bluuebunny/crossref_metadata_2025 huggingface dataset:
Accuracy of administrative databases in detecting primary breast cancer diagnoses: a systematic review
Authors: Abraha Iosief , Montedori Alessandro , Serraino Diego , Orso Massimiliano , Giovannini Gianni , Scotti Valeria , Granata Annalisa , Cozzolino Francesco , Fusco Mario , Bidoli Ettore
Published: July 2018

Objective

To define the accuracy of administrative datasets to identify primary diagnoses of breast cancer based on the International Classification of Diseases (ICD) 9th or 10th revision codes.

Design

Systematic review.

Data sources: MEDLINE, EMBASE, Web of Science and the Cochrane Library (April 2017).

Eligibility criteria

The inclusion criteria were: (a) the presence of a reference standard; (b) the presence of at least one accuracy test measure (eg, sensitivity) and (c) the use of an administrative database.

Data extraction

Eligible studies were selected and data extracted independently by two reviewers; quality was assessed using the Standards for Reporting of Diagnostic accuracy criteria.

Data analysis

Extracted data were synthesised using a narrative approach.

Results

From 2929 records screened 21 studies were included (data collection period between 1977 and 2011). Eighteen studies evaluated ICD-9 codes (11 of which assessed both invasive breast cancer (code 174.x) and carcinoma in situ (ICD-9 233.0)); three studies evaluated invasive breast cancer-related ICD-10 codes. All studies except one considered incident cases.

The initial algorithm results were: sensitivity ≥80% in 11 of 17 studies (range 57%–99%); positive predictive value was ≥83% in 14 of 19 studies (range 15%–98%) and specificity ≥98% in 8 studies. The combination of the breast cancer diagnosis with surgical procedures, chemoradiation or radiation therapy, outpatient data or physician claim may enhance the accuracy of the algorithms in some but not all circumstances. Accuracy for breast cancer based on outpatient or physician’s data only or breast cancer diagnosis in secondary position diagnosis resulted low.

Conclusion

Based on the retrieved evidence, administrative databases can be employed to identify primary breast cancer. The best algorithm suggested is ICD-9 or ICD-10 codes located in primary position.

Trial registration number

CRD42015026881.
Protected adults’ voting rights: an interdisciplinary study of medical assessment and jurisprudence in France
Authors: Bosquet Antoine , Mahé Isabelle
Published: July 2018

Objectives

The study’s objective was to describe the decision-making about voting rights of protected adults, which includes the medical assessment and the magistrate’s decision to maintain voting rights or not.

Design

This work explores using an interdisciplinary approach: first, magistrate’s decision-making with a systematic review of jurisprudence and second medical assessment with semistructured questionnaires sent to physicians assessing adults under guardianship.

Setting

France.

Participants

For jurisprudence’s analysis, all guardianship decisions found on the Legifrance.gouv.fr website and that specified the protected person’s voting rights were analysed. For the survey about medical civic assessment, an 18-item questionnaire was sent to all physicians drawing up medical certificates prior to placement under guardianship in one urban (Paris and the three surrounding departments) and one rural area of France (the 10 most rural French administrative departments).

Main outcome measures

The analysis of jurisprudence explores the situation concerning protected adults’ voting rights and the reasons for magistrates’ decision. The survey about medical civic assessment explores the means of medical assessment (persons consulted, information collected), the content of the medical certificate, the physicians’ opinions regarding their role.

Results

The analysis of the jurisprudence demonstrates that 30% (51/171) of protected adults kept the right to vote. The survey shows that medical assessment varied according to the physician’s gender, specialty and geographical location. Voting capacity was the main criterion common to both physicians and magistrates in the decision whether to maintain voting rights. 27% (34/124) of physicians would like the official texts to be more precise, and one-third (41/133) wished to have tools to facilitate assessment of civic capacity.

Conclusions

Official guides need to be drawn up to detail the criteria for and means of medical assessment of the civil capacity of protected adults, with a view to ensuring transparency and homogeneity in the exercise of justice.
Risk factors and complications of lower limb cellulitis in Africa: a systematic review
Authors: Tianyi Frank-Leonel , Mbanga Clarence Mvalo , Danwang Celestin , Agbor Valirie Ndip
Published: July 2018

Objective

To summarise available data on the risk factors, complications and the factors associated with complications of lower limb cellulitis in Africa.

Methods

We did electronic searches on PubMed, EMBASE, Scopus and African Journals Online from 1 January 1986 to 30 October 2017, extracted and summarised data on the risk factors, complications and the factors associated with the complications of lower limb cellulitis from eligible literature.

Results

A total of seven studies were retained for final review after the search and screening processes. Local risk factors of cellulitis reported were: disruption of the skin barrier, neglected wounds, toe-web intertrigo, leg ulcers, use of depigmentation drugs and leg oedema. Obesity was the only reported general risk factor of cellulitis. Five studies reported on the complications of cellulitis which included: abscess formation, necrotising fasciitis, bullae, haemorrhagic lesions, necrosis, phlebitis and amputations. Nicotine addiction, chronic use of non-steroidal anti-inflammatory drugs, delay in the initiation of antibiotic treatment and elevated erythrocyte sedimentation rate were risk factors of complications of lower limb cellulitis identified from three studies.

Conclusion

This review highlights the important role of local risk factors in the pathogenesis of lower limb cellulitis in Africa. The association between voluntary skin depigmentation and lower limb cellulitis should alert public health authorities and the general population to the health risks associated with this practice. The identification and improved management of the risk factors of lower limb cellulitis and its complications could go a long way in decreasing the morbidity and health costs incurred by lower limb cellulitis in Africa.
Trends in the utilisation of emergency departments in California, 2005–2015: a retrospective analysis
Authors: Hsia Renee Y , Sabbagh Sarah H , Guo Joanna , Nuckton Thomas J , Niedzwiecki Matthew J
Published: July 2018

Objective

To examine current trends in the characteristics of patients visiting California emergency departments (EDs) in order to better direct the allocation of acute care resources.

Design

A retrospective study.

Setting

We analysed ED utilisation trends between 2005 and 2015 in California using non-public patient data from California’s Office of Statewide Health Planning and Development.

Participants

We included all ED visits in California from 2005 to 2015.

Primary and secondary outcome measures

We analysed ED visits and visit rates by age, sex, race/ethnicity, payer and urban/rural trends. We further examined age, sex, race/ethnicity and urban/rural trends within each payer group for a more granular picture of the patient population. Additionally, we looked at the proportion of patients admitted from the ED and distribution of diagnoses.

Results

Between 2005 and 2015, the annual number of ED visits increased from 10.2 to 14.2 million in California. ED visit rates increased by 27.8% (p<0.001), with the greatest increases among patients aged 5–19 (37.4%, p<0.001) and 45–64 years (41.1%, p<0.001), non-Hispanic Black and Hispanic patients (56.8% and 48.8%, p<0.001), the uninsured and Medicaid-insured (36.1%, p=0.002; 28.6%, p<0.001) and urban residents (28.3%, p<0.001). The proportion of ED visits resulting in hospitalisation decreased by 18.3%, with decreases across all payer groups.

Conclusions

Our findings reveal an increasing demand for emergency care and may reflect current limitations in accessing care in other parts of the healthcare system. Policymakers may need to recognise the increasingly vital role that EDs are playing in the provision of care and consider ways to incorporate this changing reality into the delivery of health services.
Accurate estimation of cardiovascular risk in a non-diabetic adult: detecting and correcting the error in the reported Framingham Risk Score for the Systolic Blood Pressure Intervention Trial population
Authors: Warner Frederick , Dhruva Sanket S , Ross Joseph S , Dey Pranammya , Murugiah Karthik , Krumholz Harlan M
Published: July 2018

Objectives

To understand the discrepancy between the published 10-year cardiovascular risk and 10-year cardiovascular risk generated from raw data using the Framingham Risk Score for participants in the Systolic Blood Pressure Intervention Trial (SPRINT).

Design

Secondary analysis of SPRINT data published inThe New England Journal of Medicine(NEJM) and made available to researchers in late 2016.

Setting

SPRINT clinical trial sites.

Participants

Study participants enrolled into SPRINT.

Results

The number of SPRINT study participants identified as having ≥15% 10-year cardiovascular risk was not consistent with what was reported in the original publication. Using the data from the trial, the Framingham Risk Score indicated ≥15% 10-year cardiovascular risk for 7089 participants compared with 5737 reported in the paper, a change from 61% to 76% of the total study population.

Conclusions

The analysis of the clinical trial data by independent investigators identified an error in the reporting of the risk of the study population. The SPRINT trial enrolled a higher risk population than was reported in the initial publication, which was brought to light by data sharing.
How do Korean nursing students build knowledge? A constructivist grounded theory study
Authors: Lee Jung Jae , Clarke Charlotte L , Carson Maggie N , Yang Sook Ching
Published: July 2018

Introduction

Nursing is a knowledge-intensive profession. Therefore, to cope with the demands of the nursing role, nursing students need to become competent in managing information to build nursing knowledge. However, nursing students’ knowledge building process is poorly understood. This research aimed to explore (1) nursing students’ dynamics of how they process nursing information for knowledge building and (2) nursing students’ learning context in South Korea for their knowledge building.

Methods

A constructivist grounded theory approach was used for this research. Data collection was achieved through four rounds of intensive individual and group interviews with 16 fourth year nursing students in South Korea. The collected data were coded by initial, focused and theoretical coding methods. Constant comparison analysis between data, codes, memos and categories was applied.

Results

This research identified knowledge building dynamics consisting of three cognitive processes: connecting with information, deciding to accept information and building knowledge. Five motivational factors, including learners’ interest, necessity of information, volition to learn, utility of information and the frequency of information that influence the processes were discovered. Moreover, four knowledge stages of memorising, understanding, synthesising and applying and creating emerged.

Conclusions

This is the first empirical study on knowledge building dynamics in educational environments for healthcare professionals. The findings of this research provide nursing educators with a practical model that can be used to improve nursing curricula in facilitating students’ knowledge building processes. Moreover, a deeper understanding of sociocultural influences on nursing education can assist educators to adapt and generalise the findings to their pedagogical contexts, providing a culturally sensitive and relevant approach to nursing education.
A prospective, observational study investigating the use of carbon monoxide screening to identify maternal smoking in a large university hospital in Ireland
Authors: Reynolds Ciara Marie Edel , Egan Brendan , Kennedy Rachel AK , O’Malley Eimer G , Sheehan Sharon R , Turner Michael J
Published: July 2018

Objectives

This study evaluated breath carbon monoxide (BCO) testing in identifying maternal smokers as well as the difference between disclosers and non-disclosers of smoking status. We also investigated if other extrinsic factors affected the women’s BCO levels in pregnancy.

Design

A prospective observational study.

Setting

A university obstetric hospital in an urban setting in Ireland.

Participants

Women (n=250) and their partners (n=54) were recruited at their first antenatal visit. Women <18 years and those who did not understand English were excluded. A booking history, including recording of smoking status, was collected by midwives. Following this, women were recruited and completed a detailed research questionnaire on smoking and extrinsic/environmental BCO sources. A BCO test was performed on both the woman and her partner.

Primary and secondary outcome measures

The number of self-reported smokers and those that were positive on the BCO test. The characteristics of women who disclosed and did not disclose smoking status. The effect of extrinsic factors on the BCO test results.

Results

Based on the receiver-operating characteristic curve, a BCO cut-off point of ≥3 ppm was the optimal level to identify ongoing smoking. At booking history, 15% of women reported as current smokers. Based on BCO levels ≥3 ppm combined with self-reported smoking in the research questionnaire, the rate increased to 25%. Non-disclosers had similar characteristics to non-smokers. No extrinsic factors affected maternal BCO levels.

Conclusions

Based on self-report and BCO levels, a quarter of women presenting for antenatal care continued to smoke, but only 60% reported their smoking to midwives. BCO measurement is an inexpensive, practical method of improving identification of maternal smoking, and it was not effected by extrinsic sources of BCO. Improved identification means more smokers can be supported to stop smoking in early pregnancy potentially improving the short-term and long-term health of both mother and child.
Development and implementation of a structured ward round in acute adult psychiatry
Authors: Mattinson Anna Rebecca , Cheeseman Sarah Jane
Published: July 2018

Delivering high quality care in acute psychiatry requires a coordinated approach from a multidisciplinary team (MDT). Weekly ward rounds are an important forum for reviewing a patient’s progress and developing a personalised care plan for the coming week. In general medicine, structured ward rounds and check lists have been shown to prevent omissions and improve patient safety; however, they are not widely used in psychiatry. At the Royal Edinburgh Hospital, the format of ward rounds differed between psychiatry wards and clinical teams, and care plans were not standardised. An audit in October 2015 found only 5% of acute psychiatric inpatients had a documented nursing care plan. It was agreed that a clear multidisciplinary care plan from the weekly ward round would be beneficial. A group of consultant psychiatrists identified seven key domains for ward round (Social needs,Community Mental Health Team liaison,Assessments required,Mental Health Act,Prescriptions: medication electroconvulsive therapy (ECT), T2/T3,Engagement with relatives and carers,Risk Assessment and Pass Plans). This was given the acronymSCAMPER. Following this, a clinical MDT on a paired male and female ward, developed and introduced a structured ward round sheet. Within 8 weeks this was being used for 100% of patients. It was subsequently introduced into three other acute adult psychiatry wards and the intensive psychiatric care unit. Staff feedback was sought verbally and via a questionnaire. This was positive. The form was widely accepted and staff felt it improved patient care and ward round quality.
Mural destabilization after aneurysm treatment with a flow-diverting device: a report of two cases
Authors: Hampton Timothy , Walsh Donal , Tolias Christos , Fiorella David
Published: July 2018

Background

Flow-diverting stents have demonstrated great promise for the treatment of cerebral aneurysms; however, clinical experience with the devices remains very preliminary. We present two cases of spontaneous delayed complications—one fatal aneurysm rupture and one symptomatic increase in aneurysm volume—following the treatment of intradural aneurysms with the Pipeline Embolization Device (PED).

Presentation/intervention

Two patients with unruptured, intradural aneurysms of the carotid artery underwent uneventful treatment with the PED (eV3, Irvine, California, USA). One patient, with a giant aneurysm of the carotid terminus, experienced worsening headache 5 days after the procedure and ultimately collapsed and became unresponsive. CT of the head demonstrated acute subarachnoid and intraventricular hemorrhage. The patient died the following day. A second patient with a large left posterior communicating artery aneurysm presented with progressive memory loss 3 months after PED reconstruction of the carotid artery. Although serial CT angiograms showed progressive thrombosis of the aneurysm to near-complete occlusion, MR of the brain demonstrated marked interval growth of the collective aneurysm–intra-aneurysmal thrombus mass with extensive edema throughout the adjacent left temporal lobe.

Conclusions

Flow-diverting devices have demonstrated tremendous promise for the treatment of complex, unruptured cerebral aneurysms. However, experience with this novel approach to aneurysm treatment is preliminary and the consequences of its application within the cerebrovasculature remain incompletely defined. Mural destabilization resulting in delayed, spontaneous, aneurysm growth and/or rupture may occur in the days to weeks following the application of flow-diverting devices to treat previously unruptured intracranial aneurysms. A better understanding of the incidence and etiology of these complications is essential for this technology to be optimally applied.
Initial clinical experience with the ADAPT technique: A direct aspiration first pass technique for stroke thrombectomy
Authors: Turk Aquilla S , Spiotta Alex , Frei Don , Mocco J , Baxter Blaise , Fiorella David , Siddiqui Adnan , Mokin Maxim , Dewan Michael , Woo Henry , Turner Raymond , Hawk Harris , Miranpuri Amrendra , Chaudry Imran
Published: July 2018

Background

The development of new revascularization devices has improved recanalization rates and time but not clinical outcomes. We report our initial results with a new technique utilizing a direct aspiration first pass technique with a large bore aspiration catheter as the primary method for vessel recanalization.

Methods

A retrospective evaluation of a prospectively captured database of 37 patients at six institutions was performed on patients where the ADAPT technique was utilized. The data represent the initial experience with this technique.

Results

The ADAPT technique alone was successful in 28 of 37 (75%) cases although six cases had large downstream emboli that required additional aspiration. Nine cases required the additional use of a stent retriever and one case required the addition of a Penumbra aspiration separator to achieve recanalization. The average time from groin puncture to at least Thrombolysis in Cerebral Ischemia (TICI) 2b recanalization was 28.1 min, and all cases were successfully revascularized. TICI 3 recanalization was achieved 65% of the time. On average, patients presented with an admitting National Institutes of Health Stroke Scale (NIHSS) score of 16.3 and improved to an NIHSS score of 4.2 by the time of hospital discharge. There was one procedural complication.

Discussion

This initial experience highlights the fact that the importance of the technique with which new stroke thrombectomy devices are used may be as crucial as the device itself. The ADAPT technique is a simple and effective approach to acute ischemic stroke thrombectomy. Utilizing the latest generation of large bore aspiration catheters in this fashion has allowed us to achieve excellent clinical and angiographic outcomes.
Effect of crop and residue type on nitrous oxide emissions from rotations in the semi-arid Canadian prairies
Authors: Lemke R.L. , Liu L. , Baron V.S. , Malhi S.S. , Farrell R.E.
Published: July 2018

Crop rotations on the Canadian prairies commonly include sequences of pulses, oilseeds, and cereals; however, limited information is available regarding the influence that different crop types and sequences may have on direct nitrous oxide (N2O) emissions. A 3 yr field study was conducted on a site near Scott, SK, to compare N2O emissions from selected crop phases of rotations containing pea (Pisum sativum L.), wheat (Triticum aestivum L.), and canola (Brassica napus L.) and to examine the potential influence of these residues on N2O emissions during the subsequent crop phase. Nitrous oxide losses from N-fertilized canola or wheat crops were generally higher than losses from pea or the control treatments. Nitrous oxide losses from N-fertilized wheat or canola crops grown on pea residue were comparable or lower than losses from N-fertilized wheat or canola crops grown on wheat residues. Cumulative N2O loss over the 3 yr was significantly higher from N-fertilized wheat grown on canola compared with pea or wheat residues. Losses from wheat grown on canola residue were 67% and 56% higher than from wheat grown on pea or wheat residue, respectively. This indicates that the emission factors used to estimate direct N2O loss may need to be adjusted upwards for N-fertilized crops grown on canola compared with wheat or pea residues.
Influence of pedestrians’ jaywalking behavior on vehicle flow
Authors: Liu Gang , Lu Jiayan , Wang Jingchao , Jing Xiaodong , He Jing , Gao Peichao , Luo Zhiyong , Li Lian , Tang Min , Long Wen , Li Ru
Published: July 2018

There always exist a conflict between vehicles and pedestrians on urban streets. To study the complicated behaviors of vehicles and pedestrians is significant to understand the dynamics of traffic flow and explore efficient strategies for solving traffic problems. Based on this, this paper studies the effect of pedestrian’s jaywalking behavior on vehicle flow with no crosswalks and no traffic lights, and constructs a cellular automata model to describe the dynamic traffic flow by considering some significant traffic behaviors of pedestrians and vehicles. Experimental results show that the maximum vehicle flow will be greatly affected as long as there are jaywalking pedestrians; retreating behavior may lead to the fluctuation in vehicle flow; the maximum vehicle flow is greater if more pedestrians choose the behavior of fast crossing. This research is helpful to further study the interaction between pedestrians and vehicles.
On-chip optical isolator based on unidirectional wavelength-mode conversion waveguide
Authors: Liu Wenlong , Liu Xuebin , Yan Qiangqiang , Qiang Simiao , Pi Haifeng , Hu Bingliang , Zhang Lingxuan
Published: July 2018

Breaking Lorentz reciprocity is one necessary condition of optical isolator design. Unidirectional wavelength-mode conversion will be realized in a time-dependent system through a short operating range. Based on plasma dispersion effect, generate space-asymmetric periodical time-space modulation on silicon waveguide, and non-reciprocal propagation is realized in the waveguide. The designed unidirectional wavelength-mode conversion waveguide demonstrated that in the forward direction, input 1.55 [Formula: see text]m fundamental mode light signal and then output 1.5492 [Formula: see text]m is of 1st-order mode, while in the backward direction, input 1.5492 [Formula: see text]m is of 1st-order mode light signal and then output 1.5484 [Formula: see text]m is of fundamental mode. Based on this non-reciprocal structure, mode conversion waveguide and two-ring resonance filters were designed then, to accomplish on-chip optical isolation. The scale of the designed isolator is 160 [Formula: see text]m × 60 [Formula: see text]m, and the isolation is 21 dB, revealing perfect application potential.
Regularized sparse decomposition model for speech enhancement via convex distortion measure
Authors: Saleem Nasir , Khattak Muhammad Irfan
Published: July 2018

An important stage in speech enhancement is to estimate noise signal which is a difficult task in non-stationary and low signal-to-noise conditions. This paper presents an iterative speech enhancement approach which requires no prior knowledge of noise and is based on low-rank sparse matrix decomposition using Gammatone filterbank and convex distortion measure. To estimate noise and speech, the noisy speech is decomposed into low-rank noise and sparse-speech parts by enforcing sparsity regularization. The exact distribution of noise signals and noise estimator is not required in this approach. The experimental results demonstrate that our approach outperforms competing methods and yields better overall speech quality and intelligibility. Moreover, composite objective measure reinforced a better performance in terms of residual noise and speech distortion in adverse noisy conditions. The time-varying spectral analysis validates significant reduction of the background noise.
Thermal Zoning Based on Design Cooling Loads: Methodology and Simulation Case Study for a DOAS with Local Recirculating Units
Authors: Sarkar Mridul
Published: July 2018

A framework for creating thermal zones in a building for effective and efficient heating ventilation and air conditioning (HVAC) system design is introduced here. This method is based on simple “sort and eliminate” schemes and requires design cooling loads of conditioned spaces obtained from load calculation tools as primary input. The developed methodology is applied for creating thermal zones, determining corresponding supply conditions and ascertaining sizing of a dedicated outdoor air system (DOAS) with local recirculating units. A simulation study on a prototype-building model shows that a DOAS coupled with zoned recirculating systems that serve distinct thermal zones in a building (zoned model) perform comparatively better in controlling both space temperatures and humidity without significantly compromising HVAC energy and chiller loads than un-zoned HVAC systems serving the whole building as a single thermal block (un-zoned model). The consistency in the performance of zoned HVAC systems is verified by applying three different simulation weather files for New Delhi. Better performance along with logical and computational simplicity makes this design procedure a good alternative to traditional methodologies.
A Mobile Health System for Neurocognitive Impairment Evaluation Based on P300 Detection
Authors: Venuto D. De , Annese V. F. , Mezzina G. , Scioscia F. , Ruta M. , Sciascio E. Di , Vincentelli A. Sangiovanni
Published: July 2018

A new mobile healthcare system for neuro-cognitive function monitoring and treatment is presented. The architecture of the system features sensors to measure the brain potential, localized data analysis and filtering, and in-cloud distribution to specialized medical personnel. As such, it presents tradeoffs typical of other cyber-physical systems, where hardware, algorithms, and software implementations have to come together in a coherent fashion. The system is based on spatio-temporal detection and characterization of a specific brain potential called P300. The diagnosis of cognitive deficit is achieved by analyzing the data collected by the system with a new algorithm called tuned-Residue Iteration Decomposition (t-RIDE). The system has been tested on 17 subjects (
n
= 12 healthy,
n
= 3 mildly cognitive impaired, and
n
= 2 with Alzheimer's disease involved in three different cognitive tasks with increasing difficulty. The system allows fast diagnosis of cognitive deficit, including mild and heavy cognitive impairment: t-RIDE convergence is achieved in 79 iterations (i.e., 1.95s), yielding an 80% accuracy in P300 amplitude evaluation with only 13 trials on a single EEG channel.
Representation Learning for Classification in Heterogeneous Graphs with Application to Social Networks
Authors: Santos Ludovic Dos , Piwowarski Benjamin , Denoyer Ludovic , Gallinari Patrick
Published: July 2018

We address the task of node classification in heterogeneous networks, where the nodes are of different types, each type having its own set of labels, and the relations between nodes may also be of different types. A typical example is provided by social networks where node types may for example be users, content, or films, and relations
friendship
,
like
,
authorship
. Learning and performing inference on such heterogeneous networks is a recent task requiring new models and algorithms. We propose a model,
Labeling Heterogeneous Network (LaHNet)
, a transductive approach to classification that learns to project the different types of nodes into a common latent space. This embedding is learned so as to reflect different characteristics of the problem such as the correlation between node labels, as well as the graph topology. The application focus is on social graphs, but the algorithm is general and can be used for other domains. The model is evaluated on five datasets representative of different instances of social data.
ABRA
Authors: Riondato Matteo , Upfal Eli
Published: July 2018

ABPA
Ξ
A
Σ (
ABRAXAS
):
Gnostic word of mystic meaning
.

We present ABRA, a suite of algorithms to compute and maintain probabilistically guaranteed high-quality approximations of the betweenness centrality of all nodes (or edges) on both static and fully dynamic graphs. Our algorithms use progressive random sampling and their analysis rely on Rademacher averages and pseudodimension, fundamental concepts from statistical learning theory. To our knowledge, ABRA is the first application of these concepts to the field of graph analysis. Our experimental results show that ABRA is much faster than exact methods, and vastly outperforms, in both runtime number of samples, and accuracy, state-of-the-art algorithms with the same quality guarantees.
Fast non-intrusive memory reclamation for highly-concurrent data structures
Authors: Dice Dave , Herlihy Maurice , Kogan Alex
Published: July 2018

Current memory reclamation mechanisms for highly-concurrent data structures present an awkward trade-off. Techniques such as epoch-based reclamation perform well when all threads are running on dedicated processors, but the delay or failure of a single thread will prevent any other thread from reclaiming memory. Alternatives such as hazard pointers are highly robust, but they are expensive because they require a large number of memory barriers. This paper proposes three novel ways to alleviate the costs of the memory barriers associated with hazard pointers and related techniques. These new proposals are backward-compatible with existing code that uses hazard pointers. They move the cost of memory management from the principal code path to the infrequent memory reclamation procedure, significantly reducing or eliminating memory barriers executed on the principal code path. These proposals include (1) exploiting the operating system's memory protection ability, (2) exploiting certain x86 hardware features to trigger memory barriers only when needed, and (3) a novel hardware-assisted mechanism, called a hazard lookaside buffer (HLB) that allows a reclaiming thread to query whether there are hazardous pointers that need to be flushed to memory. We evaluate our proposals using a few fundamental data structures (linked lists and skiplists) and libcuckoo, a recent high-throughput hash-table library, and show significant improvements over the hazard pointer technique.
CBufs: efficient, system-wide memory management and sharing
Authors: Ren Yuxin , Parmer Gabriel , Georgiev Teo , Bloom Gedare
Published: July 2018

Modern systems are composed of many different protection domains separating privilege levels, subsystems, users, clients, and software of differing levels of assurance. System-wide memory management must consider not only allocation to single processes, but also efficient sharing of data across protection domains, and the allocation of memory based on the performance of applications that span multiple protection domains. This paper introduces the CBuf system for the global management of virtual and physical memory, including zero-copy sharing between protection domains. We present the design and implementation of both garbage collection techniques to enable efficient sharing, and policies that balance memory between protection domains specifically to satisfy system and application constraints such as quality of service. We show that a CBuf-enabled webserver achieves over a factor of 2.5 throughput speedup while using less processing time than Apache on Linux, and that the system can intentionally control system throughput through intelligent memory allocation.
Persistence programming models for non-volatile memory
Authors: Boehm Hans-J. , Chakrabarti Dhruva R.
Published: July 2018

It is expected that DRAM memory will be augmented, and perhaps eventually replaced, by one of several up-and-coming memory technologies. These are all non-volatile, in that they retain their contents without power. This allows primary memory to be used as a fast disk replacement. It also enables more aggressive programming models that directly leverage persistence of primary memory. However, it is challenging to maintain consistency of memory in such an environment. There is no consensus on the right programming model for doing so, and subtle differences can have large, and sometimes surprising, effects on the implementation and its performance. The existing literature describes multiple programming systems that provide point solutions to the selective persistence for user data structures. Real progress in this area requires a choice of programming model, which we cannot reasonably make without a real understanding of the design space. Point solutions are insufficient. We systematically explore what we consider to be the most promising part of the space, precisely defining semantics and identifying implementation costs. This allows us to be much more explicit and precise about semantic and implementation trade-offs that were usually glossed over in prior work. It also exposes some promising new design alternatives.
Hardware support for protective and collaborative cache sharing
Authors: Parihar Raj , Brock Jacob , Ding Chen , Huang Michael C.
Published: July 2018

Shared caches are generally optimized to maximize the overall throughput, fairness, or both, among multiple competing programs. In shared environments and compute clouds, users are often unrelated to each other. In such circumstances, an overall gain in throughput does not justify an individual loss. This paper explores cache management policies that allow conservative sharing to protect the cache occupancy for individual programs, yet enable full cache utilization whenever there is an opportunity to do so. We propose a hardware-based mechanism called cache rationing. Each program is assigned a portion of the shared cache as its ration. The hardware support protects the ration so it cannot be taken away by peer programs while in use. However, a program can exceed its pre-allocated ration, but only if another program has unused space in its allocated portion of ration. We show that rationing provides good resource protection and full cache utilization of the shared cache for a variety of co-runs.
Rust as a language for high performance GC implementation
Authors: Lin Yi , Blackburn Stephen M. , Hosking Antony L. , Norrish Michael
Published: July 2018

High performance garbage collectors build upon performance-critical low-level code, typically exhibit multiple levels of concurrency, and are prone to subtle bugs. Implementing, debugging and maintaining such collectors can therefore be extremely challenging. The choice of implementation language is a crucial consideration when building a collector. Typically, the drive for performance and the need for efficient support of low-level memory operations leads to the use of low-level languages like C or C++, which offer little by way of safety and software engineering benefits. This risks undermining the robustness and flexibility of the collector design. Rust's ownership model, lifetime specification, and reference borrowing deliver safety guarantees through a powerful static checker with little runtime overhead. These features make Rust a compelling candidate for a collector implementation language, but they come with restrictions that threaten expressiveness and efficiency. We describe our experience implementing an Immix garbage collector in Rust and C. We discuss the benefits of Rust, the obstacles encountered, and how we overcame them. We show that our Immix implementation has almost identical performance on micro benchmarks, compared to its implementation in C, and outperforms the popular BDW collector on the gcbench micro benchmark. We find that Rust's safety features do not create significant barriers to implementing a high performance collector. Though memory managers are usually considered low-level, our high performance implementation relies on very little unsafe code, with the vast majority of the implementation benefiting from Rust's safety. We see our experience as a compelling proof-of-concept of Rust as an implementation language for high performance garbage collection.
Functional reactive programming, refactored
Authors: Perez Ivan , Bärenz Manuel , Nilsson Henrik
Published: July 2018

Functional Reactive Programming (FRP) has come to mean many things. Yet, scratch the surface of the multitude of realisations, and there is great commonality between them. This paper investigates this commonality, turning it into a mathematically coherent and practical FRP realisation that allows us to express the functionality of many existing FRP systems and beyond by providing a minimal FRP core parameterised on a monad. We give proofs for our theoretical claims and we have verified the practical side by benchmarking a set of existing, non-trivial Yampa applications running on top of our new system with very good results.
Non-recursive make considered harmful: build systems at scale
Authors: Mokhov Andrey , Mitchell Neil , Peyton Jones Simon , Marlow Simon
Published: July 2018

Most build systems start small and simple, but over time grow into hairy monsters that few dare to touch. As we demonstrate in this paper, there are a few issues that cause build systems major scalability challenges, and many pervasively used build systems (e.g. Make) do not scale well.

This paper presents a solution to the challenges we identify. We use functional programming to design abstractions for build systems, and implement them on top of the Shake library, which allows us to describe build rules and dependencies. To substantiate our claims, we engineer a new build system for the Glasgow Haskell Compiler. The result is more scalable, faster, and spectacularly more maintainable than its Make-based predecessor.
Antibody Responses to Streptococcus Gallolyticus Subspecies Gallolyticus Proteins in a Large Prospective Colorectal Cancer Cohort Consortium
Authors: Butt Julia , Blot William J. , Teras Lauren R. , Visvanathan Kala , Le Marchand Loïc , Haiman Christopher A. , Chen Yu , Bao Ying , Sesso Howard D. , Wassertheil-Smoller Sylvia , Ho Gloria Y. , Tinker Lesley F. , Peek Richard M. , Potter John D. , Cover Timothy L. , Hendrix Laura H. , Huang Li-Ching , Waterboer Tim , Pawlita Michael , Epplein Meira
Published: July 2018

Background: Antibody responses to Streptococcus gallolyticus subspecies gallolyticus (SGG) proteins, especially pilus protein Gallo2178, have been consistently associated with colorectal cancer risk. Previous case–control studies and prospective studies with up to 8 years of follow-up, however, were unable to decipher the temporality of antibody responses to SGG in the context of the long-term multistep development of colorectal cancer. In this study, we analyzed a large U.S. colorectal cancer cohort consortium with follow-up beyond 10 years for antibody responses to SGG.

Methods: We applied multiplex serology to measure antibody responses to 9 SGG proteins in participants of 10 prospective U.S. cohorts (CLUE, CPSII, HPFS, MEC, NHS, NYUWHS, PHS, PLCO, SCCS, and WHI) including 4,063 incident colorectal cancer cases and 4,063 matched controls. Conditional logistic regression was used to assess whether antibody responses to SGG were associated with colorectal cancer risk, overall and by time between blood draw and diagnosis.

Results: Colorectal cancer risk was increased among those with antibody responses to Gallo2178, albeit not statistically significant [OR, 1.23; 95% confidence interval (CI), 0.99–1.52]. This association was stronger for cases diagnosed <10 years after blood draw (OR, 1.40; 95% CI, 1.09–1.79), but was not found among cases diagnosed ≥10 years after blood draw (OR, 0.79; 95% CI, 0.50–1.24).

Conclusions: In a large cohort consortium, we reproduced the association of antibody responses to SGG Gallo2178 with colorectal cancer risk for individuals diagnosed within 10 years after blood draw.

Impact: This timing-specific finding suggests that antibody responses to SGG are associated with increased colorectal cancer risk only after tumorigenesis has begun. Cancer Epidemiol Biomarkers Prev; 27(10); 1186–94. ©2018 AACR.
Two HLA Class II Gene Variants Are Independently Associated with Pediatric Osteosarcoma Risk
Authors: Zhang Chenan , Wiemels Joseph L. , Hansen Helen M. , Gonzalez-Maya Julio , Endicott Alyson A. , de Smith Adam J. , Smirnov Ivan V. , Witte John S. , Morimoto Libby M. , Metayer Catherine , Walsh Kyle M.
Published: July 2018

Background: The genetic etiology of osteosarcoma remains poorly understood despite the publication of a genome-wide association study. Association between HLA genetic variants and risk of several cancers has been observed, but HLA variation is not well captured by standard SNP arrays.

Methods: We genotyped 207 Californian pediatric osteosarcoma cases and 696 controls of European ancestry using a custom genome-wide array supplemented with approximately 6,000 additional probes across the MHC region. We subsequently imputed 4-digit classical HLA alleles using a reference panel of 5,225 individuals who underwent high-resolution HLA typing via next-generation sequencing. Case–control comparisons were adjusted for ancestry-informative principal components, and top associations from the discovery analysis underwent replication in an independent dataset of 657 cases and 1,183 controls.

Results: Three highly correlated HLA class II variants (r2 = 0.33–0.98) were associated with osteosarcoma risk in discovery analyses, including HLA-DRB1*0301 (OR = 0.52; P = 3.2 × 10−3), HLA-DQA1*0501 (OR = 0.74; P = 0.031), and HLA-DQB1*0201 (OR = 0.51; P = 2.7 × 10−3). Similar associations were observed in the replication data (Prange = 0.011–0.037). Meta-analysis of the two datasets identified HLA-DRB1*0301 as the most significantly associated variant (ORmeta = 0.62; Pmeta = 1.5 × 10−4), reaching Bonferroni-corrected statistical significance. The meta-analysis also revealed a second significant independent signal at HLA-DQA1*01:01 (ORmeta = 1.33, Pmeta = 1.2 × 10−3), and a third suggestive association at HLA-DQB1*0302 (ORmeta = 0.73, Pmeta = 6.4 × 10−3).

Conclusions: Multiple independent HLA class II alleles may influence osteosarcoma risk.

Impact: Additional work is needed to extend our observations to other patient populations and to clarify the potential causal mechanisms underlying these associations. Understanding immunologic contributions to the etiology of osteosarcoma may inform rational therapeutic targets. Cancer Epidemiol Biomarkers Prev; 27(10); 1151–8. ©2018 AACR.
Integrated Analysis of RNA and DNA from the Phase III Trial CALGB 40601 Identifies Predictors of Response to Trastuzumab-Based Neoadjuvant Chemotherapy in HER2-Positive Breast Cancer
Authors: Tanioka Maki , Fan Cheng , Parker Joel S. , Hoadley Katherine A. , Hu Zhiyuan , Li Yan , Hyslop Terry M. , Pitcher Brandelyn N. , Soloway Matthew G. , Spears Patricia A. , Henry Lynn N. , Tolaney Sara , Dang Chau T. , Krop Ian E. , Harris Lyndsay N. , Berry Donald A. , Mardis Elaine R. , Winer Eric P. , Hudis Clifford A. , Carey Lisa A. , Perou Charles M.
Published: July 2018

Purpose: Response to a complex trastuzumab-based regimen is affected by multiple features of the tumor and its microenvironment. Developing a predictive algorithm is key to optimizing HER2-targeting therapy.

Experimental Design: We analyzed 137 pretreatment tumors with mRNA-seq and DNA exome sequencing from CALGB 40601, a neoadjuvant phase III trial of paclitaxel plus trastuzumab with or without lapatinib in stage II to III HER2-positive breast cancer. We adopted an Elastic Net regularized regression approach that controls for covarying features within high-dimensional data. First, we applied 517 known gene expression signatures to develop an Elastic Net model to predict pCR, which we validated on 143 samples from four independent trials. Next, we performed integrative analyses incorporating clinicopathologic information with somatic mutation status, DNA copy number alterations (CNA), and gene signatures.

Results: The Elastic Net model using only gene signatures predicted pCR in the validation sets (AUC = 0.76). Integrative analyses showed that models containing gene signatures, clinical features, and DNA information were better pCR predictors than models containing a single data type. Frequently selected variables from the multiplatform models included amplifications of chromosome 6p, TP53 mutation, HER2-enriched subtype, and immune signatures. Variables predicting resistance included Luminal/ER+ features.

Conclusions: Models using RNA only, as well as integrated RNA and DNA models, can predict pCR with improved accuracy over clinical variables. Somatic DNA alterations (mutation, CNAs), tumor molecular subtype (HER2E, Luminal), and the microenvironment (immune cells) were independent predictors of response to trastuzumab and paclitaxel-based regimens. This highlights the complexity of predicting response in HER2-positive breast cancer. Clin Cancer Res; 24(21); 5292–304. ©2018 AACR.