Miracle-dz/UniFAR-FTUs huggingface dataset:
Convergent evolution and parallelism in plant domestication revealed by an expanding archaeological record

Significance Agriculture was a transformative development in the history of human societies and natural environments and drove the evolution of new domesticated species. Crop plants are the predominant domesticated species in most agricultural systems and are an essential component in all the food production systems that underpinned the development of urban societies. Archaeological plant remains provide a range of insights into the processes by which plants were domesticated in different parts of the world. The present paper provides a unique synthesis of evidence, including quantitative evidence on the trajectory and rate of domestication in seed crops and patterns in the development of tropical vegetatively propagated crops. Recent increases in archaeobotanical evidence offer insights into the processes of plant domestication and agricultural origins, which evolved in parallel in several world regions. Many different crop species underwent convergent evolution and acquired domestication syndrome traits. For a growing number of seed crop species, these traits can be quantified by proxy from archaeological evidence, providing measures of the rates of change during domestication. Among domestication traits, nonshattering cereal ears evolved more quickly in general than seed size. Nevertheless, most domestication traits show similarly slow rates of phenotypic change over several centuries to millennia, and these rates were similar across different regions of origin. Crops reproduced vegetatively, including tubers and many fruit trees, are less easily documented in terms of morphological domestication, but multiple lines of evidence outline some patterns in the development of vegecultural systems across the New World and Old World tropics. Pathways to plant domestication can also be compared in terms of the cultural and economic factors occurring at the start of the process. Whereas agricultural societies have tended to converge on higher population densities and sedentism, in some instances cultivation began among sedentary hunter–gatherers whereas more often it was initiated by mobile societies of hunter–gatherers or herder–gatherers.
Judicial Independence: Some Evidence from the English Court of Appeal

This paper is concerned with the existence or otherwise of conscious political interference with judicial decision taking. We produce new evidence from the English Court of Appeal to shed some light on the theoretical debate on judicial independence. This evidence rests on the fact that the procedure for promoting judges from the Court of Appeal to the House of Lords is in principle under political control: the lord chancellor, who has a key role in the promotion of judges, is a member of the cabinet and as such a political appointee. The data relate to public law decisions made by judges in the Court of Appeal over the period 1951–86. We use a competing risks survival model to establish whether the record of individual judges in deciding for or against the government was a factor that determined their promotion chances, controlling for the quality of their decision making.
Null-matching for the design of linear aperiodic arrays

In this paper the design of linear aperiodic arrays is solved imposing that the nulls of the array factor match those of a Dolph-Chebyschev reference array. With respect to a previous work published by Haupt [R.L. Haupt, 1995], the present technique permits to design aperiodic arrays with an arbitrary number of elements. The maximum sidelobe level achievable with an assigned number of array elements is identified.
Biokinetic Modeling and in Vitro–in Vivo Extrapolations

The introduction of in vitro methodologies in the toxicological risk assessment process requires a number of prerequisites regarding both the toxicodynamics and the biokinetics of the compounds under study. In vitro systems will need to be relevant for measuring those structural and physiological changes that are good indicators for adverse effects. Furthermore, the dose metric found to have an effect in the in vitro system should be relevant. One element in defining the appropriate dose metric is related to the kinetic behavior of the compound in the in vitro system: binding to proteins, binding to plastic, evaporation, and the interaction between the culture medium and the cells. Ways to measure and model “in vitro biokinetics” are described. Second, the appropriate dose metric in vitro, e.g., the effective concentration, will need to be extrapolated to relevant in vivo exposure scenarios. The application of physiologically based biokinetic modelling is essential in such extrapolations. The parameters needed to build these models often can be estimated based on nonanimal data, namely chemical properties (QSARs) and in vitro experiments.
Measures of current alcohol consumption and problems: two independent twin studies suggest a complex genetic architecture.

BACKGROUND Twin studies demonstrate that measures of alcohol consumption (AC) show evidence of genetic influence, suggesting they may be useful in gene identification efforts. The extent to which these phenotypes will be informative in identifying susceptibility genes involved in alcohol dependence depends on the extent to which genetic influences are shared across measures of AC and alcohol problems. Previous studies have demonstrated that AC reported for the period of heaviest lifetime drinking shows a large degree of genetic overlap with alcohol dependence; however, many studies with genetic material assess current AC. Further, there are many different aspects of AC that can be assessed (e.g., frequency of use, quantity of use, and frequency of intoxication). METHODS Here, we use data from 2 large, independent, population-based twin samples, FinnTwin 16 and The Virginia Adult Twin Study of Psychiatric and Substance Use Disorders, to examine the extent to which genetic influences are shared across many different measures of AC and alcohol problems. RESULTS Genetic correlations across current AC measures and alcohol problems were high across both samples. However, both samples suggest a complex genetic architecture with many different genetic factors influencing various aspects of current AC and problems. CONCLUSIONS These results suggest that careful attention must be paid to the phenotype in efforts to "replicate" genetic effects across samples or combine samples for meta-analyses of genetic effects influencing susceptibility to alcohol-related outcomes.
The effect of enteral nutrition supplements on serum voriconazole levels

This is the case of a 13-year-old Hispanic boy (34.2 kg, 1.14 m2) who had achieved stable therapeutic levels on voriconazole who later experienced levels reported as ‘none detected’ after the initiation of tube feeds. This case outlines the temporal relationship of the effect of tube feeds on voriconazole serum levels. Based on this information, voriconazole suspension should not be prescribed to patients also receiving supplemental enteral nutrition. In absence of formal animal or human pharmacokinetic studies, it is the recommendation of the author to separate this combination and to be very vigilant about checking serum voriconazole levels in patients on voriconazole suspension and enteral nutrition supplements.
Services Selection of Transactional Property for Web Service Composition

Web service composition enables seamless and dynamic integration of business applications on the web. Due to the inherent autonomy and heterogeneity of component Web services it is difficult to predict the behavior of the overall composite service. Therefore, transactional properties are crucial for selecting the web services to take part in the composition. Transactional properties ensure reliability of composite Web service. In this paper we propose a novel selection approach based on transactional properties of ensuring reliability. We build a model to implement transactional-aware service selection, and use the model composite Web service to guarantee reliable execution. We evaluate our approach experimentally using both real and synthetically generated datasets.
Hypermethylation of HPP 1 Is Associated with hMLH 1 Hypermethylation in Gastric Adenocarcinomas 1

The HPP1 gene was initially discovered because of its frequent hypermethylation in hyperplastic colon polyps, but it is also hypermethylated in colorectal adenomas and carcinomas. Expression of the DNA mismatch repair gene hMLH1 is diminished or absent in some hyperplastic polyps, and it has been suggested that HPP1 inactivation is associated with the progression of microsatellite-unstable colorectal tumors. We sought then to determine the prevalence of HPP1 silencing by DNA methylation in gastric adenocarcinomas and to define any association of this event with microsatellite instability (MSI) or hMLH1 hypermethylation. Thirty-two matched normal-gastric adenocarcinoma DNA pairs were studied for MSI status and hypermethylation of HPP1 and hMLH1. Five (100%) of 5 MSI-H tumors, 2 (50%) of 4 MSI-L tumors, and 8 (35%) of 23 MSS tumors demonstrated HPP1 hypermethylation. Eight (25%) of 32 tumors (5 of 5 MSI-H, 2 of 4 MSI-L, and 1 of 23 MSS) showed evidence of hMLH1 hypermethylation. All (8 of 8) of these hMLHI-methylated tumors demonstrated concomitant methylation at the HPP1 locus: there were no cases of hMLH1 methylation occurring in the absence of HPP1 methylation. In gastric adenocarcinoma, hypermethylation frequently targets HPP1. Moreover, hMLH1 hypermethylation occurs predominantly in the setting of HPP1 hypermethylation. HPP1 hypermethylation may represent an early event in mismatch repair-deficient gastric tumorigenesis.
Are Large Scale Training Images or Discriminative Features Important for Codebook Construction?

Advances in machine learning and image feature representations have led to great progress in pattern recognition approaches in recognising up to 1000 visual object categories. However, the human brain solves this problem effortlessly as it can recognise about 10000 to 100000 objects with a small number of examples. In recent years bag-of-features approach has proved to yield state-of-the-art performance in large scale evaluations. In such systems a visual codebook plays a crucial role. For constructing a codebook researchers cover a large-scale of training image set. But this brings up the issue of scalability. A large volume of training data becomes difficult to process whereas the high dimensional image representation could make many machine learning algorithms become inefficient or even a breakdown. In this work we investigate whether the dominant bag-of-features approach used in object recognition will continue significantly to improve with large training image set or not. We have validated a one-pass clustering algorithm to construct visual codebooks for object classification tasks on the PASCAL VOC Challenge image set. Our testing results show that adding more training images do not contribute significantly to increase the performance of classification but it increases the overall model complexity in terms of increased storage requirement and greater computational time. This study further suggests an alternative view to the community working with the patch-based object recognition to enforce retaining more discriminative descriptors rather than the reminiscent of the BIG data hypothesis.
Cytochrome P450 2C9 variants influence response to celecoxib for prevention of colorectal adenoma.

BACKGROUND & AIMS Variants in the cytochrome P450 2C9 (CYP2C9) gene are associated with impaired metabolism of celecoxib. We examined the influence of CYP2C9*2 (R144C) and CYP2C9*3 (I359L) variants on dose-related response or toxicity in a randomized trial of celecoxib. METHODS We identified individuals with CYP2C9*2 and CYP2C9*3 genotypes (>or=1 variant allele) in the Adenoma Prevention with Celecoxib trial. Following adenoma removal, patients were assigned randomly to groups given placebo or low-dose (200 mg twice daily) or high-dose (400 mg twice daily) celecoxib and underwent follow-up colonoscopies at 1 and/or 3 years. RESULTS Among 1660 patients, 21% were CYP2C9*2, and 12% were CYP2C9*3 genotypes. Overall, celecoxib was associated with a dose-dependent reduction in adenoma, compared with placebo, with relative risks (RR) of 0.65 (95% confidence interval [CI]: 0.56-0.76) for the low-dose and 0.54 (95% CI: 0.46-0.63) for the high-dose groups. However, the additional protective effect of the high dose, compared with the low-dose, was observed only in those with CYP2C9*3 genotypes (RR, 0.51; 95% CI: 0.30-0.87). The high dose, compared with low dose, was not associated with significant risk reduction among those with CYP2C9*2 (RR, 0.83; 95% CI: 0.57-1.21) or wild-type (RR, 0.89; 95% CI: 0.72-1.11) genotypes. Compared with placebo, a higher incidence of cardiovascular events was associated with both doses among patients with wild-type genotypes but only with the high dose among patients with variant genotypes. CONCLUSIONS The greater efficacy of high-dose celecoxib, compared with the low-dose, in preventing colorectal adenoma appears confined to individuals with slow metabolizer (CYP2C9*3) genotypes. Genetic variability influences susceptibility to the potential benefits and hazards of celecoxib.
Land Use Change at the National and Regional Level in China: A Scenario Analysis Based on Input-Output Modeling

Land availability is of crucial importance for China's development in the 21 century. Economic growth, urbanization, changes in life styles such diet changes, and population growth will influence both the demand for and the supply of land. In this study, an input-output model expanded by a set of land categories is developed to synthesize various scenarios of changes in the economy and society, and to evaluate their impact on land-use changes in China. The scenario analysis is conducted at both the national and regional levels and for the time horizon of over 30-years. The analysis aims to show how different development paths will influence the available land base as well as the inter-regional and international trade flows of primary products for China in the coming decades. To do this is a mixed model with supply-constraints for the major land-consuming sectors is used. Given the moderate pace of technological progress, as commonly assumed in the literature, the resultant increases in final demands and sectoral outputs would drive the associated land requirements to exceed the then available land area. Scarcity of cultivated land, grassland, and forestland will be persistent. If the traditional policy of grain and food self-sufficiency were maintained intact, to keep the farmland requirement feasible, an annual growth rate of land-productivity of about 1.28 percent would be required, which is higher than what is usually expected for the next 30 years. In addition, faster technological advancement in the livestock sector will be necessary.
Organoleptic and nutritional analysis of taro and wheat flour composite bread.

The effect of supplementing wheat flour with taro flour in the production of bread has been investigated. It is observed from the organoleptic analysis of the taro-supplemented bread samples studied in this work that generally, the preference for taro-supplemented bread decreased with the amount of taro in the bread. However, the panellists scores for the composite bread in some attributes were comparable to the control. Bread with 30 percent taro flour had the highest rating in colour while the bread with 50 percent taro flour had the highest rating in texture. Although the bread from the whole wheat flour was rated higher in many of the attributes, the taro-supplemented bread produced desirable organoleptic quality. Incorporation of taro flour to wheat flour would lead to reduction of cost of bread in Ghana. The preference of the panellists for the sensory attributes of the wheat flour bread may be due to the familiarization of consumers to the normal whole wheat flour. From the proximate analysis, it was observed that the increased amount of taro resulted in decreasing the protein content, fat, carbohydrate and energy while moisture and ash increased.
Advancing Pharmacogenomics as a Component of Precision Medicine: How, Where, and Who?

Pharmacogenomics is an important element of precision medicine. Advances in pharmacogenomics implementation have been made but significant barriers remain, including evidence, reimbursement, and clinician knowledge, among others. Widespread adoption of pharmacogenomics requires overcoming these barriers, a clinician champion group, which we propose will be pharmacists, and an easily accessible setting, which may be the community pharmacy. Whatever the path, it must be evidence‐driven and pharmacogenomics must improve drug‐related outcomes to become a standard of care.
Ontology-Mediated Querying with EL: Trichotomy and Linear Datalog Rewritability

We consider ontology-mediated queries (OMQs) based on an EL ontology and an atomic query (AQ), provide an ultimately finegrained analysis of data complexity and study rewritability into linear Datalog – aiming to capture linear recursion in SQL. Our main results are that every such OMQ is in AC0, NL-complete or PTime-complete, and that containment in NL coincides with rewritability into linear Datalog (whereas containment in AC0 coincides with rewritability into first-order logic). We establish natural characterizations of the three cases, show that deciding linear Datalog rewritability (as well as the mentioned complexities) is ExpTime-complete, give a way to construct linear Datalog rewritings when they exist, and prove that there is no constant bound on the arity of IDB relations in linear Datalog rewritings.
Motion processing in the auditory cortex of the rufous horseshoe bat: role of GABAergic inhibition

This study examined the influence of inhibition on motion‐direction‐sensitive responses of neurons in the dorsal fields of auditory cortex of the rufous horseshoe bat. Responses to auditory apparent motion stimuli were recorded extracellularly from neurons while microiontophoretically applying γ‐aminobutyric acid (GABA) and the GABAA receptor antagonist bicuculline methiodide (BMI). Neurons could respond with a directional preference exhibiting stronger responses to one direction of motion or a shift of receptive field (RF) borders depending on direction of motion. BMI influenced the motion direction sensitivity of 53% of neurons. In 21% of neurons the motion‐direction sensitivity was decreased by BMI by decreasing either directional preference or RF shift. In neurons with a directional preference, BMI increased the spike number for the preferred direction by a similar amount as for the nonpreferred direction. Thus, inhibition was not direction specific. BMI increased motion‐direction sensitivity by either increasing directional preference or magnitude of RF shifts in 22% of neurons. Ten percent of neurons changed their response from a RF shift to a directional preference under BMI. In these neurons, the observed effects could often be better explained by adaptation of excitation rather than inhibition. The results suggest, that adaptation of excitation, as well as cortex specific GABAergic inhibition, contribute to motion‐direction sensitivity in the auditory cortex of the rufous horseshoe bat.
16 x 16 VCSEL array flip-chip bonded to CMOS VLSI circuit

We report the flip-chip bonding of a 16/spl times/16 array of 970-nm vertical-cavity surface-emitting lasers (VCSELs) to an array of silicon CMOS driver circuits. The small-signal bandwidth of a flip-chip bonded VCSEL is in excess of 4 GHz. Individual VCSELs are capable of being modulated by the CMOS circuits at 1 Gb/s. The thermal impedance of the flip-chip bonded VCSELs is 1/spl deg/C/mW. The measured crosstalk suppression between channels is approximately 20 dB. Simultaneous parallel testing of up to 80 VCSELs at 1 Gb/s per VCSEL is demonstrated.
Bacterial spore structures and their protective role in biocide resistance

The structure and chemical composition of bacterial spores differ considerably from those of vegetative cells. These differences largely account for the unique resistance properties of the spore to environmental stresses, including disinfectants and sterilants, resulting in the emergence of spore‐forming bacteria such as Clostridium difficile as major hospital pathogens. Although there has been considerable work investigating the mechanisms of action of many sporicidal biocides against Bacillus subtilis spores, there is far less information available for other species and particularly for various Clostridia. This paucity of information represents a major gap in our knowledge given the importance of Clostridia as human pathogens. This review considers the main spore structures, highlighting their relevance to spore resistance properties and detailing their chemical composition, with a particular emphasis on the differences between various spore formers. Such information will be vital for the rational design and development of novel sporicidal chemistries with enhanced activity in the future.
Extraction methods and food uses of a natural red colorant from dye sorghum.

BACKGROUND The interest in stable natural colorants for food applications continues to grow. A red pigment extracted from the leaf sheaths of a sorghum variety (Sorghum bicolor) with a high content of apigeninidin is widely used as a biocolorant in processed foods in West Africa. This study compared the colour and anthocyanin composition from traditional extraction methods to determine options for improvement and use of the red biocolorant from dye sorghum in the food sector. RESULTS Sorghum biocolorant was commonly applied in fermented and heated foods. Traditional extraction methods predominantly differed in two aspects, namely the use of an alkaline rock salt (locally known as kanwu) and the temperature of the extraction water. Cool extraction using the alkaline ingredient was more efficient than hot alkaline and hot aqueous extractions in extracting anthocyanins. The apigeninidin content was three times higher in the cool and hot alkaline extracts than in the aqueous extract. CONCLUSION Cool and hot alkaline extractions at pH 8-9 were the most efficient methods for extracting apigeninidin from dye sorghum leaf sheaths. Broader use of the sorghum biocolorant in foods requires further research on its effects on nutrient bioavailability and antioxidant activity. © 2017 Society of Chemical Industry.