The oncogenic transcription factor FOXM1 and anticancer therapy

Comment on: Halasi M,et al. PLoS One 2012; 7:e31761.     

Critical role of mTOR in calcineurin inhibitor-induced renal cancer progression

Comment on: Basu A, et al. PLoS One 2011; 6:e23919     

Genetic variability in the PRKCI gene and prostate cancer risk

Comment on: Campa D, et al. PLoS One 2011; 6:e16914.     

Poor Diet in Shift Workers: A New Occupational Health Hazard?

The PLoS Medicine Editors discuss the link between shift work, diet, and type 2 diabetes, and argue that unhealthy eating should be considered a new form of occupational hazard.     

飞蝗型变分子机理研究前沿

飞蝗的型变是重要的科学问题,也是防治害虫的理论基础。近年来,我国昆虫学家围绕飞蝗型变的分子机制方面取得一系列开创性的工作进展,鉴定了多个飞蝗型变的关键基因及其生物学功能,提出了飞蝗型变的分子机制。这些研究成果在PNAS,PLoS Genetics,Genome Biology,Bioinformatics,Insect Molecular Biology,Journal of Insect Physiology,PLoS One等国际著名刊物发表,极大地提高了我国在该领域的研究水平,为今后彻底解决飞蝗型变这一科学难题奠定了基础。     

Sanitation and health

As one article in a four-part PLoS Medicine series on water and sanitation, David Trouba and colleagues discuss the importance of improved sanitation to health and the role that the health sector can play in its advocacy.     

Hygiene,Sanitation, and Water: What Needs to Be Done?

In the final article in a four-part PLoS Medicine series on water and sanitation, Sandy Cairncross and colleagues outline what needs to be done to make significant progress in providing more and better hygiene, sanitation, and water for all.     

Foxa2: the rise and fall of dopamine neurons

Understanding the development and maintenance of dopamine neurons is essential to establish novel stem cell therapies and animal models of Parkinson's disease. A recent PLoS Biology report (Kittappa et al., 2007) reveals that Foxa2 regulates dopamine neuron generation and differentiation, and that aging foxa2(+/-) mice spontaneously develop Parkinsonism.     

Repeated evolution of digital adhesion in geckos: a reply to Harrington and Reeder

We published a phylogenetic comparative analysis that found geckos had gained and lost adhesive toepads multiple times over their long evolutionary history (Gamble et al., PLoS One, 7, 2012, e39429). This was consistent with decades of morphological studies showing geckos had evolved adhesive toepads on multiple occasions and that the morphology of geckos with ancestrally padless digits can be distinguished from secondarily padless forms. Recently, Harrington & Reeder (J. Evol. Biol., 30, 2017, 313) reanalysed data from Gamble et al. (PLoS One, 7, 2012, e39429) and found little support for the multiple origins hypothesis. Here, we argue that Harrington and Reeder failed to take morphological evidence into account when devising ancestral state reconstruction models and that these biologically unrealistic models led to erroneous conclusions about the evolution of adhesive toepads in geckos.     

Genome sequence of Shigella flexneri serotype 5a strain M90T Sm

Bacteria of the genus Shigella are a major cause of death worldwide (L. von Seidlein et al., PLoS Med. 3:e353, 2006). We sequenced the genome of Shigella flexneri strain M90T Sm (serotype 5a) and compared it to the published genome sequence of S. flexneri strain 8401 (serotype 5b).     

Computational and statistical analysis of protein mass spectrometry data

High-throughput proteomics experiments involving tandem mass spectrometry produce large volumes of complex data that require sophisticated computational analyses. As such, the field offers many challenges for computational biologists. In this article, we briefly introduce some of the core computational and statistical problems in the field and then describe a variety of outstanding problems that readers of PLoS Computational Biology might be able to help solve.     

Branched-chain amino acid (BCAA) supplementation enhances adaptability to exercise training of mice with a muscle-specific defect in the control of BCAA catabolism

Branched-chain α-keto acid dehydrogenase (BCKDH) kinase (BDK) suppresses the branched-chain amino acid (BCAA) catabolism by inactivation of the BCKDH complex. The muscle-specific BDK-deficient (BDK-mKO) mice showed accelerated BCAA oxidation in muscle and decreased endurance capacity after training (Xu et al. PLoS One. 12 (2017) e0180989). We here report that BCAA supplementation overcompensated endurance capacity in BDK-mKO mice after training.     

The hypoxic response and aging

Comment on: (1) Proteasomal regulation of the hypoxic response modulates aging in C. elegans. Mehta R, Steinkraus KA, Sutphin GL, Ramos FJ, Shamieh LS, Huh A, Davis C, Chandler-Brown D, Kaeberlein M. Science;324:1196-8.

(2) HIF-1 modulates dietary restriction-mediated lifespan extension via IRE-1 in Caenorhabditis elegans. Chen D, Thomas EL, Kapahi P. PLoS Genet 2009; 5:e1000486.     

The spread of scientific information: insights from the web usage statistics in PLoS article-level metrics

The presence of web-based communities is a distinctive signature of Web 2.0. The web-based feature means that information propagation within each community is highly facilitated, promoting complex collective dynamics in view of information exchange. In this work, we focus on a community of scientists and study, in particular, how the awareness of a scientific paper is spread. Our work is based on the web usage statistics obtained from the PLoS Article Level Metrics dataset compiled by PLoS. The cumulative number of HTML views was found to follow a long tail distribution which is reasonably well-fitted by a lognormal one. We modeled the diffusion of information by a random multiplicative process, and thus extracted the rates of information spread at different stages after the publication of a paper. We found that the spread of information displays two distinct decay regimes: a rapid downfall in the first month after publication, and a gradual power law decay afterwards. We identified these two regimes with two distinct driving processes: a short-term behavior driven by the fame of a paper, and a long-term behavior consistent with citation statistics. The patterns of information spread were found to be remarkably similar in data from different journals, but there are intrinsic differences for different types of web usage (HTML views and PDF downloads versus XML). These similarities and differences shed light on the theoretical understanding of different complex systems, as well as a better design of the corresponding web applications that is of high potential marketing impact.     

Empirical Study of Data Sharing by Authors Publishing in PLoS Journals

Background

Many journals now require authors share their data with other investigators, either by depositing the data in a public repository or making it freely available upon request. These policies are explicit, but remain largely untested. We sought to determine how well authors comply with such policies by requesting data from authors who had published in one of two journals with clear data sharing policies.

Methods and Findings

We requested data from ten investigators who had published in either PLoS Medicine or PLoS Clinical Trials. All responses were carefully documented. In the event that we were refused data, we reminded authors of the journal''s data sharing guidelines. If we did not receive a response to our initial request, a second request was made. Following the ten requests for raw data, three investigators did not respond, four authors responded and refused to share their data, two email addresses were no longer valid, and one author requested further details. A reminder of PLoS''s explicit requirement that authors share data did not change the reply from the four authors who initially refused. Only one author sent an original data set.

Conclusions

We received only one of ten raw data sets requested. This suggests that journal policies requiring data sharing do not lead to authors making their data sets available to independent investigators.     

What Are the Roles and Responsibilities of the Media in Disseminating Health Information?

BACKGROUND TO THE DEBATE: In December 2004 three news stories in the popular press suggested that the side effects of single-dose nevirapine, which has been proven to prevent mother-to-child transmission of HIV, had been covered up. Many HIV experts believed that the stories were unwarranted and that they would undermine use of the drug, leading to a rise in neonatal HIV infection. The controversy surrounding these stories prompted the PLoS Medicine editors to ask health journalists, and others with an interest in media reporting of health, to share their views on the roles and responsibilities of the media in disseminating health information.     

Strategic Treatment Interruptions During Imatinib Treatment of Chronic Myelogenous Leukemia

Although imatinib is an effective treatment for chronic myelogenous leukemia (CML), and nearly all patients treated with imatinib attain some form of remission, imatinib does not completely eliminate leukemia. Moreover, if the imatinib treatment is stopped, most patients eventually relapse (Cortes et al. in Clin. Cancer Res. 11:3425–3432, 2005). In Kim et al. (PLoS Comput. Biol. 4(6):e1000095, 2008), the authors presented a mathematical model for the dynamics of CML under imatinib treatment that incorporates the anti-leukemia immune response. We use the mathematical model in Kim et al. (PLoS Comput. Biol. 4(6):e1000095, 2008) to study and numerically simulate strategic treatment interruptions as a potential therapeutic strategy for CML patients. We present the results of numerous simulated treatment programs in which imatinib treatment is temporarily stopped to stimulate and leverage the anti-leukemia immune response to combat CML. The simulations presented in this paper imply that treatment programs that involve strategic treatment interruptions may prevent leukemia from relapsing and may prevent remission for significantly longer than continuous imatinib treatment. Moreover, in many cases, strategic treatment interruptions may completely eliminate leukemic cells from the body. Thus, strategic treatment interruptions may be a feasible clinical approach to enhancing the effects of imatinib treatment for CML. We study the effects of both the timing and the duration of the treatment interruption on the results of the treatment. We also present a sensitivity analysis of the results to the parameters in the mathematical model.     

Do rhesus monkeys recognize themselves in mirrors?

Self-recognition continues to attract attention because of the evidence of a striking difference between the great apes and humans, on the one hand, and all other primates; the former are capable of self recognition,whereas no compelling evidence exists for prosimians, monkeys, or lesser apes. This is inspite of numerous attempts to facilitate mirror self-recognition in other primates. Although all previous attempts to find self-recognition in rhesus macaques have failed, a recent article [Rajala et al., PLoS One9:e12865, 2010] claimed the opposite—that adult male rhesus monkeys did recognize their own image in a mirror. We critically examine this claim, and conclude that the article fails to provide acceptable evidence for self-recognition in rhesus monkeys.     

“Knock once for yes,twice for no”

Previous studies have indicated that the expression of CCN3, a member of the CCN family of proteins, was tightly regulated during central nervous development and was associated with acquisition of cognitive functions in rats (Perbal, Mol Pathol 54(2):57–79, 2001; Su et al. Sheng Li Xue Bao 52(4):290–294, 2000) therefore suggesting that CCN3 might be involved in higher levels of physiological communication in the brain. In spite of the considerable amount of progress made into the understanding of neuronal organization and communication, reducing the knowledge gap between brain cellular biology and behavioral studies remains a huge challenge. Mind-to-mind communication has been the subject of numerous science fiction writings, intense research and emotional debates for many years. Scientists have tried for a long time to achieve transmission of messages between living subjects via non intrusive protocols. Thanks to the great progress made in imagery and neurosciences, another dimension of neuronal function in communication has now been documented. Two recent experimental demonstrations of direct brain to brain communication without physical contact (Grau et al. (2014) Conscious brain-to-brain communication in humans using non-invasive technologies. PLoS One. Aug 19;9(8)- - Rao et al. (2014) A direct brain-to-brain interface in humans. PLoS One. Nov 5;9(11)) pave the road to more sophisticated applications that could profoundly affect communications of humans with other humans, animals and machines. Although the wide use of such applications might seem a long way off, they raise quite a number of ethical, legal and societal issues.