nils-herrmann/clean_scirepeval huggingface dataset:
An Integrated TCGA Pan Cancer Clinical Data Resource to Drive High Quality Survival Outcome Analytics
Venue: Cell
Year: 2018

For a decade, The Cancer Genome Atlas (TCGA) program collected clinicopathologic annotation data along with multi platform molecular profiles of more than 11,000 human tumors across 33 different cancer types. TCGA clinical data contain key features representing the democratized nature of the data collection process. To ensure proper use of this large clinical dataset associated with genomic features, we developed a standardized dataset named the TCGA Pan Cancer Clinical Data Resource (TCGA CDR) which includes four major clinical outcome endpoints. In addition to detailing major challenges and statistical limitations encountered during the effort of integrating the acquired clinical data, we present a summary that includes endpoint usage recommendations for each cancer type. These TCGA CDR findings appear to be consistent with cancer genomics studies independent of the TCGA effort and provide opportunities for investigating cancer biology using clinical correlates at an unprecedented scale.
Data Driven Resilient Fleet Management for Cloud Asset enabled Urban Flood Control
Venue: IEEE Transactions on Intelligent Transportation Systems
Year: 2018

Emergency fleet management has become one of the determinant success factors for post disaster responses in urban flood control. However, it is challenging as multiple types of emergency vehicles are involved, and its performance is frequently threatened by the fluctuation of rescue demands and fleet capacity. Aiming at coping with the imbalances between rescue demands and vehicle supplies, and maintaining required service level of fleet management after flood occurs, this paper proposes a data driven resilient fleet management solution under the context of cloud asset enabled urban flood control. First, the problem of resilient fleet management is quantitatively defined, and then a data driven dynamic management mechanism is proposed, which is highly effective on realizing resilient fleet management. Furthermore, considering the cooperation among different types of emergency vehicles, a greedy based algorithm is proposed for resilient vehicle dispatching based on real time scenarios. Finally, a simulation case is also conducted to verify the effectiveness and performance of the proposed solution.
Interpretable, highly accurate brain decoding of subtly distinct brain states from functional MRI using intrinsic functional networks and long short term memory recurrent neural networks
Venue: NeuroImage
Year: 2019

Decoding brain functional states underlying cognitive processes from functional MRI (fMRI) data using multivariate pattern analysis (MVPA) techniques has achieved promising performance for characterizing brain activation patterns and providing neurofeedback signals. However, it remains challenging to decode subtly distinct brain states for individual fMRI data points due to varying temporal durations and dependency among different cognitive processes. In this study, we develop a deep learning based framework for brain decoding by leveraging recent advances in intrinsic functional network modeling and sequence modeling using long short term memory (LSTM) recurrent neural networks (RNNs) Particularly, subject specific intrinsic functional networks (FNs) are computed from resting state fMRI data and are used to characterize functional signals of task fMRI data with a compact representation for building brain decoding models, and LSTM RNNs are adopted to learn brain decoding mappings between functional profiles and brain states. Validation results on fMRI data from the HCP dataset have demonstrated that brain decoding models built on training data using the proposed method could learn discriminative latent feature representations and effectively distinguish subtly distinct working memory tasks of different subjects with significantly higher accuracy than conventional decoding models. Informative FNs of the brain decoding models identified as brain activation patterns of working memory tasks were largely consistent with the literature. The method also obtained promising decoding performance on motor and social cognition tasks. Our results suggest that LSTM RNNs in conjunction with FNs could build interpretable, highly accurate brain decoding models.
Comparative Analysis of Chemical Composition, Antioxidant Activity and Quantitative Characterization of Some Phenolic Compounds in Selected Herbs and Spices in Different Solvent Extraction Systems
Venue: Molecules
Year: 2018

This study evaluated the efficacy of various organic solvents (80% acetone, 80% ethanol, 80% methanol) and distilled water for extracting antioxidant phenolic compounds from turmeric, curry leaf, torch ginger and lemon grass extracts. They were analyzed regarding the total phenol and flavonoid contents, antioxidant activity and concentration of some phenolic compounds. Antioxidant activity was determined by the 2,2 diphenyl 1 picrylhydrazyl (DPPH) free radical scavenging assay and the ferric reducing antioxidant power (FRAP) assay. Quantification of phenolic compounds was carried out using high performance liquid chromatography (HPLC) All the extracts possessed antioxidant activity, however, the different solvents showed different efficiencies in the extraction of phenolic compounds. Turmeric showed the highest DPPH values (67.83 13.78% and FRAP (84.9 2.3 mg quercetin/g freeze dried crude extract) followed by curry leaf, torch ginger and lemon grass. While 80% acetone was shown to be the most efficient solvent for the extraction of total phenolic compounds from turmeric, torch ginger and lemon grass (221.68, 98.10 and 28.19 mg GA/g freeze dried crude extract, respectively) for the recovery of phenolic compounds from curry leaf (92.23 mg GA/g freeze dried crude extract) 80% ethanol was the most appropriate solvent. Results of HPLC revealed that the amount of phenolic compounds varied depending on the types of solvents used.
Reconstruction of the full length transcriptome atlas using PacBio Iso Seq provides insight into the alternative splicing in Gossypium australe
Venue: BMC Plant Biology
Year: 2019

BackgroundGossypium australe F. Mueller (2n 2x 26, G2 genome) possesses valuable characteristics. For example, the delayed gland morphogenesis trait causes cottonseed protein and oil to be edible while retaining resistance to biotic stress. However, the lack of gene sequences and their alternative splicing (AS) in G. australe remain unclear, hindering to explore species specific biological morphogenesis.ResultsHere, we report the first sequencing of the full length transcriptome of the Australian wild cotton species, G. australe, using Pacific Biosciences single molecule long read isoform sequencing (Iso Seq) from the pooled cDNA of ten tissues to identify transcript loci and splice isoforms. We reconstructed the G. australe full length transcriptome and identified 25,246 genes, 86 pre miRNAs and 1468 lncRNAs. Most genes (12,832, 50.83% exhibited two or more isoforms, suggesting a high degree of transcriptome complexity in G. australe. A total of 31,448 AS events in five major types were found among the 9944 gene loci. Among these five major types, intron retention was the most frequent, accounting for 68.85% of AS events. 29,718 polyadenylation sites were detected from 14,536 genes, 7900 of which have alternative polyadenylation sites (APA) In addition, based on our AS events annotations, RNA Seq short reads from germinating seeds showed that differential expression of these events occurred during seed germination. Ten AS events that were randomly selected were further confirmed by RT PCR amplification in leaf and germinating seeds.ConclusionsThe reconstructed gene sequences and their AS in G. australe would provide information for exploring beneficial characteristics in G. australe.
Factors influencing dwell time during source code reading: a large scale replication experiment
Venue: ETRA
Year: 2019

The paper partially replicates and extends a previous study by Busjahn et al.  on the factors influencing dwell time during source code reading, where source code element type and frequency of gaze visits are studied as factors. Unlike the previous study, this study focuses on analyzing eye movement data in large open source Java projects. Five experts and thirteen novices participated in the study where the main task is to summarize methods. The results examine semantic line level information that developers view during summarization. We find no correlation between the line length and the total duration of time spent looking on the line even though it exists between a token's length and the total fixation time on the token reported in prior work. The first fixations inside a method are more likely to be on a method's signature, a variable declaration, or an assignment compared to the other fixations inside a method. In addition, it is found that smaller methods tend to have shorter overall fixation duration for the entire method, but have significantly longer duration per line in the method. The analysis provides insights into how source code's unique characteristics can help in building more robust methods for analyzing eye movements in source code and overall in building theories to support program comprehension on realistic tasks.
The Comparison of Milk and Reproductive Performance of Saanen and Saanen x Hair Goat Crossbreds (F1, B1 B2) and Growth Performance of their Kids in Semi Intensive Production System
Venue: Turkish Journal of Agriculture Food Science and Technology
Year: 2019

The aims of this study were to evaluate the traits of reproductive, milking and growth performance of Saanen and Saanen x Hair crossbreds (F1, B1 and B2) raised at the Bandirma Sheep Research Institute. The data were collected from 868 goats for reproductive performance and milk yield and from 1077 kids for survival performance between 2009 2012. Milk components (fat, protein, lactose and non fat dry matter) of goats (n=162) and body weight changes of kid's (n=64) were evaluated for one year in 2012. Estrus rates and survival rates were similar among all genotypes. Kidding rate was significantly higher in F1 goats than Saanen goats. Saanen goat had the lowest average mean daily milk yield compared with other genotypes. The effect of year and age were significant on milk yield. Goats in F1 and B1 genotypes had higher milk protein percentage and non fat dry matter content in comparison with Saanen and B2 genotype. Milk fat and lactose contents were similar among genotypes. Birth weight and monthly live weight were similar between genotypes while weaning weight, six month live weight and yearling live weight were higher in B1 kids in comparison with Saanen kids. The effect of dam age and birth type were significant on birth weight, monthly live weight and weaning weight. The findings related to performance characteristics in goat genotypes investigated show that B1 genotype could be recommend for semi intensive production system in the Western Anatolia.
Waste separation at source and recycling potential of the hotel industry in Hoi An city, Vietnam
Year: 2019

This study focuses on assessing the practice of waste separation at source and evaluating the recycling potential of the hotel industry in Hoi An City (HAC) which is a famous tourism city in the centre of Vietnam. Five recycling scenarios were designed based on the status and intention of waste management practices of the hotels and the hierarchical structure of recycling, which was identified by the analytic hierarchy process method. This study revealed that the solid waste management (SWM) system of the hotel industry in HAC has a high potential for developing recycling practices. The high percentage of recyclable materials (84.3% the achievements of waste separation practices, and the intentions of SWM of the hoteliers are favourable conditions for enhancing recycling practices. Furthermore, this study indicated that recycling could reduce 30 70% of total hotel waste, lead to beneficial changes in waste characterisation for incineration and composting processes, and bring economic profits to the hotels. In addition, recycling strategies with the synchronous combination of improvement of waste separation at source, waste regulation promulgation, and enhancement of waste management motivation for the hotels were discussed.
Procedural Requirements of the South African Anti Dumping Law and Practice Prior to Imposition of Anti Dumping Duties: Are They Really WTO inconsistent?
Year: 2020

Dumping, which is a form of price discrimination or differential pricing of different units of the same good sold at different prices in different markets, remains a continuing problem for many countries. The World Trade Organisation (WTO) members resort to the imposition of anti dumping duties or levies to offset the effects of the dumped products on the domestic industry. This article provides a critical analysis of procedural issues in the South African anti dumping law and practice to determine if it is compatible with the WTO's Anti Dumping Agreement (ADA) It particularly focusses on procedural issues prior to the imposition of anti dumping measures by the South African International Trade Administration Commission. Some authors argue that the South African anti dumping law and practice is incompatible with its WTO obligations in areas such as the calculation of the constructed export price, the determination of material injury and a causal relationship, the imposition of provisional and definitive anti dumping duties and the procedure for review. The conclusion provided in this article is that the South African law and application of anti dumping measure is largely WTO compliant, particularly on the issues of initiation, investigation and prosecution of anti dumping complaints.
User behaviour and perception as drivers for lighting energy efficiency and performance gap reduction in higher education
Year: 2018

User behaviour and perception are key drivers for lighting energy efficiency and performance gap reduction in higher education. Changing the way we conduct post occupancy evaluation to include retrofits and understanding users' needs more thoroughly will ultimately lead to a greater reduction in CO, emissions. A pilot interview study was carried out with University of Reading Whiteknights campus with a total of 6 staff and students in 2014 and developed into a main interview study with 9 academic staff in 2015. During 2014 to 2016 data loggers were deployed for six months to 10 single occupancy offices, 13 classrooms and 14 corridor areas in 3 buildings on campus that were used for both teaching and office space. The data from the loggers was used to calculate hours of lighting use and occupancy, time of day analysis and a prompt study. The findings from interviews revealed that lighting control design in classrooms lacked consistency across the real estate portfolio; office occupants felt their spaces were neglected and; the piecemeal upgrades contributed to their frustrations of being unable to control their lighting effectively. Post occupancy evaluation in single occupancy offices, classrooms and corridors was carried out using environmental loggers to quantify the levels of hours of wasted lighting use for performance gap analysis relating this to external factor. and CO, emission savings. Significant hours of wasted lighting were found in all three task areas in the three study buildings. Interesting findings in the office study found that lighting use and occupancy patterns varied by both building and size of office. To combat this prevalent lighting waste continuous commissioning and verification were suggested as practical measures to reduce the CO, emissions and energy consumption and improve user satisfaction. Finally the prompt study exploring office occupant's habits was found to link light switching behaviours on exit to the time of day and suggested the corridor lights being off influenced the action of switching off lights in the office. This thesis contributes to knowledge by providing new significant findings in both post occupancy evaluation and human behaviour in light switching.
Lymphangioleiomyomatosis.
Venue: Seminars in respiratory and critical care medicine
Year: 2020

Lymphangioleiomyomatosis (LAM) is a slow albeit progressive rare neoplastic disease featured with diffuse thin walled cysts in lungs and angiomyolipomas in kidneys. LAM affects almost exclusively women and has one of the strongest gender predispositions of any extragenital human disease. Two forms of LAM present clinically, sporadic (S LAM) and tuberous sclerosis complex associated (TSC LAM) TSC is an autosomal dominant genetic multisystems neoplastic disease. A high prevalence of LAM can be detected in adult female TSC patients. Tremendous progress has been made in our understanding and management of this rare disease. Both LAM and TSC are TSC2 or TSC1 mutated diseases that result in overactivation of the mechanistic target of rapamycin (mTOR) pathway. Sirolimus, an mTOR inhibitor, has been approved for LAM treatment in the United States and many other countries. Therapies targeting female sex hormones have shown preclinical efficacy in animal and cell culture based experiments, but have not been properly investigated clinically. In this review, we summarize current recommendations in the diagnosis and treatment of LAM.
LoPP: Locality Preserving Projections for Moving Object Detection
Year: 2012

Automatic moving object detection and tracking is very important task in video surveillance applications. In this paper, we propose a novel scheme for moving object detection based on Locality Preserving Projections (LPP) It is also known as Laplacian eigenmaps, which optimally preserves the neighborhood structure of the data set  The proposed method was tested on standard PETS dataset and many real time video sequence and the results was satisfactory.
Conceptualizing soil organic matter into particulate and mineral associated forms to address global change in the 21st century.
Venue: Global change biology
Year: 2019

Managing soil organic matter (SOM) stocks to address global change challenges requires well substantiated knowledge of SOM behavior that can be clearly communicated between scientists, management practitioners, and policy makers. However, SOM is incredibly complex and requires separation into multiple components with contrasting behavior in order to study and predict its dynamics. Numerous diverse SOM separation schemes are currently used, making cross study comparisons difficult and hindering broad scale generalizations. Here we recommend separating SOM into particulate (POM) and mineral associated (MAOM) forms, two SOM components that are fundamentally different in terms of their formation, persistence, and functioning. We provide evidence of their highly contrasting physical and chemical properties, mean residence times in soil, and responses to land use change, plant litter inputs, warming, CO2 enrichment, and N fertilization. Conceptualizing SOM into POM versus MAOM is a feasible, well supported, and useful framework that will allow scientists to move beyond studies of bulk SOM, but also use a consistent separation scheme across studies. Ultimately, we propose the POM versus MAOM framework as the best way forward to understand and predict broad scale SOM dynamics in the context of global change challenges and provide necessary recommendations to managers and policy makers.
Inversion analysis of in situ stress field in underground cavern of hydropower station
Year: 2014

In the calculation of the stability of surrounding rock in the underground caverns,the study area of underground stress is usually large.However,the information of known parameters is limited;therefore the numerical analysis results on this basis can result in some deviations from the reality.Based on the measured data of underground stress and geological structure,and improved particle swarm optimization algorithm,an inversion model of the initial stress field was developed.The inversion results were in good agreement with the measured results,which can provide reference for the further analysis of the surrounding rock stability in the plant area.
Determination of the Network Structure of Sensor Materials Prepared by Three Different Sol Gel Routes Using Fourier Transform Infrared Spectroscopy (FT IR)
Venue: Applied spectroscopy
Year: 2013

Solid acid base sensor materials were prepared by encapsulating three pH indicators (alizarin red, brilliant yellow, and acridine) within a silica matrix using a sol gel approach through three different routes: (1) non hydrolytic, (2) acid catalyzed, and (3) base catalyzed. Raman and Fourier transform infrared spectroscopies were used to evaluate the silica indicator interactions. Because vibrational bands assigned to functional groups present in the indicator molecules were not detected, the main silica stretching mode vSi o between approximately 1300 and 1000 cm 1 was used to detect the presence of our indicators within the silica matrix. The large band centered at 1100 cm 1 was deconvoluted into four components corresponding to the longitudinal optic and transversal optic modes of the silicon monoxide (SiO)4 and (SiO)6 siloxane rings. Using the component area of each mode, it was possible to calculate the percentage of each structure. Such percentages ranged from 49% to 70% (SiO)6 for the analyzed samples, within a confidence level of 95% (p 0.05) (The confidence limits were 53 62% These results could be related to the pH indicator content, indicating that the quantity of the encapsulated molecule affects the (SiO)6 percentage values. In addition, a comparison with the radius of gyration obtained by small angle X ray scattering was done. These results indicate that the analyte accesses the receptor elements through the passages between the siloxane rings but not through the siloxane rings themselves.
Faster on scene times associated with decreased mortality in Helicopter Emergency Medical Services (HEMS) transported trauma patients
Venue: Trauma Surgery Acute Care Open
Year: 2017

The 'Golden Hour' emphasizes the importance of rapidly providing definitive care to trauma patients. Dispatch time, defined as the time it takes the Helicopter Emergency Medical Service (HEMS) to dispatch from their base and reach the patient, and on scene time, defined as the time spent with the patient prior to departure to a trauma center, can impact how quickly the patient will reach definitive care. We evaluated HEMS dispatch and on scene times by investigating the survival rates among patients transported by air to a level 1 trauma center. We hypothesize that longer HEMS dispatch and on scene times are associated with worse patient outcomes.  A retrospective, single institution analysis was performed on patients transported by HEMS. Inclusion criteria were air transported patients aged 18 years and above admitted to a level 1 trauma center from January 1, 2005 to January 1, 2015. Total dispatch time and on scene times were divided into five incremental groups and mortality data were analyzed. Mortality was defined as death during initial hospital admission. A Pearson's correlation was used to analyze relationship between dispatch times, on scene times, and mortality. Simple binary logistic regression was used to run a multivariate analysis on confounding variables of Injury Severity Score (ISS) gender, age, and Glasgow Coma Scale.  There was a strong positive linear correlation between HEMS on scene time and mortality, R=0.962, p=0.038. Additionally, there was a positive trend between HEMS dispatch time and mortality. ISS was found to be a significant confounder of mortality in our cohort with on scene times >20 min, with mortality increasing by 7.5% for every 0.1 increase in ISS score (p=0.01)  Longer HEMS on scene and dispatch times appeared to be associated with increased mortality in trauma patients. However, those with higher ISS require longer on scene times, increasing mortality. Regardless, efforts should focus on reducing on scene and dispatch times. Level of evidence and study type Level III; Therapeutic/Care Management.