Miracle-dz/UniFAR-FTUs huggingface dataset:
Clinical Pan-Cancer Assessment of Mismatch Repair Deficiency Using Tumor-Only, Targeted Next-Generation Sequencing

PURPOSE Given regulatory approval of immune checkpoint inhibitors in patients with mismatch repair–deficient (MMR-D) cancers agnostic to tumor type, it has become important to characterize occurrence of MMR-D and develop cost-effective screening approaches. Using a next-generation sequencing (NGS) panel (OncoPanel), we developed an algorithm to identify MMR-D frequency in tumor samples and applied it in a clinical setting with pathologist review. METHODS To predict MMR-D, we adapted methods described previously for use in NGS panels, which assess patterns of single base-pair insertion or deletion events occurring in homopolymer regions. Tumors assayed with OncoPanel between July 2013 and July 2018 were included. For tumors tested after June 2017, sequencing results were presented to pathologists in real time for clinical MMR determination, in the context of tumor mutation burden, other mutational signatures, and clinical data. RESULTS Of 20,301 tumors sequenced, 2.7% (553) were retrospectively classified as MMR-D by the algorithm. Of 4,404 samples with pathologist sign-out of MMR status, the algorithm classified 147 (3.3%) as MMR-D: in 116 cases, MMR-D was confirmed by a pathologist, five cases were overruled by the pathologist, and 26 were assessed as indeterminate. Overall, the highest frequencies of OncoPanel-inferred MMR-D were in endometrial (21%; 152/723), colorectal (9.7%; 169/1,744), and small bowel (9.3%; 9/97) cancers. When algorithm predictions were compared with historical MMR immunohistochemistry or polymerase chain reaction results in a set of 325 tumors sequenced before initiation of pathologist assessment, the overall sensitivity and specificity of the algorithm were 91.1% and 98.2%, respectively. CONCLUSION We show that targeted, tumor-only NGS can be leveraged to determine MMR signatures across tumor types, suggesting that broader biomarker screening approaches may have clinical value.
Agricultural terraces in the Mediterranean: intensive construction during the later Middle Ages revealed by landscape analysis with OSL profiling and dating

1 McCord Centre for Landscape, Newcastle University, Newcastle upon Tyne, NE1 7RU, UK 10 2 Earth and Environmental Sciences, University of St Andrews, St Andrews, KY16 9AL, UK 11 3 Dept of Art History, Mimar Sinan Güzel Sanatlar Üniversitesi, 34427 Beyoğlu, Istanbul, Turkey 12 4 Research Centre for Anatolian Civilizations, Koç Üniversitesi, 34433 Beyoğlu, Istanbul, Turkey; 13 School of Archaeology and Ancient History, University of Leicester, Leicester, LE1 7RH, UK 14 5 Dept of Archaeology, Mimar Sinan Güzel Sanatlar Üniversitesi, 34427 Beyoğlu, Istanbul, Turkey 15 6 Dept of Classical Archaeology, Çanakkale Onsekiz Mart Üniversitesi, Terzioğlu/Çanakkale, Turkey 16 7 Ephorate of Antiquities of the Cyclades, Mpoumpoulinas 20-22, 106 82 Athens, Greece 17 8 Dept of Archaeology, Conservation & History, University of Oslo, 0315 Oslo, Norway 18 9 School of History, Classics and Archaeology, University of Edinburgh, EH8 9AG, UK 19 10 Dept of History, University of Lleida, Plaça de Víctor Siurana 1, 25003 Lleida, Spain 20 11 Faculty of Geography and History, University of Santiago de Compostela, 15782 Santiago de 21 Compostela, Spain 22 12 Scottish Universities Environmental Research Centre, East Kilbride, Glasgow, G75 0QF, UK 23 24
A Lattice Model for COVID-19 Epidemic

Susceptible, infective, recovered, and hospitalized/isolated individuals are placed on the cells of a nxn square lattice, where each cell is occupied by a single individual or is vacant. At discrete time units (typically one day each) all susceptibles and infectives execute a random movement and when a coincidence of the two types occurs the susceptible is converted to infective status according to some probability. Infectives are labelled by the number of days since originally infected. At each time increment the age label of the infectives is increased by one unit. When the label reaches a number like 15 or 20 days the susceptibles recover with some probability or become isolated/hospitalized. Upon reaching some age the latter types either recover or die. Probabilities for the movements and conversions from one status to another are implemented by random numbergeneration. Simulations were carried out to investigate the effect of several probability and age parameters, the size of population (proportional to nxn) and density (related to fraction of occupied cells), and the size of the movements. Mid-term gradual conversion of susceptibles to isolated was explored as intervention policy.
Size distribution of Pacific cod (Gadus macrocephalus) in the North Pacific Ocean over 6 millennia

Abstract In this paper, we compile estimates of cod size distributions based on zooarchaeological data and contemporary length-frequency data to look at variability in size composition through time across the North Pacific, from the northern Kuril Islands through the Aleutian Islands to southeast Alaska. The results suggest that a strong longitudinal trend in cod size has remained consistent over time, with the largest cod found to the west. We find that five of nine sites show that overall cod length and distribution of the largest fish remain relatively unchanged. Two sites where we find truncation of the length distributions—or loss of the largest fish—are places where the modern fisheries have the longest history and have been most intense, suggesting a potential for anthropogenic impacts on these local populations. We acknowledge two limitations in these data: (1) there are differences in selectivity between the ancient and modern fisheries; and (2) seasonal variability in fish availability was observed to be an important explanatory variable in the modern data set, but the season of harvest is poorly understood for the ancient collections. Therefore, while differences observed between the two data sets suggest possible anthropogenic influence on the size structure of Pacific cod, they are not conclusive.
Enzymatic hydrolysis of the Eisenia andrei earthworm: Characterization and evaluation of its properties

Abstract Some studies have carried out in order to retrieve proteins from the by-product of animal-processing industries. Earthworms are rich in protein and usually are used in animal feed. Thus, this study aimed to optimize the hydrolysis process of Eisenia andrei earthworms by employing Alcalase enzyme. Using the response surface methodology, we evaluated the following conditions: temperature, hydrolysis time, stirring speed, and enzyme/substrate ratio. The optimal conditions for the experimental design were determined through the analysis of the foaming and emulsifying properties, in vitro starch digestibility, and antioxidant activity. The results demonstrate that the highest degree of hydrolysis (i.e., 92%) was obtained under the following conditions: pH, 9.5; temperature, 25 °C; hydrolysis time, 2.25 h; stirring speed, 200 rpm; and enzyme/substrate ratio, 1.77%, using Alcalase enzyme. Evaluation of the amino acid composition under these conditions revealed higher concentrations of aspartic acid, glutamic acid, and leucine. The in vitro protein digestibility of the hydrolysate was approximately 73%. There were no significant improvements in either foam stability or emulsification after enzymatic hydrolysis. Additional studies on the antioxidant activity are required. This bioproduct could potentially serve as a promising supplementary food product.
European Industries’ Energy Efficiency under Different Technological Regimes: The Role of CO2 Emissions, Climate, Path Dependence and Energy Mix

The assessment of industrial-level energy efficiency’s (EE) development is a critical research topic that has entrenched in the global battle against climate change. Under the Energy Efficiency Directives 2012/27/EU and 2018/2002/EU, European Commission sets specific industrial energy efficiency targets, rules and obligations for the 2020-2030 period aiming, among others, at specific energy intensity reduction and energy efficiency improvements. In this paper we use a balanced panel of fourteen European industries from twenty-seven countries for the period 1995-2011 under a metatechnology framework. The aim of this study is to evaluate, at a first stage, the industrial total factor energy efficiency (TFEE) at a national and European level by incorporating technological heterogeneity through a nonparametric approach. Reflecting the divergent views on the importance of desirable and undesirable outcomes in the pursuit of TFEE, we additionally estimate industrial performance by prioritizing either economic or environmental aspects. At the second stage of our analysis, econometric models are applied to investigate the main factors of industrial TFEE using sector specific and country characteristics while we further proceed with a ft and ^-convergence analysis for our TFEE measures. The results of this study reveal that small-scale economies exhibit persistent high TFEE scores. At the same time, TFEE determinants suggest that path dependence phenomena have a strong presence, climatic characteristics occur while energy mix displays both linear and non-linear relationship. Either considering one desirable output or consolidating the undesirable output in the production function our results indicate a strong evidence of conditional and unconditional convergence in TFEE scores.
Cultural Differences in the Construal of Suffering and the COVID-19 Pandemic

The present research examines how suffering is construed across cultures. Study 1 (N 1 = 264; N 2 = 745) asked participants to provide free associations for suffering. Chinese individuals generated more positive associations than did Euro-Canadians. Study 2 (N = 522) had participants create a hypothetical potion of suffering to represent what people would experience while suffering. Chinese participants added more positive ingredients and fewer negative ingredients than Euro-Canadians did. How would cultural differences in the construal of suffering matter in a real-life negative situation? Study 3 (N = 608) showed that Chinese participants generated a greater proportion of potential positive outcomes for the COVID-19 outbreak and reported more positive affect during the pandemic than did Euro-Canadians. Thus, Chinese construe suffering more positively than Euro-Canadians. These findings are consistent with previous research on cultural differences in dialectical thinking and lay theory of change and have implications for coping and resilience.
Robust Audio-Visual Mandarin Speech Recognition Based On Adaptive Decision Fusion And Tone Features

Audio-visual speech recognition (AVSR) integrates both audio and visual information to perform automatic speech recognition (ASR), which improves the robustness of human-robot interaction systems especially in noise environments. However, few methods and applications have paid attention to AVSR in tonal languages, in which the linguistic feature can play an important role as well as visual information. In this work, we propose a method for AVSR in Mandarin based on adaptive decision fusion as well as making full use of tone features. Firstly, we introduce tone features calculated by Constant Q trasform (CQT) and put them into a CNN-based audio network together with Mel-Frequency Cepstral Coefficient (MFCC) audio features. Then, the visual features are extracted by Discrete Cosine Transform (DCT) from mouth regions in video frames and modeled by an LSTM-based visual network. Finally, an adaptive decision fusion network combines the outputs from both streams to make final predictions. Experimental results on the PKU-AV2 dataset show that the tone features can significantly improve the robustness of Mandarin speech recognition systems, and the adaptability of the proposed method to various noise environments.
Stamps extraction using local adaptive k- means and ISODATA algorithms

One of the main difficulties facing the certified documents documentary archiving system is checking the stamps system, but, that stamps may be contains complex background and surrounded by unwanted data. Therefore, the main objective of this paper is to isolate background and to remove noise that may be surrounded stamp. Our proposed method comprises of four phases, firstly, we apply k-means algorithm for clustering stamp image into a number of clusters and merged them using ISODATA algorithm. Secondly, we compute mean and standard deviation for each remaining cluster to isolate background cluster from stamp cluster. Thirdly, a region growing algorithm is applied to segment the image and then choosing the connected region to produce a binary mask for the stamp area. Finally, the binary mask is combined with the original image to extract the stamp regions. The results indicate that the number of clusters can be determined dynamically and the largest cluster that has minimum standard deviation (i.e., always the largest cluster is the background cluster). Also, show that the binary mask can be established from more than one segment to cover are all stamp’s disconnected pieces and it can be useful to remove the noise appear with stamp region.
Effect of Trypsin on Antioxidant Activity and Gel-Rheology of Flaxseed Protein

Abstract Enzymatic hydrolysis of flaxseed protein (FP) was carried out using trypsin in order to obtain flaxseed protein hydrolysates possessing better antioxidative property and modified rheological properties. The antioxidative properties of hydrolysates were much higher than the unhydrolyzed flaxseed protein. The hydrolysis also significantly reduced the hydrodynamic diameter of the magnitude of zeta potential of the dispersions. The gelling point of the hydrolysates occurred earlier than the unhydrolyzed sample while the duration of hydrolysis (30–120 min) did not affect gelling point of the hydrolysates. Considerable decrease in the gel strength and the frequency dependence of gel strength were observed in gels produced using hydrolyzed flaxseed protein. The above findings indicate that hydrolysates possessing high degree of antioxidative properties. The gels produces from these hydrolysates will have fast gelling property and will produce gels with reasonable strength. Thus, flaxseed protein hydrolysates obtained from trypsin hydrolysis can be used in applications that require proteins with higher antioxidative properties but softer texture.
Relationship between Ancestry Inferred By Molecular Analysis, Self-Report and Hetero-Classification

Population stratification is the main cause of spurious results and the difficulty of replicating genetic association findings. In admixed populations, there is evidence that such proxies do not provide efficient control of stratification. We aimed to evaluate the statistical relationship between self-reported, hetero-classified and genetic ancestry, defined by categories of skin color and individual ancestry estimates and by the genotyping of 48 ancestry-informative indel markers in a sample of 130 volunteers from the city of Macapa in the Amazonian state of Amapa - Brazil. Five groups of self- reported skin color were defined: white, light brown, middle brown, dark brown and blacks, and three groups of predominant ancestry were defined: European, African and Native American. The results showed a significant correlation between skin color and predominant ancestry, self-reported and hetero-classified by volunteers, in comparison with the genetic ancestry, an important potential application of these AIMs in forensic investigations.
Measuring Nonapoptotic Caspase Activity with a Transgenic Reporter in Mice

Abstract The protease caspase-3 is a key mediator of apoptotic programmed cell death. But weak or transient caspase activity can contribute to neuronal differentiation, axonal pathfinding, and synaptic long-term depression. Despite the importance of sublethal, or nonapoptotic, caspase activity in neurodevelopment and neural plasticity, there has been no simple method for mapping and quantifying nonapoptotic caspase activity (NACA) in rodent brains. We therefore generated a transgenic mouse expressing a highly sensitive and specific fluorescent reporter of caspase activity, with peak signal localized to the nucleus. As a proof of concept, we first obtained evidence that NACA influences neurophysiology in an amygdalar circuit. Then focusing on the amygdala, we were able to quantify a sex-specific persistent elevation in caspase activity in females after restraint stress. This simple in vivo caspase activity reporter will facilitate systems-level studies of apoptotic and nonapoptotic phenomena in behavioral and pathologic models.
Integrating community phylogenetics and phylogenetic beta diversity to understand Amazonian trees community assembly: a biogeographical and conservation approach

Author(s): Guevara Andino, Juan Ernesto | Advisor(s): Fine, Paul V.A. | Abstract: Understanding the tree species composition and turnover in Amazon forests has fascinated ecologists and evolutionary biologists since the first botanical expeditions from the 19th century. More recently, the advent of community phylogenetics and phylogenetic beta diversity methods has been demonstrated to be powerful tools to investigate the patterns and causes of Amazonian tree species assemblies. However, the lack of a comprehensive sampling of tree species communities using well-standardized taxonomy across gradients of soils, geology and climate has precluded making conclusions about the relative importance of these environmental filters on the patterns of species and lineage composition and turnover. In addition, due to current threats that Amazon forests are experiencing an ecologically informed delineation of floristic boundaries is urgently needed to guide conservation decisions. In this dissertation, I present the results of intensive floristic sampling at two spatial scales continental and regional, and show that the complementary implementation of phylogenetic beta diversity and community phylogenetics can help us to better describe and analyze floristic patterns of Amazon tree communities. Additionally, I used this combination of methods to determine high priority conservation areas that are currently experiencing severe threats in Ecuador Amazon.
The influence of titanate coupling agent on the performance of barium titanate/PMMA denture base nanocomposites after SBF storage

Poly(methyl methacrylate) (PMMA)/nanobarium titanate (NBT) composite has potential application in denture base materials. The denture base materials should be stable in the wet environment and exhibit good mechanical properties. This study aimed to evaluate the effectiveness of titanate coupling agent (TCA) on NBT behavior after soaking in the simulated body fluid (SBF) and to determine the effect of SBF exposure on fracture toughness of the PMMA nanocomposites. Silanated (Si-NBT), titanated (Ti-NBT), and pure NBT (Un-NBT) at 5% concentration (by mass) were incorporated in the PMMA matrix. NBT was sonicated in MMA prior to mixing with PMMA. SBF absorption, solubility, and leaching were measured, and fracture toughness of the PMMA nanocomposites was evaluated after soaking. The results showed that Titanated samples displayed lower SBF absorption capability and solubility values than the silanated ones. Moreover, the leachability of filler elements (Ba and Ti) was substantially reduced by titanation (54% and 61%, respectively), whereas the Si-NBT/PMMA revealed values of 12.3% and 7% respectively. Significant differences in fracture toughness were observed among the tested samples after 6 weeks of aging in SBF (p < 0.05). Although no notable changes in the KIC of pure PMMA and Un-NBT/PMMA samples were detected, KIC was improved by 20% after titanation. In addition, the fracture toughness of the titanated samples was higher than that of the silanated ones by 26%. In conclusion, TCA exhibited better stability in moisture than silane. Degradation resistance to moisture obtained with titanated NBT could lead to the promotion of clinical longevity of the composites.
A comparative study on the performance of RCC for pavements casted in laboratory and field

ABSTRACT Due to its superior properties, usage of Roller Compacted Concrete (RCC) in pavement applications gradually increases. As the compaction effort and curing conditions applied are significantly altered between laboratory and field conditions, performance of RCC may be considerably different. Therefore, studies that are carried out to compare the laboratory and field RCC performance have crucial importance. On the other hand, number of these studies are very limited. In the presented study, a RCC mixture was designed and applied to a site in Kocaeli/Turkey. Required pavement thickness was determined based on AASHTO (1993) design methodology, and performance of laboratory and field RCC (in terms of compressive strength, splitting tensile strength, ultrasonic pulse velocity (UPV), capillarity, abrasion resistance, density, water absorption and porosity) were determined and compared. As a result of the study for almost all of the performance parameters decreased values were obtained for RCC when compared to laboratory specimens. This result was attributed to difference between field and laboratory compaction effort and curing conditions.
Ethanol from Lignocellulosic Biomass: Deacetylation, Pretreatment, and Enzymatic Hydrolysis

ii Acknowledgments. v List of Figures . xiv List of Tables . xviii List of Abbreviations . xix Chapter I Introduction . 1 I.1 Motivation . 1 I.2 Objectives . 2 Chapter II Literature Review . 4 II.1 Need for biofuels. 4 II.1. 1 Environmental concerns . 4 II.1. 2 Benefits of using biomass . 5 II.2 Biomass: types and composition . 6 II.2. 1 Types of feedstock . 6 II.2. 2 Biomass composition . 8 II.2. 3 Need for pretreatment . 11 II.3 Pretreatment effects and its types . 12
Reliability and Construct Validity of the Leipzig Short Scale of Sense of Coherence (SOC-L9) in Japanese Sample: The Rasch Measurement Model and Confirmatory Factor Analysis

The present study aimed to examine the reliability and construct validity of the “Leipzig Short Scale of Sense of Coherence” (SOC-L9) in a Japanese sample, using item analysis based on the Rasch measurement model, confirmatory factor analysis, and longitudinal correlation analysis. According to the item fit statistics, nine items and the total score were confirmed to fit the model assuming the one latent factor. Furthermore, the SOC-L9 scores significantly correlated with the original 29-item version of the SOC-L9. The factor analysis showed that, similar to the previous study, the same model which assumed covariance between errors of some items, was suitable. These results indicate that SOC-L9 had high reliability and validity.
About P‐glycoprotein: a new drugable domain is emerging from structural data

P‐glycoprotein (P‐gp) has been considered an important molecular target in the reversal of multidrug resistance (MDR). As such, the development of P‐gp modulators able to restore drug sensitivity in resistant cells is still considered one of the most promising strategies for overcoming MDR. Since the identification of the P‐gp's role in MDR, several studies have been performed in order to develop effective P‐gp modulators and understand the efflux mechanism. However, no efflux modulator is still clinically available for treating multidrug‐resistant cancers. Nevertheless, recent experimental studies suggest that MDR can be surpassed by targeting a specific region within the ABC transporter structure rather than the polyspecific drug‐binding pocket. This article will focus on the information available about this new target region and on a brief overview of which scaffolds would be suitable for modulating P‐gp at this new location. WIREs Comput Mol Sci 2017, 7:e1316. doi: 10.1002/wcms.1316