LLukas22/scidocs huggingface dataset:
How to Fit when No One Size Fits

While “no one size fits all” is a sound philosophy for system designers to follow, it poses multiple challenges for application developers and system administrators. It can be hard for an application developer to pick one system when the needs of her application match the features of multiple “one size” systems. The choice becomes considerably harder when different components of an application fit the features of different “one size” systems. Considerable manual effort goes into creating and tuning such multi-system applications. An application’s data and workload properties may change over time, often in unpredictable and bursty ways. Consequently, the “one size” system that is best for an application can change over time. Adapting to change can be hard when application development is coupled tightly with any individual “one size” system. In this paper, we make the case for developing a new breed of Database Management Systems that we term DBMS. A DBMS contains multiple “one size” systems internally. An application specifies its execution requirements on aspects like performance, availability, consistency, change, and cost to the DBMS declaratively. For all requests (e.g., queries) made by the application, the DBMS will select the execution plan that meets the application’s requirements best. A unique aspect of the execution plan in a DBMS is that the plan includes the selection of one or more “one size” systems. The plan is then deployed and managed automatically on the selected system(s). If application requirements change beyond what was planned for originally by the DBMS, then the application can be reoptimized and redeployed; usually with no additional effort required from the application developer. The DBMS approach has the potential to address the challenges that application developers and system administrators face from the vast and growing number of “one size” systems today. However, this approach poses many research challenges that we discuss in this paper. We are taking the DBMS approach in a platform, called Cyclops, that we are building for continuous query execution. We will use Cyclops throughout the paper to give concrete illustrations of the benefits and challenges of the DBMS approach. This article is published under a Creative Commons Attribution License (http://creativecommons.org/licenses/by/3.0/), which permits distribution and reproduction in any medium as well allowing derivative works, provided that you attribute the original work to the author(s) and CIDR 2013. 6 Biennial Conference on Innovative Data Systems Research (CIDR ’13) January 6-9, 2013, Asilomar, California, USA.
Multidimensional Process Mining Using Process Cubes

Process mining techniques enable the analysis of processes using event data. For structured processes without too many variations, it is possible to show a relative simple model and project performance and conformance information on it. However, if there are multiple classes of cases exhibiting markedly different behaviors, then the overall process will be too complex to interpret. Moreover, it will be impossible to see differences in performance and conformance for the different process variants. The different process variations should be analysed separately and compared to each other from different perspectives to obtain meaningful insights about the different behaviors embedded in the process. This paper formalizes the notion of process cubes where the event data is presented and organized using different dimensions. Each cell in the cube corresponds to a set of events which can be used as an input by any process mining technique. This notion is related to the well-known OLAP (Online Analytical Processing) data cubes, adapting the OLAP paradigm to event data through multidimensional process mining. This adaptation is far from trivial given the nature of event data which cannot be easily summarized or aggregated, conflicting with classical OLAP assumptions. For example, multidimensional process mining can be used to analyze the different versions of a sales processes, where each version can be defined according to different dimensions such as location or time, and then the different results can be compared. This new way of looking at processes may provide valuable insights for process optimization.
Night work and breast cancer in women: a Swedish cohort study

OBJECTIVES
Recent research has suggested a moderate link between night work and breast cancer in women, mainly through case-control studies, but non-significant studies are also common and cohort studies are few. The purpose of the present study was to provide new information from cohort data through investigating the association between the number of years with night work and breast cancer among women.


DESIGN
Cohort study of individuals exposed to night shift work in relation to incidence of breast cancer in women.


SETTING
Individuals in the Swedish Twin registry, with follow-up in the Swedish Cancer Registry.


PARTICIPANTS
13,656 women from the Swedish Twin Registry, with 3404 exposed to night work.


OUTCOME MEASURES
Breast cancer from the Swedish Cancer Registry (463 cases) during a follow-up time of 12 years.


RESULTS
A Cox proportional hazards regression analysis with control for a large number of confounders showed that the HR was HR=1.68 (95% CI 0.98 to 2.88) for the group with >20 years of night work. When the follow-up time was limited to ages below 60 years, those exposed >20 years showed a HR=1.77 (95% CI 1.03 to 3.04). Shorter exposure to night work showed no significant effects.


CONCLUSIONS
The present results, together with previous work, suggest that night work is associated with an increased risk of breast cancer in women, but only after relatively long-term exposure.
Biodentine-a novel dentinal substitute for single visit apexification

Use of an apical plug in management of cases with open apices has gained popularity in recent years. Biodentine, a new calcium silicate-based material has recently been introduced as a dentine substitute, whenever original dentine is damaged. This case report describes single visit apexification in a maxillary central incisor with necrotic pulp and open apex using Biodentine as an apical barrier, and a synthetic collagen material as an internal matrix. Following canal cleaning and shaping, calcium hydroxide was placed as an intracanal medicament for 1 mon. This was followed by placement of small piece of absorbable collagen membrane beyond the root apex to serve as matrix. An apical plug of Biodentine of 5 mm thickness was placed against the matrix using pre-fitted hand pluggers. The remainder of canal was back-filled with thermoplasticized gutta-percha and access cavity was restored with composite resin followed by all-ceramic crown. One year follow-up revealed restored aesthetics and function, absence of clinical signs and symptoms, resolution of periapical rarefaction, and a thin layer of calcific tissue formed apical to the Biodentine barrier. The positive clinical outcome in this case is encouraging for the use of Biodentine as an apical plug in single visit apexification procedures.
Mr. Bennet, his coachman, and the Archbishop walk into a bar but only one of them gets recognized: On The Difficulty of Detecting Characters in Literary Texts

Characters are fundamental to literary analysis. Current approaches are heavily reliant on NER to identify characters, causing many to be overlooked. We propose a novel technique for character detection, achieving significant improvements over state of the art on multiple datasets.
Performance of X-ray detectors with SiPM readout in cargo accelerator-based inspection systems

Existing requirements for high throughput cargo radiography inspection include high resolution images (better than 5 mm line pair resolution), penetration beyond 400 mm steel equivalent, material discrimination (organic, inorganic, high Z), high scan speeds (> 10kph, up to 60kph), low dose and small radiation exclusion zone; all in a cost effective system. To meet and exceed these requirements research into a number of new radiography methods has been initiated. Novel concepts relying on intrapulse modulated energy X-ray sources, mono-energetic gamma-ray sources, and new types of fast X-ray detectors, Scintillation-Cherenkov Detectors, are expected to be more beneficial being combined with unique features of Silicon Photomultiplier (SiPM) technology.
The global prevalence of common mental disorders: a systematic review and meta-analysis 1980-2013.

BACKGROUND
Since the introduction of specified diagnostic criteria for mental disorders in the 1970s, there has been a rapid expansion in the number of large-scale mental health surveys providing population estimates of the combined prevalence of common mental disorders (most commonly involving mood, anxiety and substance use disorders). In this study we undertake a systematic review and meta-analysis of this literature.


METHODS
We applied an optimized search strategy across the Medline, PsycINFO, EMBASE and PubMed databases, supplemented by hand searching to identify relevant surveys. We identified 174 surveys across 63 countries providing period prevalence estimates (155 surveys) and lifetime prevalence estimates (85 surveys). Random effects meta-analysis was undertaken on logit-transformed prevalence rates to calculate pooled prevalence estimates, stratified according to methodological and substantive groupings.


RESULTS
Pooling across all studies, approximately 1 in 5 respondents (17.6%, 95% confidence interval:16.3-18.9%) were identified as meeting criteria for a common mental disorder during the 12-months preceding assessment; 29.2% (25.9-32.6%) of respondents were identified as having experienced a common mental disorder at some time during their lifetimes. A consistent gender effect in the prevalence of common mental disorder was evident; women having higher rates of mood (7.3%:4.0%) and anxiety (8.7%:4.3%) disorders during the previous 12 months and men having higher rates of substance use disorders (2.0%:7.5%), with a similar pattern for lifetime prevalence. There was also evidence of consistent regional variation in the prevalence of common mental disorder. Countries within North and South East Asia in particular displayed consistently lower one-year and lifetime prevalence estimates than other regions. One-year prevalence rates were also low among Sub-Saharan-Africa, whereas English speaking counties returned the highest lifetime prevalence estimates.


CONCLUSIONS
Despite a substantial degree of inter-survey heterogeneity in the meta-analysis, the findings confirm that common mental disorders are highly prevalent globally, affecting people across all regions of the world. This research provides an important resource for modelling population needs based on global regional estimates of mental disorder. The reasons for regional variation in mental disorder require further investigation.
The effect of YOCAS©® yoga for musculoskeletal symptoms among breast cancer survivors on hormonal therapy

Up to 50 % of breast cancer survivors on aromatase inhibitor therapy report musculoskeletal symptoms such as joint and muscle pain, significantly impacting treatment adherence and discontinuation rates. We conducted a secondary data analysis of a nationwide, multi-site, phase II/III randomized, controlled, clinical trial examining the efficacy of yoga for improving musculoskeletal symptoms among breast cancer survivors currently receiving hormone therapy (aromatase inhibitors [AI] or tamoxifen [TAM]). Breast cancer survivors currently receiving AI (N = 95) or TAM (N = 72) with no participation in yoga during the previous 3 months were randomized into 2 arms: (1) standard care monitoring and (2) standard care plus the 4-week yoga intervention (2x/week; 75 min/session) and included in this analysis. The yoga intervention utilized the UR Yoga for Cancer Survivors (YOCAS©®) program consisting of breathing exercises, 18 gentle Hatha and restorative yoga postures, and meditation. Musculoskeletal symptoms were assessed pre- and post-intervention. At baseline, AI users reported higher levels of general pain, muscle aches, and total physical discomfort than TAM users (all P ≤ 0.05). Among all breast cancer survivors on hormonal therapy, participants in the yoga group demonstrated greater reductions in musculoskeletal symptoms such as general pain, muscle aches and total physical discomfort from pre- to post-intervention than the control group (all P ≤ 0.05). The severity of musculoskeletal symptoms was higher for AI users compared to TAM users. Among breast cancer survivors on hormone therapy, the brief community-based YOCAS©® intervention significantly reduced general pain, muscle aches, and physical discomfort.
Adding saxagliptin to extended-release metformin vs. uptitrating metformin dosage.

AIM
To investigate whether patients taking metformin for type 2 diabetes mellitus (T2DM) have improved glycaemic control without compromising tolerability by adding an agent with a complementary mechanism of action vs. uptitrating metformin.


METHODS
Adults with T2DM and glycated haemoglobin (HbA1c) between 7.0 and 10.5% receiving metformin extended release (XR) 1500 mg/day for ≥8 weeks were randomized to receive saxagliptin 5 mg added to metformin XR 1500 mg (n = 138) or metformin XR uptitrated to 2000 mg/day (n = 144). Endpoints were change from baseline to week 18 in HbA1c (primary), 120-min postprandial glucose (PPG), fasting plasma glucose (FPG) and the proportion of patients achieving HbA1c <7%.


RESULTS
At week 18, the adjusted mean reduction from baseline HbA1c was -0.88% for saxagliptin + metformin XR and -0.35% for uptitrated metformin XR (difference, -0.52%; p < 0.0001). For 120-min PPG and FPG, differences in adjusted mean change from baseline between saxagliptin + metformin XR and uptitrated metformin XR were -1.3 mmol/l (-23.32 mg/dl) (p = 0.0013) and -0.73 mmol/l (-13.18 mg/dl) (p = 0.0030), respectively. More patients achieved HbA1c <7.0% with saxagliptin + metformin XR than with uptitrated metformin XR (37.2 vs. 26.1%; p = 0.0459). The proportions of patients experiencing any adverse events (AEs) were generally similar between groups; neither group showed any notable difference in hypoglycaemia or gastrointestinal AEs.


CONCLUSION
Adding saxagliptin to metformin XR provided superior glycaemic control compared with uptitrating metformin XR without the emergence of additional safety concerns.
A comparison of short-term treatment with inhaled fluticasone propionate and zafirlukast for patients with persistent asthma.

PURPOSE
To compare the short-term efficacy and safety of low-dose fluticasone propionate with that of oral zafirlukast therapy for patients previously treated with beta-2-agonists alone, and to evaluate the potential therapeutic benefit of switching from zafirlukast to a low-dose inhaled corticosteroid.


SUBJECTS AND METHODS
This study consisted of a 4-week randomized, double-blind treatment period followed by a 4-week open-label period. Two hundred ninety-four patients > or =12 years old with asthma previously uncontrolled with beta-2-agonists alone were randomly assigned to treatment with low-dose inhaled fluticasone (88 microg twice daily) or oral zafirlukast (20 mg twice daily). After 4 weeks, all patients discontinued their double-blind therapy and received open-label fluticasone (88 microg twice daily). Outcomes included pulmonary function, asthma symptoms, albuterol use, asthma exacerbations, and adverse events.


RESULTS
During the double-blind treatment period, fluticasone patients had significantly greater improvements in morning peak flow (29.3 L/min vs. 18.3 L/min), percentage of symptom-free days (19.8% vs. 11.6%), and daily albuterol use (-1.8 puffs per day vs. -1.1 puffs per day) compared with zafirlukast patients (P < or =0.025, each comparison). During the open-label treatment period, patients switched from zafirlukast to fluticasone experienced additional improvements in morning peak flow (17.2 L/min), evening peak flow (13.6 L/min), and FEV(1) (0.11 liter) and daily albuterol use (-0.9 puffs daily) compared with values obtained at the end of the double-blind treatment period (P < or =0.001, each comparison).


CONCLUSION
Low-dose fluticasone was more effective than zafirlukast in improving pulmonary function and symptoms in patients with persistent asthma. In addition, switching patients from zafirlukast to fluticasone further improved clinical outcomes.
Association of Adiponectin with Adolescent Cardiovascular Health in a Dietary Intervention Study.

OBJECTIVE
To investigate whether an infancy-onset, low saturated fat-oriented dietary intervention influences serum adiponectin concentration in adolescents, and to study the association of adiponectin with subclinical markers of vascular health, and cardio-metabolic risk factors.


STUDY DESIGN
The longitudinal, randomized Special Turku Coronary Risk Factor Intervention Project aimed to modify child's dietary fat quality replacing saturated fat with unsaturated fat. Serum adiponectin (n = 521) along with weight, height, high-density lipoprotein cholesterol, C-reactive protein (CRP), triglycerides, and insulin were measured at age 15 years. Adiposity was assessed using body mass index, waist circumference, and abdominal fat thickness measured with ultrasound. Metabolic syndrome was defined according to International Diabetes Foundation criteria. Vascular ultrasound measures including carotid intima-media thickness (IMT) were assessed.


RESULTS
Adiponectin concentrations were similar in the intervention and control groups (P = .16). Adiponectin associated with carotid IMT (r = -0.13, P = .005), high-density lipoprotein cholesterol (r = 0.18, P < .0001), triglycerides (r = -0.16, P = .0004), CRP (r = -0.10, P = .02), insulin (r = -0.14, P = .002), and adiposity (r = -0.18-0.24, P ≤ .0001). When adjusted for adiposity indices, the association with carotid IMT was only marginally diluted (P = .03-.06), but the associations with insulin and CRP became nonsignificant. Adolescents with adiponectin ≤median had 4-fold risk of metabolic syndrome than peers with adiponectin >median (CI 1.8-10.2, P = .0001).


CONCLUSIONS
In healthy adolescents, low serum adiponectin is related with carotid IMT and metabolic syndrome. We found no evidence that repeated low saturated fat-oriented dietary counseling would influence serum adiponectin in adolescence.


TRIAL REGISTRATION
Registered with ClinicalTrials.gov: NCT00223600.
An Experiment in Software Prototyping Productivity ∗

We describe the results of an experiment in which several conventional programming languages, together with the functional language Haskell, were used to prototype a Naval Surface Warfare Center (NSWC) requirement for a Geometric Region Server. The resulting programs and development metrics were reviewed by a committee chosen by the Navy. The results indicate that the Haskell prototype took significantly less time to develop and was considerably more concise and easier to understand than the corresponding prototypes written in several different imperative languages, including Ada and C++. ∗This work was supported by the Advanced Research Project Agency and the Office of Naval Research under Arpa Order 8888, Contract N00014-92-C-0153.
Mindfulness based stress reduction (MBSR(BC)) in breast cancer: evaluating fear of recurrence (FOR) as a mediator of psychological and physical symptoms in a randomized control trial (RCT)

To investigate the mechanism(s) of action of mindfulness based stress reduction (MBSR(BC)) including reductions in fear of recurrence and other potential mediators. Eighty-two post-treatment breast cancer survivors (stages 0–III) were randomly assigned to a 6-week MBSR(BC) program (n = 40) or to usual care group (UC) (n = 42). Psychological and physical variables were assessed as potential mediators at baseline and at 6 weeks. MBSR(BC) compared to UC experienced favorable changes for five potential mediators: (1) change in fear of recurrence problems mediated the effect of MBSR(BC) on 6-week change in perceived stress (z = 2.12, p = 0.03) and state anxiety (z = 2.03, p = 0.04); and (2) change in physical functioning mediated the effect of MBSR(BC) on 6-week change in perceived stress (z = 2.27, p = 0.02) and trait anxiety (z = 1.98, p = 0.05). MBSR(BC) reduces fear of recurrence and improves physical functioning which reduces perceived stress and anxiety. Findings support the beneficial effects of MBSR(BC) and provide insight into the possible cognitive mechanism of action.
Genome-wide DNA methylation profile implicates potential cartilage regeneration at the late stage of knee osteoarthritis.

OBJECTIVE
The aim of this work was to characterize the genome-wide DNA methylation profile of cartilage from three regions of tibial plateau isolated from patients with primary knee osteoarthritis (OA), providing the first DNA methylation study that reflects OA progression.


METHODS
The unique model system was used to section three regions of tibial plateau: the outer lateral tibial plateau (oLT), the inner lateral tibial plateau (iLT) and the inner medial tibial plateau (iMT) regions which represented the early, intermediate and late stages of OA, respectively. Genome-wide DNA methylation profile was examined using Illumina Infinium HumanMethylation450 BeadChip array. Comparisons of the iLT/oLT and iMT/oLT groups were carried out to identify differentially methylated (DM) probes (DMPs) associated with OA progression. DM genes were analyzed to identify the gene ontologies (GO), pathways, upstream regulators and networks.


RESULTS
No significant DMPs were identified in iLT/oLT group, while 519 DMPs were identified in iMT/oLT group. Over half of them (68.2%) were hypo-methylated and enriched in enhancers and OpenSea. Upstream regulator analysis identified many microRNAs. DM genes were enriched in transcription factors, especially homeobox genes and in Wnt/β-catenin signaling pathway. These genes also showed changes in expression when analyzed with expression profiles generated from previous studies.


CONCLUSION
Our data suggested the changes in DNA methylation occurred at the late stage of OA. Pathways and networks enriched in identified DM genes highlighted potential etiologic mechanism and implicated the potential cartilage regeneration in the late stage of knee OA.