LLukas22/scidocs huggingface dataset:
A hybridized K-means clustering approach for high dimensional dataset

Due to incredible growth of high dimensional dataset, conventional data base querying methods are inadequate to extract useful information, so researchers nowadays is forced to develop new techniques to meet the raised requirements. Such large expression data gives rise to a number of new computational challenges not only due to the increase in number of data objects but also due to the increase in number of features/attributes. Hence, to improve the efficiency and accuracy of mining task on high dimensional data, the data must be preprocessed by an efficient dimensionality reduction method. Recently cluster analysis is a popularly used data analysis method in number of areas. K-means is a well known partitioning based clustering technique that attempts to find a user specified number of clusters represented by their centroids. But its output is quite sensitive to initial positions of cluster centers. Again, the number of distance calculations increases exponentially with the increase of the dimensionality of the data. Hence, in this paper we proposed to use the Principal Component Analysis (PCA) method as a first phase for K-means clustering which will simplify the analysis and visualization of multi dimensional data set. Here also, we have proposed a new method to find the initial centroids to make the algorithm more effective and efficient. By comparing the result of original and new approach, it was found that the results obtained are more accurate, easy to understand and above all the time taken to process the data was substantially reduced.
Enzymic degradation of deoxyribonucleic acid. II. Enzymic properties of thymus acid deoxyribonuclease.

Abstract The degradation of deoxyribonucleic acid by thymus acid deoxyribonuclease was studied by viscosity, formation of acid-soluble products, spectrophometry, and pH measurements. The influence of enzyme and substrate concentration is examined. Divalent cations, Mg, Mn, Ca and Zn are activators at low concentrations and inhibitors at higher ones. There is a stoichiometric relationship between the concentrations of substrate and cations at the point of maximum activation. Spectral changes and pH variation are discussed in relation with structural modifications of the degradation products. From the viscometric experiments, the mechanisms of action of the two DNases (neutral and acid) appear to be quite different.
1 Emulsion Formation, Stability, and Rheology

Emulsions are a class of disperse systems consisting of two immiscible liquids [1–3]. The liquid droplets (the disperse phase) are dispersed in a liquid medium (the continuous phase). Several classes may be distinguished: oil-in-water (O/W), water-in-oil (W/O), and oil-in-oil (O/O). The latter class may be exemplified by an emulsion consisting of a polar oil (e.g., propylene glycol) dispersed in a nonpolar oil (paraffinic oil) and vice versa. To disperse two immiscible liquids, one needs a third component, namely, the emulsifier. The choice of the emulsifier is crucial in the formation of the emulsion and its long-term stability [1–3]. Emulsions may be classified according to the nature of the emulsifier or the structure of the system. This is illustrated in Table 1.1.
A case report of a rare complication of bowel perforation in extreme lateral interbody fusion

Over the past decade, extreme lateral interbody fusion (XLIF) has gained in popularity as a minimally invasive alternative to direct anterior lumbar interbody fusion (ALIF), and ALIF’s associated morbidity. Most notably, XLIF largely avoids vascular and visceral structures that are required to be mobilized in ALIF. In this case report, the authors describe a rare complication of a bowel injury in a 70-year-old male who underwent an L3–4 and L4–5 lateral transpsoas approach for interbody fusion.
General Overview of ImageCLEF at the CLEF 2016 Labs

This paper presents an overview of the ImageCLEF 2016 evaluation campaign, an event that was organized as part of the CLEF (Conference and Labs of the Evaluation Forum) labs 2016. ImageCLEF is an ongoing initiative that promotes the evaluation of technologies for annotation, indexing and retrieval for providing information access to collections of images in various usage scenarios and domains. In 2016, the 14th edition of ImageCLEF, three main tasks were proposed: 1) identification, multi-label classification and separation of compound figures from biomedical literature; 2) automatic annotation of general web images; and 3) retrieval from collections of scanned handwritten documents. The handwritten retrieval task was the only completely novel task this year, although the other two tasks introduced several modifications to keep the proposed tasks challenging.
Predictive model-based compensation schemes for robust speech recognition

For practical applications speech recognition systems need to be insensitive to diierences between training and test acoustic conditions. Diierences in the acoustic environment may result from various sources, such as ambient background noise, channel variations and speaker stress. These diierences can dramatically degrade the performance of a speech recognition system. A wide range of techniques have been proposed for achieving noise robustness. This paper considers one particular approach to model-based compensation, predictive model-based compensation, which has been shown to achieve good noise robustness in a wide range of acoustic environments. The characteristic of these schemes is that they combine a speech model with an additive noise model, a channel model and, in the general case, a speaker stress model, to generate a corrupted-speech model. The general theory of these predictive techniques is discussed. Various approximations for rapidly performing the model combination stage have been proposed and are reviewed in this paper. The advantages and the limitations of such a predictive approach to noise robustness are also discussed. In addition, methods for combining predictive schemes with schemes which make use of speech data in the new environment, adaptive schemes, are detailed. This combined approach overcomes some of the limitations of the predictive schemes.
Invisible antennas using mesoscale conductive polymer wires embedded within OLED displays

An efficient, optically invisible antenna applied on the touch OLED display panel is presented and demonstrated for the first time in literature. A transverse magnetic (TM01) patch antenna is devised at 2.45 GHz on the display panel surface of a real-life smartwatch device and its radiation properties, optical visibility and touch functions are investigated.
An environmental impact analysis of grinding

This thesis was intended to investigate the environmental impact of grinding in the United States manufacturing industry. Grinding is an ideal method for producing parts with a fine surface finish and high dimensional accuracy and for shaping hard or brittle workpieces. There are a wide variety of different types of grinding machines, each with different applications and slightly different energy requirements. Workpieces are generally flooded with a stream of coolant while being ground or placed in a spray of coolant mist. Coolant recycling systems are used to filter ground off chips out of coolant and to remove foreign oils and bacteria which pose health hazards. Oil mist collectors both clean mist coolant and prevent the toxic coolant from being inhaled by machinists. In total, 63 * 1015 joules of energy are consumed per year by grinding in manufacturing, 57% of which is directly used in material removal. A total of 1.5* 1010 pounds of scrap chips, spent grinding wheels, and used filters are produced each year as a result of grinding, over 99% of that being scrap chips. About 2.3 million gallons of fluids per year of grinding fluids are incinerated. Grinding creates a significant environmental footprint, creating a need for methods to reduce energy use in grinding and for ways to recycle solid waste that would otherwise be sent to landfills or incinerated. Thesis Supervisor: Timothy G. Gutowski Title: Associate Department Head, Professor of Mechanical Engineering, Director, Laboratory for Manufacturing and Productivity, Thesis Supervisor
Development of Japanese version of the UCLA Prostate Cancer Index: a pilot validation study

 Methods: The Japanese version (version 1.2) of the UCLA PCI was developed through a process of translation, back-translation, and refinement after interviewing patients. Reliability and validity were examined for 125 Japanese patients with localized prostate cancer. The patients simultaneously responded to the Japanese version of the RAND 36-Item Health Survey (SF-36) and five representative questions from the International Index of Erectile Function (IIEF). Results: Internal consistency reliability was very high for both urinary and sexual function scales, and lower for bowel function. The test-retest reliability of the urinary and sexual function scales and the urinary bother scales was stable, while that of the bowel function and bother scales was relatively unstable. Sexual function scores did not correlate highly with sexual bother scores. Furthermore, poor sexual function and bother had little association with the SF-36 scores. Missing data as to urinary and bowel function/bother scales were minimal (0.8%–2.4%), while those for sexual function and bother were relatively high (4.8%–11.2%). Conclusions: The results of this pilot study, together with the previous American study, suggest ethnic or cultural difference in how impaired sexual function is integrated into overall QOL. A future cross-cultural comparative study using the UCLA PCI and SF-36 will provide useful information about the influence of cultural or ethnic differences on health-related QOL in prostate cancer patients.
Dyskinesias and motor fluctuations in Parkinson's disease. A community-based study.

We investigated the prevalence of dyskinesias and motor fluctuations, and the factors determining their occurrence, in a community-based population of patients with Parkinson's disease. Among 124 patients with Parkinson's disease, 87 (70%) had received a levodopa preparation. Among these 87 patients, 28% were experiencing treatment-induced dyskinesias and 40% response fluctuations. The prevalence of motor fluctuations was best predicted by disease duration and dose of levodopa, whereas dyskinesias could be best predicted by duration of treatment. Patients with a shorter time from symptom onset to initiation of levodopa and younger patients had developed motor complications earlier, and patients who had started treatment with a dopamine agonist had developed these treatment complications later. Although a satisfactory response to medication was associated with higher rates of motor complications, poor or moderate response was associated with lower quality of life in patients with a disease duration of </=5 years or >/=10 years. We conclude that motor fluctuations are most strongly related to disease duration and dose of levodopa, and dyskinesias to duration of levodopa treatment. However, poorer quality of life associated with inadequate dosage of levodopa may be the price for a low rate of motor complications in patients with Parkinson's disease.
Quantitatively measuring a large-scale agile transformation

Context : Agile software development continues to grow in popularity and is being adopted by more and more organizations. However, there is a need for empirical evidence on the impact, benefits and drawbacks of an agile transformation in an organization since the cost for such a transformation in terms of money, disrupted working routines and quality of development can become considerable. Currently, such evidence exists in the form of success stores and case studies, mostly of qualitative nature. Objective : Provide a metrics model to quantitatively measure the impact of an agile transformation in a software development organization. Method : The metrics model was elicited with the use of the Goal Question Metric approach. Results: A quantitative metrics model containing eight rigorously described metrics is presented and followed by its application to evaluate an agile and lean transformation in a large international telecommunication organization with 350 employees in two sites. Conclusions : The metrics model was sensitive to the changes that occurred in the organization and revealed significant improvements in six of the eight metrics and a deterioration in one of the metrics. © 2016 Elsevier Inc. All rights reserved.
Standard of Care Versus Metastases-directed Therapy for PET-detected Nodal Oligorecurrent Prostate Cancer Following Multimodality Treatment: A Multi-institutional Case-control Study.

BACKGROUND
Most prostate cancer (PCa) patients with a biochemical failure following primary multimodality treatment (surgery and postoperative radiotherapy) relapse in the nodes.


OBJECTIVE
To perform a matched-case analysis in men with lymph node recurrent PCa comparing standard of care (SOC) with metastasis-directed therapy (MDT).


DESIGN, SETTING, AND PARTICIPANTS
PCa patients with a prostate-specific antigen (PSA) progression following multimodality treatment were included in this retrospective multi-institutional analysis.


INTERVENTION
The SOC cohort (n=1816) received immediate or delayed androgen deprivation therapy administered at PSA progression. The MDT cohort (n=263) received either salvage lymph node dissection (n=166) or stereotactic body radiotherapy (n=97) at PSA progression to a positron emission tomography-detected nodal recurrence.


OUTCOME MEASUREMENTS AND STATISTICAL ANALYSIS
The primary endpoint, cancer-specific survival (CSS), was analyzed using the Kaplan-Meier method, log-rank test, Cox proportional hazards models, and propensity score-matched analyses.


RESULTS AND LIMITATIONS
At a median follow-up of 70 (interquartile range: 48-98) mo, MDT was associated with an improved CSS on univariate (p=0.029) and multivariate analysis (hazard ratio: 0.33, 95% confidence interval [CI]: 0.17-0.64) adjusted for the year of radical prostatectomy (RP), age at RP, PSA at RP, time from RP to PSA progression, Gleason score, surgical margin status, pT- and pN-stage. In total, 659 men were matched (3:1 ratio). The 5-yr CSS was 98.6% (95% CI: 94.3-99.6) and 95.7% (95% CI: 93.2-97.3) for MDT and SOC, respectively (p=0.005, log-rank). The main limitations of our study are its retrospective design and lack of standardization of systemic treatment in the SOC cohort.


CONCLUSIONS
MDT for nodal oligorecurrent PCa improves CSS as compared with SOC. These retrospective data from a multi-institutional pooled analysis should be considered as hypothesis-generating and inform future randomized trials in this setting.


PATIENT SUMMARY
Prostate cancer patients experiencing a lymph node recurrence might benefit from local treatments directed at these lymph nodes.
Impact of cancer occurrence on health-related quality of life: A longitudinal pre-post assessment

BACKGROUND
Investigations focusing and implementing on the impact of cancer on health-related quality of life (HRQoL) by the way of a mean comparison between cancer patients and subjects from the general population, are scarce and usually cross-sectional. Longitudinal application of HRQoL instruments to a general, initially healthy population allows for change to be assessed as an event occurs, rather than afterwards. The objective of the present study was to investigate the impact of new cancer on HRQoL.


METHODS
The 36-item Short Form (SF-36) and 12-item General Health Questionnaire (GHQ-12) were applied to the French SU.VI.MAX cohort in 1996 and 1998. A controlled longitudinal study was used to determine the impact on HRQoL of newly diagnosed cancer: 84 patients with cancer that occurred between the 2 HRQoL measures were compared with 420 age- and sex-matched cancer-free controls.


RESULTS
Initial HRQoL level was similar in the two groups. A new cancer had a particularly marked effect on the SF-36 Physical functioning, Role-physical and General health dimensions (more than 6.6-point difference in change in HRQoL evolution on a 0-100 scale). The Bodily pain and Vitality dimensions were less severely affected (difference in change varying from 4.4 to 6.3 points), and there was no effect on either the GHQ-12 score or the SF-36 Mental health, Role-emotional and Social functioning dimensions.


CONCLUSIONS
The negative impact of cancer on the lives of patients was assessed in terms of HRQoL. The aspects most likely to be affected were those with a physical component, and general health perceptions. These results can thus help quantify the impact of a new cancer on HRQoL evolution and potentially facilitate early intervention by identifying the most affected HRQoL domains.
Compression of soft-body animation sequences

We describe a compression scheme for the geometry component of 3D animation sequences. This scheme is based on the principle component analysis (PCA) method, which represents the animation sequence using a small number of basis functions. Second-order linear prediction coding (LPC) is applied to the PCA coefficients in order to further reduce the code size by exploiting the temporal coherence present in the sequence. Our results show that applying LPC to the PCA scheme results in significant performance improvements relative to other coding methods. The use of these codes will make animated 3D data more accessible for graphics and visualization applications. r 2003 Elsevier Ltd. All rights reserved.
Four-Junction Wafer-Bonded Concentrator Solar Cells

The highest solar cell conversion efficiencies are achieved with four-junction devices under concentrated sunlight illumination. Different cell architectures are under development, all targeting an ideal bandgap combination close to 1.9, 1.4, 1.0, and 0.7 eV. Wafer bonding is used in this work to combine materials with a significant lattice mismatch. Three cell architectures are presented using the same two top junctions of GaInP/GaAs but different infrared absorbers based on Germanium, GaSb, or GaInAs on InP. The modeled efficiency potential at 500 suns is in the range of 49-54% for all three devices, but the highest efficiency is expected for the InP-based cell. An efficiency of 46% at 508 suns was already measured by AIST in Japan for a GaInP/GaAs//GaInAsP/GaInAs solar cell and represents the highest independently confirmed efficiency today. Solar cells on Ge and GaSb are in the development phase at Fraunhofer ISE, and the first demonstration of functional devices is presented in this paper.
Heart rate and oxygen demand of powered exoskeleton-assisted walking in persons with paraplegia.

UNLABELLED
Historically, persons with paralysis have limited options for overground ambulation. Recently, powered exoskeletons have become available, which are systems that translate the user's body movements to activate motors to move the lower limbs through a predetermined gait pattern. As part of an ongoing clinical study (NCT01454570), eight nonambulatory persons with paraplegia were trained to ambulate with a powered exoskeleton. Measurements of oxygen uptake (VO2) and heart rate (HR) were recorded for 6 min each during each maneuver while sitting, standing, and walking. The average value of VO2 during walking (11.2 +/- 1.7 mL/kg/min) was significantly higher than those for sitting and standing (3.5 +/- 0.4 and 4.3 +/- 0.9 mL/kg/min, respectively; p < 0.001). The HR response during walking was significantly greater than that of either sitting or standing (118 +/- 21vs 70 +/- 10 and 81 +/- 12 beats per minute, respectively: p < 0.001). Persons with paraplegia were able to ambulate efficiently using the powered exoskeleton for overground ambulation, providing potential for functional gain and improved fitness.


CLINICAL TRIAL REGISTRATION
ClinicalTrials.gov; NCT01454570; "The ReWalk Exoskeletal Walking System for Persons with Paraplegia (VA_ReWalk)"; https://clinicaltrials.gov/ct2/show/NCT01454570.
Influence of postharvest temperatures and the rate of fruit ripening on internal postharvest rots and disorders of New Zealand Hass' avocado fruit

Postharvest rots and internal disorders of'Hass' avocado (Perseaamericana) fruit develop during the latter stages of fruit ripening, with symptoms first appearing when fruit are minimally ripe but often becoming quite severe before the fruit are oversoft. Fruit ripened at 20°C and assessed at the same stage of ripeness, just before the flesh becomes oversoft, had fewer postharvest rots if they had been previously stored at 4 or 6°C, than if they had been stored at either lower or higher temperatures. Postharvest disorders increased with increased length of storage. Fruit failed to ripen properly at 30°C. Even at 25°C (a temperature typically experienced by fruit exported from New Zealand), the level of postharvest disorders was greater than in fruit ripened at 20°C. Best final quality was obtained with fruit coolstored at 6°C and then ripened at 15 °C. However, if fruit are to be ripened at c. 25 °C, then final quality was better if the fruit were not coolstored but held at a temperature closer to the final ripening temperature. Fruit from a single orchard block, harvested, coolstored, and ripened together, individually reached minimum eating ripeness over an 8-day period. Fruit which ripened earliest had the fewest disorders, with later ripening fruit typically having high levels of postharvest rots and internal browning.
Phase I trial of the positron-emitting Arg-Gly-Asp (RGD) peptide radioligand 18F-AH111585 in breast cancer patients.

UNLABELLED
The integrin alpha v beta3 receptor is upregulated on tumor cells and endothelium and plays important roles in angiogenesis and metastasis. Arg-Gly-Asp (RGD) peptide ligands have high affinity for these integrins and can be radiolabeled for PET imaging of angiogenesis or tumor development. We have assessed the safety, stability, and tumor distribution kinetics of a novel radiolabeled RGD-based integrin peptide-polymer conjugate, 18F-AH111585, and its feasibility to detect tumors in metastatic breast cancer patients using PET.


METHODS
The biodistribution of 18F-AH111585 was assessed in 18 tumor lesions from 7 patients with metastatic breast cancer by PET, and the PET data were compared with CT results. The metabolic stability of 18F-AH111585 was assessed by chromatography of plasma samples. Regions of interest (ROIs) defined over tumor and normal tissues of the PET images were used to determine the kinetics of radioligand binding in tissues.


RESULTS
The radiopharmaceutical and PET procedures were well tolerated in all patients. All 18 tumors detected by CT were visible on the 18F-AH111585 PET images, either as distinct increases in uptake compared with the surrounding normal tissue or, in the case of liver metastases, as regions of deficit uptake because of the high background activity in normal liver tissue. 18F-AH111585 was either homogeneously distributed in the tumors or appeared within the tumor rim, consistent with the pattern of viable peripheral tumor and central necrosis often seen in association with angiogenesis. Increased uptake compared with background (P = 0.002) was demonstrated in metastases in lung, pleura, bone, lymph node, and primary tumor.


CONCLUSION
18F-AH111585 designed to bind the alpha v beta3 integrin is safe, metabolically stable, and retained in tumor tissues and detects breast cancer lesions by PET in most anatomic sites.