nils-herrmann/clean_scirepeval huggingface dataset:
Targeted Next Generation Sequencing Identifies Markers of Response to PD 1 Blockade
Venue: Cancer Immunology Research

Mutational load, by whole exome sequencing, can correlate with immunotherapy responses. Assessing melanoma mutational load of a fraction of the genome, by hybrid capture based NGS, provided an accurate surrogate for WES determinations, and predicted response to anti PD 1. Therapeutic antibodies blocking programmed death 1 and its ligand (PD 1/PD L1) induce durable responses in a substantial fraction of melanoma patients. We sought to determine whether the number and/or type of mutations identified using a next generation sequencing (NGS) panel available in the clinic was correlated with response to anti PD 1 in melanoma. Using archival melanoma samples from anti PD 1/PD L1 treated patients, we performed hybrid capture based NGS on 236 315 genes and T cell receptor (TCR) sequencing on initial and validation cohorts from two centers. Patients who responded to anti PD 1/PD L1 had higher mutational loads in an initial cohort (median, 45.6 vs. 3.9 mutations/MB; P 0.003) and a validation cohort (37.1 vs. 12.8 mutations/MB; P 0.002) compared with nonresponders. Response rate, progression free survival, and overall survival were superior in the high, compared with intermediate and low, mutation load groups. Melanomas with NF1 mutations harbored high mutational loads (median, 62.7 mutations/MB) and high response rates (74% whereas BRAF/NRAS/NF1 wild type melanomas had a lower mutational load. In these archival samples, TCR clonality did not predict response. Mutation numbers in the 315 genes in the NGS platform strongly correlated with those detected by whole exome sequencing in The Cancer Genome Atlas samples, but was not associated with survival. In conclusion, mutational load, as determined by an NGS platform available in the clinic, effectively stratified patients by likelihood of response. This approach may provide a clinically feasible predictor of response to anti PD 1/PD L1.  (c)2016 AACR.
Fuel type estimation using fuel system parameters

Balasubramanian, Shambhavi MSME, Purdue University, May 2016. Fuel Type Estimation Using Fuel System Parameters. Major Professor: Peter H. Meckl, School of Mechanical Engineering. A number of factors are responsible for an increased interest in alternative fuels for transportation and other uses. Alternative fuels, such as biodiesel and vegetable oil, are widely available and both fuels can be used to power a diesel engine. Biodiesel has higher bulk modulus, sonic speed, density and viscosity than regular diesel fuel. The fueling, injection timing, and fuel spray and consequently the emission characteristics of biodiesel are affected by these properties, when used in a diesel engine. Estimation of fuel type is critical to the performance of the engine. Knowing the fuel type allows the engine controller to determine the proper fuel quantity, injection timing, injection duration, amongst other settings, to provide the best balance of performance, emissions and fuel economy. Based on the fuel type, the calorific value will change. Knowing this, the engine controller can use the best air fuel mix and injection pressure for that type of fuel. The type of injection system and the fuel properties (such as the density of fuel, viscosity, bulk modulus and sonic speed) affect fuel injection characteristics. The objective of this project is to estimate fuel properties that can determine whether the fuel is diesel or biodiesel. Bulk modulus is the critical parameter used for characterizing the fuel. This thesis seeks to devise suitable strategies to estimate the bulk modulus to determine the fuel type. Using sensors available on the Cummins XPI fuel system, this is accomplished by observing the effect that bulk modulus has on pressure rise associated with pumping events for different fuels. In this research, the pressure rise is extracted from filtered raw rail pressure data. It has been found
2016 Comprehensive Update of the Banff Working Group on Liver Allograft Pathology: Introduction of Antibody Mediated Rejection
Venue: American journal of transplantation official journal of the American Society of Transplantation and the American Society of Transplant Surgeons

The Banff Working Group on Liver Allograft Pathology reviewed and discussed literature evidence regarding antibody mediated liver allograft rejection at the 11th (Paris, France, June 5 10, 2011) 12th (Comandatuba, Brazil, August 19 23, 2013) and 13th (Vancouver, British Columbia, Canada, October 5 10, 2015) meetings of the Banff Conference on Allograft Pathology.  The primary goal was to introduce guidelines and consensus criteria for the diagnosis of liver allograft antibody mediated rejection and provide a comprehensive update of all Banff Schema recommendations. Included are new recommendations for complement component 4d tissue staining and interpretation, staging liver allograft fibrosis, and findings related to immunosuppression minimization. In an effort to create a single reference document, previous unchanged criteria are also included.
Longitudinal experience with WHO Grade III (anaplastic) meningiomas at a single institution
Venue: Journal of Neuro Oncology

To retrospectively analyze and assess the outcomes and prognostic factors in patients with anaplastic meningioma (AM) (WHO Grade III) Clinical data and outcome [overall (OS) and progression free (PFS) survival] from 18 patients with Grade III meningioma (AM, based on World Health Organization 2016 definition) initially treated between March 2000 and June 2015 were analyzed. Eleven patients (61% were male, median age at diagnosis was 63 (range 48 86) and 55% (10/18 patients) had good performance status (KPS 80) Eight patients (45% had lower grade disease (Grade I n 2; Grade II n 6) prior to being upgraded to AM. Ten patients had fractionated radiation after primary surgery, eight patients had salvage fractionated RT, stereotactic radiosurgery (SRS) boost along with primary RT in 1 patient, and salvage SRS to 18 separate areas in 14 patients. Salvage chemotherapy was mainly considered in third or fourth recurrences. 13 (72% patients recurred and 10 (56% have died. Median PFS was 14.5 months (95% CI 6.9 22.2) The 5 year survival rate was 40 15% and median OS was 55.8 months (95% CI 27.7 80.3) Of all factors examined, only Karnofsky performance status (KPS) affected outcome (PFS p 0.0003; OS p 0.0003) With median OS of 55 months (4.6 years) our results are consistent with existing reports of the poor outcomes for AM patients. From the available data, surgical resection followed by RT and salvage radiosurgery and/or chemotherapy can lead to extended survival; however the benefit may decrease with successive treatments.
Association between the interleukin 4 gene 590C>T promoter polymorphism and asthma in Xinjiang Uighur children.
Venue: Genetics and molecular research GMR

We investigated the association between the interleukin 4 gene (IL 4) 590C>T polymorphism and forced expiratory volume in one second (FEV1) values, immunoglobulin E (IgE) levels, and susceptibility to asthma in Uighur children. IL 4 590C>T frequencies were analyzed in 38 bronchial asthmatic patients and 35 non asthmatic controls. Polymerase chain reaction and direct sequencing were applied to determine the residue at position 590 of IL 4. Total serum IgE levels were detected by enzyme linked immunosorbent assay, while lung function was examined by professionals. There were significant differences in the distribution of IL 4 590C>T genotypes and alleles between patient and control groups (genotypes: chi square 11.476, P 0.05; alleles: chi square 14.572, P 0.05) Frequencies of CC, CT, and TT genotypes were 21, 29, and 50% among patients, and 49, 37, and 14% among controls, respectively, indicating that the T allele was significantly more frequent in the asthma group than in the control group. Total serum IgE levels were significantly higher (P 0.05) and FEV1 values were significantly lower (F 13.294, P 0.05) in patients than in control subjects of the same genotype. In conclusion, the IL 4 590C>T polymorphism is related to bronchial asthma in Uighur children, and the T allele may constitute a susceptibility factor in this group. Furthermore, this genetic variant can result in raised IgE levels and decreased FEV1 values, suggesting that both factors are associated with bronchial asthma in Uighur children.
Factors influencing the utilization of focused antenatal care services in Malindi and Magarini sub counties of Kilifi county, Kenya
Venue: The Pan African medical journal

Globally, pregnancy related complications contribute to more than half of the deaths among women annually. Antenatal care (ANC) is important for the prevention of maternal and fetal mortality and morbidity. This study identifies the socio demographic and economic characteristics; knowledge and attitude and; health service provision for focused antenatal care (FANC) services.  A cross sectional comparative study conducted among 385 women of reproductive age who visited 5 public health facilities in Malindi and Magarini Sub Counties. Data collection was conducted between June 2013 and September 2013 through structured questionnaires, Key Informant Interviews (KIIs) and Focused Group Discussions (FGDs) and analyzed through descriptive summary statistics and test of associations of the various variables using chi square.  About 35% of women sought 1st and 2nd ANC services at the health facilities. These women went ahead to complete the recommended 4 minimum visits as recommended by World Health Organization (WHO) Compared to Catholics, Muslims were less likely to attend a rural health facility (Odds ratio (OR) 0.25, 95% Confidence Interval (CI) 0.10, 0.62, p=0.003) According to education levels, those with secondary (OR=0.07, 95% CI 0.03, 0.18, p<0.001) or tertiary (OR=0.09, 95% CI 0.03 0.17, p<0.001) levels of education were less likely to seek FANC at rural facility. Women seeking rural ANC services started at 2nd or 3rd trimester (OR=5.40 95% CI 2.97 10.06, p<0.001) while those in urban setup start at 1st trimester. Among the women who were aware of FANC, only 27% utilized its services. Long waiting hours, unavailability of services, and departmental disharmony were major causes of dissatisfaction to mothers visiting the facilities.  Utilization and awareness of FANC services in both rural and urban health facilities among women in Malindi and Magarini Sub Counties continues to be low which is associated by socio demographic characteristics, and health facility inefficiencies. Thus there is need to standardize services across health facilities and increase awareness on FANC in both rural and urban.
Acute resistance exercise with blood flow restriction effects on heart rate, double product, oxygen saturation and perceived exertion
Venue: Clinical physiology and functional imaging

The aim of this study was to compare the acute effect of resistance exercise (RE) with and without blood flow restriction (BFR) on heart rate (HR) double product (DP) oxygen saturation (SpO2) and rating of perceived exertion (RPE) Twenty four men (21*79 3*21 years) performed three experimental protocols in a random order (crossover) (i) high intensity RE at 80% of 1RM (HI) (ii) low intensity RE at 20% of 1RM (LI) and (iii) low intensity RE at 20% of 1RM combined with partial blood flow restriction (LI+BFR) HR, blood pressure, SpO2 and RPE were assessed. The data were analysed using repeated measures analysis of variance and the Wilcoxon test for RPE. The results indicated that all protocols significantly increased HR, both immediately postexercise and during the subsequent 60 min (P<0*05) and postexercise DP (P<0*05) but there were no differences between protocols. The protocols of LI and LI+BFR reduced postexercise SpO2 (P 0*033, P 0*007) and the LI+BFR protocol presented a perception of greater exertion in the lower limbs compared with HI (P 0*022) We conclude that RE performed at low intensity combined with BFR seems to reduce the SpO2 after exercise and increase HR and DP while maintaining a perception of greater exertion on the lower limbs.
Reverse micellar extraction of bromelain from pineapple peel Effect of surfactant structure.
Venue: Food chemistry

Pineapple peel is generally disposed or used as compost. This study was focused on extracting bromelain from pineapple peel by using reverse micelles. It was found that gemini surfactant C12 8 C12*2Br (octamethylene a,o bis(dimethyldodecylammonium bromide) showed distinctive advantage over its monomeric counterpart DTAB (dodecyl trimethyl ammonium bromide) under optimized condition, the bromelain extracted with C12 8 C12*2Br reverse micelle had an activity recovery of 163% and a purification fold of 3.3, while when using DTAB reverse micelle, the activity recovery was 95% and the purification fold was 1.7. Therefore, the spacer of gemini surfactant should play a positive role in bromelain extraction and may suggest the potential of gemini surfactant in protein separation since it has been so far rarely used in relative experiments or technologies.
Loss Cause Identification by Evaluating Backscattered Modal Loss Ratio Obtained With 1 mm Band Mode Detection OTDR
Venue: Journal of Lightwave Technology

We propose a novel diagnostic technique that uses 1 mm band mode detection optical time domain reflectometry (1 mm OTDR) to identify the loss causes such as macrobends and fusion splices, of single mode fibers. 1 mm OTDR, which employs 1 mm band probe pulses and a mode selective coupler operating in the same band, enables us to individually observe the fundamental (LP01) and the second order (LP11) modes of the backscattered light generated in the two mode region of single mode fibers. Evaluating the ratio of losses occurring in the LP01 to LP11 modes of the backscattered light allows us to determine whether the cause of loss is a macrobend or a fusion splice. A proof of concept demonstration is performed for two kinds of widely used single mode fibers, and the results show that macrobending and fusion splice losses can be clearly identified.
The dynamic effect of rural to urban migration on inequality in source villages: System GMM estimates from rural China

Using a newly constructed panel dataset that covers the 14 year period from 1997 to 2011 for more than 100 villages in China, this study analyzes the dynamic effect of rural to urban migration on inequality in source villages. Given that income inequality is time persisting, we use a system GMM framework. We found that the dynamic relationship between migration and income inequality is inversely U shaped. Specifically, contemporary migration increases income inequality, whereas lagged migration has a strong income inequality reducing effect on the sending villages. A 50 percent increase in the lagged migration rate translates into a one ninth to one tenth standard deviation reduction in income inequality.
The quality of work life of registered nurses in Canada and the United States: a comprehensive literature review
Venue: International journal of occupational and environmental health

Workplace environment is related to the physical and psychological well being, and quality of work life (QWL) for nurses.  The aim of this paper was to perform a comprehensive literature review on nurses' quality of work life to identify a comprehensive set of QWL predictors for nurses employed in the United States and Canada.  Using publications from 2004 2014, contributing factors to American and Canadian nurses' QWL were analyzed. The review was structured using the Work Disability Prevention Framework. Sixty six articles were selected for analysis.  Literature indicated that changes are required within the workplace and across the health care system to improve nurses' QWL. Areas for improvement to nurses' quality of work life included treatment of new nursing graduates, opportunities for continuing education, promotion of positive collegial relationships, stress reduction programs, and increased financial compensation.  This review's findings support the importance of QWL as an indicator of nurses' broader work related experiences. A shift in health care systems across Canada and the United States is warranted where health care delivery and services are improved in conjunction with the health of the nurses working in the system.
Testing for unit roots in nonlinear heterogeneous panels with smoothly changing trends: an application to Scandinavian unemployment rates

This paper derives panel unit root tests, based on the unit root tests in single time series by He and Sandberg ( 2006) in a nonlinear dynamic heterogeneous panel accommodating smooth structural changes in the intercepts, in the dynamics, and in the trends. The finite sample size properties of the tests are satisfactory, and the tests are conspicuously more powerful than the panel data unit root tests by Im et al. ( 2003;  2005) and Pesaran ( 2007) in panels subject to structural changes. To accommodate panels with cross section dependent idiosyncratic errors, a bootstrap version of the tests is considered. The tests are applied to unemployment rates in Scandinavia, and strong evidence against the hysteresis hypothesis is found. This is not the case if panel unit root tests based on a linear panel or a nonlinear panel with a break in the intercept are applied.
On the influence of hard leverage in a soft leverage bargaining game: The importance of credible claims
Venue: Games Econ. Behav.

What makes a bargaining proposal credible? We study how hard leverage (binding commitment) influences soft leverage (appealing to a focal point) in a rich context bargaining game known to exhibit competing claims to focality. In three treatments, our experiment varies one bargainer's ability to commit, holding the soft leverage condition fixed. As in previous studies, we observe that opening offers are consistent with the available soft leverage. The influence of hard leverage is most evident in the concessionary stage. Hard and soft leverage interact to influence outcomes: Hard leverage advantages its holder, yet settlements largely stay between the two focal points. We posit that focal points induce mutual expectations of bargainer social preferences that, when combined with the Nash bargaining solution, imply the comparative statics concerning the settlements observed. A similarly modified version of the Zeuthen Harsanyi model of the bargaining process, agrees with the comparative statics on opening offers and concessions.
Analysis and Design of a Long Range PTFE Substrate UHF RFID Tag for Cargo Container Identification

In this paper, a high performances microstrip antenna for UHF (ultra high frequency) RFID (radio frequency identification) tag is designed, prototyped and tested. The antenna consists of two main components: a 1.52 mm RT/duroid 5880 laminate substrate on which the antenna is designed and a 10 mm polytetrafluoroethylene (PTFE) dielectric material placed as a separator between the antenna and the reference ground plane for the microstrip antenna. With this structure, the RFID tag can reach a maximum reading distance of 19 m, although the antenna has a compact size of 80 mm x 50 mm. The long reading distance is obtained by attaching to the antenna an RFID chip that can provide a reading sensitivity of 20.5 dBm. The high bandwidth from 677 MHz to 947 MHz measured at 10 dB, makes the tag being usable worldwide especially for cargo container identification, the main purpose of this research.
Fixed Point Quantization of Deep Convolutional Networks
Venue: ICML

In recent years increasingly complex architectures for deep convolution networks (DCNs) have been proposed to boost the performance on image recognition tasks. However, the gains in performance have come at a cost of substantial increase in computation and model storage resources. Fixed point implementation of DCNs has the potential to alleviate some of these complexities and facilitate potential deployment on embedded hardware. In this paper, we propose a quantizer design for fixed point implementation of DCNs. We formulate and solve an optimization problem to identify optimal fixed point bit width allocation across DCN layers. Our experiments show that in comparison to equal bitwidth settings, the fixed point DCNs with optimized bit width allocation offer 20%reduction in the model size without any loss in accuracy on CIFAR 10 benchmark. We also demonstrate that fine tuning can further enhance the accuracy of fixed point DCNs beyond that of the original floating point model. In doing so, we report a new state of the art fixed point performance of 6.78% error rate on CIFAR 10 benchmark.
Learning separable fixed point kernels for deep convolutional neural networks
Venue: 2016 IEEE International Conference on Acoustics, Speech and Signal Processing (ICASSP)

Deep convolutional neural networks have shown outstanding performance in several speech and image recognition tasks. However they demand high computational complexity which limits their deployment in resource limited machines. The proposed work lowers the hardware complexity by constraining the learned convolutional kernels to be separable and also reducing the word length of these kernels and other weights in the fully connected layers. To compensate for the effect of direct quantization, a retraining scheme that includes filter separation and quantization inside of the adaptation procedure is developed in this work. The filter separation reduces the number of parameters and arithmetic operations by 60% for a 5 x 5 kernel, and the quantization further lowers the precision of storage and arithmetic by more than 80 to 90deg% when compared to a floating point algorithm. Experimental results on MNIST and CIFAR 10 datasets are presented.
Hierarchical Compression of Deep Convolutional Neural Networks on Large Scale Visual Recognition for Mobile Applications

This paper present hierarchical compression scheme in deep convolutional neural networks (DCNN) on the ImageNet Large Scale Visual Recognition Challenge (ILSVRC) for mobile devices. In hierarchical compression, we reduce the size of parameters and layers in VGG16 and GoogLeNet by using the iterative synapse pruning and grouping and quantization schemes hierarchically. We use the own simulation framework based on caffe to execute the hierarchical network compression and compare the test accuracy of reference model with compressed ones. The proposed scheme reduces the network parameter size to 91.61% and 67% in VGG and GoogLeNet, respectively. And with less 16bit fixed point parameters, we achieve good compression rates again, with only negligible loss of classification accuracy.