bluuebunny/crossref_metadata_2025_split huggingface dataset:
Republished review: Next generation sequencing for clinical diagnostics and personalised medicine: implications for the next generation cardiologist
Authors: Ware James S , Roberts Angharad M , Cook Stuart A 
Published: March 2012

AbstractThe fast moving field of genomic medicine is already impacting on clinical care and cardiologists are fortunate to be in a position to benefit early from the transformative advances in genomics. However, the challenges associated with genomics in the clinic in general, and with next generation sequencing technologies in particular, are significant and cardiologists need to be prepared if they wish to surf the wave of genomic opportunity. This paper presents an overview of the implications of next generation sequencing for clinical diagnostics and personalised medicine in the cardiology clinic.
Coronary artery spasm and ventricular arrhythmias
Authors: Looi Khang Li , Grace Andrew , Agarwal Sharad 
Published: March 2012

Abstract
Coronary artery spasm (CAS) is characterised by chest pain at rest and transient ST segment elevation on the ECG. The natural history of variant angina is not fully understood. Patients with CAS are younger, mostly female subjects and usually do not have traditional cardiovascular risk factors other than cigarette smoking. Cardiac arrhythmias are known to be associated with CAS. Ventricular arrhythmia is a well-recognised complication and sudden cardiac death has also been documented. The most important diagnostic tool in CAS is coronary angiography. 24 h ECG Holter monitoring can be very useful in the diagnosis of ventricular arrhythmias caused by CAS. The mainstay therapy for CAS is calcium channel blockers and nitrates. The use of β-blockers, especially the non-selective group, can promote attacks or prolong vasospastic state. The indication for implantable cardioverter defibrillator (ICD) implantation in a patient with CAS is still not clearly established. The role of primary prevention with the use of ICD is controversial; however, ICD implantation should be considered in high risk patients despite optimal medical treatment.
Sex work and the public health impacts of the 2010 Olympic Games: Table 1
Authors: Deering Kathleen N , Chettiar Jill , Chan Keith , Taylor Matthew , Montaner Julio SG , Shannon Kate 
Published: March 2012

ObjectivesThe authors examined the impact of exposure to the 2010 Winter Olympics time period on outcomes measuring disruption of local sex work environments in Vancouver, Canada.MethodsThe authors conducted a before-and-after study, using multivariable logistic regression, to assess the relationship between exposure to the Olympics period (19 January–14 March 2010) versus the post-Olympics period (1 April–1 July 2010) and outcomes.ResultsThis study included 207 youth (14+ years) and adult sex workers (SWs) (Olympics: n=107; post-Olympics: n=100). SWs in the two periods were statistically similar, with an overall median age of 33 years (IQR: 28–40), and 106 (51.2%) of indigenous ancestry or ethnic minority. In separate multivariable logistic regression models, the Olympics period remained statistically significantly associated with perceived heightened police harassment of SWs without arrest (adjusted ORs (AOR): 3.95, 95% CIs 1.92 to 8.14), decreased availability of clients (AOR: 1.97, 95% CIs 1.11 to 3.48) and increased difficulty meeting clients due to road closures/construction (AOR: 7.68, 95% CIs 2.46 to 23.98). There were no significantly increased odds in perceived reports of new (0.999), youth (0.536) or trafficked SWs (zero reports) in the Olympic period.ConclusionsTo reduce potential adverse public health impacts of enhanced police harassment and displacement of local sex work markets, results suggest that evidence-based public health strategies need to be adopted for host cities of future events (eg, the London 2012 Olympic Games), such as the removal of criminal sanctions targeting sex work and the piloting and rigorous evaluation of safer indoor work spaces.
Access to and use of unauthorised online HIV self-tests by internet-using French-speaking men who have sex with men
Authors: Greacen Tim , Friboulet David , Fugon Lionel , Hefez Serge , Lorente Nicolas , Spire Bruno 
Published: March 2012

ObjectivesAlthough not authorised in France, HIV self-tests are easily available online. The authors questioned French-speaking internet-using men who have sex with men (MSM) concerning their access to and use of such tests.MethodsOnline questionnaire on sex websites and gay and HIV community websites. A multivariate logistic regression for rare events was used to identify factors associated with accessing self-tests.Results9169 MSM completed the questionnaire. 2748 (30%) were aware of online self-tests, but only 82 of those aware and not already HIV positive (3.5%) declared having accessed one and only 69 using it. In the multivariate model, living one's sex-life with men in absolute secrecy (odds ratio (OR)=3.90, 95% CI 1.73 to 8.76), knowing of the tests via a sex partner (OR=3.42, CI 1.39 to 8.41) or an internet search engine (OR=2.18, CI 1.26 to 3.74) but not through the general (OR=0.21, CI 0.11 to 0.42) or the gay press (OR=0.34, CI 0.16 to 0.73), having unprotected anal intercourse with a casual partner in the preceding year (OR=1.90, CI 1.17 to 3.06), using self-tests for other diseases (OR=2.66, CI 1.43 to 4.90), using poppers (OR=2.23, CI 1.35 to 3.67) and doping products (OR=3.53, CI 1.55 to 8) in the preceding year, having done a traditional HIV test but not in the preceding year (OR=1.93, CI 1.14 to 3.32), never having had suicidal thoughts (OR=0.54, CI 0.32 to 0.90) and living in the provinces (OR=1.80, CI 1.01 to 3.25) were all independently associated with accessing self-tests.ConclusionsAlthough readiness to admit use of unauthorised medical products may have influenced results, few MSM aware of the existence of self-tests actually declared having accessed one. Accessing the self-test was independently associated with both living one's sex-life with men in total secrecy and having had unprotected anal intercourse in the last 12 months, indicating that autonomous self-testing may reduce barriers to testing for this vulnerable population.
Pregnancy and contraceptive use among women participating in an HIV prevention trial in Tanzania
Authors: Odutola Aderonke , Baisley Kathy , Hayes Richard J , Rusizoka Mary , Tanton Clare , Weiss Helen A , Changalucha John , Ross David A , Watson-Jones Deborah 
Published: March 2012

ObjectivesInformation on pregnancy rates and factors associated with pregnancy and contraceptive use is important for clinical trials in women in sub-Saharan Africa where withdrawal of investigational products may be required in the event of pregnancy with a consequent effect on sample size and trial power.MethodsA prospective cohort analysis of pregnancy and contraceptive use was conducted in Tanzanian women enrolled in a randomised placebo-controlled trial of herpes simplex virus-suppressive therapy with acyclovir to measure the effect on HIV incidence in HIV-negative women and on genital and plasma HIV viral load in HIV-positive women. The cohort was followed every 3 months for 12–30 months. Women at each visit were categorised into users or non-users of contraception. Pregnancy rates and factors associated with pregnancy incidence and contraceptive use were measured.ResultsOverall 254 of 1305 enrolled women became pregnant at least once during follow-up (pregnancy rate: 12.0/100 person-years). Younger age, being unmarried, higher baseline parity and changes in contraceptive method during follow-up were independently associated with pregnancy. Having paid sex and being HIV positive were associated with lower risk of pregnancy. Uptake of contraception was associated with young age, being unmarried, occupation, parity and the number and type of sexual partners.ConclusionsData on use of contraceptive methods and risk factors for pregnancy can help to guide decisions on trial eligibility and the need for additional counselling. Mandatory reliable contraceptive use in study participants may be required to reduce pregnancy rates in studies where pregnancy is contraindicated.
THE STOCHASTIC RESETTING AND MASTER NONLINEAR FOKKER–PLANCK IN DISCRETE SPECTROSCOPY OF ULTRATHIN SILICON DIOXIDE FILM
Authors: BAHARI ALI 
Published: March 2012

In this paper, we consider a particle (carrier) which is stochastically reset to its initial position at a constant rate r. It leads toward a non-equilibrium stationary state with non-Gaussian fluctuations for the particle position and enhance escape rate of particles through the ultrathin film. Here we explore strongly-correlated random sequences. It is based on Master — nonlinear Fokker–Planck and chemical reaction equations. In that case compounding moments can set useful constraints to synchrotron radiation spectra of ultrathin film (SRSUTF). This mechanism is explained within a fitting process where both diffusion and reaction occur in discrete cells, and with both Si and O 2 treated as moving and reacting species for the very thin oxides.
India's Palaeoproterozoic legacy
Authors: Santosh M. 
Published: March 2012

Abstract

The Indian lithospheric plate assembles the history of geological events covering almost the entire history of our planet. The proto-Indian continent was an integral part of the Palaeoproterozoic supercontinent Columbia. Global mantle warming beneath this supercontinent triggered rising plumes that led to rifting and the emplacement of mafic dyke swarms and large igneous provinces in many of the major cratons of Peninsular India. Continued rifting and separation of crustal blocks led to the formation of thick passive margin successions. The opening of ocean basins and their eventual closure are recorded in the travelogue of oceanic plates from mid-ocean ridge to the trench in the form of ‘ocean plate stratigraphy’ in Proterozoic belts, including the association of dismembered ophiolites, pelagic sediments and continental margin sequences that were imbricated into accretionary belts such as those in the Aravalli–Delhi domain (Western India Suture), the Central India Tectonic Zone (Central India Suture) and the eastern margin of the East Dharwar Craton (Eastern India Suture). Recent U–Pb zircon chronology from ophiolitic rocks in the eastern margin of the Dharwar Craton shows ages spanning from 1.85 to 1.33 Ga suggesting a prolonged Wilson cycle of subduction–accretion processes before the final collisional event and the extrusion of high-grade metamorphic orogens. The extruded high pressure–temperature (
P–T
) metamorphic belts are often associated with mafic/ultramafic units with an abyssal signature. The available geophysical information from the Indian Palaeoproterozoic belts, particularly deep seismic reflection data, provides important clues on the architecture of these orogens and the subduction polarity. Whereas the Palaeoproterozoic convergent margins in the NW and SE sectors of the Indian peninsula were characterized by the westward subduction of oceanic plates, ocean closure along the Central India Tectonic Zone probably involved a double-sided subduction. The Wilson cycle traces a continuum from Palaeoproterozoic through Mesoproterozoic to Neoproterozoic in some of these belts, with a prolonged subduction–accretion history similar to the ongoing convergent margin processes in the western Pacific region. Peninsular India thus preserves a complete record from Pacific-type accretionary tectonics along the margins of the Columbia supercontinent to Himalayan-style collisional assembly within the Neoproterozoic Rodinia supercontinent.
Mesoarchaean–Palaeoproterozoic stratigraphic record of the Singhbhum crustal province, eastern India: a synthesis
Authors: Mazumder R. , Van Loon A. J. , Mallik L. , Reddy S. M. , Arima M. , Altermann W. , Eriksson P. G. , De S. 
Published: March 2012

Abstract
The Mesoarchaean–Palaeoproterozoic stratigraphic record of the Singhbhum crustal province, eastern India, implies sedimentation and volcanism in a changing tectonic scenario, and thus assumes immense geological significance. Although efforts have been made by many researchers in the past several decades to summarize various geological aspects of the Singhbhum crustal province, a critical synthesis of various stratigraphic issues was long overdue. The present contribution is an updated critical synthesis of the Mesoarchaean–Palaeoproterozoic stratigraphic record of the Singhbhum crustal province. We have pointed out the problematic stratigraphic issues of the Singhbhum crustal province that deserve careful scrutiny in order to gain better insights into the mode of stratigraphic sequence building.
Native iron in the Palaeoproterozoic Chaibasa Formation: primary or secondary?
Authors: Abbott Dallas H. , Mazumder Rajat , Breger Dee 
Published: March 2012

Abstract
Native Fe in the Chaibasa Formation may be the oldest native Fe ever found. The Chaibasa Formation contains pre-1.6 Ga offshore shelf sediments from the Singhbhum Craton in India. The sediments are light green in colour, consistent with a low content of organic matter and a metamorphic grade of greenschist–lower amphibolite facies. The native Fe grains are enclosed in fibrous mica. The native Fe occurs with magnetite crystals, evidence of relatively oxidizing conditions in the Chaibasa Formation during diagenesis. (Mn,Fe)S, a compound characteristic of reducing conditions, is found within the native Fe. The native Fe contains small amounts of native Si. Most grains of native Fe have rough edges. One bulbous grain has smooth edges and an internal wavy structure that is suggestive of a drop of melted iron. The melting temperature of pure Fe is 1535 °C. We also found native Fe with small amounts of carbon in it that appears to have a plate-like, pearlitic structure. Pearlite typically forms at temperatures of 723–500 °C. All of these temperatures are too high to be achieved during greenschist-facies metamorphism. As a result, we infer that the native Fe is primary rather than secondary. Our work and that of others suggests a primary, impact origin for the native Fe.
Metamorphic evolution of the Chotanagpur Granite Gneiss Complex of the East Indian Shield: current status
Authors: Sanyal S. , Sengupta P. 
Published: March 2012

Abstract

Geological information on the Chotanagpur Granite Gneiss Complex (CGGC) has been reviewed with a view to: (a) identifying the different metamorphic episodes; (b) developing an event stratigraphy in the high-grade blocks; and (c) correlating the different metamorphic episodes with the globally extensive orogenic processes. Integrating the existing geological information, the geological evolution of the high-grade block of the CGGC has been divided into four stages associated with four distinct metamorphic events (
M
I
−
M
IV
). The earliest metamorphic event (
M
I
) that is recorded in granulite enclaves in the regionally extensive felsic gneisses culminated in ultrahigh temperatures (>900 °C at
c
. 5–8 kbar) at around 1.87 Ga. In the second stage, voluminous felsic magmas were intruded – the
M
I
granulites – and were metamorphosed to form migmatitic felsic gneisses (
M
II
) within about 1.66–1.55 Ga. The third stage witnessed intrusions of a suite of anorthosite and porphyritic granitoids (
c
. 1.55–1.51 Ga), followed by high-grade metamorphism (700±50 °C, 6.5±1 kbar,
M
III
) during approximately 1.2–0.93 Ga. The fourth stage (
M
IV
) is marked by the intrusion of a suite of mafic dykes, followed by infiltration-driven metamorphism (600–750 °C at 7±1) during 0.87–0.78 Ga. The proposed metamorphic events have been correlated with the supercontinental cycles in the Proterozoic time.
Palaeoproterozoic sedimentation in the Cuddapah Basin, south India and regional tectonics: a review
Authors: Saha Dilip , Tripathy Vikash 
Published: March 2012

Abstract
The Proterozoic Cuddapah Basin of south India hosts a number of unconformity-bound sequences deposited over continental crust. The Palaeoproterozoic Papaghani Group with basal polymict conglomerate unconformably overlies the Archaean Peninsular Gneiss and set the stage for Palaeoproterozoic sedimentation following a long hiatus. Two cycles of fluvial–shallow-marine psammite–carbonate–pelite sedimentation in the western part of the basin (Papaghni sub-basin) is punctuated at different levels by mafic flows, sills and dykes, and less common acidic tuffs. Each of the sedimentation cycles fosters extensive carbonate platforms with dolomitic stromatolites and algal laminites. Emplacement of shallow crustal intrusives at the end of the first cycle was possibly linked to thermal anomalies in the mantle and associated widespread crustal extension in south India. Brittle fault-slip analysis from the western Cuddapah indicates repetitive extensional to strike-slip regimes. This paper proposes a likely late Palaeoproterozoic shallow-marine sedimentary sequence of the Nallamalai Fold Belt as allochthonous, thrusted over the successions of the Papaghni sub-basin and the Kurnool Group in the western part of the basin. Inversion of the Papaghni sub-basin and the development of regional erosional unconformities is discussed in the context of Palaeoproterozoic and early Mesoproterozoic orogenic events at the SE margin of India.
The power of computing; design guidelines in CS education
Authors: Reed Daniel , Guzdial Mark 
Published: March 2012

The
Communications
Web site, http://cacm.acm.org, features more than a dozen bloggers in the BLOG@CACM community. In each issue of
Communications
, we'll publish selected posts or excerpts.

twitter

Follow us on Twitter at http://twitter.com/blogCACM
http://cacm.acm.org/blogs/blog-cacm
Daniel Reed writes about how computing systems increase human intellect and abilities. Mark Guzdial discusses the need to avoid polarized and extreme positions in education and the trend toward design-based research.
Gender Influences the Class III and V β-Tubulin Ability to Predict Poor Outcome in Colorectal Cancer
Authors: Mariani Marisa , Zannoni Gian Franco , Sioletic Stefano , Sieber Steven , Martino Candice , Martinelli Enrica , Coco Claudio , Scambia Giovanni , Shahabi Shohreh , Ferlini Cristiano 
Published: March 2012

AbstractPurpose: Colorectal cancer is one of the deadliest diseases in Western countries. To predict the outcome of therapy, we assessed the role of class III (TUBB3) and class V β-tubulin (TUBB6) as predictive biomarkers.Experimental Design: Using immunohistochemistry and nanofluidics, the expression of TUBB3 and TUBB6 was assessed in two cohorts of 180 and 134 patients, respectively. The CYP17A1 RS743572 was genotyped to identify GG carriers with enhanced androgen levels. TUBB3 and TUBB6 were investigated in 22 colorectal cancer cell lines in basal conditions and after serum starvation, the latter serving as activator of this prosurvival pathway. To ascertain the role of androgen receptor (AR) in such regulation, we silenced AR and checked TUBB3 and TUBB6 expression and sensitivity to chemotherapy.Results: There was a link between poor survival, the expression of TUBB3/TUBB6, and AR only in females. Conversely, only in males carriers of the GG phenotype exhibited the worst outcome. Importantly, male cell lines were resistant to serum starvation and exhibited higher levels of TUBB6, thereby suggesting that the pathway is activated by androgens. In female cells this phenomenon was absent. In both genders, AR was the main driver of TUBB3/TUBB6 expression, as constitutive silencing of AR was associated with downregulation of TUBB3/TUBB6 expression and increased sensitivity to oxaliplatin and SN-38.Conclusions: The involvement of androgens in the TUBB3 pathway opens the way for clinical trials to assess the efficacy of antiandrogens for increasing the efficacy of chemotherapy in male colorectal cancer patients. Clin Cancer Res; 18(10); 2964–75. ©2012 AACR.
For Breast Cancer Prognosis, Immunoglobulin Kappa Chain Surfaces to the Top
Authors: Whiteside Theresa L. , Ferrone Soldano 
Published: March 2012

Abstract
The stromal immunoglobulin kappa chain (IGKC) has been validated as an immunologic biomarker of prognosis and response to therapy in human breast cancer and other cancers. This validation emphasizes the key role of humoral immunity in control of cancer progression and has major implications for determining prognosis of patients with cancer. Clin Cancer Res; 18(9); 2417–9. ©2012 AACR.
Functional Metabolic Screen Identifies 6-Phosphofructo-2-Kinase/Fructose-2,6-Biphosphatase 4 as an Important Regulator of Prostate Cancer Cell Survival
Authors: Ros Susana , Santos Claudio R. , Moco Sofia , Baenke Franziska , Kelly Gavin , Howell Michael , Zamboni Nicola , Schulze Almut 
Published: March 2012

Abstract
Alterations in metabolic activity contribute to the proliferation and survival of cancer cells. We investigated the effect of siRNA-mediated gene silencing of 222 metabolic enzymes, transporters, and regulators on the survival of 3 metastatic prostate cancer cell lines and a nonmalignant prostate epithelial cell line. This approach revealed significant complexity in the metabolic requirements of prostate cancer cells and identified several genes selectively required for their survival. Among these genes was 6-phosphofructo-2-kinase/fructose-2,6-biphosphatase 4 (PFKFB4), an isoform of phosphofructokinase 2 (PFK2). We show that PFKFB4 is required to balance glycolytic activity and antioxidant production to maintain cellular redox balance in prostate cancer cells. Depletion of PFKFB4 inhibited tumor growth in a xenograft model, indicating that it is required under physiologic nutrient levels. PFKFB4 mRNA expression was also found to be greater in metastatic prostate cancer compared with primary tumors. Taken together, these results indicate that PFKFB4 is a potential target for the development of antineoplastic agents.
Significance: Cancer cells undergo several changes in their metabolism that promote growth and survival. Using an unbiased functional screen, we found that the glycolytic enzyme PFKFB4 is essential for prostate cancer cell survival by maintaining the balance between the use of glucose for energy generation and the synthesis of antioxidants. Targeting PFKFB4 may therefore present new therapeutic opportunities. Cancer Discov; 2(4); 328–43. ©2012 AACR.
Read the Commentary on this article by Dang, p. 304
This article is highlighted in the In This Issue feature, 288
Infections and inflammatory diseases as risk factors for venous thrombosis
Authors: Kluin-Nelemans Hanneke J. C. , Meijer Karina , Tichelaar Y. I. G. Vladimir 
Published: March 2012

SummaryInflammation and venous thrombosis are intertwined. Only in the recent 15 years clinical epidemiological studies have focussed on inflammatory or infectious diseases as risk factors for venous thrombosis. Although a few reviews and many case reports or studies on these topic has been written, a review reporting relative or absolute risks for venous thrombosis has not been published yet. We performed a systematic review using Medline, Pubmed and Embase and found 31 eligible articles. Inflammatory bowel disease, ANCA-associated vasculitis, infections in general and more specifically, human immunodeficiency virus, pneumonia and urinary tract infections are associated with an increased risk of venous thrombosis.