Miracle-dz/UniFAR-FTUs huggingface dataset:
Identification and Validation of Reference Genes for RT-qPCR Analysis in Non-Heading Chinese Cabbage Flowers

Non-heading Chinese cabbage (Brassica rapa ssp. chinensis Makino) is an important vegetable member of Brassica rapa crops. It exhibits a typical sporophytic self-incompatibility (SI) system and is an ideal model plant to explore the mechanism of SI. Gene expression research are frequently used to unravel the complex genetic mechanism and in such studies appropriate reference selection is vital. Validation of reference genes have neither been conducted in Brassica rapa flowers nor in SI trait. In this study, 13 candidate reference genes were selected and examined systematically in 96 non-heading Chinese cabbage flower samples that represent four strategic groups in compatible and self-incompatible lines of non-heading Chinese cabbage. Two RT-qPCR analysis software, geNorm and NormFinder, were used to evaluate the expression stability of these genes systematically. Results revealed that best-ranked references genes should be selected according to specific sample subsets. DNAJ, UKN1, and PP2A were identified as the most stable reference genes among all samples. Moreover, our research further revealed that the widely used reference genes, CYP and ACP, were the least suitable reference genes in most non-heading Chinese cabbage flower sample sets. To further validate the suitability of the reference genes identified in this study, the expression level of SRK and Exo70A1 genes which play important roles in regulating interaction between pollen and stigma were studied. Our study presented the first systematic study of reference gene(s) selection for SI study and provided guidelines to obtain more accurate RT-qPCR results in non-heading Chinese cabbage.
Decomposable Modeling in Natural Language Processing

In this paper, we describe a framework for developing probabilistic classifiers in natural language processing. Our focus is on formulating models that capture the most important interdependencies among features, to avoid overfitting the data while also characterizing the data well. The class of probability models and the associated inference techniques described here were developed in mathematical statistics, and are widely used in artificial intelligence and applied statistics. Our goal is to make this model selection framework accessible to researchers in NLP, and provide pointers to available software and important references. In addition, we describe how the quality of the three determinants of classifier performance (the features, the form of the model, and the parameter estimates) can be separately evaluated. We also demonstrate the classification performance of these models in a large-scale experiment involving the disambiguation of 34 words taken from the HECTOR word sense corpus (Hanks 1996). In 10-fold cross-validations, the model search procedure performs significantly better than naive Bayes on 6 of the words without being significantly worse on any of them.
Resistance phenotype and clinical molecular epidemiology of carbapenem-resistant Klebsiella pneumoniae among pediatric patients in Shanghai

Background Carbapenem-resistant Klebsiella pneumoniae (CRKP) has caused wide global disseminations and serious clinical outcomes in pediatric patients, and the purpose of this study was to analyze drug resistance, molecular epidemiology, and clinical characteristics of CRKP from children in Shanghai, China. Methods A retrospective study was conducted from January 2016 to December 2017, and a total of 170 CRKP isolates were collected. Antimicrobial susceptibility was determined by the broth microdilution method. MAST D73C and polymerase chain reaction were used for the analysis of carbapenemase types. Multilocus sequence typing of K. pneumoniae was performed for genetic relationship. Clinical data were also reviewed. Results Of the 170 CRKP isolates, blaOXA-232 was mainly detected with a proportion of 42.35%, followed by blaNDM-1 (20.59%), blaKPC-2 (17.65%), blaNDM-5 (16.47%), and blaIMP-4 (1.18%). The predominant gene was blaOXA-232 in 2016 (54.46%; 55/101) and blaNDM-1 in 2017 (31.88%; 22/69). All these 170 CRKP isolates showed high resistance to cephalosporins and carbapenems (>95%), except for tigecycline and colistin. Sixteen distinct sequence types were observed with ST15 being mostly identified (41.76%). Most CRKP harboring OXA-232 type carbapenemase belonged to ST15, while NDM-1 type belonged to ST37 and KPC-2 type belonged to ST11. Furthermore, other β-lactamase genes including blaTEM, blaCTX-M, and DHA-1 were also found in this study. Clinical data reviewed that more than half of the patients produced clinical infections (112/170), mainly lower respiratory tract (58/112) and bloodstream (21/112) infections. A majority of these children had received therapy of antibiotics before CRKP isolation, especially for carbapenems (76/170) and β-lactam/β-lactamase inhibitor combinations (91/170). Conclusions Our data revealed the increasing incidence of OXA-232-producing K. pneumoniae from pediatric patients in Shanghai, and infection control measures should be conducted to limit the spread of CRKP strains.
Heterogeneity of antibiotic resistance in mucoid isolates of Pseudomonas aeruginosa obtained from cystic fibrosis patients: role of outer membrane proteins

Mucoid Pseudomonas aeruginosa strains isolated from cystic fibrosis patients are very heterogeneous and include a class which is hypersusceptible to carbenicillin (minimum inhibitory concentration, less than or equal to 1 microgram/ml). Hypersusceptible mucoid P. aeruginosa isolates were found in 12 of 22 cystic fibrosis patients examined. In cystic fibrosis patients having both resistant and hypersusceptible mucoid strains, 24 of 54 mucoid colonies obtained from a sputum sample were found to belong to the hypersusceptible class. In most instances, hypersusceptible and resistant strains isolated from the same sputum sample were indistinguishable, aside from their antibiotic susceptibilities, by classical methods. A particular pair of mucoid isolates (one hypersusceptible and one resistant) was chosen for further study. The hypersusceptibility was not limited to carbenicillin but was found to extend to other penicillins, tetracycline, and trimethoprim but not to the aminoglycosides gentamicin and tobramycin. The hypersusceptibility of the mucoid strain was found to be unrelated to amount or ability to synthesize alginate. The hypersusceptible strain was found to have two additional outer membrane proteins (32,000 and 25,000 daltons) as compared with the resistant strain. The 32,000-dalton protein, termed protein N1, was found to be correlated to the hypersusceptibility phenotype, as all spontaneous mutants of the hypersusceptible mucoid strain which were capable of growing in the presence of 50 microgram of carbenicillin per ml had lost the 32,000-dalton outer membrane protein. The possible origins of the hypersusceptibility phenotype and the implications of the heterogeneity of mucoid P. aeruginosa in the pathogenesis of P. aeruginosa are discussed.
Shallow Bounding Volume Hierarchies for Fast SIMD Ray Tracing of Incoherent Rays

Photorealistic image synthesis is a computationally demanding task that relies on ray tracing for the evaluation of integrals. Rendering time is dominated by tracing long paths that are very incoherent by construction. We therefore investigate the use of SIMD instructions to accelerate incoherent rays. SIMD is used in the hierarchy construction, the tree traversal and the leaf intersection. This is achieved by increasing the arity of acceleration structures, which also reduces memory requirements. We show that the resulting hierarchies can be built quickly and are smaller than acceleration structures known so far while at the same time outperforming them for incoherent rays. Our new acceleration structure speeds up ray tracing by a factor of 1.6 to 2.0 compared to a highly optimized bounding interval hierarchy implementation, and 1.3 to 1.6 compared to an efficient kd‐tree. At the same time, the memory requirements are reduced by 10–50%. Additionally we show how a caching mechanism in conjunction with this memory efficient hierarchy can be used to speed up shadow rays in a global illumination algorithm without increasing the memory footprint. This optimization decreased the number of traversal steps up to 50%.
Limited Capital Market Participation and Human Capital Risk

The non-tradability of human capital is often cited for the failure of traditional asset pricing theory to explain agents' portfolio holdings. In this paper we argue that the opposite might be true --- traditional models might not be able to explain agent portfolio holdings because they do not explicitly account for the fact that human capital does trade (in the form of labor contracts). We derive wages endogenously as part of a dynamic equilibrium in a production economy. Risk is shared in labor markets because firms write bilateral labor contracts that insure workers, allowing agents to achieve a Pareto optimal allocation even when the span of asset markets is restricted to just stocks and bonds. Capital markets facilitate this risk sharing because it is there that firms offload the labor market risk they assumed from workers. In effect, by investing in capital markets investors provide insurance to wage earners who then optimally choose not to participate in capital markets. The model can produce some of the most important stylized facts in asset pricing: (1) limited asset market participation, (2) the seemingly high equity risk premium, (3) the very large disparity in the volatility of consumption and the volatility of asset prices, and (4) the time dependent correlation between consumption growth and asset returns.
Effects of Soybean Agglutinin on Intestinal Barrier Permeability and Tight Junction Protein Expression in Weaned Piglets

This study was developed to provide further information on the intestinal barrier permeability and the tight junction protein expression in weaned piglets fed with different levels of soybean agglutinin (SBA). Twenty-five weaned crossbred barrows (Duroc × Landrace × Yorkshire) were selected and randomly allotted to five groups, each group with five replicates. The piglets in the control group were not fed with leguminous products. 0.05, 0.1, 0.15 and 0.2% SBA was added to the control diet to form four experimental diets, respectively. After the experimental period of 7 days (for each group), all the piglets were anesthetized with excess procaine and slaughtered. The d-lactic acid in plasma and the Ileal mucosa diamine oxidase (DAO) was analyzed to observe the change in the intestinal permeability. The tight junction proteins occludin and ZO-1 in the jejunum tissue distribution and relative expression were detected by immunohistochemistry and Western Blot. The results illustrated that a high dose of SBA (0.1–0.2%) could increase the intestinal permeability and reduce piglet intestinal epithelial tight junction protein occludin or ZO-1 expression, while low dose of SBA (0.05% of total diet) had no significant affects. The contents of DAO, d-lactic acid, occludin or ZO-1, had a linear relationship with the SBA levels (0–0.2%) in diets. The high dose SBA (0.1–0.2%) could increase the intestinal permeability and reduce piglet intestinal epithelial tight junction protein occludin or ZO-1 expression, while low dose of SBA (0.05% of total diet) had no affects.
Through the Eyes of the Wounded: A Narrative Analysis of Children’s Sexual Abuse Experiences and Recovery Process

Numerous children receive counseling for sexual abuse, yet their personal perspectives related to the abuse, the impact of making the disclosure, and the recovery process are noticeably absent from the scholarly literature. This study addressed this gap by analyzing trauma narratives written by children as part of a counseling intervention. Qualitative analysis revealed three themes: memories of the abuse, the disclosure and subsequent events, and the healing journey. Children’s descriptions of their thoughts, feelings, and beliefs about their experiences are delineated and recommendations are provided for counseling professionals to increase the efficacy of care provided.
Pioglitazone hydrochloride inhibits cholesterol absorption and lowers plasma cholesterol concentrations in cholesterol-fed rats

Diabetes is associated with altered cholesterol metabolism that may contribute to cardiovascular complications. Treatment of rats with pioglitazone hydrochloride, a novel antidiabetic compound that improves the general response of target cells to insulin, significantly lowered cholesterol levels in rats fed a hypercholesterolemic diet and produced a significant reduction in cholesterol absorption. Drug treatment was ineffective in rats that were not given dietary cholesterol. To determine whether these effects of pioglitazone hydrochloride might be related to the known ability of this compound to improve the response to circulating insulin, similar studies were conducted in streptozocin-induced diabetic rats with and without insulin replacement. Diabetic rats absorbed a greater percentage of dietary cholesterol than control rats. Treatment of insulin-deficient diabetic rats with pioglitazone alone did not affect cholesterol absorption; however, the combination of insulin and pioglitazone was synergistic to lower absorption of cholesterol and circulating cholesterol and triglycerides. Treatment of either normal rats or diabetic rats receiving insulin with pioglitazone hydrochloride produced a twofold decrease in the ratio of total cholesterol to high-density lipoprotein cholesterol. These results suggest that treatments that improve insulin sensitivity may also have a positive impact on coronary artery disease associated with diabetes.
Challenges from Variation across Regions in Cost Effectiveness Analysis in Multi-Regional Clinical Trials

Economic evaluation in the form of cost-effectiveness analysis has become a popular means to inform decisions in healthcare. With multi-regional clinical trials in a global development program becoming a new venue for drug efficacy testing in recent decades, questions in methods for cost-effectiveness analysis in the multi-regional clinical trials setting also emerge. This paper addresses some challenges from variation across regions in cost effectiveness analysis in multi-regional clinical trials. Several discussion points are raised for further attention and a multi-regional clinical trial example is presented to illustrate the implications in industrial application. A general message is delivered to call for a depth discussion by all stakeholders to reach an agreement on a good practice in cost-effectiveness analysis in the multi-regional clinical trials. Meanwhile, we recommend an additional consideration of cost-effectiveness analysis results based on the clinical evidence from a certain homogeneous population as sensitivity or scenario analysis upon data availability.
Minimally Needed Evidence for Complex Event Recognition in Unconstrained Videos

This paper addresses the fundamental question -- How do humans recognize complex events in videos? Normally, humans view videos in a sequential manner. We hypothesize that humans can make high-level inference such as an event is present or not in a video, by looking at a very small number of frames not necessarily in a linear order. We attempt to verify this cognitive capability of humans and to discover the Minimally Needed Evidence (MNE) for each event. To this end, we introduce an online game based event quiz facilitating selection of minimal evidence required by humans to judge the presence or absence of a complex event in an open source video. Each video is divided into a set of temporally coherent microshots (1.5 secs in length) which are revealed only on player request. The player's task is to identify the positive and negative occurrences of the given target event with minimal number of requests to reveal evidence. Incentives are given to players for correct identification with the minimal number of requests. Our extensive human study using the game quiz validates our hypothesis - 55% of videos need only one microshot for correct human judgment and events of varying complexity require different amounts of evidence for human judgment. In addition, the proposed notion of MNE enables us to select discriminative features, drastically improving speed and accuracy of a video retrieval system.
Analysis of Bone Plate with Different Material in Terms of Stress Distribution

One of the most used in the field of medicine for the treatment of tibial shaft fractures internal fixation methods is by osteosynthesis plates, the most common plate limited contact dynamic compression (DCP-LC) [1]. This paper presents the results of the fracture site grade 1, where the contact plate and the bone callus area on plates made of bone (LVM stainless steel, titanium alloy different biomedical materials and cobalt alloy), in recovery conditions 1% (one week of recovery), 50% (three weeks of recovery), 75% (six weeks of recovery) and 100%. The fractured tibia bone was modeled with an ideal geometry in CAD [2], modeling of commercial DCP-LC plate was obtained by parameterization of the part using a coordinate machine equipment for the exact geometry. The finite element method for the analysis of each case under the same loads and boundary conditions is used, the results were used to determine stress concentrations in the displacement plate and the fracture callus in the load direction, to have a starting point in the optimization of the geometry from a commercial plate minimizing mass while determining that the material has faster and better biocompatibility with the human body recovery. The results obtained show that the plate under the conditions of three different types of biomaterials has a greater stress concentration in the part located in the fracture zone from stage with 1% recovery between the surfaces of the bone callus upper and lower, keeping this a significant effect on the recovery of the fracture. The compression and tension strength that occur in the intact part of the bone and the tibial fracture interface at different stages of osseous healing have been investigated, The results were compared and presented, showing that the stress distribution in the callus to 1% recovery in the stainless steel plate indicate considerable compression in the area of the callus with this causing deterioration in the area fracture because the callus is not strengthened by contact between fractured bone by increasing the recovery time, the results also indicate that the titanium plate is the one with the lower shielding effect [3] according to the distribution of contact stresses according to the recovery period in the part of callus, making it the material of which the best adaptability to the bone is obtained.
Agricultural Productivity and Structural Transformation. Evidence from Brazil

We study the effects of the adoption of new agricultural technologies on structural transformation. To guide empirical work, we present a simple model where the effect of agricultural productivity on industrial development depends on the factor bias of technical change. We test the predictions of the model by studying the introduction of genetically engineered soybean seeds in Brazil, which had heterogeneous effects on agricultural productivity across areas with different soil and weather characteristics. We find that technical change in soy production was strongly labor saving and lead to industrial growth, as predicted by the model.
Word Lookup on the Basis of Associations : from an Idea to a Roadmap

Word access is an obligatory step in language production. In order to achieve his communicative goal, a speaker/writer needs not only to have something to say, he must also find the corresponding word(s). Yet, knowing a word, i.e. having it stored in a data-base or memory (human mind or electronic device) does not imply that one is able to access it in time. This is a clearly a case where computers (electronic dictionaries) can be of great help. In this paper we present our ideas of how an enhanced electronic dictionary can help people to find the word they are looking for. The yet-to-be-built resource is based on the age-old notion of association: every idea, concept or word is connected. In other words, we assume that people have a highly connected conceptuallexical network in their mind. Finding a word amounts thus to entering the network at any point by giving the word or concept coming to their mind (source word) and then following the links (associations) leading to the word they are looking for(target word). Obviously, in order to allow for this kind of access, the resource has to be built accordingly. This requires at least two things: (a) indexing words by the associations they evoke, (b) identification and labeling of the most frequent/useful associations. This is precisely our goal. Actually, we propose to build an associative network by enriching an existing electronic dictionary (essentially) with (syntagmatic) associations coming from a corpus, representing the average citizen's shared, basic knowledge of the world (encyclopedia). Such an enhanced electronic database resembles in many respects our mental dictionary. Combining the power of computers and the flexibility of the human mind (omnidirectional navigation and quick jumps), it emulates to some extent the latter in its capacity to navigate quickly and efficiently in a large data base. While the notions of association and spreading activation are fairly old, their use to support word access via computer is new. The resource still needs to be built, and this is not a trivial task. We discuss here some of the strategies and problems involved in accomplishing it with the help of people and computers (automation).
Charge Cluster-to-Alanine Scanning of UL128 for Fine Tuning of the Endothelial Cell Tropism of Human Cytomegalovirus

ABSTRACT The viral genes UL128, UL130, and UL131A have been identified as major determinants of endothelial cell (EC) tropism of human cytomegalovirus (HCMV), with deletion of either gene causing a null phenotype. We hypothesized that a functional scanning of these genes by minor genetic modifications would allow for the generation of mutants with an intermediate phenotype. By combining charge cluster-to-alanine (CCTA) mutagenesis with markerless mutagenesis of a bacterial artificial chromosome-cloned endotheliotropic HCMV strain, we analyzed UL128 in order to identify functional sites and hence enable targeted modulation of the EC tropism of HCMV. A total of nine mutations in eight charge clusters were tested. Three of the CCTA mutations severely reduced EC tropism, three were irrelevant, two had a weak effect on cell tropism, and one mutation in the most C-terminal cluster caused an intermediate phenotype. All of the highly effective mutations were located in a core region (amino acids 72 to 106) which appears to be particularly crucial for EC tropism. The intermediate effect of mutations in the C-terminal cluster could be modulated by varying the number of amino acids replaced with alanine. This study provides a rational approach for targeted modulation of HCMV cell tropism, which may aid in the development of HCMV strains with a desired degree of attenuation.