nils-herrmann/clean_scirepeval huggingface dataset:
Malignant transformation of oral leukoplakia: a systematic review of observational studies.
Venue: Journal of oral pathology medicine official publication of the International Association of Oral Pathologists and the American Academy of Oral Pathology

The aim of this systematic review was to ascertain the malignant transformation rate of oral leukoplakia and the associated risk factors. METHOD Published literature was searched through several search engines from 1960 to the end of December 2013. The inclusion criteria included 'leukoplakia' 'pre cancer' 'malignant transformation' 'follow up' and 'outcome' Two reviewers extracted the data independently and also assessed the quality of evidence.  The search strategy resulted in 1032 abstracts or full text articles, of which 24 met the inclusion criteria. There was much variation in the definitions used by the various authors in their original reports to define oral leukoplakia or in the criteria used to recruit their patients for follow up. The estimated overall (mean) malignant transformation rate for the total population described in these 24 studies amounts to 3.5% (405/11423) with a wide range between 0.13% and 34.0% Based on the evidence presented, the features that stand out as significant determinants contributing to malignant potential of OL include advanced age, female sex, leukoplakia exceeding 200 mm(2) non homogeneous type (eg. erythroleukoplakia) and the higher grades of dysplasia.  The review indicates that drawing meaningful evidence based conclusions are difficult from retrospective studies of this nature. However, many of the determinants exposed in the review require further investigation by well designed prospective studies.
ASD v3.0: unraveling allosteric regulation with structural mechanisms and biological networks
Venue: Nucleic Acids Res.

Allosteric regulation, the most direct and efficient way of regulating protein function, is induced by the binding of a ligand at one site that is topographically distinct from an orthosteric site. Allosteric Database (ASD, available online at http:/mdl.shsmu.edu.cn/ASD) has been developed to provide comprehensive information featuring allosteric regulation. With increasing data, fundamental questions pertaining to allostery are currently receiving more attention from the mechanism of allosteric changes in an individual protein to the entire effect of the changes in the interconnected network in the cell. Thus, the following novel features were added to this updated version: (i) structural mechanisms of more than 1600 allosteric actions were elucidated by a comparison of site structures before and after the binding of an modulator; (ii) 261 allosteric networks were identified to unveil how the allosteric action in a single protein would propagate to affect downstream proteins; (iii) two of the largest human allosteromes, protein kinases and GPCRs, were thoroughly constructed; and (iv) web interface and data organization were completely redesigned for efficient access. In addition, allosteric data have largely expanded in this update. These updates are useful for facilitating the investigation of allosteric mechanisms, dynamic networks and drug discoveries.
Cryptanalysis of a Theorem: Decomposing the Only Known Solution to the Big APN Problem
Venue: CRYPTO

The existence of Almost Perfect Non linear APN permutations operating on an even number of bits has been a long standing open question until Dillon et al. who work for the NSA, provided an example on 6 bits in 2009. In this paper, we apply methods intended to reverse engineer S Boxes with unknown structure to this permutation and find a simple decomposition relying on the cube function over $GF2^3$ More precisely, we show that it is a particular case of a permutation structure we introduce, the butterfly. Such butterflies are 2n bit mappings with two CCZ equivalent representations: one is a quadratic non bijective function and one is a degree $n+1$ permutation. We show that these structures always have differential uniformity at most 4 when n is odd. A particular case of this structure is actually a 3 round Feistel Network with similar differential and linear properties. These functions also share an excellent non linearity for $n=3,5,7$ Furthermore, we deduce a bitsliced implementation and significantly reduce the hardware cost of a 6 bit APN permutation using this decomposition, thus simplifying the use of such a permutation as building block for a cryptographic primitive.
Homogeneous Charge Compression Ignition (HCCI) Engine Technology A Review

The paper discusses about homogeneous charge compression ignition (HCCI) engine technology. Due to increasing emissions of greenhouse gases from automobile engines it is required to develop clean technology in automobiles with lower fuel consumption and higher efficiency for ambient air quality improvement, greenhouse gases reduction and energy security. The factors to be considered while designing this kind of technology are, high compression ratio, lean homogeneous air fuel mixture, complete and instantaneous combustion, which lead to homogeneous charge compression ignition (HCCI).HCCI combines the characteristics of Spark Ignition (SI) and Compression Ignition (CI).HCCI engines can operate on gasoline, diesel fuel, and most alternative fuels. This paper reviews the technology involved in HCCI engine development, its advantages and disadvantages. The challenges involved in HCCI and the future developments in the same are also discussed in the paper.
Data driven contextual modeling for 3D scene understanding
Venue: Comput. Graph.

The recent development of fast depth map fusion technique enables the realtime, detailed scene reconstruction using commodity depth camera, making the indoor scene understanding more possible than ever. To address the specific challenges in object analysis at subscene level, this work proposes a data driven approach to modeling contextual information covering both intra object part relations and inter object object layouts. Our method combines the detection of individual objects and object groups within the same framework, enabling contextual analysis without knowing the objects in the scene a priori. The key idea is that while contextual information could benefit the detection of either individual objects or object groups, both can contribute to object extraction when objects are unknown.Our method starts with a robust segmentation and partitions a subscene into segments, each of which represents either an independent object or a part of some object. A set of classifiers are trained for both individual objects and object groups, using a database of 3D scene models. We employ the multiple kernel learning (MKL) to learn per category optimized classifiers for objects and object groups. Finally, we perform a graph matching to extract objects using the classifiers, thus grouping the segments into either an object or an object group. The output is an object level labeled segmentation of the input subscene. Experiments demonstrate that the unified contextual analysis framework achieves robust object detection and recognition over cluttered subscenes. Graphical abstractDisplay Omitted HighlightsTo address the specific challenges in object analysis at subscene level, this work proposes a data driven approach to modeling contextual information covering both intra object part relations and inter object object layouts.our method combines the detection of individual objects and object groups within the same framework, enabling contextual analysis without knowing objects.The key idea is that while contextual information could benefit the detection of either individual objects or object groups, when object are unknown, both can contribute to object extraction.
Analysing the Impact of Interactive Machine Translation on Post editing Effort

The combination of temporal, technical and cognitive effort has been proposed as metrics to evaluate the feasibility of post editing on machine translation (MT) output (Krings, 2001) In this study, we investigate the impact of interactive machine translation on the post editing effort required to post edit two specialized texts under experimental conditions and correlate it with Translation Edit Rate (TER) scores. Using the CasMaCat workbench as a post editing tool in conjunction with a Tobii T60 eye tracker, process data were collected from 16 participants with some training on postediting. They were asked to carry out post editing tasks under two different conditions: i) traditional post editing (MT) and ii) interactive post editing (IMT) In the IMT condition, as the user types, the MT system suggests alternative target translations which the post editor can interactively accept or overwrite, whereas in the traditional MT condition no aids are provided to the user while editing the raw MT output. Temporal effort is measured by the total time spent to complete the task whereas technical effort is measured by the number of keystrokes and mouse events performed by each participant. In turn, cognitive effort is measured by fixation duration and the number of eye fixations (fixation count) in each task. Results show that IMT post editing had significantly lower fixation duration and fewer fixation counts in comparison to traditional post editing.
Safety, Tolerability, Blinding Efficacy and Behavioural Effects of a Novel MRI Compatible, High Definition tDCS Set Up
Venue: Brain Stimulation

High definition transcranial direct current stimulation (HD tDCS) may allow more specific neural modulation than conventional tDCS.  We compared safety, tolerability, blinding efficacy and cognitive effects of a novel HD tDCS set up to that of conventional tDCS and established compatibility with simultaneous functional magnetic resonance imaging (fMRI)  Two groups of healthy participants completed a visual flanker task either with conventional (N 30) or HD tDCS (N 30) administered to the right dorsolateral prefrontal cortex (1 mA) in a double blind, sham tDCS controlled, cross over design. HD tDCS was administered with a one channel DC stimulator using a small conductive rubber "centre" electrode and a circular return electrode, mimicking the frequently used 4 x 1 HD tDCS set up. Tolerability, adverse effects, impact on performance and blinding efficacy were compared within and between the two montages. In a separate experiment, potential heating and impact on image quality of the novel HD tDCS set up were assessed during simultaneous fMRI.  Both montages elicited only mild adverse effects and those were less pronounced for the novel HD tDCS set up. Participant and investigator blinding was achieved with both montages. Only HD tDCS resulted in significant modulation of the conflict adaptation effect during the flanker task; however, no differences were found for the direct comparison of the two montages. No significant heating occurred during fMRI and only minor effects on image quality were observed during HD tDCS.  This study confirmed safety, tolerability and blinding efficacy of a novel, re usable and MRI compatible HD tDCS set up. It also highlights its potential to exert beneficial effects on behavioural performance. Use of this novel set up during simultaneous fMRI in future studies will help clarify the neural mechanisms by which this HD tDCS impacts on behavioural and neural function.
Challenges in the implementation of dense wavelength division multiplexed (DWDM) optical interconnects using resonant silicon photonics
Venue: SPIE OPTO

Small silicon photonics micro resonator modulators and filters hold the promise for multi terabit per second interconnects at energy consumptions well below 1 pJ/bit. To date, no products exist and little known commercial development is occurring using this technology. Why? In this talk, we review the many challenges that remain to be overcome in bringing this technology from the research labs to the field where they can overcome important commercial, industrial, and national security limitations of existing photonic technologies.
Stories in the Cloth: Art Therapy and Narrative Textiles

In this article I weave together the relevance of narrative textile work in therapeutic and human rights contexts; showcase Common Threads, an international nonprofit that uses story cloths with survivors of gender based violence; outline a master's level art therapy course in story cloths; and relate how textiles helped build a sibling relationship. Although seemingly unrelated, these elements are tied together within the context of culture, time, and purpose, shown in the article through stories and mythology, current practices, and personal experience. Art therapists and other mental health practitioners are increasingly using sewing as a medium, particularly in places where it is culturally relevant, to help people tell their stories graphically. Though art therapists may use textiles and fabric in practice, little is found in the art therapy literature that addresses textile work with trauma survivors. Similar to traditional art therapy groups and open studio, making story cloths in community provides connection with others and an opportunity to create, process, and cope with traumatic events.
Optimizing Statistical Machine Translation for Text Simplification
Venue: TACL

Most recent sentence simplification systems use basic machine translation models to learn lexical and syntactic paraphrases from a manually simplified parallel corpus. These methods are limited by the quality and quantity of manually simplified corpora, which are expensive to build. In this paper, we conduct an in depth adaptation of statistical machine translation to perform text simplification, taking advantage of large scale paraphrases learned from bilingual texts and a small amount of manual simplifications with multiple references. Our work is the first to design automatic metrics that are effective for tuning and evaluating simplification systems, which will facilitate iterative development for this task.
Performance and bacterial community dynamics of a CANON bioreactor acclimated from high to low operational temperatures

In this study, a lab scale CANON bioreactor was operated for 260 days, decreasing operational temperature from 35 degC to 15 degC and from 466 to 100 mg N L 1 ammonium. This was done in order to check the feasibility of the acclimation of CANON biomass treating anaerobic digestion supernatant to B stage influent wastewater operational conditions. Results showed that decrease in temperature posed an impact over the performance of the CANON bioreactor as well as over its bacterial assemblage. Nitrogen removal efficiency showed a moderate decrease when the system was acclimated from 35 degC to 25 degC, but it decreased dramatically in the acclimation from 25 degC to 15 degC. The decrease in temperature and influent ammonium concentration posed an impact over the bacterial community structure of the system. Ammonium oxidizing bacteria changed from Nitrosomonas Nitrosospira or Nitrosovibrio genera at high temperature and influent ammonium to Prosthecobacter at low temperature and low ammonium. As well, dominant anammox bacteria genus changed from Candidatus Brocadia to Candidatus Anammoxoglobus during acclimation. Proliferation of nitrite oxidizing bacteria only occurred under low temperature and influent ammonium conditions with growth of Rhodanobacter genus.
Menstrual diseases as stated in canon fil Tibb

The aim of present study is to overview vaginal diseases as stated in canon fil Tibb.Computerized search of published articles was performed using PubMed, Google Scholar, Scopus and Web of Science, Medline data bases as well as local references from 1990to 2015 .The search terms used were vaginal, disorders, diseases, Canon fil Tibb, Avicenna. Additional sources were identified through cross referencing. The result of this study was indicated that there are many gynecologic diseases as mentioned by Avicenna s book i.e. canon fil Tibb as: Amenorrhea (absence of menstruation) Hypomenorrhoea (low menstruation) Dysmenorrhea (painful menstruation) Premenstruation syndrome (PMS) Leucorrhoea (vaginal discharge) Menorrhagia (excessive menstruation) and Menopause related problems. while the modern medicine put its emphasis on treating gynecologic disorders through chemical drugs ,Iranian traditional medicine, mainly Avicenna, emphasized on traditional, complementary and alternative medicine especially use of herbal medicine in the treatment of such disorders.
Effect of inorganic carbon on nitrogen removal and microbial communities of CANON process in a membrane bioreactor.
Venue: Bioresource technology

In this study, a membrane bioreactor (MBR) was adopted for completely autotrophic nitrogen removal over nitrite (CANON) process. Inorganic carbon (IC) was step wise decreased to analyze the IC influence on nitrogen removal and microbial communities, finally IC was elevated to study its recovery capability. The bioactivities of functional organisms were detected by batch experiments. Results showed that the bioactivity and biodiversity of aerobic ammonia oxidizing bacteria (AOB) and anaerobic ammonia oxidizing bacteria (AAOB) both decreased due to the IC shortage, while nitrite oxidizing bacteria bioactivity showed a contrary result. When the concentration ratio of IC to nitrogen (IC/N) decreased to 1.0, the nitrogen removal sharply deteriorated, which then recovered when the ratio increased to 2.5. Denaturing gradient gel electrophoresis results showed that Nitrosomonas sp. of AOB and Candidatus Brocadia fulgida of AAOB could survive in the condition of IC deficit. The prominent IC/N ratio for high rate and stable CANON was between 1.5 2.0.
Analysis of the transport of imported food in Spain and its contribution to global warming

Through the process of globalization, food has experienced an intense territorial restructuring process. Local agric food links have weakened at the same time as daily products arrived from distant lands. There is presently a wide international debate on the importance of transport in the configuration of the agric food system and its contribution in terms of greenhouse gas (GHG) The direct environmental costs of the transport of imported food, that is the 'external food miles' have been estimated in kilometer (km) ton (t) ton kilometer (t km) and GHG in Spain between 1995 and 2011. The analysis is made by ten food groups including 136 products, with special attention to the most important ones (cereals and animal feed) as well as by means of transport (air, rail, road and water) and from 113 different countries belonging to six geographical areas. Two phases are identified during this period: an expansive phase (1995 2007) in which the t km of imported food increased from 81.8 to 147.8 million t km and environmental pressure rose from 3.1 to 5.4 million CO 2 eq t, and a recession phase (2007 2011) in which environmental pressure subsided as a consequence of the reduction of imports, even though it still remained above the 1995 level. The article reveals a clear interrelation between amounts, distances and modal distribution when it comes to determining the environmental cost of transporting food imports in the two periods studied. It also reflects on the role of the external food miles in the Spanish agri food system from a sustainability perspective.
Childhood Anxiety Disorders: Developmental Risk Factors and Predictors of Treatment Response

Cognitive Behavioral Therapy (CBT) is the evidence based treatment of choice for childhood anxiety disorders. Its blend of cognitive and behavioral coping strategies for anxiety management has more empirical support than any other intervention approach. Yet even after receiving CBT, more than 40% of anxious children still meet criteria for their anxiety disorder. Research is needed to identify factors associated with treatment response and non response, and ultimately to inform treatment improvement. Three studies, reflecting this broad objective, focus on factors that may relate to child treatment response environmental, biological, and cognitive factors suggested by theoretical models of anxiety and potentially relevant to treatment effectiveness research. Study 1 examined whether parental anxiety is a negative predictor, and child perception of control a positive predictor, of treatment outcome in CBT within a randomized controlled trial for childhood anxiety disorders. We found that parental anxiety and child perception of control were not associated with treatment outcomes in the CBT or Usual Care treatment conditions with the exception of child perceived social control. In addition, parental anxiety levels did not change from preto post treatment but child perceived control increased from preto post treatment in response to both CBT and Usual Care. Study 2 examined biological stress response in the context of exposure, the treatment component widely regarded as the heart of CBT for anxiety. Analyses of salivary analytes focused on activation of biological systems implicated in the social stress response (i.e. the hypothalamic pituitaryadrenal axis and the autonomic nervous system) in children with Social Anxiety Disorder and
New insights into the prognostic value of Ki 67 labeling index in patients with triple negative breast cancer
Venue: Oncotarget

The clinicopathological importance of the Ki 67 labeling index (LI) in breast cancer has been studied intensely; however, its prognostic significance in triple negative breast cancer (TNBC) is unclear. We aimed to determine the optimal Ki 67 cut off point to demonstrate its prognostic relevance for breast cancer specific survival (BCSS) in TNBC patients. A total of 571 female TNBC patients underwent diagnosis and surgery at our institution from January 2002 to June 2011. Clinicopathological information for all patients was available and categorized by Ki 67 LI and age at diagnosis. The cut off values for Ki 67 LI and age were selected using the medians. A varying coefficient Cox model was used to describe the effect of Ki 67 LI on BCSS outcomes changing with age after adjustment for disease characteristics. For survival analysis, the Kaplan Meier method and the log rank test were used. Cox proportional hazards models were applied to determine the association of Ki 67 LI and age with BCSS outcomes after adjustment for disease characteristics. Median age was 50 years, and median Ki 67 LI was 35% (range, 0 97.5% There was no prognostic significance of stratification by Ki 67 LI in all patients. When analyzing age at diagnosis as a continuous variable, the log transformed HRKi67 35% vs. 35% for BCSS increased in an S shaped curve with increasing age up to about 50 years old and remained higher risk for high Ki 67 LI. After adjusting for clinicopathological risk factors, low Ki 67 LI was a poor prognostic factor for BCSS (HR: 0.36, 95% CI: 0.14 0.96, P 0.042) in patients of 50 years, but not in patients diagnosed at 50 years (hazard ratio [HR] 1.57, 95% CI: 0.76 3.22, P 0.241) In conclusion, lower Ki 67 LI has poor prognosis relevance in TNBC patients diagnosed at 50 years old. Further validation of the clinical significance of Ki 67 LI in TNBC is required.