LLukas22/scidocs huggingface dataset:
High-precision prostate cancer irradiation by clinical application of an offline patient setup verification procedure, using portal imaging.

PURPOSE
To investigate in three institutions, The Netherlands Cancer Institute (Antoni van Leeuwenhoek Huis [AvL]), Dr. Daniel den Hoed Cancer Center (DDHC), and Dr, Bernard Verbeeten Institute (BVI), how much the patient setup accuracy for irradiation of prostate cancer can be improved by an offline setup verification and correction procedure, using portal imaging.


METHODS AND MATERIALS
The verification procedure consisted of two stages. During the first stage, setup deviations were measured during a number (Nmax) of consecutive initial treatment sessions. The length of the average three dimensional (3D) setup deviation vector was compared with an action level for corrections, which shrunk with the number of setup measurements. After a correction was applied, Nmax measurements had to be performed again. Each institution chose different values for the initial action level (6, 9, and 10 mm) and Nmax (2 and 4). The choice of these parameters was based on a simulation of the procedure, using as input preestimated values of random and systematic deviations in each institution. During the second stage of the procedure, with weekly setup measurements, the AvL used a different criterion ("outlier detection") for corrective actions than the DDHC and the BVI ("sliding average"). After each correction the first stage of the procedure was restarted. The procedure was tested for 151 patients (62 in AvL, 47 in DDHC, and 42 in BVI) treated for prostate carcinoma. Treatment techniques and portal image acquisition and analysis were different in each institution.


RESULTS
The actual distributions of random and systematic deviations without corrections were estimated by eliminating the effect of the corrections. The percentage of mean (systematic) 3D deviations larger than 5 mm was 26% for the AvL and the DDHC, and 36% for the BVI. The setup accuracy after application of the procedure was considerably improved (percentage of mean 3D deviations larger than 5 mm was 1.6% in the AvL and 0% in the DDHC and BVI), in agreement with the results of the simulation. The number of corrections (about 0.7 on the average per patient) was not larger than predicted.


CONCLUSION
The verification procedure appeared to be feasible in the three institutions and enabled a significant reduction of mean 3D setup deviations. The computer simulation of the procedure proved to be a useful tool, because it enabled an accurate prediction of the setup accuracy and the required number of corrections.
Time-delay systems: an overview of some recent advances and open problems

After presenting some motivations for the study of time-delay system, this paper recalls modi.cations (models, stability, structure) arising from the presence of the delay phenomenon. A brief overview of some control approaches is then provided, the sliding mode and time-delay controls in particular. Lastly, some open problems are discussed: the constructive use of the delayed inputs, the digital implementation of distributed delays, the control via the delay, and the handling of information related to the delay value. ? 2003 Elsevier Ltd. All rights reserved.
An ARM based wireless sensors network for monitoring of plants health

In current era, with the latest technological developments, the Internet of Things (IoT) is becoming an important part of our daily life. The aim of this project is to use the IoT with an intelligent wireless sensors network in order to monitor the health of plants and to observe the population of larva in a remote crop field. In this framework, a wireless sensors network is proposed to detect larva and measure other system parameters like Acoustic Complexity Index (ACI), temperature, humidity and soil moisture. The sensors' data is collected by the front end sensing node, developed with a STM32F407VG board, via a serial port. The STM32F407VG board is based on the ARM processor. The data from the node is transmitted to a base station by using a wireless ZigBee interface. The base station collects data from a group of sensor nodes. This data is transmitted to the Central Processing Unit (CPU) via the USB liaison between the base station and the CPU. On CPU this data is analyzed via the MATLAB based specifically developed application. The findings are displayed and stored on the CPU and are also logged on the cloud via Thingspeak liaison. It allows accessing this data globally at any time. It is done to realize a timely interaction and cure of the intended crop field. The system parameters are adjusted in order to achieve the effective modules integration and performance. The proposed system operation is tested with an experimental setup. Results have confirmed a proper system functionality.
Palatability of hydrolysates and Other substitution formulas for cow's milk-allergic children: a comparative study of taste, smell, and texture evaluated by healthy volunteers.

BACKGROUND
Hydrolyzed formulas used to feed infants with cow's milk-allergy can be classified as soy based, extensively hydrolyzed (casein, whey and mixed), and amino-acid based. Their unsatisfactory taste is reported by parents and physicians.


OBJECTIVE
The aim of this study was to ascertain the palatability of these formulas in a double-blind taste test.


MATERIALS AND METHODS
Fifty healthy volunteers performed a randomized-order double-blind test with 12 different milks. The taste, smell, smell, and texture of each formula were evaluated o n scales ranging from 1 (worst) t o 5 (best). The Pearson correlation coefficient between the peptide weight of each formula and the score obtained for each evaluated attribute was calculated.


RESULTS
The soy formulas and rice formula had the best taste scores, followed by the whey hydrolysates; the mixed hydrolysates and the casein hydrolysates had the lowest taste scores. Individually the most palatable formula was mixed hydrolysate 1, by total score. We found a statistically significant correlation between peptide weight, reflecting the degree of hydrolysis of each formula, and the scores obtained for taste, texture, and overall palatability.


CONCLUSION
The palatability of formulas is determined by the amount of bitter peptides obtained through hydrolysis. Flavorings and sweeteners may also contribute to palatability. Further studies are needed in order to determine how to modify the organoleptic properties of these products with the purpose of improving their palatability.
Diagnostics in Semantic Segmentation

Abstract. Over the past years, computer vision community has contributed to enormous progress in semantic image segmentation, a perpixel classification task, crucial for dense scene understanding and rapidly becoming vital in lots of real-world applications, including driverless cars and medical imaging. Most recent models are now reaching previously unthinkable numbers (e.g., 89% mean iou on PASCAL VOC, 83% on CityScapes), and, while intersection-over-union and a range of other metrics provide the general picture of model performance, in this paper we aim to extend them into other meaningful and important for applications characteristics, answering such questions as ‘how accurate the model segmentation is on small objects in the general scene?’, or ‘what are the sources of uncertainty that cause the model to make an erroneous prediction?’. Besides establishing a methodology that covers the performance of a single model from different perspectives, we also showcase several extensions that can be worth pursuing in order to further improve current results in semantic segmentation.
AgdbNet – antigen sequence database software for bacterial typing

Bacterial typing schemes based on the sequences of genes encoding surface antigens require databases that provide a uniform, curated, and widely accepted nomenclature of the variants identified. Due to the differences in typing schemes, imposed by the diversity of genes targeted, creating these databases has typically required the writing of one-off code to link the database to a web interface. Here we describe agdbNet, widely applicable web database software that facilitates simultaneous BLAST querying of multiple loci using either nucleotide or peptide sequences. Databases are described by XML files that are parsed by a Perl CGI script. Each database can have any number of loci, which may be defined by nucleotide and/or peptide sequences. The software is currently in use on at least five public databases for the typing of Neisseria meningitidis, Campylobacter jejuni and Streptococcus equi and can be set up to query internal isolate tables or suitably-configured external isolate databases, such as those used for multilocus sequence typing. The style of the resulting website can be fully configured by modifying stylesheets and through the use of customised header and footer files that surround the output of the script. The software provides a rapid means of setting up customised Internet antigen sequence databases. The flexible configuration options enable typing schemes with differing requirements to be accommodated.
Mutual Fund Attributes and Investor Behavior

I study the dynamics of investor cash flows in socially responsible mutual funds. Consistent with anecdotal evidence of loyalty, the monthly volatility of investor cash flows is lower in socially responsible funds than conventional funds. I find strong evidence that cash flows into socially responsible funds are more sensitive to lagged positive returns than cash flows into conventional funds, and weaker evidence that cash outflows from socially responsible funds are less sensitive to lagged negative returns. These results indicate that investors derive utility from the socially responsible attribute, especially when returns are positive. Mutual fund companies continually introduce new types of funds in an effort to attract investor capital and maximize assets under management. The decision to introduce a new type of fund is affected by a number of variables, including investor demand for the fund’s attributes. As argued by Khorana and Servaes (1999), new fund types in high demand generate capital inflows and incremental revenue for the fund company. Subsequent investor behavior, however, may affect the operating costs and viability of the new funds. If a new fund type draws myopic investors, for example, then shareholder subscription and redemption activity may be more volatile and difficult to manage. In this paper, I study a specific fund type – socially responsible equity mutual funds – in order to explore investor decision making in new funds. According to the Social Investment Forum (2001, hereafter “SIF”), assets invested in all socially screened portfolios exceeded $2 trillion in 2001, with $136 billion invested in mutual funds, reflecting increased awareness of social responsibility and corporate ethics in the investment community. Socially responsible investing integrates personal values and societal concerns with the investment decision via shareholder activism, community investment, and, most visibly, investing with social screens. Social
Kinematics of Robot Fingers with Circular Rolling Contact Joints

This paper examines the kinematics of robot fingers that use RR subassemblies coupled by rolling contact to provide versatile one degree-of-freedom mechanical joints. A three degree-of-freedom robot finger constructed with these joints is a 6R planar chain with the R-joints coupled together in pairs. The focus is on coupling based on pure rolling of circular cylinders which can be realized by friction contact, gearing, or cable tendons. We derive the forward, inverse and rate kinematics for this 3(RR) open chain. We then focus on the two degree-of-freedom 2(RR) case to illustrate the geometry of the system. An example design of a robot finger that incorporates these joints in order to provide compact movement is provided. © 2003 Wiley Periodicals, Inc. • • • • • • • • • • • • • • • • • • • • • • • • • • • • • • •
The usefulness of bright light therapy for patients after oesophagectomy.

OBJECTIVES
The prevention of delirium is an important issue in the field of perioperative nursing. The objective of this study was to verify the usefulness of acute-stage bright light exposure on patients following oesophagectomy.


METHODS
The participants were oesophagectomy patients that were removed from their ventilators the day after surgery. After extubation, we assigned the participants to either the exposure group or control group. At Day 2 after surgery, the exposure group underwent two hours of bright light exposure for four days. In both groups, we monitored physical activity and autonomic activity. In addition, we scored the participants on the NEECHAM Scale and evaluated their postoperative delirium and postoperative arrhythmia.


RESULTS
On the nights of Days 4 and 5, the amount of activity of the exposure group was significantly lower and The sympathetic nervous index was significantly lower on the night of Day 5. The level of arrhythmia was lower in the exposure group and we observed a significant difference on the night of Day 4 and the daytime of Day 5 after surgery. The occurrence rate of postoperative delirium tended to be lower in the exposure group, but there was no significant difference. None of the participants in the exposure group had NEECHAM Scale scores below the cut-off value from the night of Day 4 onwards.


CONCLUSION
We conclude that postoperative bright light exposure adjusted the sleep-wakefulness cycle and improved the bed rest of patients. It was also indicated that bright light therapy is useful for reducing postoperative delirium.
A double-blind, placebo-controlled trial assessing the efficacy of varenicline tartrate for alcohol dependence.

OBJECTIVES
To assess the efficacy and safety of varenicline (Chantix) for the treatment of alcohol dependence. Varenicline is a partial α4β2 nicotinic acetylcholine agonist approved by the Food and Drug Administration for smoking cessation. It has reduced drinking in animal studies and in small studies of humans who were both heavy drinkers and smokers. This is the first multisite clinical trial of varenicline in a population of smokers and nonsmokers with alcohol dependence.


METHODS
Men and women (n = 200) meeting the criteria for alcohol dependence were recruited across 5 clinical sites. Patients received double-blind varenicline or placebo and a computerized behavioral intervention. Varenicline was titrated during the first week to 2 mg/d, which was maintained during weeks 2 to 13.


RESULTS
The varenicline group had significantly lower weekly percent heavy drinking days (primary outcome) (adjusted mean difference = 10.4), drinks per day, drinks per drinking day, and alcohol craving compared with the placebo group (P < 0.05). The average treatment effect on alcohol use was similar for smokers and nonsmokers. Varenicline was well-tolerated; adverse events were expected and mild.


CONCLUSIONS
Varenicline significantly reduced alcohol consumption and craving, making it a potentially viable option for the treatment of alcohol dependence.
Word Embeddings as Metric Recovery in Semantic Spaces

Continuous word representations have been remarkably useful across NLP tasks but remain poorly understood. We ground word embeddings in semantic spaces studied in the cognitive-psychometric literature, taking these spaces as the primary objects to recover. To this end, we relate log co-occurrences of words in large corpora to semantic similarity assessments and show that co-occurrences are indeed consistent with an Euclidean semantic space hypothesis. Framing word embedding as metric recovery of a semantic space unifies existing word embedding algorithms, ties them to manifold learning, and demonstrates that existing algorithms are consistent metric recovery methods given co-occurrence counts from random walks. Furthermore, we propose a simple, principled, direct metric recovery algorithm that performs on par with the state-of-the-art word embedding and manifold learning methods. Finally, we complement recent focus on analogies by constructing two new inductive reasoning datasets—series completion and classification—and demonstrate that word embeddings can be used to solve them as well.
Knowledge, attitude, and behavior among Saudis toward cancer preventive practice

OBJECTIVE
To examine self-reported knowledge, attitude, and preventive practices on cancer among Saudis.


MATERIALS AND METHODS
Data was collected from Saudis aged 15 years or more, who attended one of the randomly selected 20 Primary Health Centers (PHC) or the four major private hospitals located in the Riyadh region, either as patients or their escorts. The association between the variables was evaluated by the Chi square test.


RESULTS
The study population consisted of 618 males and 719 females. Among the female respondents 23.1% reported that they practiced breast self-examination (BSE); 14.2 and 8.1%, respectively, had clinical breast examination (CBE) and mammography. However, 10.0 and 16.1% of the females, aged 40 years and older, reported having had mammograms and CBE, respectively. The BSE performers were more educated, knew someone with cancer, and had heard of the cancer warning signal. Both educational level and 'heard of cancer warning signal' were significantly related to CBE. Cancer information was received from television / radio by 65.1% and from the physician by 29.4%. Even though 69.4% believed that cancer could be detected early, a vast majority (95.8%) felt early detection of cancer was extremely desirable and 55.1% said their participation was definite in any screening program. A majority of the respondents (92.6%) insisted on the need for physician recommendation to participate and 78.1% expected that any such program should be conducted in the existing hospitals / clinics.


CONCLUSION
Culturally sensitive health education messages should be tailored to fulfill the knowledge gap among all population strata. Saudis will benefit from partnerships between public health educators and media to speed up the dissemination of cancer information.
Smoking and severity of hepatic fibrosis in nonalcoholic fatty liver disease.

BACKGROUND & AIMS
Although many predictors of disease severity of nonalcoholic fatty liver disease (NAFLD) have been proposed, studies of the potential effects of specific environmental exposures on human NAFLD are lacking. Smoking increases insulin resistance. Given the pathophysiological role of insulin resistance in NAFLD, characterization of the influence of smoking in NAFLD is warranted. The aim of this paper was to study the potential association between cigarette smoking and advanced fibrosis in NAFLD.


METHODS
All adults enrolled in the NASH CRN studies, between October 2004 and February 2008, who had liver biopsies, were included (n=1091). Advanced fibrosis was defined as stages 3-4. Analyses were performed.


RESULTS
Significant bivariate associations were demonstrated between advanced fibrosis and age, gender, ethnicity, diabetes, and smoking history. History of smoking ≥ 10 pack-years was more common (p <0.0001) among patients with advanced fibrosis. Multivariate analysis demonstrated an association between smoking history of ≥ 10 pack-years and advanced fibrosis (OR=1.63). Among non-diabetics, history of ≥ 10 pack-years was associated with an OR of 2.48 for advanced fibrosis. High frequencies of advanced fibrosis were observed among diabetics (with or without ≥ 10 pack-years history) and non-diabetics with ≥ 10 pack-years history as compared to non-diabetics without significant smoking history.


CONCLUSIONS
Smoking history was associated with advanced liver fibrosis in this large multicenter cohort of NAFLD patients. The results indicate that smoking may enhance the progression of NAFLD partly through its effect on insulin resistance. Our results are consistent with recent animal studies suggesting that cigarette smoke may aggravate fatty liver. To our knowledge, this is the first study to show that cigarette smoking is associated with increased fibrosis severity in human NALFD, suggesting it may accelerate disease progression. These results may support a formal recommendation of smoking cessation in patients with NAFLD.
A Diel Flux Balance Model Captures Interactions between Light and Dark Metabolism during Day-Night Cycles in C3 and Crassulacean Acid Metabolism Leaves.

Although leaves have to accommodate markedly different metabolic flux patterns in the light and the dark, models of leaf metabolism based on flux-balance analysis (FBA) have so far been confined to consideration of the network under continuous light. An FBA framework is presented that solves the two phases of the diel cycle as a single optimization problem and, thus, provides a more representative model of leaf metabolism. The requirement to support continued export of sugar and amino acids from the leaf during the night and to meet overnight cellular maintenance costs forces the model to set aside stores of both carbon and nitrogen during the day. With only minimal constraints, the model successfully captures many of the known features of C3 leaf metabolism, including the recently discovered role of citrate synthesis and accumulation in the night as a precursor for the provision of carbon skeletons for amino acid synthesis during the day. The diel FBA model can be applied to other temporal separations, such as that which occurs in Crassulacean acid metabolism (CAM) photosynthesis, allowing a system-level analysis of the energetics of CAM. The diel model predicts that there is no overall energetic advantage to CAM, despite the potential for suppression of photorespiration through CO2 concentration. Moreover, any savings in enzyme machinery costs through suppression of photorespiration are likely to be offset by the higher flux demand of the CAM cycle. It is concluded that energetic or nitrogen use considerations are unlikely to be evolutionary drivers for CAM photosynthesis.
A method for estimating rain rate and drop size distribution from polarimetric radar measurements

Polarimetric radar measurements are sensitive to the size, shape and orientation of raindrops and provide information about drop size distribution (DSD), canting angle distribution and rain rate. In this paper, we propose and demonstrate a method for retrieving DSD parameters for calculating rain rate and the characteristic particle size. The DSD is assumed to be a Gamma distribution and the governing parameters are retrieved from radar measurements: reflectivity ( ), differential reflectivity ( ), and a constrained relation between the shape () and slope ( ) parameters derived from video disdrometer observations. The estimated rain rate is compared with that obtained from more traditional methods and the calculated characteristic size is compared with the measured values. The calculated based on the retrieved Gamma DSD is also compared with measurements. The proposed method shows improvement over the existing models and techniques because it can retrieve all three parameters of the Gamma distribution. For maintaining the continuity of earlier published results, raindrop shape is assumed to be equilibrium.
Running on an unpredictable irregular surface changes lower limb biomechanics and subjective perception compared to running on a regular surface

Background Irregular surface conditions, for instance, are present during trail running. Modified treadmills can be used to produce such surface conditions in a laboratory environment [1]. Gait variability on uneven shoe-surface interfaces is increased in walking [2,3], hence the same may apply to running. This study examined the effects of an unpredictable irregular surface (UIS) on lower limb biomechanics, locomotion variability, and subjective perception during treadmill running.