bluuebunny/crossref_metadata_2025_split huggingface dataset:
Xpert MTB/RIF Assay Shows Faster Clearance of Mycobacterium tuberculosis DNA with Higher Levels of Rifapentine Exposure
Authors: Jayakumar A. , Savic R. M. , Everett C. K. , Benator D. , Alland D. , Heilig C. M. , Weiner M. , Friedrich S. O. , Martinson N. A. , Kerrigan A. , Zamudio C. , Goldberg S. V. , Whitworth W. C. , Davis J. L. , Nahid P. 
Published: October 2016

ABSTRACT

The Xpert MTB/RIF assay is both sensitive and specific as a diagnostic test. Xpert also reports quantitative output in cycle threshold (

C
T

) values, which may provide a dynamic measure of sputum bacillary burden when used longitudinally. We evaluated the relationship between Xpert

C
T

trajectory and drug exposure during tuberculosis (TB) treatment to assess the potential utility of Xpert

C
T

for treatment monitoring. We obtained serial sputum samples from patients with smear-positive pulmonary TB who were consecutively enrolled at 10 international clinical trial sites participating in study 29X, a CDC-sponsored Tuberculosis Trials Consortium study evaluating the tolerability, safety, and antimicrobial activity of rifapentine at daily doses of up to 20 mg/kg of body weight. Xpert was performed at weeks 0, 2, 4, 6, 8, and 12. Longitudinal

C
T

data were modeled using a nonlinear mixed effects model in relation to rifapentine exposure (area under the concentration-time curve [AUC]). The rate of change of

C
T

was higher in subjects receiving rifapentine than in subjects receiving standard-dose rifampin. Moreover, rifapentine exposure, but not assigned dose, was significantly associated with rate of change in

C
T

(
P
= 0.02). The estimated increase in

C
T

slope for every additional 100 μg · h/ml of rifapentine drug exposure (as measured by AUC) was 0.11

C
T

/week (95% confidence interval [CI], 0.05 to 0.17). Increasing rifapentine exposure is associated with a higher rate of change of Xpert

C
T

, indicating faster clearance of
Mycobacterium tuberculosis
DNA. These data suggest that the quantitative outputs of the Xpert MTB/RIF assay may be useful as a dynamic measure of TB treatment response.
Commentary: Molecular Assay Validation Using Genomic Sequence Databases
Authors: Dekker John P. 
Published: October 2016

ABSTRACT

Whole-genome sequence databases offer new
in silico
approaches for designing and validating PCR assays in the clinical microbiology laboratory. An article in this issue of the
Journal of Clinical Microbiology
(M. J. Jansen van Rensburg, C. Swift, A. J. Cody, C. Jenkins, and M. C. J. Maiden, J Clin Microbiol, 54:2882–2890, 2016,
http://dx.doi.org/10.1128/JCM.01522-16
) demonstrates the use of publicly available genomic sequence data to evaluate a PCR assay for distinguishing
Campylobacter
species.
A modeling case for high atmospheric oxygen concentrations during the Mesozoic and Cenozoic
Authors: Mills Benjamin J.W. , Belcher Claire M. , Lenton Timothy M. , Newton Robert J. 
Published: October 2016

Abstract
Changes in atmospheric oxygen concentration over Earth history are commonly related to the evolution of animals and plants. But there is no direct geochemical proxy for O2 levels, meaning that estimations rely heavily on modeling approaches. The results of such studies differ greatly, to the extent that today’s atmospheric mixing ratio of 21% might be either the highest or lowest level during the past 200 m.y. Long term oxygen sources, such as the burial in sediments of reduced carbon and sulfur species, are calculated in models by representation of nutrient cycling and estimation of productivity, or by isotope mass balance (IMB)—a technique in which burial rates are inferred in order to match known isotope records. Studies utilizing these different techniques produce conflicting estimates for paleoatmospheric O2, with nutrient-weathering models estimating concentrations close to, or above, that of the present day, and IMB models estimating low O2, especially during the Mesozoic. Here we reassess the IMB technique using the COPSE biogeochemical model. IMB modelling is confirmed to be highly sensitive to assumed carbonate δ13C, and when this input is defined following recent compilations, predicted O2 is significantly higher and in reasonable agreement with that of non-IMB techniques. We conclude that there is no model-based support for low atmospheric oxygen concentrations during the past 200 m.y. High Mesozoic O2 is consistent with wildfire records and the development of plant fire adaptions, but links between O2 and mammal evolution appear more tenuous.
Trace elements in fluid inclusions of sediment-hosted gold deposits indicate a magmatic-hydrothermal origin of the Carlin ore trend
Authors: Large Simon J.E. , Bakker Edine Y.N. , Weis Philipp , Wälle Markus , Ressel Mike , Heinrich Christoph A. 
Published: October 2016

Abstract
The Carlin-type deposits in Nevada (western USA) constitute the world’s second-largest gold ore province. These structurally and stratigraphically controlled, sediment-hosted ore bodies are characterized by carbonate dissolution attending hydrothermal precipitation of gold-rich arsenian pyrite. The origin of the mineralizing fluids and the source of the gold remain debated. Conceptual models, favoring either sedimentary, metamorphic, or magmatic fluid sources, are based on isotopic tracers, giving ambiguous results. Here we use the trace element compositions of fluid inclusions to separate geochemical signals of the large-scale fluid source from effects of deposit-scale fluid interaction with the sedimentary host rocks. Specifically, we compare the ratios of Rb, K, B, As, Sr, and Ba between clearly magmatic-hydrothermal Cu-Au ores at Copper Canyon in the Battle Mountain–Eureka trend with the Gold Quarry and Chukar Footwall deposits on the Carlin trend that contain high-grade gold in similar sedimentary host rocks. Results indicate that both ore districts can be related to upper crustal hydrous magmatic intrusions, but are now exposed at different levels of erosion and formed at different distances from their magmatic fluid source. Fluid compositions are best explained by separation of a deep magmatic fluid into Rb-K–enriched brine and B-As-Au–enriched vapor, followed by cooling and contraction of the magmatic vapor phase to an epithermal liquid, which reacted with Sr-Ba–bearing sedimentary rocks during ascent and eventual precipitation of Au-rich arsenian pyrite.
Reconsultation, self-reported health status and costs following treatment at a musculoskeletal Clinical Assessment and Treatment Service (CATS): a 12-month prospective cohort study
Authors: Roddy Edward , Jordan Kelvin P , Oppong Raymond , Chen Ying , Jowett Sue , Dawes Peter , Hider Samantha L , Packham Jon , Stevenson Kay , Zwierska Irena , Hay Elaine M 
Published: October 2016

ObjectivesTo determine (1) reconsultation frequency, (2) change in self-reported health status, (3) baseline factors associated with reconsultation and change in health status and (4) associated healthcare costs and quality-adjusted life-years (QALYs), following assessment at a musculoskeletal Clinical and Assessment Treatment Service (CATS).DesignProspective cohort study.SettingSingle musculoskeletal CATS at the primary–secondary care interface.Participants2166 CATS attenders followed-up by postal questionnaires at 6 and 12 months and review of medical records.Outcome measuresPrimary outcome was consultation in primary care with the same musculoskeletal problem within 12 months. Secondary outcome measures were consultation at the CATS with the same musculoskeletal problem within 12 months, physical function and pain (Short Form-36), anxiety and depression (Hospital Anxiety and Depression Scale), time off work, healthcare costs and QALYs.ResultsOver 12 months, 507 (38%) reconsulted for the same problem in primary care and 345 (26%) at the CATS. Primary care reconsultation in the first 3 months was associated with baseline pain interference (relative risk ratio 5.33; 95% CI 3.23 to 8.80) and spinal pain (1.75; 1.09 to 2.82), and after 3–6 months with baseline assessment by a hospital specialist (2.06; 1.13 to 3.75). Small mean improvements were seen in physical function (1.88; 95% CI 1.44 to 2.32) and body pain (3.86; 3.38 to 4.34) at 6 months. Poor physical function at 6 months was associated with obesity, chronic pain and poor baseline physical function. Mean (SD) 6-month cost and QALYs per patient were £422.40 (660.11) and 0.257 (0.144), respectively.ConclusionsWhile most patients are appropriate for a ‘one-stop shop’ model, those with troublesome, disabling pain and spinal pain commonly reconsult and have ongoing problems. Services should be configured to identify and address such clinical complexity.
Outcomes of endovascular treatment of basilar artery occlusion in the stent retriever era: a systematic review and meta-analysis
Authors: Phan Kevin , Phan Steven , Huo Ya Ruth , Jia Fangzhi , Mortimer Alex 
Published: October 2016

BackgroundStent retriever thrombectomy has recently been found to be effective for anterior circulation strokes, but its efficacy for basilar artery occlusion (BAO) is unclear.ObjectiveTo carry out a systematic review and meta-analysis to analyze the available evidence for the use of stent retrievers for BAO.MethodsTwo independent reviewers searched six databases for studies reporting outcomes following endovascular treatment for BAO.ResultsA total of 17 articles (6 prospective and 11 retrospective) were included. The weighted mean age of patients was 67 years (range 59–82) and 59% were male. Thrombolytic drugs were administered intravenously and intra-arterially in 46% (range 0–88%) and 38% (range 0–90%) of patients, respectively. Weighted pooled estimates of successful recanalization (TICI 2b–3) and good outcome (modified Rankin Scale ≤2) were 80.0% (95% CI 70.7% to 88.0%; I2=80.28%; p<0.001) and 42.8% (95% CI 34.0% to 51.8%; I2=61.83%; p=0.002), respectively. Pooled mortality was 29.4% (95% CI 23.9% to 35.3%; I2=37.01%; p=0.087). Incidence of procedure-related complications and symptomatic hemorrhage was 10.0% (95% CI 3.7% to 18.3%; I2=61.05%; p=0.017) and 6.8% (95% CI 3.5% to 10.8%; I2=37.99%; p=0.08), respectively.ConclusionsStent retriever thrombectomy achieves a high rate of recanalization and functional independence while being relatively safe for patients with BAO. Future prospective studies with long-term follow-up are warranted.
Vaccination practices in patients with inflammatory bowel disease among general internal medicine physicians in the USA
Authors: Gurvits Grigoriy E , Lan Gloria , Tan Amy , Weissman Arlene 
Published: October 2016

ABSTRACTBackgroundIncreasing prevalence of inflammatory bowel disease (IBD) poses significant challenges to medical community. Preventive medicine, including vaccination against opportunistic infections, is important in decreasing morbidity and mortality in patients with IBD. We conduct first study to evaluate general awareness and adherence to immunisation guidelines by primary care physicians in the USA.MethodsWe administered an electronic questionnaire to the research panel of the American College of Physicians (ACP) assessing current vaccination practices, barriers to vaccination and provider responsibility for administering vaccinations and compared responses with the European Crohn’s and Colitis Organization consensus guidelines and expert opinion from the USA.ResultsAll of surveyed physicians (276) had experience with patients with IBD and spent majority of their time in direct patient care. 49% of physicians took immunisation history frequently or always, and 76% reported never or rarely checking immunisation antibody titres with only 2% doing so routinely. 65% of physicians believed that primary care providers (PCPs) were responsible for determining patient’s immunisation. Vaccine administration was felt to be the duty of primary care doctor 80% of the time. 2.5% of physicians correctly recommended vaccinations all the time. Physicians were more likely to recommend vaccination to immunocompetent than immunocompromised patients. Up to 23% of physicians would incorrectly recommend live vaccine to immunocompromised patients with IBD.ConclusionsCurrent knowledge and degree of comfort among PCPs in the USA in preventing opportunistic infections in IBD population remain low. Management of patients with IBD requires structured approach to their healthcare maintenance in everyday practice, including enhanced educational policy aimed at primary care physicians.
Interhospital transfer neurological deterioration in patients with spontaneous intracerebral haemorrhage: incidence and risk factors
Authors: Fan Ju-Sing , Chen Yen-Chia , Huang Hsien-Hao , Yen David Hung-Tsang , How Chorng-Kuang , Huang Mu-Shuan 
Published: October 2016

ABSTRACTObjectiveTo explore the incidence and risk factors for interhospital transfer neurological deterioration (IHTND) in patients with spontaneous intracerebral haemorrhage (SICH).MethodsConsecutive adult patients with first-ever SICH referred to our emergency department (ED) and transported by ambulance from July 2011 through June 2015 were eligible for this prospective observational study. Enrolled patients had SICH with elapsed time &lt;12 hours and a nearly normal Glasgow Coma Scale (GCS) score (≥13) at presentation. IHTND was defined as GCS score drop ≥2 points during the time from last GCS measure in first ED (shortly before transport) and first measure in second ED (shortly after arrival), which was confirmed by the accompanying nurse practitioner. The potential risk factors for IHTND were screened by χ2 test, unpaired t test (parametric data) or Mann–Whitney U test (non-parametric data) in univariate analysis. Multiple logistic regression analysis was used to adjust for other covariates.ResultsAmong 217 enrolled patients, 36 (16.6%) had IHTND. After adjustment for other covariates in multiple logistic regression analysis, the significant predictors of IHTND were arrival systolic blood pressure ≥180 mm Hg (p=0.026, OR=2.741, 95% CI 1.126 to 6.674), infratentorial ICH (p=0.015, OR=3.182, 95% CI 1.248 to 8.113), presence of intraventricular haemorrhage (p=0.023, OR=2.533, 95% CI 1.137 to 5.645) and larger ICH (by 1 mL increment of haematoma, p=0.013, OR=1.027, 95% CI 1.006 to 1.048).ConclusionsAbout one-sixth of referred not comatose patients with SICH developed IHTND. Some risk factors were identified for the first time. Modifying procedures for proper transfer of patients at high-risk for IHTND might help in safely transferring patients with SICH.
Effects of nonmetal doping on electronic structures of NaNbO3 based on hybrid density functional calculation
Authors: Shi Haifeng , Lan Benyue , Zhang Chengliang , Ye Enjia , Nie Yanguang , Bian Baoan 
Published: October 2016

The influences of a series of anion doping on the electronic structures of sodium niobate (NaNbO3) have been systematically investigated by density functional theory (DFT) calculations with the hybrid B3LYP functional. As for B[Formula: see text](C,[Formula: see text]P)-doped NaNbO3, the isolated B 2p (C 2p, P 3p) states were formed above the valence band maximum (VBM) of NaNbO3, which were too weak to mix with O 2p states and thus produced band gap narrowing. While the band gap of NaNbO3 was slightly narrowed after F doping. As for S-doped NaNbO3, the S 3p states mixed with O 2p states well and thus reduced the band gap energy. According to the calculation results, we tentatively put forward that S doping would be appropriate for single anion doping NaNbO3, while the B[Formula: see text](C,[Formula: see text]P) elements would be suitable candidates for co-doping NaNbO3.
Metamorphic evolution of the Ilomantsi greenstone belt in the Archaean Karelia Province, eastern Finland
Authors: Hölttä Pentti , Lehtonen Elina , Lahaye Yann , Sorjonen-Ward Peter 
Published: October 2016

Abstract

The Ilomantsi greenstone belt is a Neoarchaean,
c.
2.75–2.70 Ga volcanic–sedimentary complex in which metamorphic grade increases from staurolite grade in the SW of the belt to sillimanite grade in the NE. In the staurolite zone, prograde garnet zoning indicates pressure and temperature increases from 480–500°C at 2–4 kbar to 560–570°C at 6–7 kbar. Within the sillimanite zone temperatures peaked at 660–670°C at pressures of around 6 kbar. The U–Pb age determinations on monazite from the sillimanite zone yielded both Archaean and Proterozoic ages. One sample contains an exclusively Archaean monazite population of 2620±24 Ma, while another sample has two generations of monazite, with ages of 2664±33 Ma and 1837±13 Ma. The monazite data confirm that the Ilomantsi greenstone belt was metamorphosed simultaneously with the surrounding Neoarchaean migmatite complexes. The apparent clockwise
PT
path and medium
P
/
T
-type metamorphism are consistent with collisional tectonic settings, but the two distinct metamorphic events recorded by monazite indicate that a second, Palaeoproterozoic thermal event caused recrystallization and new mineral growth, in line with previous evidence from other isotopic systems. Accordingly, great care is necessary in defining metamorphic evolutionary
P–T–t
paths in rocks with complex mineral assemblages, to ensure correct identification of truly coeval mineral assemblages.
Transparent offloading and mapping (TOM)
Authors: Hsieh Kevin , Ebrahimi Eiman , Kim Gwangsun , Chatterjee Niladrish , O'Connor Mike , Vijaykumar Nandita , Mutlu Onur , Keckler Stephen W. 
Published: October 2016

Main memory bandwidth is a critical bottleneck for modern GPU systems due to limited off-chip pin bandwidth. 3D-stacked memory architectures provide a promising opportunity to significantly alleviate this bottleneck by directly connecting a logic layer to the DRAM layers with high bandwidth connections. Recent work has shown promising potential performance benefits from an architecture that connects multiple such 3D-stacked memories and offloads bandwidth-intensive computations to a GPU in each of the logic layers. An unsolved key challenge in such a system is how to enable computation offloading and data mapping to
multiple
3D-stacked memories
without burdening the programmer
such that
any application
can transparently benefit from near-data processing capabilities in the logic layer.

Our paper develops two new mechanisms to address this key challenge. First, a compiler-based technique that automatically identifies code to offload to a logic-layer GPU based on a simple cost-benefit analysis. Second, a software/hardware cooperative mechanism that predicts which memory pages will be accessed by offloaded code, and places those pages in the memory stack closest to the offloaded code, to minimize off-chip bandwidth consumption. We call the combination of these two programmer-transparent mechanisms TOM: Transparent Offloading and Mapping.
Our extensive evaluations across a variety of modern memory-intensive GPU workloads show that, without requiring any program modification, TOM significantly improves performance (by 30% on average, and up to 76%) compared to a baseline GPU system that cannot offload computation to 3D-stacked memories.
Dynamo
Authors: Wu Qiang , Deng Qingyuan , Ganesh Lakshmi , Hsu Chang-Hong , Jin Yun , Kumar Sanjeev , Li Bin , Meza Justin , Song Yee Jiun 
Published: October 2016

Data center power is a scarce resource that often goes underutilized due to conservative planning. This is because the penalty for overloading the data center power delivery hierarchy and tripping a circuit breaker is very high, potentially causing long service outages. Recently, dynamic server power capping, which limits the amount of power consumed by a server, has been proposed and studied as a way to reduce this penalty, enabling more aggressive utilization of provisioned data center power. However, no real at-scale solution for data center-wide power monitoring and control has been presented in the literature.
In this paper, we describe Dynamo -- a data center-wide power management system that monitors the entire power hierarchy and makes coordinated control decisions to safely and efficiently use provisioned data center power. Dynamo has been developed and deployed across all of Facebook's data centers for the past three years. Our key insight is that in real-world data centers, different power and performance constraints at different levels in the power hierarchy necessitate coordinated data center-wide power management.
We make three main contributions. First, to understand the design space of Dynamo, we provide a characterization of power variation in data centers running a diverse set of modern workloads. This characterization uses fine-grained power samples from tens of thousands of servers and spanning a period of over six months. Second, we present the detailed design of Dynamo. Our design addresses several key issues not addressed by previous simulation-based studies. Third, the proposed techniques and design have been deployed and evaluated in large scale data centers serving billions of users. We present production results showing that Dynamo has prevented 18 potential power outages in the past 6 months due to unexpected power surges; that Dynamo enables optimizations leading to a 13% performance boost for a production Hadoop cluster and a nearly 40% performance increase for a search cluster; and that Dynamo has already enabled an 8% increase in the power capacity utilization of one of our data centers with more aggressive power subscription measures underway.
Energy efficient data encoding in DRAM channels exploiting data value similarity
Authors: Seol Hoseok , Shin Wongyu , Jang Jaemin , Choi Jungwhan , Suh Jinwoong , Kim Lee-Sup 
Published: October 2016

As DRAM data bandwidth increases, tremendous energy is dissipated in the DRAM data bus. To reduce the energy consumed in the data bus, DRAM interfaces with asymmetric termination, such as Pseudo Open Drain (POD) and Low Voltage Swing Terminated Logic (LVSTL), have been adopted in modern DRAMs. In interfaces using asymmetric termination, the amount of termination energy is proportional to the hamming weight of the data words. In this work, we propose Bitwise Difference Encoding (BD-Encoding), which decreases the hamming weight of data words, leading to a reduction in energy consumption in the modern DRAM data bus. Since smaller hamming weight of the data words also reduces switching activity, switching energy and power noise are also both reduced.
BD-Encoding exploits the similarity in data words in the DRAM data bus. We observed that similar data words (i.e. data words whose hamming distance is small) are highly likely to be sent over at similar times. Based on this observation, BD-coder stores the data recently sent over in both the memory controller and DRAMs. Then, BD-coder transfers the bitwise difference between the current data and the most similar data. In an evaluation using SPEC 2006, BD-Encoding using 64 recent data reduced termination energy by 58.3% and switching energy by 45.3%. In addition, 55% of the LdI/dt noise was decreased with BD-Encoding.