LLukas22/scidocs huggingface dataset:
The Colletotrichum gloeosporioides species complex

UNLABELLED
The limit of the Colletotrichum gloeosporioides species complex is defined genetically, based on a strongly supported clade within the Colletotrichum ITS gene tree. All taxa accepted within this clade are morphologically more or less typical of the broadly defined C. gloeosporioides, as it has been applied in the literature for the past 50 years. We accept 22 species plus one subspecies within the C. gloeosporioides complex. These include C. asianum, C. cordylinicola, C. fructicola, C. gloeosporioides, C. horii, C. kahawae subsp. kahawae, C. musae, C. nupharicola, C. psidii, C. siamense, C. theobromicola, C. tropicale, and C. xanthorrhoeae, along with the taxa described here as new, C. aenigma, C. aeschynomenes, C. alatae, C. alienum, C. aotearoa, C. clidemiae, C. kahawae subsp. ciggaro, C. salsolae, and C. ti, plus the nom. nov. C. queenslandicum (for C. gloeosporioides var. minus). All of the taxa are defined genetically on the basis of multi-gene phylogenies. Brief morphological descriptions are provided for species where no modern description is available. Many of the species are unable to be reliably distinguished using ITS, the official barcoding gene for fungi. Particularly problematic are a set of species genetically close to C. musae and another set of species genetically close to C. kahawae, referred to here as the Musae clade and the Kahawae clade, respectively. Each clade contains several species that are phylogenetically well supported in multi-gene analyses, but within the clades branch lengths are short because of the small number of phylogenetically informative characters, and in a few cases individual gene trees are incongruent. Some single genes or combinations of genes, such as glyceraldehyde-3-phosphate dehydrogenase and glutamine synthetase, can be used to reliably distinguish most taxa and will need to be developed as secondary barcodes for species level identification, which is important because many of these fungi are of biosecurity significance. In addition to the accepted species, notes are provided for names where a possible close relationship with C. gloeosporioides sensu lato has been suggested in the recent literature, along with all subspecific taxa and formae speciales within C. gloeosporioides and its putative teleomorph Glomerella cingulata.


TAXONOMIC NOVELTIES
Name replacement - C. queenslandicum B. Weir & P.R. Johnst. New species - C. aenigma B. Weir & P.R. Johnst., C. aeschynomenes B. Weir & P.R. Johnst., C. alatae B. Weir & P.R. Johnst., C. alienum B. Weir & P.R. Johnst, C. aotearoa B. Weir & P.R. Johnst., C. clidemiae B. Weir & P.R. Johnst., C. salsolae B. Weir & P.R. Johnst., C. ti B. Weir & P.R. Johnst. New subspecies - C. kahawae subsp. ciggaro B. Weir & P.R. Johnst. Typification: Epitypification - C. queenslandicum B. Weir & P.R. Johnst.
Infertility and the provision of infertility medical services in developing countries

BACKGROUND
Worldwide more than 70 million couples suffer from infertility, the majority being residents of developing countries. Negative consequences of childlessness are experienced to a greater degree in developing countries when compared with Western societies. Bilateral tubal occlusion due to sexually transmitted diseases and pregnancy-related infections is the most common cause of infertility in developing countries, a condition that is potentially treatable with assisted reproductive technologies (ART). New reproductive technologies are either unavailable or very costly in developing countries. This review provides a comprehensive survey of all important papers on the issue of infertility in developing countries.


METHODS
Medline, PubMed, Excerpta Medica and EMBASE searches identified relevant papers published between 1978 and 2007 and the keywords used were the combinations of 'affordable, assisted reproduction, ART, developing countries, health services, infertility, IVF, simplified methods, traditional health care'.


RESULTS
The exact prevalence of infertility in developing countries is unknown due to a lack of registration and well-performed studies. On the other hand, the implementation of appropriate infertility treatment is currently not a main goal for most international non-profit organizations. Keystones in the successful implementation of infertility care in low-resource settings include simplification of diagnostic and ART procedures, minimizing the complication rate of interventions, providing training-courses for health-care workers and incorporating infertility treatment into sexual and reproductive health-care programmes.


CONCLUSIONS
Although recognizing the importance of education and prevention, we believe that for the reasons of social justice, infertility treatment in developing countries requires greater attention at National and International levels.
ENERGY PRODUCTION IN THE FORMATION OF A FINITE THICKNESS COSMIC STRING

The classical electromagnetic modes outside a long, straight, superconducting cosmic string are calculated, assuming the string to be surrounded by a superconducting cylindric surface of radius R. Thereafter, by use of a Bogoliubov-type argument, the electromagnetic energy W produced per unit length in the lowest two modes is calculated when the string is formed ”suddenly”. The essential new element in the present analysis as compared with prior work of Parker [Phys. Rev. Lett. 59, 1369 (1987)] and Brevik and Toverud [Phys. Rev. D 51, 691 (1995)], is that the radius a of the string is assumed finite, thus necessitating Neumann functions to be included in the fundamental modes. We find that the theory is changed significantly: W is now strongly concentrated in the lowest mode (m,s) = (0,1), whereas the proportionality W ∝ (Gµ/t) 2 that is characteristic for zero-width strings is found in the next mode (1,1). Here G is the gravitational constant, µ the string mass per unit length, and t the GUT time.
Probabilistic Power Flow Studies for Transmission Systems With Photovoltaic Generation Using Cumulants

This paper applies a probabilistic power flow (PPF) algorithm to evaluate the influence of photovoltaic (PV) generation uncertainty on transmission system performance. PV generation has the potential to cause a significant impact on power system reliability in the near future. A cumulant-based PPF algorithm suitable for large systems is used to avoid convolution calculations. Correlation among input random variables is considered. Specifically correlation between adjacent PV resources are considered. Three types of approximation expansions based on cumulants, namely the Gram-Charlier expansion, the Edgeworth expansion, and the Cornish-Fisher expansion, are compared, and their properties, advantages, and deficiencies are discussed. Additionally, a novel probabilistic model of PV generation is developed to obtain the probability density function (PDF) of the PV generation production based on the environmental conditions. The proposed approaches with the three expansions are compared with Monte Carlo simulations (MCS) with results for a 2497-bus representation of the Arizona area of the Western Electricity Coordinating Council (WECC) system.
To catch a fake: Curbing deceptive Yelp ratings and venues

The popularity and influence of reviews, make sites like Yelp ideal targets for malicious behaviors. We present Marco, a novel system that exploits the unique combination of social, spatial and temporal signals gleaned from Yelp, to detect venues whose ratings are impacted by fraudulent reviews. Marco increases the cost and complexity of attacks, by imposing a tradeoff on fraudsters, between their ability to impact venue ratings and their ability to remain undetected. We contribute a new dataset to the community, which consists of both ground truth and gold standard data. We show that Marco significantly outperforms state-of-the-art approaches, by achieving 94% accuracy in classifying reviews as fraudulent or genuine, and 95.8% accuracy in classifying venues as deceptive or legitimate. Marco successfully flagged 244 deceptive venues from our large dataset with 7,435 venues, 270,121 reviews and 195,417 users. Furthermore, we use Marco to evaluate the impact of Yelp events, organized for elite reviewers, on the hosting venues. We collect data from 149 Yelp elite events throughout the US. We show that two weeks after an event, twice as many hosting venues experience a significant rating boost rather than a negative impact. © 2015 Wiley Periodicals, Inc. Statistical Analysis and Data Mining 0: 000–000, 2015
Radiologically determined orthodontically induced external apical root resorption in incisors after non-surgical orthodontic treatment of class II division 1 malocclusion: a systematic review

This study aims to critically evaluate orthodontically induced external apical root resorption (OIEARR) in incisors of patients undergoing non-surgical orthodontic treatment of class II division 1 malocclusion by a systematic review of the published data. An electronic search of two databases was performed; the bibliographies of relevant articles were also reviewed. Studies were included if they examined the amount of OIEARR in incisors produced during non-surgical orthodontic treatment of individuals with class II division I malocclusion in the permanent dentition. Individuals had no previous history of OIEARR, syndromes, pathologies, or general diseases. Study selections, risk of bias assessment, and data extraction were performed in duplicate. Eight studies of moderate methodological quality were finally included. An increased prevalence (65.6% to 98.1%) and mild to moderate severity of OIEARR (<4 mm and <1/3 original root) were reported. No sex difference in root resorption was found. For the maxillary incisors, there was no evidence that either the central or lateral incisor was more susceptible to OIEARR. A weak to moderate positive correlation between treatment duration and root resorption, and anteroposterior apical displacement and root resorption was found. Current limited evidence suggests that non-surgical comprehensive orthodontic treatment to correct class II division 1 malocclusions causes increased prevalence and severity of OIEARR the more the incisor roots are displaced and the longer this movement takes.
Risk factors for conjunctival squamous cell neoplasia: a matched case-control study.

AIMS
To identify roles of human papillomavirus (HPV) infection and solar elastosis as the risk factors for conjunctival squamous cell neoplasia (CSCN).


METHODS
30 consecutive pathological specimens, ranging from conjunctival intraepithelial neoplasia, carcinoma in situ, to invasive squamous cell carcinoma were retrieved from tissue archives. 30 controls were disease free conjunctiva from age and sex matched patients undergoing extracapsular cataract extraction. Two masked pathologists studied haematoxylin and eosin stains on paraffin embedded conjunctival tissues. Elastic stain for solar elastosis was blindly interpreted in comparison with negative and positive controls. HPV infection was studied by polymerase chain reaction and dot hybridisation.


RESULTS
The mean age of CSCN patients was 54.9 years. The male to female ratio was 1:1. Solar elastosis was seen in 53.3% of CSCN and in 3.3% of controls with an odds ratio of 16.0 (95% CI, 2.49 to 670.96; p value = 0.0003). HPV DNA were not detected in any of the specimens.


CONCLUSION
Solar elastosis is much more frequently found in CSCN cases than in their matched controls and is a risk factor for CSCN. These data are insufficient to conclude that HPV infection is a risk factor for CSCN.
Applying proxemics to mediate people's interaction with devices in ubiquitous computing ecologies

Through vastly increasing availability of digital devices in people’s everyday life, ubiquitous computing (ubicomp) ecologies are emerging. An important challenge here is the design of adequate techniques that facilitate people’s interaction with these ubicomp devices. In my research, I explore how the knowledge of people’s and devices’ spatial relationships – called proxemics – can be applied to interaction design. I introduce concepts of proxemic interactions that consider fine-grained information of proxemics to mediate people’s interactions with digital devices, such as large digital surfaces or portable personal devices. In particular, my work considers four dimensions that are essential to determine basic proxemic relationships of people and devices: position, orientation, movement, and identity. I outline my previous and current work towards a framework of proxemic interaction, the design of adequate development tools, and the implementation and evaluation of applications that illustrate concepts of proxemic interactions. ACM Classification: H.5.2 [Information interfaces and presentation]: User Interfaces: Input devices and strategies. General terms: Design, Human Factors
Multicentre surveillance study on feasibility, safety and efficacy of antifungal combination therapy for proven or probable invasive fungal diseases in haematological patients: the SEIFEM real-life combo study.

UNLABELLED
This multicentre observational study evaluated the feasibility, efficacy and toxicity of antifungal combination therapy (combo) as treatment of proven or probable invasive fungal diseases (IFDs) in patients with haematological malignancies. Between January 2005 and January 2010, 84 cases of IFDs (39 proven and 45 probable) treated with combo were collected in 20 Hematological Italian Centres, in patients who underwent chemotherapy or allogeneic haematopoietic stem cell transplantation for haematological diseases. Median age of patients was 34 years (range 1-73) and 37% had less than 18 years. Acute leukaemia was the most common underlying haematological disease (68/84; 81%). The phase of treatment was as follows: first induction in 21/84 (25%), consolidation phase in 18/84 (21%) and reinduction/salvage in 45/84 (54%). The main site of infection was lung with or without other sites. The principal fungal pathogens were as follows: Aspergillus sp. 68 cases (81%), Candida sp. six cases (8%), Zygomycetes four cases (5%) and Fusarium sp. four cases (5%). The most used combo was caspofungin+voriconazole 35/84 (42%), caspofungin + liposomal amphotericin B (L-AmB) 20/84 (24%) and L-AmB+voriconazole 15/84 (18%). The median duration of combo was 19 days (range 3-180). The overall response rate (ORR) was 73% (61/84 responders) without significant differences between the combo regimens. The most important factor that significantly influenced the response was granulocyte (PMN) recovery (P 0.009). Only one patient discontinued therapy (voriconazole-related neurotoxicity) and 22% experienced mild and reversible adverse events (hypokalaemia, ALT/AST increase and creatinine increase). The IFDs-attributable mortality was 17%. This study indicates that combo was both well tolerated and effective in haematological patients. The most used combo regimens were caspofungin + voriconazole (ORR 80%) and caspofungin + L-AmB (ORR 70%). The ORR was 73% and the mortality IFD related was 17%. PMN recovery during combo predicts a favourable outcome.


CLINICAL TRIALS REGISTRATION
NCT00906633.
On the Soviet Contribution to the Discovery of Quark Color (Against One False Revision)

A critical discussion of recent attempts to revise the modern physics history is presented.
Building Commissioning: A Golden Opportunity for Reducing Energy Costs and Greenhouse-gas Emissions

Commissioning is arguably the single most cost-effective strategy for reducing energy, costs, and greenhouse gas emissions in buildings today. Although commissioning has earned increased recognition in recent years, it remains an enigmatic practice whose visibility severely lags its potential. The application of commissioning to new buildings ensures that they deliver or exceed the performance and energy savings promised by their design and intended operation. When applied to existing buildings, commissioning identifies deficiencies and the almost inevitable “drift” from intended performance over time, and carries out interventions to put the building back on course. More formally, commissioning is a systematic, forensic approach to quality assurance and performance risk management, rather than a technology per se. This article presents the world’s largest compilation and meta-analysis of commissioning experience and the associated literature, comprising 643 non-residential buildings, 99 million ft of floorspace, $43 million in commissioning expenditures, and the work of 37 commissioning providers. The median normalized cost to deliver commissioning is $0.30/ft ($2009 currencies) for existing buildings and $1.16/ft for new construction (or 0.4% of the overall construction cost). The one third of projects for which data are available reveal over 10,000 energy-related deficiencies, the correction of which resulted in 16% median wholebuilding energy savings in existing buildings and 13% in new construction, with payback times of 1.1 and 4.2 years, respectively. Because energy savings exceed commissioning costs, the associated reductions in greenhouse gas emissions come at a “negative” cost of −$110/tonne CO2 for new buildings and −$25/tonne for new construction. Cases with comprehensive commissioning attained nearly twice the overall median level of savings and five times the savings of the least-thorough projects. Significant non-energy benefits such as improved indoor air quality are also achieved. Applying the median whole-building energysaving values to the US non-residential buildings stock corresponds to an annual energy-saving potential of $30 billion (and 340 Mt of CO2) by the year 2030.
Positive pressure--analysing the effect of the addition of non-invasive ventilation (NIV) to home airway clearance techniques (ACT) in adult cystic fibrosis (CF) patients.

BACKGROUND
There is no published literature on the frequency of use of non-invasive ventilation (NIV) with airway clearance techniques (ACT) throughout the cystic fibrosis (CF) population; 3.9% (191 people of 5062 registered) of the United Kingdom CF population older than 16 years are reported to use NIV in registry data; however, it is not specified if this is for ACT or respiratory failure. Using NIV with ACT decreases work of breathing and fatigue during in-patient admissions for CF patients. We hypothesised these effects could be replicated at home, potentially reducing hospital admissions.


METHOD
Fourteen adult patients with CF scored ease of clearance and breathlessness with ACT before and after addition of NIV to normal ACT routine using a visual analog scale. Patient views on NIV with ACT were collected via a structured interview. Number of home intravenous (IV) antibiotic courses and days in hospital was collected for one year pre- and post-NIV provision.


RESULTS
Patients reported statistically significant improvements in ease of clearance (p = 0.011) and reduced breathlessness during ACT using NIV (p = 0.011). Structured interview results indicated patient reports of sputum clearance improved. In-patient days were lower, while home IV days were higher after NIV was set up, although not statistically significant.


CONCLUSION
This study is limited by small numbers; however, trends towards less hospital admissions and greater patient ease while using NIV with ACT warrant further investigation.
Explaining Asset Pricing Puzzles Associated with the 1987 Market Crash

The 1987 market crash was associated with a dramatic and permanent steepening of the implied volatility curve for equity index options, despite minimal changes in aggregate consumption. We explain these events within a general equilibrium framework in which expected endowment growth and economic uncertainty are subject to rare jumps. The arrival of a jump triggers the updating of agents’ beliefs about the likelihood of future jumps, which produces a market crash and a permanent shift in option prices. Consumption and dividends remain smooth, and the model is consistent with salient features of individual stock options, equity returns, and interest rates.
No . 89 The Process of Innovation

SUMMARY The paper argues that innovation processes can be cognitive, organisational and/or economic. They happen in conditions of uncertainty and (in the capitalist system) of competition. Three broad, overlapping sub-processes of innovation are identified: the production of knowledge; the transformation of knowledge into products, systems, processes and services; and the continuous matching of the latter to market needs and demands. The paper identifies key trends in each of these areas: (1) increasing specialisation in knowledge production; (2) increasing complexity in physical artefacts, and in the knowledge bases underpinning them; and (3) the difficulties of matching technological opportunities with market needs and organisational practices. Despite advances in scientific theory and information and communication technologies (ICTs), innovation processes remain unpredictable and difficult to manage. They also vary widely according to the firm's sector and size. Only two innovation processes remain generic: coordinating and integrating specialised knowledge, and learning in conditions of uncertainty. The paper also touches on the key challenges now facing 'innovation managers' within modern industrial corporations, bearing in mind the highly contingent nature of innovation. 3 1. INTRODUCTION This paper concerns the processes (or more accurately 'processes') of innovation within (mainly) large corporations with headquarters located in the advanced industrialised countries. 1 The aim is to provide an interpretation of how innovation processes have evolved historically and the key challenges now facing 'innovation managers' within modern industrial corporations. 2 In so far as it is possible, the paper draws lessons from studies of innovation processes within and between firms, bearing in mind the highly contingent nature of innovation. It examines many of the different problems facing innovation mangers within the modern corporation and shows how these have been, and are being, reacted to. The structure of the paper explains its logic and focus. Part 1 presents a short introduction to the many theories and empirical studies of innovation. This is used in
Free/Libre Open Source Software in Health Care: A Review

OBJECTIVES
To assess the current state of the art and the contribution of Free/Libre Open Source Software in health care (FLOSS-HC).


METHODS
The review is based on a narrative review of the scientific literature as well as sources in the context of FLOSS-HC available through the Internet. All relevant available sources have been integrated into the MedFLOSS database and are freely available to the community.


RESULTS
The literature review reveals that publications about FLOSS-HC are scarce. The largest part of information about FLOSS-HC is available on dedicated websites and not in the academic literature. There are currently FLOSS alternatives available for nearly every specialty in health care. Maturity and quality varies considerably and there is little information available on the percentage of systems that are actually used in health care delivery.


CONCLUSIONS
The global impact of FLOSS-HC is still very limited and no figures on the penetration and usage of FLOSS-HC are available. However, there has been a considerable growth in the last 5 to 10 years. While there where only few systems available a decade ago, in the meantime many systems got available (e.g., more than 300 in the MedFLOSS database). While FLOSS concepts play an important role in most IT related sectors (e.g., telecommunications, embedded devices) the healthcare industry is lagging behind this trend.