LLukas22/scidocs huggingface dataset:
A Robust System for Noisy Image Classification Combining Denoising Autoencoder and Convolutional Neural Network

Image classification, a complex perceptual task with many real life important applications, faces a major challenge in presence of noise. Noise degrades the performance of the classifiers and makes them less suitable in real life scenarios. To solve this issue, several researches have been conducted utilizing denoising autoencoder (DAE) to restore original images from noisy images and then Convolutional Neural Network (CNN) is used for classification. The existing models perform well only when the noise level present in the training set and test set are same or differs only a little. To fit a model in real life applications, it should be independent to level of noise. The aim of this study is to develop a robust image classification system which performs well at regular to massive noise levels. The proposed method first trains a DAE with low-level noise-injected images and a CNN with noiseless native images independently. Then it arranges these two trained models in three different combinational structures: CNN, DAE-CNN, and DAE-DAECNN to classify images corrupted with zero, regular and massive noises, accordingly. Final system outcome is chosen by applying the winner-takes-all combination on individual outcomes of the three structures. Although proposed system consists of three DAEs and three CNNs in different structure layers, the DAEs and CNNs are the copy of same DAE and CNN trained initially which makes it computationally efficient as well. In DAE-DAECNN, two identical DAEs are arranged in a cascaded structure to make the structure well suited for classifying massive noisy data while the DAE is trained with low noisy image data. The proposed method is tested with MNIST handwritten numeral dataset with different noise levels. Experimental results revealed the effectiveness of the proposed method showing better results than individual structures as well as the other related methods. Keywords—Image denoising; denoising autoencoder; cascaded denoising autoencoder; convolutional neural network
Hemostatic changes in pediatric neurosurgical patients as evaluated by thrombelastograph.

UNLABELLED
Thromboembolic events are a known complication in neurosurgical patients. There is evidence to suggest that a hypercoagulable state may develop perioperatively. Thrombelastograph (TEG) coagulation analysis is a reliable method of evaluating hypercoagulability. We evaluated coagulation by using TEG data in pediatric neurosurgical patients undergoing craniotomy to determine whether a hypercoagulable state develops intraoperatively or postoperatively. Thirty children undergoing craniotomy for removal of a tumor or seizure focus were studied. Blood was analyzed with TEG) data by using native and celite techniques, at three time points for each patient: preoperatively after induction of anesthesia; intraoperatively during closure of the dura; and on the first postoperative day. Compared with preoperative indices, closing and postoperative celite TEG values were indicative of hypercoagulability with shortened coagulation time values (P < 0.001), prolonged alpha angle divergence values (P < 0.001), and above-normal TEG coagulation indices (P < or = 0.002). Reaction time values were shortened, and maximal amplitude of clot strength values were prolonged but did not reach statistical significance. Hypercoagulation develops early after resection of brain tissue in pediatric neurosurgical patients as assessed by using TEG data. Further studies are needed to determine the clinical significance of this hypercoagulable state.


IMPLICATIONS
Hypercoagulability in postoperative neurosurgical patients has been demonstrated in the adult population, but few studies have dealt with the pediatric population. We found that children undergoing craniotomy for focal resection, lobectomy, and hemispherectomy are hypercoagulable as detected by thrombelastograph coagulation analysis. Further studies are needed to determine whether this is clinically significant.
Location of PD sources in power transformers by UHF and acoustic measurements

The paper presents the experience of unconventional methods for partial discharge (PD) measurement to detect and localise PD sources in power transformers. The UHF PD measurement method is usable as stand-alone measurement and as a supporting measurement for off- and on-line PD detection. The sensitivity of UHF PD measurements is sufficient and is normally not affected by external disturbances. Especially in noisy surrounding it might be a very helpful method to support other PD measurement techniques for example dissolved gas analysis and acoustic location of PD. Propagation time of UHF signals can be used for geometrical PD location. The accuracy seems to be adequate to determine the phase limb where the PD is located. Additionally, different measurable UHF amplitudes support an estimation of the PD location. However, since transformers rarely possess more than three oil valves for installation of UHF probes, an additional acoustic measurement is usually required for location. Using the knowledge gained from the UHF location, acoustic sensors can be placed near to the PD source at the transformer tank. The paper explains first the fundamentals of PD measurements and PD source location and presents two case studies.
Queue scheduling and advance reservations with COSY

Summary form only given. Most of current job scheduling systems for supercomputers and clusters provide batch queuing support. With the development of metacomputing and grid computing, users require resources managed by multiple local job schedulers. Advance reservations are becoming essential for job scheduling systems to be utilized within a large-scale computing environment with geographically distributed resources. COSY is a lightweight implementation of such a local job scheduler with support for both queue scheduling and advance reservations. COSY queue scheduling utilizes the FCFS algorithm with backfilling mechanisms and priority management. Advance reservations with COSY can provide effective QoS support for exact start time and latest completion time. Scheduling polices are defined to reject reservations with too short notice time so that there is no start time advantage to making a reservation over submitting to a queue. Further experimental results show that as a larger percentage of reservation requests are involved, a longer mandatory shortest notice time for advance reservations must be applied in order not to sacrifice queue scheduling efficiency.
Prediction of potential for organ donation after cardiac death in patients in neurocritical state: a prospective observational study

BACKGROUND
Successful donation of organs after cardiac death (DCD) requires identification of patients who will die within 60 min of withdrawal of life-sustaining treatment (WLST). We aimed to validate a straightforward model to predict the likelihood of death within 60 min of WLST in patients with irreversible brain injury.


METHODS
In this multicentre, observational study, we prospectively enrolled consecutive comatose patients with irreversible brain injury undergoing WLST at six medical centres in the USA and the Netherlands. We assessed four clinical characteristics (corneal reflex, cough reflex, best motor response, and oxygenation index) as predictor variables, which were selected on the basis of previous findings. We excluded patients who had brain death or were not intubated. The primary endpoint was death within 60 min of WLST. We used univariate and multivariable logistic regression analyses to assess associations with predictor variables. Points attributed to each variable were summed to create a predictive score for cardiac death in patients in neurocritical state (the DCD-N score). We assessed performance of the score using area under the curve analysis.


FINDINGS
We included 178 patients, 82 (46%) of whom died within 60 min of WLST. Absent corneal reflexes (odds ratio [OR] 2·67, 95% CI 1·19-6·01; p=0·0173; 1 point), absent cough reflex (4·16, 1·79-9·70; p=0·0009; 2 points), extensor or absent motor responses (2·99, 1·22-7·34; p=0·0168; 1 point), and an oxygenation index score of more than 3·0 (2·31, 1·10-4·88; p=0·0276; 1 point) were predictive of death within 60 min of WLST. 59 of 82 patients who died within 60 min of WLST had DCD-N scores of 3 or more (72% sensitivity), and 75 of 96 of those who did not die within this interval had scores of 0-2 (78% specificity); taking into account the prevalence of death within 60 min in this population, a score of 3 or more was translated into a 74% chance of death within 60 min (positive predictive value) and a score of 0-2 translated into a 77% chance of survival beyond 60 min (negative predictive value).


INTERPRETATION
The DCD-N score can be used to predict potential candidates for DCD in patients with non-survivable brain injury. However, this score needs to be tested specifically in a cohort of potential donors participating in DCD protocols.


FUNDING
None.
Question Dependent Recurrent Entity Network for Question Answering

Question Answering is a task which requires building models capable of providing answers to questions expressed in human language. Full question answering involves some form of reasoning ability. We introduce a neural network architecture for this task, which is a form of Memory Network, that recognizes entities and their relations to answers through a focus attention mechanism. Our model is named Question Dependent Recurrent Entity Network and extends Recurrent Entity Network by exploiting aspects of the question during the memorization process. We validate the model on both synthetic and real datasets: the bAbI question answering dataset and the CNN & Daily News reading comprehension dataset. In our experiments, the models achieved a State-ofThe-Art in the former and competitive results in the latter.
Identification of robust focus measure functions for the automated capturing of focused images from Ziehl-Neelsen stained sputum smear microscopy slide.

Capturing of the best-focused image using focus measure function (FMF) from a stack of images acquired at different focus distances is a crucial step in automatic microscopy development. Detection of bacilli present in Ziehl-Neelsen (ZN) stained sputum smears conventional microscope (CM) images is critical to disease diagnosis. Studies have revealed that the performances of FMFs are sensitive to image contents and background noise. In this article, 24 diverse FMFs were implemented on 31 stacks of CM's field of view images acquired from three different microscopes to determine the best-focused one. Seven FMFs achieved the accuracies of greater than 90%. Accuracy, focus error, and false maxima were calculated for each FMF, and overall score and ranking were also calculated for better interpretation. Preprocessing techniques such as filtering and image distortions (noise, contrast, saturation, illumination, etc.) were performed to evaluate the robustness of every FMF. Gaussian derivative, steerable filters, Tenengrad, and Hemli and Scherer's mean FMFs were identified as the most robust and accurate functions with the accuracy >90%. These FMFs have a relatively less focus error and false maxima rate. Full widths at half maximum of these four FMFs were also computed to determine their efficacy for the optimization process. These four FMFs can be implemented for automated capturing of the image from ZN-stained sputum smear slide. Gaussian derivative FMF can also be used effectively for both CM and fluorescence microscope's field of view image stacks to determine the best-focused one from each stack. © 2017 International Society for Advancement of Cytometry.
Interexaminer reliability of three methods of combining test results to determine side of sacral restriction, sacral base position, and innominate bone position.

CONTEXT
Sacroiliac joint dysfunction is diagnosed based on the combined results of several palpatory examinations. Previous studies have compared the interexaminer reliability of only one of these methods of diagnosis.


OBJECTIVE
To compare the interexaminer reliability of three methods of combining palpatory examinations to determine the side of sacroiliac joint dysfunction, sacral base position, and innominate bone position.


DESIGN
Blinded single-cohort reliability study.


METHODS
Patients with low back pain underwent two identical sets of palpatory examinations given by two physicians, separately, at a university spine center. The results of each set were compiled and interpreted by three methods: using the test result with the highest interexaminer reliability (method 1), requiring at least one test result to be abnormal for the variable to be abnormal (method 2), and requiring all test results to be abnormal for the variable to be abnormal (method 3). The kappa was calculated for each method.


RESULTS
There were 24 subjects (mean age, 68.3 years), of which 15 (62%) were women. The kappa was consistently higher with method 1, at 0.47, 0.08, and 0.32 for the sacral position, innominate bone position, and side of sacroiliac joint dysfunction, respectively. Corresponding values for method 2 were 0.09, 0.4, and 0.16, and for method 3 were 0.16, 0.1, and -0.33.


CONCLUSION
Using the results of the most reliable examination consistently has the best interexaminer reliability.
Reliability of body temperature measurements in hospitalised older patients.

AIMS AND OBJECTIVES
To compare different body temperature assessment methods in older people and to assess the role of cognitive and functional characteristics in temperature recordings.


BACKGROUND
Axillary gallium-in-glass thermometers are commonly used. Their accuracy depends on the proper placement of the device and their permanence in place for eight minutes. With adequate instruction, well-functioning patients can measure their axillary temperature by themselves, while in cognitively and functionally impaired older people, inadequate understanding of instructions and misplacement of the thermometer might determine significant recording errors. Electronic ear and axillary temperature measurements are faster, but their accuracy has not been demonstrated convincingly with older people.


METHODS
Patients (n = 107; aged 65-104 years) were recruited. Barthel Index and Short Portable Mental Status Questionnaire (SPMSQ) scores were obtained for each patient. Temperature readings were obtained using: the axillary gallium-in-glass thermometer, with (T(nurse)) and without (T(self)) the nurse's assistance; the electronic axillary thermometer (T(el)) and the infrared tympanic thermometer (T(tymp)). The T(nurse) was considered as the reference method.


RESULTS
Mean difference and standard deviation (mean +/- SD) in temperature recordings between the different techniques and T(nurse) differed significantly from zero for T(self) (-0.40 SD 0.42) and T(tymp) (+0.19 SD 0.48). No significant differences in temperature recordings emerged between T(nurse) and T(el). In simple linear regression models, the difference between T(self) and T(nurse) significantly correlated with age, gender, SPMSQ score and Barthel Index. Multiple linear regression analysis showed an underestimation of body temperature in older patients with cognitive impairments.


CONCLUSION
Unassisted gallium-in-glass axillary temperature assessment is inadequate, in older patients. The differences between T(self) and T(nurse) are significantly influenced by age and mental decline. T(el) provides adequate accuracy. Relevance to clinical practice. In geriatric settings, the electronic axillary thermometer is a safe and accurate alternative to the more traditional gallium-in-glass thermometer, with the advantage of saving time (five seconds in recording vs. eight minutes).
Progression of hepatic fibrosis in patients with hepatitis C: a prospective repeat liver biopsy study.

BACKGROUND
The natural history of hepatitis C virus (HCV) infection remains uncertain. Previous data concerning rates of progression are from studies using estimated dates of infection and single liver biopsy scores. We prospectively studied the rate of progression of fibrosis in HCV infected patients by repeat liver biopsies without intervening treatment.


PATIENTS
We studied 214 HCV infected patients (126 male; median age 36 years (range 5-8)) with predominantly mild liver disease who were prospectively followed without treatment and assessed for risk factors for progression of liver disease. Interbiopsy interval was a median of 2.5 years. Paired biopsies from the same patient were scored by the same pathologist.


RESULTS
Seventy of 219 (33%) patients showed progression of at least 1 fibrosis point in the Ishak score; 23 progressed at least 2 points. Independent predictors of progression were age at first biopsy and any fibrosis on first biopsy. Factors not associated with progression were: necroinflammation, duration of infection, alcohol consumption, alanine aminotransferase levels, current or past hepatitis B virus infection, ferritin, HCV genotype, and steatosis or iron deposition in the initial biopsy.


CONCLUSIONS
One third of patients with predominantly mild hepatitis C showed significant fibrosis progression over a median period of 30 months. Histologically, mild hepatitis C is a progressive disease. The overall rate of fibrosis progression in patients with hepatitis C was low but increased in patients who were older or had fibrosis on their index biopsy. These data suggest that HCV infection will place an increasing burden on health care services in the next 20 years.
Intakes of meat, fish, poultry, and eggs and risk of prostate cancer progression.

BACKGROUND
Processed meat and fish have been shown to be associated with the risk of advanced prostate cancer, but few studies have examined diet after prostate cancer diagnosis and risk of its progression.


OBJECTIVE
We examined the association between postdiagnostic consumption of processed and unprocessed red meat, fish, poultry, and eggs and the risk of prostate cancer recurrence or progression.


DESIGN
We conducted a prospective study in 1294 men with prostate cancer, without recurrence or progression as of 2004-2005, who were participating in the Cancer of the Prostate Strategic Urologic Research Endeavor and who were followed for an average of 2 y.


RESULTS
We observed 127 events (prostate cancer death or metastases, elevated prostate-specific antigen concentration, or secondary treatment) during 2610 person-years. Intakes of processed and unprocessed red meat, fish, total poultry, and skinless poultry were not associated with prostate cancer recurrence or progression. Greater consumption of eggs and poultry with skin was associated with 2-fold increases in risk in a comparison of extreme quantiles: eggs [hazard ratio (HR): 2.02; 95% CI: 1.10, 3.72; P for trend = 0.05] and poultry with skin (HR: 2.26; 95% CI: 1.36, 3.76; P for trend = 0.003). An interaction was observed between prognostic risk at diagnosis and poultry. Men with high prognostic risk and a high poultry intake had a 4-fold increased risk of recurrence or progression compared with men with low/intermediate prognostic risk and a low poultry intake (P for interaction = 0.003).


CONCLUSIONS
Our results suggest that the postdiagnostic consumption of processed or unprocessed red meat, fish, or skinless poultry is not associated with prostate cancer recurrence or progression, whereas consumption of eggs and poultry with skin may increase the risk.
Anti-inflammatory, antioxidant, and antimicrobial activities of Cocos nucifera var. typica

BACKGROUND
Teas from the husk fiber of Cocos nucifera are used in the folk medicine to treat arthritis and other inflammatory processes. Some works show that some varieties have biological activities. However, one of the main variety of the species, C. nucifera var. typica, known in Brazil as "gigante", was not studied yet. Thus, this study evaluates if this variety has the anti-inflammatory and antimicrobial activities already reported in other varieties.


METHODS
C. nucifera aqueous crude extract (10, 50, and 100 mg/kg) and the reference drugs morphine (1 mg/kg) and acetylsalicylic acid (100 mg/kg) were evaluated in models of inflammation (formalin-induced licking and subcutaneous air pouch). The antioxidant activity was evaluated by 2,2-diphenyl-1-picryl-hydrazyl-hydrate (DPPH) photometric assay and compared with those of the standards (quercetin, rutin, and ascorbic acid). The extract was also screened against Candida albicans, Escherichia coli, Staphylococcus aureus, and methicillin-resistant Staphylococcus aureus (MRSA), in the agar diffusion method. The minimal inhibitory concentration (MIC) and minimal bactericidal concentration (MBC) were determined by the broth micro-dilution assay. Activities of combinations of the extract and antibiotics (methicillin or vancomycin) against MRSA were evaluated using checkerboard assays.


RESULTS
The extract significantly inhibited the time that the animals spent licking the formalin-injected paws (second phase). The extract also inhibited the inflammatory process induced by subcutaneous carrageenan injection by reducing cell migration, protein extravasation, and TNF-α production. Additionally, the extract showed an antioxidant potential in vitro as good as standards in their antioxidant activity. The extract was active only against S. aureus and MRSA. MIC and the bactericidal concentrations were identical (1,024 μg/ml). The extract and methicillin acted synergistically against the clinical MRSA isolate, whereas an indifferent effect was detected when the extract was combined with vancomycin.


CONCLUSIONS
The extract exhibits anti-inflammatory activity through the inhibition of the cell migration. The mixture of extract constituents and methicillin could lead to the development of a new combination antibiotic against MRSA infections.