nils-herrmann/clean_scirepeval huggingface dataset:
Expression of AE1/p16 promoted degradation of AE2 in gastric cancer cells
Venue: BMC Cancer

BackgroundHuman anion exchanger 1 and 2 (AE1 and AE2) mediate the exchange of Cl /HCO3 across the plasma membrane and regulate intracellular pH (pHi) AE1 is specifically expressed on the surface of erythrocytes, while AE2 is widely expressed in most tissues, and is particularly abundant in parietal cells. Previous studies showed that an interaction between AE1 and p16 is a key event in gastric cancer (GC) progression, but the importance of AE2 in GC is unclear.MethodsThe relationship among AE1, AE2 and p16 in GC cells was characterized by molecular and cellular experiments. AE2 expression and pHi were measured after knockdown or forced expression of AE1 or p16 in GC cells. The effect of AE2 on GC growth and the correlation of AE2 expression with differentiation and prognosis of GC were also evaluated. The effect of gastrin on AE2 expression and GC growth was investigated in cellular experiments and mouse xenograft models.Resultsp16 binds to both AE1 and AE2 simultaneously. AE1 or p16 silencing elevated AE2 expression on the plasma membrane where it plays a role in pHi regulation and GC suppression. AE2 expression was decreased in GC tissue, and these decreased levels were correlated with poor differentiation and prognosis of GC. The low AE2 protein levels are due to rapid ubiquitin mediated degradation that was facilitated in the presence of p16. Gastrin inhibited the growth of GC cells at least partially through up regulation of AE2 expression.ConclusionAE1/p16 expression promoted AE2 degradation in GC cells. Gastrin is a potential candidate drug for targeted therapies for AE1 and p16 positive GC.
JASPAR 2016: a major expansion and update of the open access database of transcription factor binding profiles
Venue: Nucleic Acids Res.

JASPAR (http:/jaspar.genereg.net) is an open access database storing curated, non redundant transcription factor (TF) binding profiles representing transcription factor binding preferences as position frequency matrices for multiple species in six taxonomic groups. For this 2016 release, we expanded the JASPAR CORE collection with 494 new TF binding profiles (315 in vertebrates, 11 in nematodes, 3 in insects, 1 in fungi and 164 in plants) and updated 59 profiles (58 in vertebrates and 1 in fungi) The introduced profiles represent an 83% expansion and 10% update when compared to the previous release. We updated the structural annotation of the TF DNA binding domains (DBDs) following a published hierarchical structural classification. In addition, we introduced 130 transcription factor flexible models trained on ChIP seq data for vertebrates, which capture dinucleotide dependencies within TF binding sites. This new JASPAR release is accompanied by a new web tool to infer JASPAR TF binding profiles recognized by a given TF protein sequence. Moreover, we provide the users with a Ruby module complementing the JASPAR API to ease programmatic access and use of the JASPAR collection of profiles. Finally, we provide the JASPAR2016 R/Bioconductor data package with the data of this release.
Entrepreneurial Intentions of Students in Poland in the View of Ajzen's Theory of Planned Behaviour

The purpose of this study is to empirically verify the Ajzen's in Polish realities, however the TPB was extended of one more variable attitude towards risk.  We decided to use the survey questionnaire among students. The survey was conducted among seven universities in Krakow. Out of 1100 sent questionnaires, we received 719 fully completed and corrected questionnaires, it means that the return rate is 65.4% The questionnaire was divided into 14 thematic blocks their elements explain the entrepreneurial intentions.  The statistical calculations confirmed that three Ajzen's independent variables such as attitude towards entrepreneurship, subjunctive norms and perceived behavioural control determine entrepreneurial intensions of investigated students. Additionally we found out that the risk attitude is also an determinant in a similar way, as well as the entrepreneurial intentions differ between business and non business students.  Shaping entrepreneurial mindset of young people is one of the most important role of contemporary education system, including the tertiary education. Future studies should seek new factors influencing entrepreneurial intentions of students, facts that will be complementary to TPB and EEM models.  The study extended Ajzen's TPB of risk propensity as a separate variable describing attitude towards entrepreneurship.
Early Time GPR: A Method to Monitor Spatial Variations in Soil Water Content during Irrigation in Clay Soils

We used a recent ground penetrating radar (GPR) methodology, early time amplitude analysis, with the goal of monitoring changes in soil water content (SWC) in response to irrigation in clayey soils. We hypothesized that early time analysis could be used to monitor changes in SWC in clay rich soil where ground wave and reflection based GPR methods traditionally fail. An overnight irrigation experiment was performed in a 20 by 14 m section of natural grassland at the Samford Ecological Research Facility in southeastern Queensland, Australia. Both GPR reflection surveys and ground wave velocity analysis were ineffective at the site due to the signal attenuation associated with the clay rich soil. We collected daily GPR and time domain reflectometry (TDR) data sets during a 5 d period in August 2014, with soil samples collected for gravimetric analysis at the conclusion of data collection. The GPR data display a clear response of the early time signal amplitude to changes in SWC. The GPR data sets exhibit a strong correlation with SWC, as measured by TDR and gravimetric analysis of soil cores, which is consistent with the dependence of GPR early time amplitude on relative permittivity. The results suggest that the early time method can be used to obtain spatially distributed information on subsurface moisture content in clay rich soils.
In situ unsaturated zone water stable isotope 2 H and 18 O) measurements in semi arid environments: a soil water balance

Stable isotopes (deuterium, 2H, and oxygen 18, 18O) of soil water were measured in the field using a liquid water isotope analyzer (tunable off axis integrated cavity output spectroscope, OA ICOS, LGR) and commercially available soil gas probes (BGL 30, UMS, Munich) in the semi arid Cuvelai Etosha Basin (CEB) Namibia. Results support the applicability of an in situ measurement system for the determination of stable isotopes in soil pore water. High spatial and temporal resolution was achieved in the study area with reasonable accuracy and measurements were in agreement with laboratory based cryogenic vacuum extraction and subsequent cavity ring down laser spectroscopic isotope analysis (CRDS, L2120 i, Picarro Inc. After drift and span correction of the in situ isotope data, precision for over 140 measurements taken during two consecutive field campaigns (June and November 2014) was 1.8 and 0.48 %0 for d2H and d18O, respectively. Mean measurement trueness is determined using quality check standards and was 5 and 0.3 %0 for d2H and d18O, respectively. The isotope depth profiles are used quantitatively to calculate a soil water balance. The contribution of transpiration to total evapotranspiration ranged between 72 and 92 Shortly after a rain event, the contribution of transpiration was much lower, at 35 to 50 Potential limitations of such an in situ system are related to environmental conditions which could be minimized by using a temperature controlled chamber for the laser spectrometer. Further, the applicability of the system using previously oven dried soil material might be limited by physicochemical soil properties (i.e. clay minerals) Uncertainty in the in situ system is suggested to be reduced by improving the calibration procedure and further studying fractionation effects influencing the isotope ratios in the soil water, especially at low water contents. Furthermore, the influence of soil respired CO2 on isotope values within the root zone could not be deduced from the data.
Mulching practices for reducing soil water erosion: A review

Among the soil conservation practices that are used, mulching has been successfully applied to reduce soil and water losses in different contexts, such as agricultural lands, fire affected areas, rangelands and anthropic sites. In these contexts, soil erosion by water is a serious problem, especially in semi arid and semi humid areas of the world. Although the beneficial effects of mulching are known, further research is needed to quantify them, especially in areas where soil erosion by water represents a severe threat. In the literature, there are still some uncertainties about how to maximize the effectiveness of mulching to reduce the soil and water loss rates. Given the seriousness of soil erosion by water and the uncertainties that are still associated with the correct use of mulching, this study review aims to (i) develop a documented and global database on the use of mulching with vegetative residues; (ii) quantify the effects of mulching on soil and water losses based on different measurement methods and, consequently, different spatial scales; (iii) evaluate the effects of different types of mulches on soil and water losses based on different measurement methods; and (iv) provide suggestions for more sustainable soil management. The data published in the literature have been collected. The results showed the beneficial effects of mulching in combating soil erosion by water in all of the environments considered here, with reduction rates in the average sediment concentration, soil loss and runoff volume that, in some cases, exceeded 90% However, the economic feasibility of mulching application was not readily available in the literature. Therefore, more research should be performed to help both farmers and land managers by providing them with evidence based means for implementing more sustainable soil management practices.
Does the stress gradient hypothesis hold water? Disentangling spatial and temporal variation in plant effects on soil moisture in dryland systems

The nature of the relationship between water limitation and facilitation has been one of the most contentious debates surrounding the stress gradient hypothesis (SGH) which states that plant plant interactions shift from competition to facilitation with increasing environmental stress. We take a closer look at the potential role of soil moisture in mediating plant plant interaction outcomes by assessing effects of climate and soil texture on plant modulation of soil moisture. Using an empirically parameterized soil moisture model, we simulated soil moisture dynamics beneath shrubs and in un vegetated coarse and fine soils for 1000 sites in the Western United States with <700 mm mean annual precipitation. This threshold reflects the transition from dryland <600 mm precipitation) to mesic ecosystems. Positive effects of shrubs on shallow soil moisture (i.e. the difference between shrub and interspace soil moisture) decreased along the aridity gradient when long term average conditions were considered, contrary to expectations based on the SGH. Negative effects of shrubs on deeper soil moisture also increased with aridity. However, when extreme years were considered, positive effects of shrub on soil moisture were greatest at intermediate points along the spatial aridity gradient, consistent with a hump backed model of plant plant interactions. When viewed through time within a site, shrub effects on shallow soil moisture were positively related to precipitation, with more complex relationships exhibited in deeper soils Taken together, the results of this simulation study suggest that plant effects on soil moisture are predictable based on relatively general relationships between precipitation inputs and differential evaporation and transpiration rates between plant and interspace microsites that are largely driven by temperature. In particular, this study highlights the importance of differentiating between temporal and spatial variation in weather and climate, respectively, in determining plant effects on available soil moisture. Rather than focusing on the somewhat coarse scale predictions of the SGH, it may be more beneficial to explicitly incorporate plant effects on soil moisture into predictive models of plant plant interaction outcomes in drylands.
Convolutional Tables Ensemble: classification in microseconds
Venue: ArXiv

We study classifiers operating under severe classification time constraints, corresponding to 1 1000 CPU microseconds, using Convolutional Tables Ensemble (CTE) an inherently fast architecture for object category recognition. The architecture is based on convolutionally applied sparse feature extraction, using trees or ferns, and a linear voting layer. Several structure and optimization variants are considered, including novel decision functions, tree learning algorithm, and distillation from CNN to CTE architecture. Accuracy improvements of 24 45% over related art of similar speed are demonstrated on standard object recognition benchmarks. Using Pareto speed accuracy curves, we show that CTE can provide better accuracy than Convolutional Neural Networks (CNN) for a certain range of classification time constraints, or alternatively provide similar error rates with 5 200X speedup.
Historical document digitization through layout analysis and deep content classification
Venue: 2016 23rd International Conference on Pattern Recognition (ICPR)

Document layout segmentation and recognition is an important task in the creation of digitized documents collections, especially when dealing with historical documents. This paper presents an hybrid approach to layout segmentation as well as a strategy to classify document regions, which is applied to the process of digitization of an historical encyclopedia. Our layout analysis method merges a classic top down approach and a bottom up classification process based on local geometrical features, while regions are classified by means of features extracted from a Convolutional Neural Network merged in a Random Forest classifier. Experiments are conducted on the first volume of the "Enciclopedia Treccani" a large dataset containing 999 manually annotated pages from the historical Italian encyclopedia.
AN IMPROVED HYBRID BINARIZATION TECHNIQUE FOR DEGRADED DOCUMENT DIGITIZATION

In document analysis, binary image representation is essential format. In previous studies, different techniques are implemented and tried and true for different types of degradation in document image. But none of these methods are competent to properly extract the text from degraded background. However, few thresholding techniques are available but due to complex nature it cannot solve all binarization problems. This paper evaluates a hybrid document image binarization technique which uses both local and global thresholding that divides the text from badly degraded document images accurately. The proposed method involves specialized evaluation technique for binarization to test samples from DIBCO 2009 13 dataset which have contrast parameter selection.The method uses both local image contrast and gradient to enhance the poor quality old script images and define edge pixels correctly. To evaluate the proposed work performance, we compare it with Otsu, Sauvola, Niblack, Bernsen and LMM method. The proposed method adapts all the binarization problems and brings highest 94.97% accuracy and gives superior performance compare to all other state of art techniques.
High resolution CSR GRACE RL05 mascons

The determination of the gravity model for the Gravity Recovery and Climate Experiment (GRACE) is susceptible to modeling errors, measurement noise, and observability issues. The ill posed GRACE estimation problem causes the unconstrained GRACE RL05 solutions to have north south stripes. We discuss the development of global equal area mascon solutions to improve the GRACE gravity information for the study of Earth surface processes. These regularized mascon solutions are developed with a 1deg resolution using Tikhonov regularization in a geodesic grid domain. These solutions are derived from GRACE information only, and no external model or data is used to inform the constraints. The regularization matrix is time variable and will not bias or attenuate future regional signals to some past statistics from GRACE or other models. The resulting Center for Space Research (CSR) mascon solutions have no stripe errors and capture all the signals observed by GRACE within the measurement noise level. The solutions are not tailored for specific applications and are global in nature. This study discusses the solution approach and compares the resulting solutions with postprocessed results from the RL05 spherical harmonic solutions and other global mascon solutions for studies of Arctic ice sheet processes, ocean bottom pressure variation, and land surface total water storage change. This suite of comparisons leads to the conclusion that the mascon solutions presented here are an enhanced representation of the RL05 GRACE solutions and provide accurate surface based gridded information that can be used without further processing.
Validation of GRACE based groundwater storage anomaly using in situ groundwater level measurements in India

In this study, we tried to validate groundwater storage (GWS) anomaly obtained from a combination of GRACE and land surface model based estimates, for the first time, with GWS anomaly obtained from a dense network of in situ groundwater observation wells within 12 major river basins in India. We used seasonal data from >15,000 groundwater observation wells between 2005 and 2013, distributed all over the country. Two recently released GRACE products, RL05 spherical harmonics (SH) and RL05 mascon (MS) products are used for comparison with in situ data. To our knowledge, this is the first study of comparing the performance of two independent GRACE products at a sub continental scale. Also for the first time, we have created a high resolution (0.1 0 x 0.1 0 map of specific yield for the entire country that was used for calculating GWS. Observed GWS anomalies have been computed using water level anomalies and specific yield information for the locale of individual observation wells that are up scaled to basin scale in order to compare with GRACE based estimates. In general GRACE based estimates match well (on the basis of the statistical analyses performed in the study) with observed estimates in most of the river basins. On comparing with observed GWS anomaly, GRACE SH estimates match well in terms of RMSE, while GRACE MS estimates show better association in terms of correlation, while the output of skewness, kurtosis, coefficient of variation (CV) and scatter analyses remain inconclusive for inter comparison between two GRACE estimates. We used a non parametric trend estimation approach, the Hodrick Prescott (HP) filter, to further assess the performance of the two GRACE estimates. GRACE MS estimates clearly outperform GRACE SH estimates for reproducing observed GWS anomaly trends with significantly >95% confidence level) strong association in 10 out of 12 basins for GRACE MS estimates, on the other hand, GRACE SH estimates show significantly >95% confidence level) strong association in 6 out of 12 basins. On the basis of the study output, we recommend using GRACE MS estimates for groundwater studies over the region and other regions of the globe with similar climatic, hydrogeologic or groundwater withdrawal conditions.
Mass Flux Solution in the Tibetan Plateau Using Mascon Modeling
Venue: Remote. Sens.

Mascon modeling is used in this paper to produce the mass flux solutions in the Tibetan Plateau. In the mascon modeling, the pseudo observations and their covariance matrices are derived from the GRACE monthly gravity field models. The sampling density of the pseudo observations is determined based on the eigenvalues of the covariance matrices. In the Tibetan Plateau, the sampling density of per 1.5deg is the most appropriate among all choices. The mass flux variations from 2003 to 2014 are presented in this paper, which show large mass loss (about 15.5 Gt/year) in Tianshan, North India, and Eastern Himalaya, as well as strong positive signals (about 9 Gt/year) in the Inner Tibetan Plateau. After the glacier isostatic adjustment effects from Pau 5 AUT model are removed, the mass change rates in the Tibetan Plateau derived from CSR RL05, JPL RL05, GFZ RL05a, and Tongji GRACE02 monthly models are 6.41 4.74 Gt/year, 5.87 4.88 Gt/year, 6.08 4.65 Gt/year, and 11.50 4.79 Gt/year, respectively, which indicate slight mass loss in this area. Our results confirm that mascon modeling is efficient in the recovery of time variable gravity signals in the Tibetan Plateau.
Forecasting electricity consumption in Pakistan: the way forward

Growing shortfall of electricity in Pakistan affects almost all sectors of its economy. For proper policy formulation, it is imperative to have reliable forecasts of electricity consumption.  Results reveal that Holt Winter is the appropriate model for forecasting electricity consumption in Pakistan. It also suggests that electricity consumption would continue to increase throughout the projected period and widen the consumption production gap in case of failure to respond the issue appropriately. It further reveals that demand would be highest in the household sector as compared to all other sectors and the increase in the energy generation would be less than the increase in total electricity consumption throughout the projected period. The study discuss various options to reduce the demand supply gap and provide reliable electricity to different sectors of the economy.
Real time patient experience surveys of hospitalized medical patients.
Venue: Journal of hospital medicine

Real time feedback about patients' perceptions of the quality of the care they are receiving could provide physicians the opportunity to address concerns and improve these perceptions as they occur, but physicians rarely if ever receive feedback from patients in real time.  To evaluate if real time patient feedback to physicians improves patient experience.  Prospective, randomized, quality improvement initiative.  University affiliated, public safety net hospital.  Patients and hospitalist physicians on general internal medicine units.  Real time daily patient feedback to providers along with provider coaching and revisits of patients not reporting optimal satisfaction with their care.  Patient experience scores on 3 provider specific questions from daily surveys on all patients and Hospital Consumer Assessment of Healthcare Providers and Systems (HCAHPS) scores and percentiles on randomly selected patients.  Changes in HCAHPS percentile ranks were substantial (communication from doctors: 60th percentile versus 39th, courtesy and respect of doctors: 88th percentile versus 23rd, doctors listening carefully to patients: 95th percentile versus 57th, and overall hospital rating: 87th percentile versus 6th (P 0.02 for overall differences in percentiles) but we found no statistically significant difference in the top box proportions for the daily surveys or the HCAHPS survey. The median [interquartile range] top box score for the overall hospital rating question on the HCAHPS survey was higher in the intervention group than in the control group (10 [9, 10] vs 9 [8, 10] P 0.04)  Real time feedback, followed by coaching and patient revisits, seem to improve patient experience.