credit, a reputed publisher can grant an expectation value of citations that otherwise would remain fantastic for a newcomer. All those who have really made it in science took advantage of such a credit at some point of their career. Remarkably, though, publishers granting credits in terms of guaranteed attention income are entering, and thus opening, the business field of finance in the scientific economy of attention.Regarding the promotion of the talented, importing the business model of finance is certainly among the commendable functions of publishers in the scientific economy of attention. By acting as bankers, however, they are active in wealth management as well. They are managing the wealth of scientists by translating the accumulated wage of fame (account of citations) into an asset yielding interest. Wealth yielding interest is wealth activated as a capital enhancing itself according to size. The bigger the size, the bigger, as a rule, is the rate of growth. Renown that has reached the critical mass for triggering self-enhancement gives rise, thus, to economies of scale in building up renown. Markets where suppliers realize economies of scale will be shot through by moments of monopolistic competition.In fact, since the citation process is monitored and charted statistically, a remarkably uneven distribution of citations is observed. There are few who receive many citations and many who get only a few. Robert Merton (1968) called this conspicuously uneven distribution the “Matthew effect in science.” The Matthew effect refers to the biblical parable of being entrusted with talents, the text reading that “those who have will be given and those who have not will be taken away” (Matthew 25:14–30).The skewed distribution of citations is not reducible to the uneven distribution of publications authors call their own. The explanation lies in the working of reputation as an income-generating asset. The Matthew effect denotes the role that hype plays in science. It is due not to extraordinary productivity, but to the homage that scientists, as do other people, pay to renown, prominence, fame. If you have grown prominent, you will be cited not only for the discovery you owe your prominence to, but just for being a celebrity. To be paid attention for being a celebrity means to be given because of having.The gains generated by the Matthew effect are shared between author and publisher. These gains are monopoly profits. Since the publisher is engaged in both the market where information is exchanged for attention and in the market where information is exchanged for money, he is particularly well-equipped to translate his monopoly position in the economy of attention into a monopoly position in commercial economy. This translation cannot be suppressed by toughening competition on the commercial market. The only way of pre-empting monopoly due to renown would lie in preventing the Matthew effect.If there are any means to suppress the Matthew effect, open access is certainly not among them. Nor is it clear, however, whether it makes sense at all to fight the manifestations of celebrity culture in science. In order to do so, you would have to start with abolishing the distinguished awards such as the Nobel prize and the Fields medal. You would have to ban any talk of excellence and even suppress the publication of citation indices and other ratings. Even working for the wage of fame would have to be frowned upon. Finally, social media’s way of amassing entourage would have to be suspected politically incorrect.Open access, to sum up, is far from a revolutionary innovation. It is a mode of redistributing the costs incurred by the publisher for delivering the services of marketing and pre-selection. Scientists eager to publish in renowned journals can be exploited, as libraries eager to make accessible renowned journals can. Since, as a rule, the publication outlays of the scientists will be borne by the same institution as the acquisitions of the libraries, the conversion risks to be just a switch between cost centers.     

Negative molecular ion of deuterium D<Stack><Subscript>2</Subscript><Superscript>−</Superscript></Stack>

D₂⁻ ions produced in collisions of D⁻ ions with relative energies of 2.5–9.2 eV were detected for the first time. It is shown that the effective cross section for this reaction is no less than 1.5 × 10⁻¹⁴ cm². Along with the theoretically predicted short-lived state of negative molecular deuterium ions, a state existing for more than 1 μs was observed.