LLukas22/scidocs huggingface dataset:
Automating Construction of Machine Learning Models With Clinical Big Data: Proposal Rationale and Methods

BACKGROUND
To improve health outcomes and cut health care costs, we often need to conduct prediction/classification using large clinical datasets (aka, clinical big data), for example, to identify high-risk patients for preventive interventions. Machine learning has been proposed as a key technology for doing this. Machine learning has won most data science competitions and could support many clinical activities, yet only 15% of hospitals use it for even limited purposes. Despite familiarity with data, health care researchers often lack machine learning expertise to directly use clinical big data, creating a hurdle in realizing value from their data. Health care researchers can work with data scientists with deep machine learning knowledge, but it takes time and effort for both parties to communicate effectively. Facing a shortage in the United States of data scientists and hiring competition from companies with deep pockets, health care systems have difficulty recruiting data scientists. Building and generalizing a machine learning model often requires hundreds to thousands of manual iterations by data scientists to select the following: (1) hyper-parameter values and complex algorithms that greatly affect model accuracy and (2) operators and periods for temporally aggregating clinical attributes (eg, whether a patient's weight kept rising in the past year). This process becomes infeasible with limited budgets.


OBJECTIVE
This study's goal is to enable health care researchers to directly use clinical big data, make machine learning feasible with limited budgets and data scientist resources, and realize value from data.


METHODS
This study will allow us to achieve the following: (1) finish developing the new software, Automated Machine Learning (Auto-ML), to automate model selection for machine learning with clinical big data and validate Auto-ML on seven benchmark modeling problems of clinical importance; (2) apply Auto-ML and novel methodology to two new modeling problems crucial for care management allocation and pilot one model with care managers; and (3) perform simulations to estimate the impact of adopting Auto-ML on US patient outcomes.


RESULTS
We are currently writing Auto-ML's design document. We intend to finish our study by around the year 2022.


CONCLUSIONS
Auto-ML will generalize to various clinical prediction/classification problems. With minimal help from data scientists, health care researchers can use Auto-ML to quickly build high-quality models. This will boost wider use of machine learning in health care and improve patient outcomes.
A Method for Computing Optimal SetPoint Schedule for HVAC Systems

We propose a method for model-based control of building air conditioning systems that minimizes energy costs while maintaining occupant comfort. The method uses a building thermal model in the form of a thermal circuit identified from collected sensor data, and reduces the building thermal dynamics to a Markov decision process (MDP) whose decision variables are the sequence of temperature set-points over a suitable horizon, for example one day. The main advantage of the resulting MDP model is that it is completely discrete, which allows for a very fast computation of the optimal sequence of temperature set-points. Experiments on thermal models demonstrate savings that can exceed 50% with respect to usual control strategies in buildings such as night setup. 2013 REHVA World Congress (CLIMA) This work may not be copied or reproduced in whole or in part for any commercial purpose. Permission to copy in whole or in part without payment of fee is granted for nonprofit educational and research purposes provided that all such whole or partial copies include the following: a notice that such copying is by permission of Mitsubishi Electric Research Laboratories, Inc.; an acknowledgment of the authors and individual contributions to the work; and all applicable portions of the copyright notice. Copying, reproduction, or republishing for any other purpose shall require a license with payment of fee to Mitsubishi Electric Research Laboratories, Inc. All rights reserved. Copyright c © Mitsubishi Electric Research Laboratories, Inc., 2013 201 Broadway, Cambridge, Massachusetts 02139 A Method for Computing Optimal Set-Point Schedules for HVAC Systems Daniel Nikovski#1, Jingyang Xu#2, and Mio Nonaka∗3 #Mitsubishi Electric Research Laboratories, 201 Broadway, Cambridge, MA 02139, USA {1nikovski,2jxu}@merl.com ∗Mitsubishi Electric Corporation, 8-1-1, Tsukaguchi-Honmachi, Hyogo 661-8661, Japan 3nonaka.mio@dc.mitsubishielectric.co.jp Abstract We propose a method for model-based control of building air conditioning systems that minimizes energy costs while maintaining occupant comfort. The method uses a building thermal model in the form of a thermal circuit identified from collected sensor data, and reduces the building thermal dynamics to a Markov decision process (MDP) whose decision variables are the sequence of temperature set-points over a suitable horizon, for example one day. The main advantage of the resulting MDP model is that it is completely discrete, which allows for a very fast computation of the optimal sequence of temperature set-points. Experiments on thermal models demonstrate savings that can exceed 50% with respect to usual control strategies in buildings such as night setup.
Effects of Chinese Liquors on Cardiovascular Disease Risk Factors in Healthy Young Humans

OBJECTIVES
To elucidate whether consumption of two Chinese liquors, tea-flavor liquor (TFL) and traditional Chinese liquor (TCL) have protective effects on cardiovascular disease (CVD) risk factors in healthy human subjects.


METHODS
Forty-five healthy subjects (23 men, 22 women), aged 23-28, were recruited and randomized into two groups: TFL and TCL, and consumed 30 mL/day (45% (v/v) alcohol) of either liquor for 28 days.


RESULTS
Serum high-density lipoprotein cholesterol/low-density lipoprotein cholesterol (HDL-C/LDL-C) and apolipoprotein A1 were significantly increased, and total cholesterol (TC) and TC/HDL-C were significantly decreased after the intervention in both groups (P < 0.05). Serum uric acid (P = 0.004 for TFL, P = 0.001 for TCL), glucose (P < 0.001 for TFL, P < 0.001 for TCL) and endothelial adhesion molecules (P < 0.05) were significantly decreased after the intervention. ADP-induced whole blood platelet aggregation was also significantly decreased after the intervention in both TFL and TCL groups (P < 0.05).


CONCLUSIONS
TFL and TCL consumption had protective effects on CVD risk factors in young humans. However, the results were valid only for 28 days, and that the possibility of adverse effect (liver, kidney) of chronic alcohol consumption should be considered.
Heterogenous mismatch-repair status in colorectal cancer

BACKGROUND
Immunohistochemical staining for mismatch repair proteins is efficient and widely used to identify mismatch repair defective tumors. The tumors typically show uniform and widespread loss of MMR protein staining. We identified and characterized colorectal cancers with alternative, heterogenous mismatch repair protein staining in order to delineate expression patterns and underlying mechanisms.


METHODS
Heterogenous staining patterns that affected at least one of the mismatch repair proteins MLH1, PMS2, MSH2 and MSH6 were identified in 14 colorectal cancers. Based on alternative expression patterns macro-dissected and micro-dissected tumor areas were separately analyzed for microsatellite instability and MLH1 promoter methylation.


RESULTS
Heterogenous retained/lost mismatch repair protein expression could be classified as intraglandular (within or in-between glandular formations), clonal (in whole glands or groups of glands) and compartmental (in larger tumor areas/compartments or in between different tumor blocks). These patterns coexisted in 9/14 tumors and in the majority of the tumors correlated with differences in microsatellite instability/MLH1 methylation status.


CONCLUSIONS
Heterogenous mismatch repair status can be demonstrated in colorectal cancer. Though rare, attention to this phenomenon is recommended since it corresponds to differences in mismatch repair status that are relevant for correct classification.


VIRTUAL SLIDES
The virtual slide(s) for this article can be found here: http://www.diagnosticpathology.diagnomx.eu/vs/1771940323126788.
Effect of Mo and Nb on the phase equilibrium of the Ti–Cr–V ternary system in the non-burning β-Ti alloy region

Abstract The phase equilibria of the ternary Ti–M1–M2 (M1=Cr, V and M2=Mo, Nb) systems are described thermodynamically, especially in the non-burning β-Ti alloy region, and the ternary interaction parameters of the β-phase are derived. The phase diagrams reported previously are compared with the presented results and good agreement is found. The effect of Mo or Nb additions on the properties of the Ti–Cr–V system was studied. Molybdenum is effective in terms of non-burning. It does not form an intermediate phase but expands the β-phase field. The effect of Nb addition on the Ti–Cr–V ternary system was weak.
Alterations in plasma essential trace elements selenium, manganese, zinc, copper, and iron concentrations and the possible role of these elements on oxidative status in patients with childhood asthma

The aim of the present study is to evaluate the status of plasma essential trace element selenium (Se), manganese (Mn), copper (Cu), zinc (Zn), and iron (Fe) concentrations and the effect of these elements on oxidative status in patients with childhood asthma. Plasma Se, Mn, Cu, and Zn concentrations were determined by atomic absorption spectrophotometry (AAS) and Fe concentrations, malondialdehyde (MDA), and total antioxidant capacity (TAC) were determined by the colorimetric method. The plasma MDA/TAC ratio was calculated as an index of oxidative status. Plasma albumin levels were measured to determine nutritional status. Plasma Fe concentrations, MDA levels and the MDA/TAC ratio were significantly higher (p<0.001, p<0.001, and p<0.01, respectively) and Se and Mn concentrations and TAC were lower (p<0.01, p<0.05, and p<0.01, respectively) in patients when compared to the healthy subjects. Plasma Zn, Cu, and albumin levels were not found to be significantly different in patients and controls (p>0.05). There were positive relationships between plasma MDA and Fe (r=0.545, p<0.001) and TAC and Se (r=0.485, p<0.021), and a negative correlation between TAC and MDA values (r= −0.337, p<0.031) in patients with childhood asthma. However, there was no correlation between these trace elements and albumin content in patient groups. These observations suggest that increased Fe and decreased Se concentrations in patients with childhood asthma may be responsible for the oxidant/antioxidant imbalance.
Analyses of heart rate variability in young soccer players: The effects of sport activity

BACKGROUND
The use of heart rate variability (HRV) in the management of sport training is a practice which tends to spread, especially in order to prevent the occurrence of states of fatigue.


OBJECTIVE
To estimate the HRV parameters obtained using a heart rate recording, according to different loads of sporting activities, and to make the possible link with the appearance of fatigue.


METHODS
Eight young football players, aged 14.6 years+/-2 months, playing at league level in Rhône-Alpes, training for 10 to 20 h per week, were followed over a period of 5 months, allowing to obtain 54 recordings of HRV in three different conditions: (i) after rest (ii) after a day with training and (iii) after a day with a competitive match.


RESULTS
Under the effect of a competitive match, the HRV temporal indicators (heart rate, RR interval, and pNN50) were significantly altered compared to the rest day. The analysis of the sympathovagal balance rose significantly as a result of the competitive constraint (0.72+/-0.17 vs. 0.90+/-0.20; p<0.05).


CONCLUSION
The main results obtained show that the HRV is an objective and non-invasive monitoring of management of the training of young sportsmen. HRV analysis allowed to highlight any neurovegetative adjustments according to the physical loads. Thus, under the effect of an increase of physical and psychological constraints that a football match represents, the LF/HF ratio rises significantly; reflecting increased sympathetic stimulation, which beyond certain limits could be relevant to prevent the emergence of a state of fatigue.
Association of vegetable, fruit, and grain intakes with colorectal cancer: the Multiethnic Cohort Study.

BACKGROUND
It is uncertain whether or not vegetables, fruit, or grains protect against colorectal cancer.


OBJECTIVE
In a large prospective study, we investigated the association of vegetable, fruit, and grain intakes with colorectal cancer risk.


DESIGN
Between 1993 and 1996, 85 903 men and 105 108 women completed a quantitative food-frequency questionnaire that included approximately 180 foods and beverages in the Multiethnic Cohort Study. A diagnosis of colorectal cancer was made in 1138 men and 972 women after an average follow-up of 7.3 y. Cox proportional hazards models were used to calculate multivariate-adjusted relative risks and 95% CIs for colorectal cancer.


RESULTS
In men, multivariate adjustment for energy intake, dietary, and nondietary variables resulted in relative risks in the highest quintile group of 0.74 (95% CI: 0.59, 0.93; P for trend = 0.02) for vegetables and fruit combined, 0.80 (95% CI: 0.64, 0.99; P for trend = 0.09) for fruit alone, and 0.85 (95% CI: 0.69, 1.05; P for trend = 0.05) for vegetables alone. When colon and rectal cases were separated among men, the inverse associations were stronger for colon than for rectal cancer. In women, none of the associations with vegetables, fruit, or vegetables and fruit combined were significant. Grain intake was not associated with colorectal cancer for either men or women.


CONCLUSION
The intake of vegetables and fruit was inversely related to colorectal cancer risk among men but not among women. The association appears stronger for colon than for rectal cancer.
Randomized trial of a comprehensive asthma education program after an emergency department visit.

BACKGROUND
Patients with asthma who visit the emergency department (ED) may benefit from education that optimizes self-management and treatment.


OBJECTIVE
To conduct a randomized trial of asthma education (AE) after an ED visit.


METHODS
Patients who present with acute asthma and history consistent with moderate to severe persistent asthma or recent ED visits were stratified by age (adult, child) and randomly assigned to intervention or usual care during the ED visit. The intervention was conducted by trained asthma educators and included a facilitated office visit with the primary care physician followed by a home visit. Intention-to-treat analysis was conducted, with time to first asthma relapse (either ED or unscheduled urgent office visit) during the 6-month follow-up period used as the primary outcome.


RESULTS
Of the 239 patients analyzed, 46% were adults, 46% were male, 30% were African American, and 56% had moderate to severe persistent asthma. Follow-up information was obtained on 191 patients (80%) at 6 months; 23.1% of the intervention group vs 31.1% of the usual care group had an urgent asthma visit (hazard ratio [HR], 0.79; 95% confidence interval [CI], 0.48-1.29). Overall, 39% of the 117 patients assigned to the intervention group did not comply with any of the post-ED activities. Subgroup analysis suggested greater benefit among children (HR, 0.62; 95% CI, 0.33-1.19) than adults (HR, 1.08; 95% CI, 0.50-2.33).


CONCLUSIONS
Delivery of a comprehensive AE program after an ED visit was ineffective in adult patients; however, it may be effective in children. Further research on alternative AE delivery strategies appears warranted to reduce the burden of asthma visits to the ED.
Nasoseptal flap takedown and reuse in revision endoscopic skull base reconstruction.

OBJECTIVES/HYPOTHESIS
To provide a description of the techniques and limitations of nasoseptal flap takedown and reuse during second-stage and revision endoscopic skull base surgery and review the institutional experience with the use of this reconstructive technique.


STUDY DESIGN
: Case series.


METHODS
A retrospective analysis of cerebrospinal fluid (CSF) leak outcomes was performed for a consecutive series of patients who underwent the nasoseptal flap takedown technique during endoscopic skull base surgery at two tertiary care skull base centers.


RESULTS
Twenty-eight consecutive cases with nasoseptal flap takedown procedures for endoscopic skull base reconstruction were collected and evaluated for flap viability and CSF leak outcomes. This cohort was composed of 14 revision surgeries and 14 planned second-stage procedures. There were no cases of flap loss. Twenty cases involved the presence of intraoperative CSF leaks. Twelve of these 20 cases were second-stage surgeries, and eight were revision or recurrent-tumor procedures. Nineteen of 20 had successful skull base reconstruction without a postoperative CSF leak. One patient required revision endoscopic CSF leak repair and bolstering of the defect with a fat graft 3 days after the initial surgery. Endoscopic skull base reconstructive techniques and limitations of flap takedowns are discussed.


CONCLUSIONS
Expansion of the limits of endoscopic skull base surgery must be accompanied by the development of new reconstructive options. This report illustrates the ability to take down and reuse the nasoseptal flap in staged and revision cases with a high success rate and minimal additional nasal morbidity.
Feasibility of fully automated detection of fiducial markers implanted into the prostate using electronic portal imaging: a comparison of methods.

PURPOSE
To investigate the feasibility of fully automated detection of fiducial markers implanted into the prostate using portal images acquired with an electronic portal imaging device.


METHODS AND MATERIALS
We have made a direct comparison of 4 different methods (2 template matching-based methods, a method incorporating attenuation and constellation analyses and a cross correlation method) that have been published in the literature for the automatic detection of fiducial markers. The cross-correlation technique requires a-priory information from the portal images, therefore the technique is not fully automated for the first treatment fraction. Images of 7 patients implanted with gold fiducial markers (8 mm in length and 1 mm in diameter) were acquired before treatment (set-up images) and during treatment (movie images) using 1MU and 15MU per image respectively. Images included: 75 anterior (AP) and 69 lateral (LAT) set-up images and 51 AP and 83 LAT movie images. Using the different methods described in the literature, marker positions were automatically identified.


RESULTS
The method based upon cross correlation techniques gave the highest percentage detection success rate of 99% (AP) and 83% (LAT) set-up (1MU) images. The methods gave detection success rates of less than 91% (AP) and 42% (LAT) set-up images. The amount of a-priory information used and how it affects the way the techniques are implemented, is discussed.


CONCLUSIONS
Fully automated marker detection in set-up images for the first treatment fraction is unachievable using these methods and that using cross-correlation is the best technique for automatic detection on subsequent radiotherapy treatment fractions.
Implementation and performance analysis of various VM placement strategies in CloudSim

Infrastructure as a Service (IaaS) has become one of the most dominant features that cloud computing offers nowadays. IaaS enables datacenter’s hardware to get virtualized which allows Cloud providers to create multiple Virtual Machine (VM) instances on a single physical machine, thus improving resource utilization and increasing the Return on Investment (ROI). VM consolidation includes issues like choosing appropriate algorithm for selection of VMs for migration and placement of VMs to suitable hosts. VMs need to be migrated from overutilized host to guarantee that demand for computer resources and performance requirements are accomplished. Besides, they need to be migrated from underutilized host to deactivate that host for saving power consumption. In order to solve the problem of energy and performance, efficient dynamic VM consolidation approach is introduced in literature. In this work, we have proposed multiple redesigned VM placement algorithms and introduced a technique by clustering VMs to migrate by taking account both CPU utilization and allocated RAM. We implement and study the performance of our algorithms on a cloud computing simulation toolkit known as CloudSim using PlanetLab workload data. Simulation results demonstrate that our proposed techniques outperform the default VM Placement algorithm designed in CloudSim.
Salvage of failed resection arthroplasties of the distal radioulnar joint using an ulnar head prosthesis: long-term results.

PURPOSE
The aim of this prospective multicenter study was to evaluate the long-term outcome of the Herbert ulnar head prosthesis for painful instability of the distal radioulnar joint (DRUJ) following resection of the ulnar head.


METHODS
Twenty-three patients were treated with a Herbert ulnar head prosthesis in 3 international hand centers. One patient was excluded from the study because a septic prosthesis had to be removed after 3 months. Sixteen of the remaining 22 patients could be assessed at 2 follow-up times, 28 months (range, 10-43 mo) and 11 years and 2 months (range, 97-158 mo) after surgery, for DRUJ stability, forearm rotation, grip strength, pain level (0-10), and satisfaction (0-10). Standardized radiographs of the wrist were evaluated for displacement of the ulnar head and loosening or bony reactions at the sigmoid notch or the ulna shaft.


RESULTS
All patients demonstrated a clinically stable DRUJ at the latest examination, and no patient required further surgery at the DRUJ since the short-term evaluation in 1999. Average pain measured 3.7 before surgery, 1.7 at the short-term follow-up, and 1.7 at the long-term follow-up; patients' satisfaction, 2.2, 8.2, and 8.9; pronation, 73°, 86°, and 83°; supination, 52°, 77°, and 81°; and grip strength, 42%, 72%, and 81% of the unaffected side. All clinical parameters improved significantly from before surgery to the short-term follow-up, with no further statistically significant change between the short-term and long-term follow-up. Radiographs demonstrated no signs of stem loosening or incongruity of the DRUJ.


CONCLUSIONS
The previously reported short-term results with the Herbert prosthesis did not deteriorate in the long term. Reconstruction of the DRUJ with this prosthesis in painful radioulnar impingement following ulnar head resection is a reliable and reproducible procedure with lasting results.
The history of twins, as a criterion of the relative powers of nature and nurture (1,2).

In the article ?The History of Twins, As a Criterion of the Relative Powers of Nature and Nurture,? Francis Galton [2] describes his study of twins. Published in 1875 in Fraser?s Magazine in London, England, the article lays out Galton?s use of twins to examine and distinguish between the characteristics people have at birth and the characteristics they receive from the circumstances of life and experience. Galton calls those factors nature and nurture. Based on his study, Galton concluded that nature has a larger effect than nurture on development. By studying twins, Galton introduced a way to examine the effects of nature and nurture in people who were born with similar traits, which allowed him to focus on the effects of experience on a person?s development.