LLukas22/scidocs huggingface dataset:
Comparison of Support Vector Machine and Artificial Neural Network Systems for Drug/Nondrug Classification

Support vector machine (SVM) and artificial neural network (ANN) systems were applied to a drug/nondrug classification problem as an example of binary decision problems in early-phase virtual compound filtering and screening. The results indicate that solutions obtained by SVM training seem to be more robust with a smaller standard error compared to ANN training. Generally, the SVM classifier yielded slightly higher prediction accuracy than ANN, irrespective of the type of descriptors used for molecule encoding, the size of the training data sets, and the algorithm employed for neural network training. The performance was compared using various different descriptor sets and descriptor combinations based on the 120 standard Ghose-Crippen fragment descriptors, a wide range of 180 different properties and physicochemical descriptors from the Molecular Operating Environment (MOE) package, and 225 topological pharmacophore (CATS) descriptors. For the complete set of 525 descriptors cross-validated classification by SVM yielded 82% correct predictions (Matthews cc = 0.63), whereas ANN reached 80% correct predictions (Matthews cc = 0.58). Although SVM outperformed the ANN classifiers with regard to overall prediction accuracy, both methods were shown to complement each other, as the sets of true positives, false positives (overprediction), true negatives, and false negatives (underprediction) produced by the two classifiers were not identical. The theory of SVM and ANN training is briefly reviewed.
The whole versus the sum of some of the parts: toward resolving the apparent controversy of clitoral versus vaginal orgasms

BACKGROUND
The nature of a woman's orgasm has been a source of scientific, political, and cultural debate for over a century. Since the Victorian era, the pendulum has swung from the vagina to the clitoris, and to some extent back again, with the current debate stuck over whether internal sensory structures exist in the vagina that could account for orgasms based largely on their stimulation, or whether stimulation of the external glans clitoris is always necessary for orgasm.


METHOD
We review the history of the clitoral versus vaginal orgasm debate as it has evolved with conflicting ideas and data from psychiatry and psychoanalysis, epidemiology, evolutionary theory, feminist political theory, physiology, and finally neuroscience.


RESULTS
A new synthesis is presented that acknowledges the enormous potential women have to experience orgasms from one or more sources of sensory input, including the external clitoral glans, internal region around the "G-spot" that corresponds to the internal clitoral bulbs, the cervix, as well as sensory stimulation of non-genital areas such as the nipples.


CONCLUSIONS
With experience, stimulation of one or all of these triggering zones are integrated into a "whole" set of sensory inputs, movements, body positions, autonomic arousal, and partner- and contextual-related cues, that reliably induces pleasure and orgasm during masturbation and copulation. The process of integration is iterative and can change across the lifespan with new experiences of orgasm.
Late Jurassic age for the Morokweng impact structure, southern Africa

Abstract A roughly 70 km diameter circular feature buried beneath the Kalahari sands in South Africa is revealed on regional aeromagnetic maps. Boreholes drilled into the centre of the structure intercept a ∼ 250 m thick sheet of quartz norite, interpreted as an impact melt, which overlies brecciated and shock metamorphosed basement granite. Zircons recovered from the quartz norite, yield U-Pb ages of 145 ± 0.8 Ma, and biotites provide Ar-Ar ages of 144 ± 4 Ma. These data provide strong evidence for the occurrence of a Late Jurassic impact crater (the Morokweng impact structure) ∼ 100 m beneath the surface.
CaaS: Caching as a Service for 5G Networks

In recent years, demands for rich multimedia services over mobile networks have been soaring at a tremendous pace. Traditional dedicated networking equipment may not be able to efficiently support the phenomenal growth of the traffic load and user demand dynamics while consuming an unnecessarily large amount of energy resources. Recently, mobile content caching, whereby popular contents are cached inside the mobile front-haul and back-haul networks so that demands for these contents from users in proximity can be easily accommodated without redundant transmissions from the remote sources, has emerged as an efficient technique for multimedia content delivery. Mobile content caching is particularly suitable for fifth generation (5G) mobile systems that are being designed to incorporate advanced cloud computing technologies and network function virtualization techniques. Therefore, in this paper, we first propose the concept of “Caching-as-a-Service” (CaaS) based on cloud-based radio access networks, and virtualized evolved packet core, which provides the capability to cache anything at anytime, anywhere in the cloud-based 5G mobile systems to satisfy user demands from any service location with high elasticity and adaptivity, and to empower third-party service providers with flexible controllability and programmability. Then, we study the potential techniques related to the virtualization of caching, and discuss the technical details of virtualization and optimization of CaaS in 5G mobile networks. Some novel schemes for CaaS are proposed to target different mobile applications and services. We also explore new opportunities and challenges for further research.
Business Improvement Districts: Should Lexington Establish One?

EXECUTIVE SUMMARY Downtown districts are falling victim to surges of new development increasingly taking place outside the city as people seek to escape fast‐paced city life for a more peaceful life in the suburbs. As people move to the suburbs, they either take the businesses with them or the businesses fail to maintain profitability in empty downtowns. Downtown Lexington has been no exception. The recent developments of Hamburg Place and, more recent the developments around Fayette Mall have attracted even more business owners away from downtown. A new implementation approach for revitalization is gaining momentum, as downtowns are introducing policies that enable Business Improvement Districts (BID). In this approach to revitalization, property owners in a district file a petition to impose an additional assessment on themselves. This assessment is used to provide services supplemental to services being provided by the city government. Most BIDs seek to promote the economic development of downtowns, while providing services such as maintenance, street cleaning, security, marketing, and special events. This report seeks to determine if the establishment of a BID has an effect on businesses in downtown districts, while also examining the issue of whether or not Lexington should establish a BID. To determine this, I have analyzed data from the Economic Census Zip Code Business Patterns. I conducted both a two‐sample t‐test with equal variances and a difference in difference regression to estimate if there was a statistically significant difference in the means of BID and Non‐BID cities pre and post‐ BID establishment for the average annual growth rates for number of establishments, number of employees, and average payroll. The studies both failed to estimate that there is a statistically significant difference in the means of BID and Non‐BID cities pre and post‐BID establishment for the average annual growth rates of number of establishments, number of employees, and average payroll. However, there was a low variance in the difference of the BID cities and the Non‐BID comparison cities, meaning that the cities were well matched. Based on my analysis, I would recommend further study of BIDs before establishing a BID in Lexington, perhaps using these same cities, but examining the sales tax receipts or the type of business establishments might provide a better analysis of the impact that BIDs have on businesses.
Who will buy smart glasses? Empirical results of two pre-market-entry studies on the role of personality in individual awareness and intended adoption of Google Glass wearables

Recent market studies reveal that augmented reality (AR) devices, such as smart glasses, will substantially influence the media landscape. Yet, little is known about the intended adoption of smart glasses, particularly: Who are the early adopters of such wearables? We contribute to the growing body of research that investigates the role of personality in predicting media usage by analyzing smart glasses, such as Google Glass or Microsoft Hololens. First, we integrate AR devices into the current evolution of media and technologies. Then, we draw on the Big Five Model of human personality and present the results from two studies that investigate the direct and moderating effects of human personality on the awareness and innovation adoption of smart glasses. Our results show that open and emotionally stable consumers tend to be more aware of Google Glass. Consumers who perceive the potential for high functional benefits and social conformity of smart glasses are more likely to adopt such wearables. The strength of these effects is moderated by consumers’ individual personality, particularly by their levels of openness to experience, extraversion and neuroticism. This article concludes with a discussion of theoretical and managerial implications for research on technology adoption, and with suggestions for avenues for future research. 2015 Elsevier Ltd. All rights reserved.
Risk Factors for Long-Term Mortality after Hospitalization for Community-Acquired Pneumonia: A 5-Year Prospective Follow-Up Study

BACKGROUND
Contributors to long-term mortality in patients with community-acquired pneumonia (CAP) remain unclear, with little attention paid to pneumonia etiology. We examined long-term survival, causes of death, and risk factors for long-term mortality in adult patients who had been hospitalized for CAP, with emphasis on demographic, clinical, laboratory, and microbiological characteristics.


METHODS
Two hundred and sixty-seven consecutive patients admitted in 2008-2011 to a general hospital with CAP were prospectively recruited and followed up. Patients who died during hospital stay were excluded. Demographic, clinical, and laboratory data were collected within 48 hours of admission. Extensive microbiological work-up was performed to establish the etiology of CAP in 63% of patients. Mortality data were obtained from the Norwegian Cause of Death Registry. Cox regression models were used to identify independent risk factors for all-cause mortality.


RESULTS
Of 259 hospital survivors of CAP (median age 66 years), 79 (30.5%) died over a median of 1,804 days (range 1-2,520 days). Cumulative 5-year survival rate was 72.9% (95% CI 67.4-78.4%). Standardized mortality ratio was 2.90 for men and 2.05 for women. The main causes of death were chronic obstructive pulmonary disease (COPD), vascular diseases, and malignancy. Independent risk factors for death were the following (hazard ratio, 95% CI): age (1.83 per decade, 1.47-2.28), cardiovascular disease (2.63, 1.61-4.32), COPD (2.09, 1.27-3.45), immunocompromization (1.98, 1.17-3.37), and low serum albumin level at admission (0.75 per 5 g/L higher, 0.58-0.96), whereas active smoking was protective (0.32, 0.14-0.74); active smokers were younger than non-smokers (P < 0.001). Microbial etiology did not predict mortality.


CONCLUSIONS
Results largely confirm substantial comorbidity-related 5-year mortality after hospitalization for CAP and the impact of several well-known risk factors for death, and extend previous findings on the prognostic value of serum albumin level at hospital admission. Pneumonia etiology had no prognostic value, but this remains to be substantiated by further studies using extensive diagnostic microbiological methods in the identification of causative agents of CAP.
pplacer: linear time maximum-likelihood and Bayesian phylogenetic placement of sequences onto a fixed reference tree

Likelihood-based phylogenetic inference is generally considered to be the most reliable classification method for unknown sequences. However, traditional likelihood-based phylogenetic methods cannot be applied to large volumes of short reads from next-generation sequencing due to computational complexity issues and lack of phylogenetic signal. "Phylogenetic placement," where a reference tree is fixed and the unknown query sequences are placed onto the tree via a reference alignment, is a way to bring the inferential power offered by likelihood-based approaches to large data sets. This paper introduces pplacer, a software package for phylogenetic placement and subsequent visualization. The algorithm can place twenty thousand short reads on a reference tree of one thousand taxa per hour per processor, has essentially linear time and memory complexity in the number of reference taxa, and is easy to run in parallel. Pplacer features calculation of the posterior probability of a placement on an edge, which is a statistically rigorous way of quantifying uncertainty on an edge-by-edge basis. It also can inform the user of the positional uncertainty for query sequences by calculating expected distance between placement locations, which is crucial in the estimation of uncertainty with a well-sampled reference tree. The software provides visualizations using branch thickness and color to represent number of placements and their uncertainty. A simulation study using reads generated from 631 COG alignments shows a high level of accuracy for phylogenetic placement over a wide range of alignment diversity, and the power of edge uncertainty estimates to measure placement confidence. Pplacer enables efficient phylogenetic placement and subsequent visualization, making likelihood-based phylogenetics methodology practical for large collections of reads; it is freely available as source code, binaries, and a web service.
Pioglitazone treatment enlarges subcutaneous adipocytes in insulin-resistant patients.

CONTEXT
Obesity-related insulin resistance is associated with an increase in adipocyte size. In rodent models, treatment with the insulin-sensitizers thiazolidinediones (TZDs) leads to the appearance of small, insulin-sensitive adipocytes. Whether such TZD-dependent morphological changes occur in adipose tissue of insulin-resistant patients is unclear.


OBJECTIVE
The objective of the study was to study the effects of treatment with the TZD pioglitazone on sc adipose tissue morphology and function in insulin-resistant subjects.


DESIGN
This was a placebo-controlled, randomized crossover study.


SETTING
The study was conducted at a university medical center.


PATIENTS
Twelve adult patients with congenital adrenal hyperplasia (CAH) characterized by insulin resistance were included in this study.


INTERVENTION
After a 4-wk run-in phase, patients were treated with pioglitazone (45 mg/d) followed by placebo, each for 16 wk or vice versa.


MAIN OUTCOME MEASURES
After both placebo and pioglitazone treatment, insulin sensitivity was determined by hyperinsulinemic euglycemic clamp and abdominal sc adipose tissue was obtained to measure adipocyte cell surface and expression of genes involved in glucose uptake and inflammation.


RESULTS
Pioglitazone treatment significantly improved the insulin sensitivity index (placebo: 0.35 +/- 0.16 micromol/kg . min per milliunit per liter; pioglitazone 0.53 +/- 0.16 micromol/kg . min per milliunit per liter, P < 0.001) and increased mRNA expression levels of adiponectin and glucose transporter-4 in adipose tissue. The increase in insulin sensitivity was accompanied by a significant enlargement of the sc adipocyte cell surface (placebo: 2323 +/- 725 microm(2); pioglitazone 2821 +/- 885 microm(2), P = 0.03).


CONCLUSIONS
In the human situation, treatment of insulin-resistant subjects with pioglitazone improves insulin sensitivity, whereas at the same time, sc adipocyte cell surface increases.
Are metformin, statin and aspirin use still associated with overall mortality among colorectal cancer patients with diabetes if adjusted for one another?

Background:Metformin, statin and aspirin use seem associated with decreased mortality in cancer patients, though, without adjusting for one another. Independent associations of these drugs with overall mortality after colorectal cancer (CRC) diagnosis within glucose-lowering drugs (GLDs) users were assessed.Methods:Patients starting GLDs before CRC diagnosis (1998–2011) were selected from the Eindhoven Cancer Registry linked with the PHARMO Database Network. The Cox regression model, with time since CRC diagnosis, included time-dependent variables of cumulative exposure to metformin, statins and aspirin after cancer diagnosis and time-dependent ever-never terms for drug exposure.Results:A total of 1043 patients used GLDs before CRC diagnosis; 666 (64%) used metformin, 639 (61%) used statins and 490 (47%) used aspirin after CRC diagnosis. Multivariable analyses revealed that longer cumulative exposure to metformin was not associated with overall mortality (HRCumulative exposure/6 months 1.02; 95% CI 0.97–1.07), whereas the favourable effect of statins increased with cumulative exposure (HRCumulative exposure/6 months 0.93; 95% CI 0.89–0.98). No association between aspirin use and overall mortality was seen (HRCumulative exposure/6 months 0.98; 95% CI 0.93–1.03).Conclusions:No independent association between cumulative exposure to metformin, aspirin and overall mortality was found. Cumulative exposure to statins after CRC diagnosis was associated with lower overall mortality, supporting a drug effect of statins among GLDs users.
Stakeholder Prioritization, Strategic Corporate Social Responsibility and Company Performance: Further Evidence

Using KLD data on more than 900 company's performance over a nine-year period in seven areas of corporate social responsibility (environment, community, corporate governance, diversity, employee relations, human rights, and product quality), this research note re-tests Michelon et al. proxies for prioritization and strategic approaches to CSR. The results show that, when a company pursues CSR initiatives that are linked to stakeholder preferences and allocates resources to these initiatives in a strategic way, the positive effect of its CSR initiatives on financial corporate performance (CP) strengthen. The analysis of KLD's variance and top tiers is thus proposed as a parsimonious way to measure when companies link their CSR initiatives to salient stakeholder preferences and undertake the corporate social actions that are ultimately relevant to the company's strategy and financials. Copyright © 2014 John Wiley & Sons, Ltd and ERP Environment
Potentials of on-line repositioning based on implanted fiducial markers and electronic portal imaging in prostate cancer radiotherapy

BACKGROUND
To evaluate the benefit of an on-line correction protocol based on implanted markers and weekly portal imaging in external beam radiotherapy of prostate cancer. To compare the use of bony anatomy versus implanted markers for calculation of setup-error plus/minus prostate movement. To estimate the error reduction (and the corresponding margin reduction) by reducing the total error to 3 mm once a week, three times per week or every treatment day.


METHODS
23 patients had three to five, 2.5 mm Ø spherical gold markers transrectally inserted into the prostate before radiotherapy. Verification and correction of treatment position by analysis of orthogonal portal images was performed on a weekly basis. We registered with respect to the bony contours (setup error) and to the marker position (prostate motion) and determined the total error. The systematic and random errors are specified. Positioning correction was applied with a threshold of 5 mm displacement.


RESULTS
The systematic error (1 standard deviation [SD]) in left-right (LR), superior-inferior (SI) and anterior-posterior (AP) direction contributes for the setup 1.6 mm, 2.1 mm and 2.4 mm and for prostate motion 1.1 mm, 1.9 mm and 2.3 mm. The random error (1 SD) in LR, SI and AP direction amounts for the setup 2.3 mm, 2.7 mm and 2.7 mm and for motion 1.4 mm, 2.3 mm and 2.7 mm. The resulting total error suggests margins of 7.0 mm (LR), 9.5 mm (SI) and 9.5 mm (AP) between clinical target volume (CTV) and planning target volume (PTV). After correction once a week the margins were lowered to 6.7, 8.2 and 8.7 mm and furthermore down to 4.9, 5.1 and 4.8 mm after correcting every treatment day.


CONCLUSION
Prostate movement relative to adjacent bony anatomy is significant and contributes substantially to the target position variability. Performing on-line setup correction using implanted radioopaque markers and megavoltage radiography results in reduced treatment margins depending on the online imaging protocol (once a week or more frequently).
Localization of ictal onset zones in Lennox-Gastaut syndrome using directional connectivity analysis of intracranial electroencephalography

INTRODUCTION
Neuroscientists are becoming interested in the application of computational EEG analysis to the identification of ictal onset zones; however, most studies have focused on the localization of ictal onset zones in focal epilepsy. The present study aimed to estimate the ictal onset zone of Lennox-Gastaut syndrome (LGS) with bilaterally synchronous epileptiform discharges from intracranial electroencephalography (iEEG) recordings using directional connectivity analysis.


METHODS
We analyzed ictal iEEG data acquired from three LGS patients who underwent epileptic surgery with favorable surgical outcomes. To identify the ictal onset zones, we estimated the functional directional connectivity network among the intracerebral electrodes using the directed transfer function (DTF) method.


RESULTS
The analysis results demonstrated that areas with high average outflow values corresponded well with the surgical resection areas identified using electrophysiologic data and conventional neuroimaging modalities.


DISCUSSIONS
Our results suggest that the DTF analysis can be a useful auxiliary tool for determining surgical resection areas prior to epilepsy surgery in LGS patients. This is the first research article demonstrating that directional connectivity analysis of iEEG recording data can be used for delineating surgical resection areas in generalized epilepsy patients who need surgical treatment.