LLukas22/scidocs huggingface dataset:
The Late Oligocene-Early Miocene Himalayan belt Constraints deduced from isotopic compositions of Early Miocene turbidites in the Bengal Fan

We present a mineralogical and isotopic study of Early Miocene turbidites from the Bengal Fan, which are the oldest sediments recovered during ODP Leg 116. Clay fractions are dominated by illite and chlorite and have low di80 (11-16%o). The clays are dominantly derived from a metamorphic precursor by physical erosion, and have undergone only minor low-T water-rock exchange and chemical weathering. Sr and Nd isotope analysis of silt and clay fractions and coarse muscovite, biotite and feldspar fractions are remarkably similar to those of the presently exposed High Himalaya Crystalline (HHC) sequence. The data show that a close analogue of the HHC was already subaerially exposed to active erosion during Early Miocene. Rb-Sr data on the biotite separates has been used to evaluate the time elapsed between cooling through the closure temperature for Sr in biotite in the HI-IC (ca. 325°C) and final sedimentation in the Bengal Fan. Despite the large uncertainties in the initial S7Sr/S6Sr values of sedimentary mixtures, our estimates of the elapsed time between cooling and deposition are short (4-14 Ma). Assuming a transport time scale (<1 Ma), deduced exhumation rates are in the same range of modern values (1-3 mm/yr) since ca. 30 Ma. Given that (a) the rocks exposed at the surface, (b) the style of weathering, and (c) rates of exhumation were similar to the present, we infer that the factors controlling erosion of the Early Miocene Himalayan belt were also similar to the present. The data suggest that the Early Miocene Himalayan belt had significant relief and induced orographic effects on precipitation similar to the modern mountain range. It appears that the thrusting along the Main Central Thrust (MCT) or similar structures has uplifted metamorphic basement analogous to the present HHC at sufficiently high rate to maintain steep relief throughout Miocene time, despite high average erosion rates.
SpEED: fast computation of sensitive spaced seeds

SUMMARY
Multiple spaced seeds represent the current state-of-the-art for similarity search in bioinformatics, with applications in various areas such as sequence alignment, read mapping, oligonucleotide design, etc. We present SpEED, a software program that computes highly sensitive multiple spaced seeds. SpEED can be several orders of magnitude faster and computes better seeds than the existing leading software programs.


AVAILABILITY
The source code of SpEED is freely available at www.csd.uwo.ca/~ilie/SpEED/ CONTACT: ilie@csd.uwo.ca


SUPPLEMENTARY INFORMATION
Supplementary data are available at Bioinformatics online.
Optimal Redistricting Under Geographical Constraints: Why 'Pack and Crack' Does Not Work

We show that optimal partisan redistricting with geographical constraints is a computationally intractable (NP-complete) problem. In particular, even when voter’s preferences are deterministic, a solution is generally not obtained by concentrating opponent’s supporters in “unwinnable” districts (“packing”) and spreading one’s own supporters evenly among the other districts in order to produce many slight marginal wins (“cracking”).
Learning a Mahalanobis distance metric for data clustering and classification

Article history: Received 7 October 2007 Received in revised form 27 February 2008 Accepted 16 May 2008
Description and design considerations of a randomized clinical trial investigating the effect of a multidisciplinary cognitive-behavioural intervention for patients undergoing lumbar spinal fusion surgery

BACKGROUND
The ideal rehabilitation strategy following lumbar spinal fusion surgery has not yet been established. This paper is a study protocol, describing the rationale behind and the details of a cognitive-behavioural rehabilitation intervention for lumbar spinal fusion patients based on the best available evidence. Predictors of poor outcome following spine surgery have been identified to provide targets for the intervention, and the components of the intervention were structured in accordance with the cognitive-behavioural model. The study aims to compare the clinical and economical effectiveness of a cognitive-behavioural rehabilitation strategy to that of usual care for patients undergoing lumbar spinal fusion surgery.


METHODS/DESIGN
The study is a randomized clinical trial including 96 patients scheduled for lumbar spinal fusion surgery due to degenerative disease or spondylolisthesis. Patients were recruited in the period October 2011 to July 2013, and the follow-up period is one year from date of surgery. Patients are allocated on a 1:2 ratio (control: intervention) to either treatment as usual (control group), which implies surgery and the standard postoperative rehabilitation, or in addition to this, a patient education focusing on pain behaviour and pain coping (intervention group). It takes place in a hospital setting, and consists of six group-based sessions, managed by a multidisciplinary team of health professionals.The primary outcomes are disability (Oswestry Disability Index) and sick leave, while secondary outcomes include coping (Coping Strategies Questionnaire), fear-avoidance belief (Fear Avoidance Belief Questionnaire), pain (Low Back Pain Rating Scale, pain index), mobility during hospitalization (Cumulated Ambulation Score), generic health-related quality of life (EQ-5D) and resource use. Outcomes are measured using self report questionnaires, medical records and national registers.


DISCUSSION
It is expected that the intervention can provide better functional outcome, less pain and earlier return to work after lumbar spinal fusion surgery. By combining knowledge and evidence from different knowledge areas, the project aims to provide new knowledge that can create greater consistency in patient treatment. We expect that the results can make a significant contribution to development of guidelines for good rehabilitation of patients undergoing lumbar spinal fusion.


TRIAL REGISTRATION
Current Controlled Trials ISRCTN42281022.
Development of a HIV-1 lipopeptide antigen pulsed therapeutic dendritic cell vaccine.

In the search for a therapeutic HIV-1 vaccine, we describe herein the development of a monocyte-derived dendritic cell (DC) vaccine loaded with a mixture of HIV-1-antigen lipopeptides (ANRS HIV-LIPO-5 Vaccine). LIPO-5 is comprised of five HIV-1-antigen peptides (Gag(17-35), Gag(253-284), Nef(66-97), Nef(116-145), and Pol(325-355)), each covalently linked to a palmitoyl-lysylamide moiety. Monocytes enriched from HIV-1-infected highly active antiretroviral therapy (HAART)-treated patients were cultured for three days with granulocyte-macrophage colony-stimulating factor and alpha-interferon. At day 2, the DCs were loaded with ANRS HIV-LIPO-5 vaccine, activated with lipopolysaccharide, harvested at day 3 and frozen. Flow cytometry analysis of thawed DC vaccines showed expression of DC differentiation markers: CD1b/c, CD14, HLA-DR, CD11c, co-stimulatory molecule CD80 and DC maturation marker CD83. DCs were capable of eliciting an HIV-1-antigen-specific response, as measured by expansion of autologous CD4(+) and CD8(+) T-cells. The expanded T-cells secreted gamma-IFN and interleukin (IL)-13, but not IL-10. The safety and immunogenicity of this DC vaccine are being evaluated in a Phase I/II clinical trial in chronically HIV-1-infected patients on HAART (clinicaltrials.gov identifier: NCT00796770).
SUBDUCTION INFLUENCE ON MAGMA SUPPLY AT THE EAST SCOTIA RIDGE

Despite a spreading rate of 65-70 km Ma-‘, the East Scotia Ridge has, along most of its length, a form typically associated with slower rates of sea floor spreading. This may be a consequence of cooler than normal mantle upwelling, which could be a feature of back-arc spreading. At the northern end of the ridge, recently acquired sonar data show a complex, rapidly evolving pattern of extension within 100 km of the South Sandwich Trench. New ridge segments appear to be nucleating at or near the boundary between the South American and Scotia Sea plates and propagating southwards, supplanting older segments. The most prominent of these, north of 56’3O’S, has been propagating at a rate of approximately 60 km Ma-’ for at least 1 Ma, and displays a morphology unique on this plate boundary. A 40 km long axial high exists at the centre of this segment, forming one of the shallowest sections of the East Scotia Ridge. Beneath it, seismic reflection profiles reveal an axial magma chamber, or AMC, reflector, similar to those observed beneath the East Pacific Rise and Valu Fa Ridge. Simple calculations indicate the existence here of a narrow (< 1 km wide) body of melt at a depth of approximately 3 km beneath the sea floor. From the topographic and seismic data, we deduce that a localised mantle melting anomaly lies beneath this segment. Rates of spreading in the east Scotia Sea show little variation along axis. Hence, the changes in melt supply are related to the unique tectonic setting, in which the South American plate is tearing to the east, perhaps allowing mantle flow around the end of the subducting slab. Volatiles released from the tom plate edge and entrained in the flow are a potential cause of the anomalous melting observed. A southward mantle flow may have existed beneath the axis of the East Scotia Ridge throughout its history.
Parental and neonatal risk factors for atopy, airway hyper-responsiveness, and asthma.

BACKGROUND
Previous studies have not resolved the importance of several potential risk factors for the development of childhood atopy, airway hyperresponsiveness, and wheezing, which would allow the rational selection of interventions to reduce morbidity from asthma. Risk factors for these disorders were examined in a birth cohort of 1037 New Zealand children.


METHODS
Responses to questions on respiratory symptoms and measurements of lung function and airway responsiveness were obtained every two to three years throughout childhood and adolescence, with over 85% cohort retention at age 18 years. Atopy was determined by skin prick tests at age 13 years. Relations between parental and neonatal factors, the development of atopy, and features of asthma were determined by comparison of proportions and logistic regression.


RESULTS
Male sex was a significant independent predictor for atopy, airway hyper-responsiveness, hay fever, and asthma. A positive family history, especially maternal, of asthma strongly predicted childhood atopy, airway hyperresponsiveness, asthma, and hay fever. Maternal smoking in the last trimester was correlated with the onset of childhood asthma by the age of 1 year. Birth in the winter season increased the risk of sensitisation to cats. Among those with a parental history of asthma or hay fever, birth in autumn and winter also increased the risk of sensitisation to house dust mites. The number of siblings, position in the family, socioeconomic status, and birth weight were not consistently predictive of any characteristic of asthma.


CONCLUSIONS
Male sex, parental atopy, and maternal smoking during pregnancy are risk factors for asthma in young children. Children born in winter exhibit a greater prevalence of sensitisation to cats and house dust mites. These data suggest possible areas for intervention in children at risk because of parental atopy.
The chemistry of tea flavonoids.

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Pb Neurotoxicity: Neuropsychological Effects of Lead Toxicity

Neurotoxicity is a term used to describe neurophysiological changes caused by exposure to toxic agents. Such exposure can result in neurocognitive symptoms and/or psychiatric disturbances. Common toxic agents include heavy metals, drugs, organophosphates, bacterial, and animal neurotoxins. Among heavy metal exposures, lead exposure is one of the most common exposures that can lead to significant neuropsychological and functional decline in humans. In this review, neurotoxic lead exposure's pathophysiology, etiology, and epidemiology are explored. In addition, commonly associated neuropsychological difficulties in intelligence, memory, executive functioning, attention, processing speed, language, visuospatial skills, motor skills, and affect/mood are explored.
Isocyanate-crosslinked silica aerogel monoliths: preparation and characterization

Polymerization of diand tri-isocyanates can be templated onto the mesoporous surface of a preformed network of sol–gelderived silica nanoparticles, resulting in a conformal crosslinked coating that renders the interparticle neck zone wider. Upon drying, these crosslinked networks yield aerogels which are up to 3· more dense than native aerogels based on the underlying silica framework, but also up to 10· less hygroscopic and they may take more than 300· the force to break. These results have been obtained with one-step based-catalyzed sol–gel silica networks, as well as with gels derived through a two-step process involving an acid-catalyzed sol and a based-catalyzed gel. Furthermore, it has been also found that crosslinking increases the dielectric constant only by 35% relative to values reported in the literature for native silica aerogels of about the same porosity. Chemical investigations into the polymerization reaction have shown that the process of crosslinking involves reaction of the isocyanate with: (a) AOH groups at the surface of silica to form carbamate; and (b) adsorbed water, to form an amine and carbon dioxide. This amine then reacts with additional isocyanates resulting in polymer chain extension and bridging of particles with urethane-terminated polyurea. 2004 Elsevier B.V. All rights reserved. PACS: 81.05.Qk; 81.05.Rm; 81.05.Zx; 81.07. b; 81.20.Fw; 81.40.Tv; 82.35.Np
Vaccines are not associated with autism: an evidence-based meta-analysis of case-control and cohort studies.

There has been enormous debate regarding the possibility of a link between childhood vaccinations and the subsequent development of autism. This has in recent times become a major public health issue with vaccine preventable diseases increasing in the community due to the fear of a 'link' between vaccinations and autism. We performed a meta-analysis to summarise available evidence from case-control and cohort studies on this topic (MEDLINE, PubMed, EMBASE, Google Scholar up to April, 2014). Eligible studies assessed the relationship between vaccine administration and the subsequent development of autism or autism spectrum disorders (ASD). Two reviewers extracted data on study characteristics, methods, and outcomes. Disagreement was resolved by consensus with another author. Five cohort studies involving 1,256,407 children, and five case-control studies involving 9,920 children were included in this analysis. The cohort data revealed no relationship between vaccination and autism (OR: 0.99; 95% CI: 0.92 to 1.06) or ASD (OR: 0.91; 95% CI: 0.68 to 1.20), nor was there a relationship between autism and MMR (OR: 0.84; 95% CI: 0.70 to 1.01), or thimerosal (OR: 1.00; 95% CI: 0.77 to 1.31), or mercury (Hg) (OR: 1.00; 95% CI: 0.93 to 1.07). Similarly the case-control data found no evidence for increased risk of developing autism or ASD following MMR, Hg, or thimerosal exposure when grouped by condition (OR: 0.90, 95% CI: 0.83 to 0.98; p=0.02) or grouped by exposure type (OR: 0.85, 95% CI: 0.76 to 0.95; p=0.01). Findings of this meta-analysis suggest that vaccinations are not associated with the development of autism or autism spectrum disorder. Furthermore, the components of the vaccines (thimerosal or mercury) or multiple vaccines (MMR) are not associated with the development of autism or autism spectrum disorder.
Accelerating last-mile web performance with popularity-based prefetching

As broadband speeds increase, latency is becoming a bottleneck for many applications—especially for Web downloads. Latency affects many aspects of Web page load time, from DNS lookups to the time to complete a three-way TCP handshake; it also contributes to the time it takes to transfer the Web objects for a page. Previous work has shown that much of this latency can occur in the last mile [2]. Although some performance bottlenecks can be mitigated by increasing downstream throughput (e.g., by purchasing a higher service plan), in many cases, latency introduces performance bottlenecks, particularly for connections with higher throughput. To mitigate latency bottlenecks in the last mile, we have implemented a system that performs DNS prefetching and TCP connection caching to the Web sites that devices inside a home visit most frequently, a technique we call popularity-based prefetching. Many devices and applications already perform DNS prefetching and maintain persistent TCP connections, but most prefetching is predictive based on the content of the page, rather than on past site popularity. We evaluate the optimizations using a simulator that we drive from traffic traces that we collected from five homes in the BISmark testbed [1]. We find that performing DNS prefetching and TCP connection caching for the twenty most popular sites inside the home can double DNS and connection cache hit rates.
Skip-Thought Memory Networks

Question Answering (QA) is fundamental to natural language processing in that most nlp problems can be phrased as QA (Kumar et al., 2015). Current weakly supervised memory network models that have been proposed so far struggle at answering questions that involve relations among multiple entities (such as face-book's bAbi qa5-three-arg-relations in (Weston et al., 2015)). To address this problem of learning multi-argument multi-hop semantic relations for the purpose of QA, we propose a method that combines the jointly learned long-term read-write memory and attentive inference components of end-to-end memory networks (MemN2N) (Sukhbaatar et al., 2015) with distributed sentence vector representations encoded by a Skip-Thought model (Kiros et al., 2015). This choice to append Skip-Thought Vectors to the existing MemN2N framework is motivated by the fact that Skip-Thought Vectors have been shown to accurately model multi-argument semantic relations (Kiros et al., 2015).
Designing a desirable smart bracelet for older adults

In this paper, we present the design process of a smart bracelet that aims at enhancing the life of elderly people. The bracelet acts as a personal assistant during the user's everyday life, monitoring the health status and alerting him or her about abnormal conditions, reminding medications and facilitating the everyday life in many outdoor and indoor activities.
MusicXML: An internet-friendly format for sheet music

The downloadable sheet music market has been constrained by reliance on proprietary binary formats. MusicXML is a new Internet-friendly format for representing sheet music and music notation. We introduce the basics of MusicXML design, using examples from current software to illustrate MusicXML's advantages over previous music interchange formats. We conclude by discussing the new types of music use that MusicXML makes possible, and how this fits in with ongoing XML development efforts. 1. The Need for a New Music Interchange Format Common Western music notation is a symbolic method of representing music for performers and listeners. Besides its use in publishing sheet music, musical scores and parts, it has been encoded in different computer formats for over 30 years. The book Beyond MIDI describes over 20 of these published musical codes. There are also many more unpublished, proprietary codes. Given the high costs of traditional music publication, many companies have seen that Internet distribution has the potential to increase both the size and profitability of the sheet music market. To date, the Internet sheet music market has been hobbled by its reliance on a proliferation of proprietary binary formats. The most common format, Portable Document Format (PDF) , contains no musical semantics and can only be viewed on screen or printed on paper. Companies like Sunhawk, MusicNotes, Sibelius, and Noteheads all have different proprietary music formats for their sheet music players. If you buy sheet music from them or their partners today, you can play it, view it, or print it only with that single proprietary player. This provides little valueadded to consumers when compared to printed music on paper. We believe this has fragmented the online sheet music market and contributed significantly to its disappointing sales through 2001. Electronic musical instruments such as synthesizers faced a similar problem in the 1980s, when there was no way to get musical instruments from different vendors to work or play together. The invention of the Musical Instrument Digital Interface (MIDI) format [MIDI 1996]solved this problem, and led to the rapid growth of the electronic musical instrument market. The introduction of General MIDI led to even further levels of compatibility, interchange, and growth in the instrument market. Today, MIDI remains the only symbolic music interchange format in wide use today. But MIDI, designed to solve problems in music performance, cannot represent much of what is found in sheet music. MP3 and other audio formats represent music recordings, not music notation.