LLukas22/scidocs huggingface dataset:
A Multiple Resampling Method for Learning from Imbalanced Data Sets

Re-Sampling methods are commonly used for dealing with the class-imbalance problem. Their advantage over other methods is that they are external and thus, easily transportable. Although such approaches can be very simple to implement, tuning them most effectively is not an easy task. In particular, it is unclear whether oversampling is more effective than undersampling and which oversampling or undersampling rate should be used. This paper presents an experimental study of these questions and concludes that combining different expressions of the re-sampling approach is an effective solution to the tuning problem. The proposed combination scheme is evaluated on imbalanced subsets of the Reuters-21578 text collection and is shown to be quite effective for these problems. Introduction In a conceptlearning problem, the data set is said to present a class imbalance if it contains many more examples of one class than the other. Such a situation poses challenges for typical classifiers such as Decision Tree Induction Systems or Multi-Layer Perceptrons that are designed to optimize overall accuracy without taking into account the relative distribution of each class (Japkowicz & Stephen 2002; Estabrooks 2000). As a result, these classifiers tend to ignore small classes while concentrating on classifying the large ones accurately. Unfortunately, this problem is quite pervasive as many domains are cursed with a class imbalance. This is the case, for example, with text classification tasks whose training sets typically contain much fewer documents of interest to the reader than on irrelevant topics. Other domains suffering from class imbalances include target detection, fault detection, or fraud detection problems, which, again, typically contain much fewer instances of the event of interest than of irrelevant events. ∗ Corresponding author
Alterations in nerve terminal glutamate immunoreactivity in the nucleus accumbens and ventral tegmental area following single and repeated doses of cocaine

Abstract Rationale and objectives. Previous studies have demonstrated that sensitization to repeated doses of cocaine results in prolonged changes in glutamate transmission. However, little is known about long-term changes in glutamate transmission following a single dose of cocaine. Our laboratory has previously reported that a single dose of cocaine, but not repeated cocaine, decreased the density of presynaptic nerve terminal glutamate immunolabeling in the nucleus accumbens when measured 3 days later. This study extends the results of our previous work by examining nerve terminal glutamate immunoreactivity 17 days after the last dose of cocaine. Methods. Quantitative electron-microscopic immunocytochemistry was used to determine the density of presynaptic nerve terminal glutamate immunoreactivity in rats that received single or repeated doses of cocaine followed by 17 days of withdrawal. Animals that received repeated cocaine were separated into behaviorally sensitized and non-sensitized groups based on individual differences between cocaine-stimulated locomotor activity on the first and last days of cocaine administration. Results. There were significant decreases in the density of presynaptic nerve terminal glutamate immunoreactivity in the nucleus accumbens core of the group that received a single dose of cocaine. The repeat cocaine groups had significant decreases in nerve terminal glutamate immunolabeling in the ventral tegmental area. Conclusions. Acute cocaine administration resulted in a significant loss of nerve terminal glutamate immunoreactivity that was persistent in the nucleus accumbens core, but there were only transient changes in the shell. Nerve terminal glutamate immunoreactivities in the behaviorally sensitized and non-sensitized groups were not significantly different from one another, which suggests that cocaine-induced alterations in presynaptic glutamate immunoreactivity may not be sufficient for the expression of behavioral sensitization.
Population pharmacokinetics of bevacizumab in children with osteosarcoma: implications for dosing.

PURPOSE
To describe sources of interindividual variability in bevacizumab disposition in pediatric patients and explore associations among bevacizumab pharmacokinetics and clinical wound healing outcomes.


EXPERIMENTAL DESIGN
Before tumor resection, three doses of bevacizumab (15 mg/kg) were administered to patients (median age, 12.2 years) enrolled in a multi-institutional osteosarcoma trial. Serial sampling for bevacizumab pharmacokinetics was obtained from 27 patients. A population pharmacokinetic model was fit to the data, and patient demographics and clinical chemistry values were systematically tested as predictive covariates on model parameters. Associations between bevacizumab exposure and wound healing status were evaluated by logistic regression.


RESULTS
Bevacizumab concentration-time data were adequately described by a two-compartment model. Pharmacokinetic parameter estimates were similar to those previously reported in adults, with a long median (range) terminal half-life of 12.2 days (8.6 to 32.4 days) and a volume of distribution indicating confinement primarily to the vascular space, 49.1 mL/kg (27.1 to 68.3 mL/kg). Body composition was a key determinant of bevacizumab exposure, as body mass index percentile was significantly (P < 0.05) correlated to body-weight normalized clearance and volume of distribution. Furthermore, bevacizumab exposure before primary tumor resection was associated with increased risk of major wound healing complications after surgery (P < 0.05).


CONCLUSION
A population pharmacokinetic model for bevacizumab was developed, which demonstrated that variability in bevacizumab exposure using weight-based dosing is related to body composition. Bevacizumab dosage scaling using ideal body weight would provide an improved dosing approach in children by minimizing pharmacokinetic variability and reducing likelihood of major wound healing complications.
Therapeutic effects of acupuncture in patients with rheumatoid arthritis: a prospective study using (18)F-FDG-PET.

OBJECTIVE
The purpose of this study was to investigate whether improvement of regional inflammatory findings in knee joints of rheumatoid arthritis (RA) could be detected by positron-emission tomography (PET) using (18)F-Fluorodeoxyglucose (FDG) after acupuncture treatments, as well as improvement of systemic inflammatory markers.


METHODS
Six RA patients (all female, 61 +/- 12 years old) received 10 acupuncture treatments in 2 months, to 11 traditional acupuncture points around a knee joint considered effective on RA. A visual analogue scale (VAS) for intensity of pain, knee joint range of motion (ROM), face scale for patient mood, and modified health assessment questionnaire (MHAQ) for disability of daily activities were assessed just before and after acupuncture. Maximum standardized uptake value (SUV(max)) and the volume with SUV more than 1.0 [Volume(SUV > 1)] on FDG-PET images as well as erythrocyte sedimentation rate (ESR) and C-reactive protein (CRP) levels were also measured before and after the treatments.


RESULTS
VAS, ROM, face scale and MHAQ improved in all patients and significantly after acupuncture, but no significant change was detected in ESR, CRP, SUV(max), or Volume(SUV > 1).


CONCLUSIONS
Acupuncture relieves symptom, remedies physical function, and improves quality of life in RA patients, but may have no or very limited anti-inflammatory effect systemically. The regional effects of acupuncture are unlikely to be induced through reduction of regional inflammation. We believe this clinical study is the first step for elucidating therapeutic mechanisms of acupuncture, which must be important for the rational use and further development of acupuncture.
Coalition-Based Approach to Task Allocation of Multiple Robots With Resource Constraints

We propose a coalition-based approach to solve the task allocation problem of multiple robots with resource constraints. The resources required by task execution characterize the robots and tasks. Robots must form coalitions to accomplish the assigned tasks because individually, each robot may not complete the task independently due to resource limitation. We consider both online and offline assignment manners of the task allocation problem. For online assignment, a sequential coalition method is proposed to select efficiently the suitable robots to form coalitions for the assigned task. For offline assignment, a holistic coalition method is proposed for global optimization of all the assigned tasks. Both sequential and holistic coalition methods are compared with existing approaches. Numerous simulations and experiments performed on heterogeneous multiple mobile robots demonstrate the effectiveness of the proposed coalition-based task allocation methods. Note to Practitioners - Task allocation into a group of heterogeneous mobile robots for implementing multiple tasks is a challenge in multirobot applications. To find and organize the most suitable coalition for each task, we need to well organize the coalition for each task to maximize the robot group utility and optimize the task allocation solution. The sequential and holistic coalition methods presented in this paper provide both online and offline solutions for optimal multirobot task allocation. The advantage of the sequential coalition method lies in its efficiency in selecting best-fitted robots during coalition forming, and the advantage of the holistic coalition method lies in its effectiveness in finding the global optimal solution for all tasks. We illustrate the effectiveness of the proposed methods through numerous case studies with comparisons in this paper.
Validation of a prediction rule for development of rheumatoid arthritis in patients with early undifferentiated arthritis.

OBJECTIVE
To validate a model which predicts progression from undifferentiated arthritis (UA) to RA, in a Canadian UA cohort.


METHODS
The prediction rule, comprising variables which are scored from 0 to 13, with higher scores reflecting an increased risk of RA, was applied to baseline characteristics of all patients with UA. Progression to RA was determined at 6 months.


RESULTS
105 patients were identified. By 6 months, 80 (76%) had developed RA while 25 (24%) had developed another diagnosis. Number of tender and swollen joints, rheumatoid factor positivity, anti-cyclic citrullinated peptide positivity, poor functional status and high disease activity were associated with development of RA (p<0.01). Median prediction score was 8.0 for progressors, 5.0 for non-progressors. With these cut-off points, 18 (72%) patients with scores < or =5 did not develop RA, while 35 (97%) with scores > or =8 did develop RA.


CONCLUSIONS
High scores in our cohort predicted those who progressed to RA by 6 months. Baseline scores > or =8 corresponded with higher rates of progression.
Intravenous versus intra-articular tranexamic acid in total knee arthroplasty: A double-blinded randomised controlled noninferiority trial.

BACKGROUND
Despite the proven efficacy of both intravenous (IV) and intra-articular (IA) tranexamic acid (TXA) in reducing blood loss during total knee arthroplasty (TKA), the ideal route of administration remained debatable. This study aimed to compare the effect of IV versus IA TXA on transfusion incidences, perioperative blood loss and postoperative lower limb swelling during TKA.


METHODS
One hundred patients were prospectively randomised into two groups: 1) IV TXA; and 2) IA TXA. In both groups, TXA was administered intraoperatively after cementing the prostheses. The perioperative blood loss was calculated using the haemoglobin balance method. The thigh, suprapatellar, and calf girths were measured preoperatively and on postoperative day (POD) 4.


RESULTS
Two patients in the IV group and one patient in the IA group required blood transfusion (p=0.500). The median and interquartile range (IQR) of perioperative blood loss on POD1 and POD4 was 530 (IQR 386,704) and 730 (IQR 523,925) ml for the IV group, compared with 613 (IQR 506,703) and 799 (IQR 563,1067) ml for the IA group (p=0.090 and p=0.232 respectively). The median increment in thigh, suprapatellar, and calf girths were 1.5 (IQR 0, 3.0), 2.0 (IQR 0.5, 4.0) and 0 (IQR 0, 1.0) cm for the IV group, compared to 2.0 (IQR 1.0, 4.0), 2.0 (IQR 0, 4.5) and 0 (IQR 0, 1.5) cm for the IA group (p=0.246, p=0.562, and p=0.937 respectively).


CONCLUSIONS
Both IV and IA TXA had comparable effect on transfusion incidences, perioperative blood loss, and postoperative lower limb swelling during TKA. IA TXA is an alternative to IV TXA.


LEVEL OF EVIDENCE
I.
Identification of rice diseases using deep convolutional neural networks

The automatic identification and diagnosis of rice diseases are highly desired in the field of agricultural information. Deep learning is a hot research topic in pattern recognition and machine learning at present, it can effectively solve these problems in vegetable pathology. In this study, we propose a novel rice diseases identification method based on deep convolutional neural networks (CNNs) techniques. Using a dataset of 500 natural images of diseased and healthy rice leaves and stems captured from rice experimental field, CNNs are trained to identify 10 common rice diseases. Under the 10-fold cross-validation strategy, the proposed CNNs-based model achieves an accuracy of 95.48%. This accuracy is much higher than conventional machine learning model. The simulation results for the identification of rice diseases show the feasibility and effectiveness of the proposed method. © 2017 Elsevier B.V. All rights reserved.
Folate, vitamin B12, and serum total homocysteine levels in confirmed Alzheimer disease.

BACKGROUND
Recent studies suggest that vascular disease may contribute to the cause of Alzheimer disease (AD). Since elevated plasma total homocysteine (tHcy) level is a risk factor for vascular disease, it may also be relevant to AD.


OBJECTIVE
To examine the association of AD with blood levels of tHcy, and its biological determinants folate and vitamin B12.


DESIGN
Case-control study of 164 patients, aged 55 years or older, with a clinical diagnosis of dementia of Alzheimer type (DAT), including 76 patients with histologically confirmed AD and 108 control subjects.


SETTING
Referral population to a hospital clinic between July 1988 and April 1996.


MAIN OUTCOME MEASURES
Serum tHcy, folate, and vitamin B12 levels in patients and controls at entry; the odds ratio of DAT or confirmed AD with elevated tHcy or low vitamin levels; and the rate of disease progression in relation to tHcy levels at entry.


RESULTS
Serum tHcy levels were significantly higher and serum folate and vitamin B12 levels were lower in patients with DAT and patients with histologically confirmed AD than in controls. The odds ratio of confirmed AD associated with a tHcy level in the top third (> or = 14 micromol/L) compared with the bottom third (< or = 11 micromol/L) of the control distribution was 4.5 (95% confidence interval, 2.2-9.2), after adjustment for age, sex, social class, cigarette smoking, and apolipoprotein E epsilon4. The corresponding odds ratio for the lower third compared with the upper third of serum folate distribution was 3.3 (95% confidence interval, 1.8-6.3) and of vitamin B12 distribution was 4.3 (95% confidence interval, 2.1-8.8). The mean tHcy levels were unaltered by duration of symptoms before enrollment and were stable for several years afterward. In a 3-year follow-up of patients with DAT, radiological evidence of disease progression was greater among those with higher tHcy levels at entry.


CONCLUSIONS
Low blood levels of folate and vitamin B12, and elevated tHcy levels were associated with AD. The stability of tHcy levels over time and lack of relationship with duration of symptoms argue against these findings being a consequence of disease and warrant further studies to assess the clinical relevance of these associations for AD.
Effects of Nutritional Supplementation on Fatigue, and Autonomic and Immune Dysfunction in Patients with End-Stage Renal Disease: A Randomized, Double-Blind, Placebo-Controlled, Multicenter Trial

BACKGROUND
Fatigue is a predictor of cardiovascular events in patients with end-stage renal disease (ESRD) undergoing hemodialysis treatment. We hypothesized that multinutritional support would improve quality of life, fatigue symptoms, and potential quantitative measures including endocrine, immune and autonomic functions in patients with ESRD undergoing hemodialysis.


METHODS
Two hundred and two hemodialysis patients were randomly assigned to receive active treatment (containing vitamin B1, vitamin B2, niacin, vitamin B6, vitamin B12, folic acid, vitamin C, carnitine, coenzyme Q10, naïve galacto-oligosaccharide, and zinc) or placebo after each dialysis session for 12 weeks. The patients and attending physicians were blinded to the treatment, and 172 patients (86 in each group) completed the study. Fatigue was evaluated via fatigue questionnaire at 0, 4, and 12 weeks. To assess human herpes virus (HHV) 6 and 7 reactivation, numbers of viral DNA copies were determined in saliva by polymerase chain reaction at weeks 0 and 12. Autonomic function was determined via measurement of beat-to-beat variation by using acceleration plethysmography.


RESULTS
Clinical characteristics, changes in fatigue, quality of life score, endocrine functions, and laboratory data did not differ significantly between the two groups. Several parameters of heart rate variability significantly increased after nutritional treatment compared to placebo. Nutritional drink for 12 weeks significantly suppressed HHV7 DNA copy numbers. Similarly, HHV6 DNA copy numbers tended to be decreased by treatment but without reaching statistical significance.


CONCLUSIONS
Nutritional supplementation may modulate immune and autonomic dysfunction in ESRD patients undergoing hemodialysis.
Single stage surgical treatment of amniotic band syndrome – Case report.

Introduction
Amniotic band syndrome is a rare congenital disorder with clinical presentation of constricting
bands in different parts of extremities or whole extremities. Conservative or surgical treatment
is provided depending on the type and severity of the anomaly.


Case Outline
The paper presents the case of a neonate patient with constriction bands localized on the
left leg. During the second week of life, a surgery was indicated, and a single-stage multiple Z-plasty was
performed to correct the anomalies on the left lower leg. Postoperative edema in the distal part of the
lower leg was easily managed by incisions and drainage. Two months later, the correction of the stricture
of the left thigh was managed using the same procedure. The postoperative course was uneventful and
the outcome was satisfactory after a two-year follow-up.


Conclusion
Evaluation of a patient with amniotic band syndrome, as well as diagnosis, monitoring, treatment
and postoperative care, should always be multidisciplinary. A single-stage correction approach
provided satisfactory both functional and aesthetic results. Given many morphological variations of the
syndrome, a decision on the strategy of treatment should be made individually for each patient.
Pain assessment for pediatric patients in the emergency department.

OBJECTIVE
To examine the relationship between pediatric patient visit characteristics and pain score documentation in the emergency department (ED) and determine whether documentation of a pain score is associated with increased analgesic use.


METHODS
A cross-sectional analysis was conducted of ED visits for pediatric patients from the National Hospital Ambulatory Medical Care Survey (1997-2000). Survey weighted regression first was used to assess the association between patient visit characteristics and pain score documentation. The regression then was repeated to determine the association between documentation of a pain score and analgesic use, adjusting for visit characteristics.


RESULTS
A total of 24,707 visits were included. Only 44.5% of visits had documented pain scores. In the regression analysis, younger age, self-pay, visits to pediatric facilities, and visits that were not designated as injury related were associated with decreased pain score documentation. Documentation of pain score was associated with increased odds of an analgesic prescription and opioid prescription. When no pain score was documented, the odds of receiving any analgesic was similar to visits with pain documented as mild.


CONCLUSION
ED pain score documentation is suboptimal in the pediatric population. Infants and toddlers are at particular risk for not having a pain score documented. There is a significant association between pain score documentation and the use of any analgesic, particularly opioids. Improvements in pain documentation for acutely ill and injured children are needed to improve pain management.
Geodesic Flow Kernel Support Vector Machine for Hyperspectral Image Classification by Unsupervised Subspace Feature Transfer

Alim Samat 1,2,*, Paolo Gamba 3, Jilili Abuduwaili 1,2, Sicong Liu 4 and Zelang Miao 5 1 State Key Laboratory of Desert and Oasis Ecology, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi 830011, China; jilil@ms.xjb.ac.cn 2 Chinese Academy of Sciences Research Center for Ecology and Environment of Central Asia, Urumqi 830011, China 3 Department of Electrical, Computer and Biomedical Engineering, University of Pavia, 27100 Pavia, Italy; paolo.gamba@unipv.it 4 College of Surveying and Geoinformatics, Tongji University, Shanghai 200092, China; sicongliu.rs@gmail.com 5 Department of Land Surveying and Geo-Informatics, Hong Kong Polytechnic University, Kowloon, Hong Kong 999077, China; cumtzlmiao@gmail.com * Correspondence: alim.smt@gmail.com; Tel.: +86-991-788-5432
A systematic literature review on features of deep learning in big data analytics

Context: Deep Learning (DL) is a division of machine learning techniques that based on algorithms for learning multiples level of representations. Big Data Analytics (BDA) is the process of examining large scale of data and variety of data types. Objectives: The aims of this study are to identify the existing features of DL approaches for using in BDA and identify the key features that affect the effectiveness of DL approaches. Method: A Systematic Literature Review (SLR) was carried out and reported based on the preferred reporting items for systematic reviews. 4065 papers were retrieved by manual search in four databases which are Google Scholar, Taylor & Francis, Springer Link and Science Direct. 34 primary studies were finally included. Result: From these studies, 70% were journal articles, 25% were conference papers and 5% were contributions from the studies consisted of book chapters. Five features of DL were identified and analyzed. The features are (1) hierarchical layer, (2) high-level abstraction, (3) process high volume of data, (4) universal model and (5) does not over fit the training data. Conclusion: This review delivers the evidence that DL in BDA is an active research area. The review provides researchers with some guidelines for future research on this topic. It also provides broad information on DL in BDA which could be useful for practitioners.