LLukas22/scidocs huggingface dataset:
Water Budgets to Inform Sustainable Water Management

Abstract Any plan for increasing the provision of water for the environment can be greatly aided by the preparation of a water budget that clarifies how much water is available, how much is being consumed and for what purposes, how water demands may change over time and how much water remains within the ecosystem of interest. This chapter highlights important considerations and challenges in constructing a water budget, and illustrates how a water budget can inform strategies for returning water to the environment. However, any strategies for restoring environmental water should carefully consider the changing economic, social, and cultural context in which restoration strategies will be pursued.
Deep Reinforcement Learning for Dynamic Multichannel Access

We consider the problem of dynamic multichannel access in a Wireless Sensor Network (WSN) containing N correlated channels, where the states of these channels follow a joint Markov model. A user at each time slot selects a channel to transmit a packet and receives a reward based on the success or failure of the transmission, which is dictated by the state of the selected channel. The objective is to find a policy that maximizes the expected long-term reward. The problem can be formulated as a partially observable Markov decision process (POMDP), which is PSPACE-hard and intractable. As a solution, we apply the concept of online learning and implement a Deep Q-Network (DQN) that can deal with large state space without any prior knowledge of the system dynamics. We compare the performance of DQN with a myopic policy and a Whittle Index-based heuristic through simulations and show that DQN can achieve nearoptimal performance. We also evaluate the performance of DQN on traces obtained from a real indoor WSN deployment. We show that DQN has the capability to learn a good policy in complex real scenarios, which do not necessarily show Markovian dynamics.
Screening Microalgae Strains for Biodiesel Production: Lipid Productivity and Estimation of Fuel Quality Based on Fatty Acids Profiles as Selective Criteria

The viability of algae-based biodiesel industry depends on the selection of adequate strains in regard to profitable yields and oil quality. This work aimed to bioprospecting and screening 12 microalgae strains by applying, as selective criteria, the volumetric lipid productivity and the fatty acid profiles, used for estimating the biodiesel fuel properties. Volumetric lipid productivity varied among strains from 22.61 to 204.91 mg l−1 day−1. The highest lipid yields were observed for Chlorella (204.91 mg l−1 day1) and Botryococcus strains (112.43 and 98.00 mg l−1 day−1 for Botryococcus braunii and Botryococcus terribilis, respectively). Cluster and principal components analysis analysis applied to fatty acid methyl esters (FAME) profiles discriminated three different microalgae groups according to their potential for biodiesel production. Kirchneriella lunaris, Ankistrodesmus fusiformis, Chlamydocapsa bacillus, and Ankistrodesmus falcatus showed the highest levels of polyunsaturated FAME, which incurs in the production of biodiesels with the lowest (42.47–50.52) cetane number (CN), the highest (101.33–136.97) iodine values (IV), and the lowest oxidation stability. The higher levels of saturated FAME in the oils of Chlamydomonas sp. and Scenedesmus obliquus indicated them as source of biodiesel with higher oxidation stability, higher CN (63.63–64.94), and lower IV (27.34–35.28). The third group, except for the Trebouxyophyceae strains that appeared in isolation, are composed by microalgae that generate biodiesel of intermediate values for CN, IV, and oxidation stability, related to their levels of saturated and monosaturated lipids. Thus, in this research, FAME profiling suggested that the best approach for generating a microalgae-biodiesel of top quality is by mixing the oils of distinct cell cultures.
Transcatheter tricuspid valve-in-valve in patients with transvalvular device leads.

OBJECTIVE
To describe the effects of percutaneously implanted valve-in-valve in the tricuspid position for patients with pre-existing transvalvular device leads.


METHODS
In this case series, we describe implantation of the Melody valve and SAPIEN XT valve within dysfunctional bioprosthetic tricuspid valves in three patients with transvalvular device leads.


RESULTS
In all cases, the valve was successfully deployed and device lead function remained unchanged. In 1/3 cases with 6-month follow-up, device lead parameters remain unchanged and transcatheter valve-in-valve function remains satisfactory.


CONCLUSIONS
Transcatheter tricuspid valve-in-valve is feasible in patients with pre-existing transvalvular devices leads. Further study is required to determine the long-term clinical implications of this treatment approach.
Correlation between intracoronary ultrasound and fractional flow reserve in long coronary lesions. A three-dimensional intracoronary ultrasound study.

INTRODUCTION AND OBJECTIVES
Intracoronary ultrasound estimation of the functional significance of intermediate angiographic lesions has mainly been based on measuring the minimal lumen area. These estimates take no account of lesion length and pay insufficient attention to long coronary lesions.


METHODS
We included 61 lesions with visual angiographic stenosis of 40% to 70% that required treatment with a ≥20mm stent, studied with ultrasound and fractional flow reserve. Three-dimensional analysis of the ultrasound study was conducted offline and blinded to fractional reserve values. Angiographic and ultrasound parameters were correlated with fractional reserve.


RESULTS
From the angiography we obtained data on mean reference diameter (2.87 [0.57] mm), length (29.8 [10.01] mm), and severity of stenosis (50.3% [8.7]%). Mean fractional flow reserve was 0.78 (0.09). We found a weak linear correlation (R) between fractional reserve and the ultrasound parameters that did not include lesion length: fractional reserve-minimal luminal area (R=0.4; P=.003). The correlation was stronger when lesion length was included: fractional reserve-volume of plaque (R=-0.65; P<.0005); fractional reserve-length/mean luminal area (R=0.73; P<.0005). The strongest correlation came from the product of mean stenosis by area multiplied by lesion length (R=-0.78; P<.0005).


CONCLUSIONS
In long coronary lesions, the correlation between ultrasound-measured minimal lumen area and functional significance is weak. In these cases, estimates of functional significance should incorporate lesion length or be derived from direct fractional flow reserve measurement.
Enabling the Internet of Things

Merging the virtual World Wide Web with nearby physical devices that are part of the Internet of Things gives anyone with a mobile device and the appropriate authorization the power to monitor or control anything.
Multicenter evaluation of an investigational prostate cancer methylation assay.

PURPOSE
Prostate specific antigen tests have low specificity, which frequently results in unnecessary biopsy and typically limits screening to patients with prostate specific antigen greater than 4.0 ng/ml. We evaluated an investigational prostate cancer methylation specific polymerase chain reaction assay that detects aberrant methylation in 3 markers (GSTP1, RARbeta2 and APC) that indicate the presence of prostate cancer.


MATERIALS AND METHODS
The assay was evaluated in 337 post-digital rectal examination urine samples (178 cancer and 159 noncancer) collected prospectively at a total of 9 clinical sites. Samples were processed wholly or after division into equal portions. Subject prostate specific antigen was 2.0 to 10.0 ng/ml. All subjects underwent transrectal ultrasound guided needle biopsy with 6 or greater cores sampled. Detection of 1 or greater markers indicated positivity.


RESULTS
Methylation specific polymerase chain reaction assay performance was better in whole than in divided urine cohorts (p = 0.035). Assay AUC was 0.72 in the whole urine cohort and 0.67 in the combined population. These values were higher than those of prostate specific antigen alone using 4.0 ng/ml as the cutoff (p = 0.00 and 0.01, respectively). Moreover, the assay together with the Prostate Cancer Prevention Trial risk calculator or a standard nomogram significantly improved AUC in the whole urine cohort and the combined population vs predictive algorithms alone (p <0.05). Assay positive predictive value was 54% in whole urine cohort with prostate specific antigen 2.0 to 4.0 ng/ml and negative predictive value was 87% with prostate specific antigen 4.1 to 10.0 ng/ml. Assay positive predictive value was higher in subjects with all 3 methylation markers positive.


CONCLUSIONS
These data demonstrate that this investigational assay used in conjunction with current screening algorithms may potentially add value to the biopsy decision making process.
The new aestheticism

List of Contributors The new aestheticism: An introduction - John J. Joughin and Simon Malpas PART ONE: Positions 1. Aesthetic education and the demise of experience - Thomas Docherty 2. Towards a contemporary aesthetic - Jonathan Dollimore 3. Mimesis in black and white: Feminist aesthetics, negativity and semblance - Ewa Plonowska Ziarek 4. What comes after art - Andrew Bowie 5. Touching art: Aesthetics, fragmentation and community - Simon Malpas PART TWO: READINGS 6. The Alexandrian aesthetic - Howard Caygill 7. Defending poetry, or is there an early modern aesthetic? - Mark Robson 8. Shakespeare's genius: 'Hamlet', adaptation and the work of following - John J. Joughin 9. Critical knowledge, scientific knowledge and the truth of literature - Robert Eaglestone 10. Melancholy as form: Towards an archaeology of modernism - Jay Bernstein 11. Kant and the ends of criticism - Gary Banham 12. Including transformation: Notes on the art of the contemporary - Andrew Benjamin 13. Aesthetics and politics: Between Adorno and Heidegger - Joanna Hodge
Enriching the sequence substitution matrix by structural information.

A fundamental step in homology modeling is the comparison of two protein sequences: a probe sequence with an unknown structure and function and a template sequence for which the structure and function are known. The detection of protein similarities relies on a substitution matrix that scores the proximity of the aligned amino acids. Sequence-to-sequence alignments use symmetric substitution matrices, whereas the threading protocols use asymmetric matrices, testing the fitness of the probe sequence into the structure of the template protein. We propose a linear combination of threading and sequence-alignment scoring function, to produce a single (mixed) scoring table. By fitting a single parameter (which is the relative contribution of the BLOSUM 50 matrix and the threading energy table of THOM2) we obtain a significant increase in prediction capacity in the twilight zone of homology modeling (detecting sequences with <25% sequence identity and with very similar structures). For a difficult test of 176 homologous pairs, with no signal of sequence similarity, the mixed model makes it possible to detect between 40 and 100% more protein pairs than the number of pairs that are detected by pure threading. Surprisingly, the linear combination of the two models is performing better than threading and than sequence alignment when the percentage of sequence identity is low. We finally suggest that further enrichment of substitution matrices, combing more structural descriptors such as exposed surface area, or secondary structure is expected to enhance the signal as well.
The sva package for removing batch effects and other unwanted variation in high-throughput experiments

Heterogeneity and latent variables are now widely recognized as major sources of bias and variability in high-throughput experiments. The most well-known source of latent variation in genomic experiments are batch effects-when samples are processed on different days, in different groups or by different people. However, there are also a large number of other variables that may have a major impact on high-throughput measurements. Here we describe the sva package for identifying, estimating and removing unwanted sources of variation in high-throughput experiments. The sva package supports surrogate variable estimation with the sva function, direct adjustment for known batch effects with the ComBat function and adjustment for batch and latent variables in prediction problems with the fsva function.
Smartphone use in neurosurgery? APP-solutely!

BACKGROUND
A number of smartphone medical apps have recently emerged that may be helpful for the neurosurgical patient, practitioner, and trainee. This study aims to review the current neurosurgery-focused apps available for the iPhone, iPad, and Android platforms as of December 2013.


METHODS
Two of the most popular smartphone app stores (Apple Store and Android Google Play Store) were surveyed for neurosurgery-focused apps in December 2013. Search results were categorized based on their description page. Data were collected on price, rating, app release date, target audience, and medical professional involvement in app design. A review of the top apps in each category was performed.


RESULTS
The search resulted in 111 unique apps, divided into these 7 categories: 16 (14%) clinical tools, 17 (15%) conference adjunct, 27 (24%) education, 18 (16%) literature, 15 (14%) marketing, 10 (9%) patient information, and 8 (7%) reference. The average cost of paid apps was $23.06 (range: $0.99-89.99). Out of the 111 apps, 71 (64%) were free, 48 (43%) had reviews, and 14 (13%) had more than 10 reviews. Seventy-three (66%) apps showed evidence of medical professional involvement. The number of apps being released every year has been increasing since 2009.


CONCLUSIONS
There are a number of neurosurgery-themed apps available to all audiences. There was a lack of patient information apps for nonspinal procedures. Most apps did not have enough reviews to evaluate their quality. There was also a lack of oversight to validate the accuracy of medical information provided in these apps.
Vitamin D deficiency is independently associated with the extent of coronary artery disease.

BACKGROUND
Vitamin D (25-OH D3) deficiency represents a rising social and economic problem in Western countries. Vitamin D has been recently reported to modulate inflammatory processes, endothelium and smooth muscle cell proliferation and even platelet function, thus potentially modulating atherothrombosis. Great interest has been addressed on its impact on cardiovascular outcome, with contrasting results. The aim of current study was to evaluate the relationship between 25-OH D3 and the extent of coronary artery disease (CAD) in a consecutive cohort of patients undergoing coronary angiography.


MATERIALS AND METHODS
Patients undergoing elective coronary angiography were included in a cross-sectional study. Fasting samples were collected for 25-OH D3 levels assessment. Significant CAD was defined as at least 1 vessel stenosis > 50%, while severe CAD as left main and/or trivessel disease, as evaluated by quantitative coronary angiography.


RESULTS
Hypovitaminosis D was observed in 70·4% of 1484 patients. Patients were divided according to vitamin D tertiles (< 9·6; 9·6-18·4; ≥ 18·4). Lower vitamin D levels were associated with age, female gender (P < 0·001), renal failure (P = 0·05), active smoking (P = 0·001), acute coronary syndrome at presentation (P < 0·001), therapy with calcium antagonists (P = 0·02) and diuretics (P < 0·001), less beta-blockers (P = 0·02) and statins (P = 0·001) use. Vitamin D was directly related to haemoglobin (P < 0·001) and inversely with platelet count (P = 0·002), total and low-density-lipoprotein cholesterol (P = 0·002 and P < 0·001) and triglycerides (P = 0·01). Vitamin D did not influence angiographic features of coronary lesions, but was associated with higher prevalence of left main or right CAD (P = 0·03). Vitamin D deficiency was significantly associated with higher prevalence of CAD (adjusted OR [95%CI] = 1·32[1·1-1·6], P = 0·004) and severe CAD (adjusted OR [95%CI] = 1·18[1-1·39], P = 0·05).


CONCLUSION
Hypovitaminosis D was observed in the vast majority of patients undergoing coronary angiography. Vitamin D deficiency is significantly associated with the prevalence and extent of CAD, especially for patients with values < 10 ng/mL. Therefore, future large studies are needed to evaluate whether vitamin D supplementation may prevent CAD and its progression.
Representing General Relational Knowledge in ConceptNet 5

ConceptNet is a knowledge representation project, providing a large semantic graph that describes general human knowledge and how it is expressed in natural language. This paper presents the latest iteration, ConceptNet 5, including its fundamental design decisions, ways to use it, and evaluations of its coverage and accuracy.
Stabilization and Regulation of Nonlinear Systems [Bookshelf]

This book is organized into ten chapters, and many of the chapters, especially those in the second half of the book, present the results of the authors’ work that has been published in scientific journals. Chapter 1 is an introduction to the book, and Chapter 10 presents a specific application of the methods introduced in the book for attitude control of a rigid spacecraft. The rest of book can be roughly divided into two parts; Chapters 2–6 are on stabilization of nonlinear systems, and Chapters 7–9 are on output regulation of nonlinear systems. Stabilization and regulation are important topics in control systems design. The stabilization of nonlinear systems deals with feedback control design to ensure the stability of closed-loop dynamic systems, and there have been significant developments in control design methods in the past two decades. Overall, the book is well organized, and it systematically presents several key results on output regulation and disturbance rejection published in literature in the past 15 years. Those who have a research interest in the area of output regulation and disturbance rejection of nonlinear systems should certainly read this book. The text contains problems at the end of each chapter that will help the readers understand the technical contents. The book is aimed at the advanced textbook level, but it would likely be a challenge to use it as a textbook for an M.Sc. unit in most U.K. universities.
The effect of intraoperative dexmedetomidine on postoperative catheter-related bladder discomfort in patients undergoing transurethral bladder tumour resection: A double-blind randomised study.

BACKGROUND
Catheter-related bladder discomfort (CRBD) due to an indwelling urinary catheter causes postoperative distress. Dexmedetomidine is used as an anaesthetic adjuvant during general anaesthesia and has an antimuscarinic effect, which may be beneficial for the prevention and treatment of CRBD.


OBJECTIVE
To determine the effect of intraoperative dexmedetomidine administration on the incidence of CRBD.


DESIGN
A double-blind, placebo-controlled, randomised study.


SETTING
A tertiary care teaching hospital.


PATIENTS
One-hundred and nine patients undergoing transurethral bladder tumour excision (TURB).


INTERVENTIONS
Patients were randomly allocated to two groups: control group (n = 55) received placebo and dexmedetomidine group (n = 54) received intraoperative dexmedetomidine (1 μg kg(-1) loading dose followed by 0.5 μg kg(-1) h(-1) continuous infusion).


MAIN OUTCOME MEASURES
The incidence and severity (mild, moderate, severe) of CRBD assessed at 0, 1, 6 and 24 h postoperatively.


RESULTS
The incidence of CRBD was significantly higher in the control group at 0 (78 vs. 50%; P = 0.004), 1 (86 vs. 57%; P = 0.002) and 6 h (82 vs. 63%; P = 0.047) postoperatively. The incidence of moderate to severe CRBD was higher in the control group at 0 (38 vs. 11%; P = 0.002) and 1 h (29 vs. 7%; P = 0.006) postoperatively. The number of patients having CRBD treated with tramadol was higher in the control group (24 vs. 12; P = 0.006). The mean end-tidal desflurane concentration during the surgery was higher in the control group (4.5 vs. 3.9%; P = 0.04). The postoperative pain score (numerical rating scale: 0 to 10) was higher in the control group at 0 (4.6 vs. 2.7; P = 0.002), and 1 h (3.8 vs. 2.7; P = 0.041). The number of patients treated with opioids was higher in the control group (21 vs. 8; P = 0.011).


CONCLUSION
Intraoperative dexmedetomidine administration decreased the incidence and severity of early postoperative CRBD as well as intraoperative desflurane and postoperative opioid requirements in patients undergoing TURB.


TRIAL REGISTRATION IDENTIFIER
NCT01991223 (www.clinicaltrials.gov).
Topics in Quantum Geometry of Riemann Surfaces: Two-Dimensional Quantum Gravity

Lectures given at International School of Physics ``Enrico Fermi'', Varenna, Villa Monastero, June 28-July 7 1994
Solitary painful osseous metastases: correlation of imaging features with pain palliation after radiofrequency ablation--a multicenter american college of radiology imaging network study.

PURPOSE
To identify the correlation of pre- and postablation imaging features with pain relief, pain intensity, and patient mood after radiofrequency (RF) ablation of solitary painful osseous metastases.


MATERIALS AND METHODS
This prospective, multicenter group trial was approved by each institutional review board. Participants were enrolled between November 1, 2001, and April 6, 2006. Written informed consent was obtained from all subjects, and patient confidentiality protocols were followed in compliance with HIPAA. Computed tomography (CT)-guided RF ablation and contrast material-enhanced 1-month follow-up CT and/or magnetic resonance imaging were performed in 49 subjects (24 men, 25 women; age range, 34-83 years) with a confirmed malignant solitary bone lesion of maximum dimension of 8 cm or smaller that was causing intractable pain. Pain intensity and patient mood were measured before and after RF ablation. Tumor imaging features were recorded. Unadjusted and adjusted linear mixed-effects models, with a random intercept for each subject, were used to model patient mood, pain relief, and pain intensity scores at three times after ablation as a function of each tumor characteristic.


RESULTS
Decreased postablation tumor pain correlated with preablation tumor volume (P = .02) and pathologic fracture (P = .01), while pain relief correlated with pathologic fracture (P = .03) and percentage of bone-tumor interface (BTI) ablated (P = .02). Conversely, presence of an irregular rim after ablation (P = .02) and rim thickness (P = .01) correlated with increased pain. There was no evidence in this study that RF ablation of larger tumor percentage or larger volume leads to better pain relief or decreased pain (P > .05).


CONCLUSION
Existing pathologic fracture and smaller tumor size appear to be predictive parameters of success when selecting patients for palliative RF ablation of painful solitary osseous metastases. Successful palliation also appears to be related to the percentage of BTI ablated.