Miracle-dz/UniFAR-FTUs huggingface dataset:
Gene Expression Profiling in Breast Cancer and Its Effect on Therapy Selection in Early-Stage Breast Cancer.

Breast cancer is a heterogeneous disease. The purpose of adjuvant therapy for early-stage breast cancer is to provide maximum benefit with minimum side effects and not to under-treat or over-treat. The clinical progresses of patients with the same clinical and pathological characteristics who are given similar treatments may show major differences. This fact indicates that the prognostic and predictive factors that we have used until recent years for therapy selection are not really sufficient, we need new markers, every disease and every individual are unique and that treatment should be individualized. The gene expression profiling, which has come into clinical use in recent years, is beneficial in therapy selection for luminal breast cancer cases. A differentiation can be made among patients for whom only endocrine treatment would be adequate and those who should also receive chemotherapy in addition to endocrine treatment. Several new gene expression analysis studies targeted at gaining the ability to determine drug selection in chemotherapy, endocrine treatment and neo-adjuvant therapy are also currently ongoing. The staging system for new breast cancer that is to be published in the year 2018 also includes gene expression analyses within the prognostic panel and the stage changes depending on the result. The statement 'Treat the patient, not the disease. ' is becoming increasingly entrenched in our clinical practice. This article briefly summarizes the gene expression profiles, which are validated and used in the selection of therapy for early-stage breast cancer.
Prevalence, Antimicrobial Resistance, and Relatedness of Salmonella Isolated from Chickens and Pigs on Farms, Abattoirs, and Markets in Sichuan Province, China.

This study aims at investigating the distribution, antimicrobial resistance, and genetic relationship of Salmonella isolated from 18 farms, their downstream abattoirs, and markets of chickens and pigs in Sichuan province, China. A total of 193 Salmonella isolates were identified from 693 samples with an isolation rate of 26.27% (88/335) in chickens and 29.33% (105/358) in pigs. Salmonella was isolated more frequently in abattoirs and markets than from farms. Serotypes were determined according to the White-Kauffmann-Le Minor scheme and 16 different serotypes were identified, with Derby being the most common, followed by Typhimurium and Meleagridis. Antimicrobial resistance phenotypes and genotypes were studied by using the disk diffusion method and polymerase chain reaction (PCR) amplification, respectively. Overall, 44.04% (n = 85) of all isolates were multidrug resistant (MDR) and resistance to nalidixic acid (51.30%) was the most frequently observed. blaCTX-M-55 was the most prevalent extended-spectrum β-lactamases gene, and polymyxin resistance gene mcr-1 was present in strains with various serotypes. Multilocus sequence typing indicated that sequence type (ST) had a close relationship with serotype, and 34.20% of all strains were ST40, which was the most prevalent. The unweighted pair group method with arithmetic means (UPGMA) dendrogram of pulsed-field gel electrophoresis showed that Salmonella isolates belonging to the same serovar from different parts of the production chain were highly genetic related, indicating that Salmonella as well as resistance genes could potentially be transmitted from farms to markets. Our study highlights the fact that Salmonella isolates from chicken and pig production chain were frequently exhibiting MDR profiles, and the dissemination of MDR Salmonella from farm to market could pose significant threats to food safety and public health.
Positive effects of plant diversity on soil microbial biomass and activity are associated with more root biomass production

ABSTRACT This study aims to explore relationships between plant diversity and soil microbial function and the factors that mediate the relationships. Artificial plant communities (1, 2, 4 and 8 species) were established filled with natural and mine tailing soils, respectively. After 12 months, the plant species richness positively affected the soil microbial functional diversity in both soil environments but negatively affected microbial biomass and soil basal respiration in the natural soil. The root biomass positively correlated with the microbial biomass, cultural bacterial activity and soil basal respiration in both soil environments. Moreover, the Di (deviations between observed performances and expected performances from the monoculture performance of each species of mixture) of microbial biomass, cultural bacterial activity and soil basal respiration positively correlated with the Di of root biomass in both soil environments. Consistent with stress-gradient hypothesis, the Dmix (over-function index) of aboveground biomass positively correlated plant species richness in the mine tailing soil. Results suggest that the root biomass production is an important mechanism that affects the effects of plant diversity on soil microbial functions. Different responses of soil microbial function to increasing plant diversity may be due to root biomass production mediated by other factors.
Ecological drivers of body size evolution and sexual size dimorphism in short-horned grasshoppers (Orthoptera: Acrididae)

Sexual size dimorphism (SSD) is widespread and variable in nature. Although female-biased SSD predominates among insects, the proximate ecological and evolutionary factors promoting this phenomenon remain largely unstudied. Here, we employ modern phylogenetic comparative methods on 8 subfamilies of Iberian grasshoppers (85 species) to examine the validity of different models of evolution of body size and SSD and explore how they are shaped by a suite of ecological variables (habitat specialization, substrate use, altitude) and/or constrained by different evolutionary pressures (female fecundity, strength of sexual selection, length of the breeding season). Body size disparity primarily accumulated late in the history of the group and did not follow a Brownian motion pattern, indicating the existence of directional evolution for this trait. We found support for the converse of Rensch’s rule across all taxa but not within the two most speciose subfamilies (Gomphocerinae and Oedipodinae), which showed an isometric pattern. Our results do not provide support for the fecundity or sexual selection hypotheses and we did not find evidence for significant effects of habitat use. Contrary to that expected, we found that species with narrower reproductive window are less dimorphic in size than those that exhibit a longer breeding cycle, suggesting that male protandry cannot solely account for the evolution of female-biased SSD in Orthoptera. Our study highlights the need to consider alternatives to the classical evolutionary hypotheses when trying to explain why in certain insect groups males remain small.
New Algorithms for Macromolecular Structure Determination

Detailed three dimensional information of macromolecules is often crucial to the study of biological systems. Structural data have for example been used to elucidate the basis of diseases resulting from variant forms of proteins and design drugs to inhibit molecules involved in diseases. However, given a purified macromolecule under investigation there still is no trivial way to experimentally "image" the three dimensional structure directly. All currently available methods (such as X-ray crystallography, single particle cryo-electron microscopy or nuclear magnetic resonance) deliver experimental data which first have to computationally processed prior to obtaining a meaningful three dimensional structure. Thus, the quality and efficiency of computational methods in structure biology have a major impact on the whole field. Recent advantages in technical setup and computational power allow for the design of new methods which were virtually infeasible to use before. This especially holds true in the field of cryo-EM which computationally is most demanding compared to all other methods mentioned above. In the work presented here new methods for managing and processing the huge amounts of image data produced by the cryo-EM technique are introduced and discussed. Algorithms aiming for accuracy improvements during image processing were implemented using state-of-the-art technology (such as parallel programming on graphic processing devices) and were embedded in a flexible, object-oriented image-processing suite delivering a high degree of operational flexibility and simplicity. Most importantly an algorithm was designed which is able to automatically identify and remove individual images which, upon inclusion, would reduce the overall quality of the final 3D structure.
Somatotype differences between mapuche and non-mapuche children aged 10 to 12 years living in the province of cautín-araucanía

The studies of the somatotype allow us to know the quantified description of the morphological configuration of the individual, through endomorphy, mesomorphy and ectomorphy. Due to the acquisition of new eating habits along with a greater sedentarism in the child and adolescent population, it has been speculated that they have generated modifications in the morpho functional structure. This therefore, has encouraged a study that allows to determine the difference between the somatotype of the Mapuche children and the non Mapuche that inhabit the Province of Cautín, IX region of Chile. The subjects who participated in this study were 350 healthy children with a mean age of 11±1 years of age, height of 140.5±4.7 cm and a weight of 39.5±5 kg. All anthropometric measures were based on the protocol of the International Society for the Development of Cineanthropometry (ISAK). According to somatotype calculations. The following classifications were present: Group 10 years old; Endomorph-mesomorph, 11 years, age group, endomorph-mesomorph, 12 years, age group, and mesomorph-endomorph. The results indicate that the 10-year-old Mapuche children had lower values of endomorphy and higher values for mesomorphy (p≤0.01) than non-Mapuche children. The 11-year-old Mapuche children had lower values of endomorphy and higher values for mesomorphy (p≤0.01), compared to non-Mapuche children. The 12-year-old Mapuche children had lower values of endomorphy and mesomorphy (p≤0.05) than non-Mapuche children. In conclusion, the Mapuche schoolchildren present a mesomorphic predominance, however, nonMapuche children present predominance of the endomorphic component.
Collider Scope: How selection bias can induce spurious associations

1. MRC Integrative Epidemiology Unit at the University of Bristol, Bristol, United Kingdom. 2. UK Centre for Tobacco and Alcohol Studies, School of Experimental Psychology, University of Bristol, Bristol, United Kingdom. 3. School of Social and Community Medicine, University of Bristol, Bristol, United Kingdom. 4. University of Queensland Diamantina Institute, Translational Research Institute, Brisbane, Queensland 4102, Australia.
Impact of Clinical Salmonellosis in Veal Calves on the Recovery of Salmonella in Lymph Nodes at Harvest.

Abstract The objective of this study was to determine the prevalence, serotypes, antimicrobial resistance phenotypes, and pulsed-field gel electrophoresis (PFGE) patterns of Salmonella recovered in feces and mesenteric and prefemoral lymph nodes (LNs) from cohorts of calves with and without a confirmed outbreak of salmonellosis. In a prospective cohort study, 160 calves from four farms without a reported outbreak (nonoutbreak farms) were sampled at farm and harvest. In addition, harvest samples from 80 calves of two farms with a confirmed outbreak (outbreak farms) were collected. A culture protocol for Salmonella isolation was applied for all samples and recovered isolates were further characterized by serotyping, antimicrobial susceptibility testing, and PFGE. Among nonoutbreak farms, Salmonella was recovered from 0% (0/160) farm fecal samples, 3.7% (6/160) harvest fecal swabs, 21.9% (35/160) mesenteric LNs, and 0.6% (1/160) prefemoral LNs. Serotypes identified in nonoutbreak herds included Salmonella Ty.
Radiation driven winds with rotation: the oblate finite disc correction factor

Abstract We have incorporated the oblate distortion of the shape of the star due to the stellar rotation, which modifies the finite disk correction factor (fD) in the m-CAK hydrodynamical model. We implement a simplified version for the fD allowing us to solve numerically the non–linear m-CAK momentum equation. We solve this model for a classical Be star in the polar and equatorial directions. The star's oblateness modifies the polar wind, which is now much faster than the spherical one, mainly because the wind receives radiation from a larger (than the spherical) stellar surface. In the equatorial direction we obtain slow solutions, which are even slower and denser than the spherical ones. For the case when the stellar rotational velocity is about the critical velocity, the most remarkable result of our calculations is that the density contrast between the equatorial density and the polar one, is about 100. This result could explain a long-standing problem on Be stars.
The emerging role of cell-derived microvesicles in stem cell research and therapy.

Microvesicles (MVs) or microparticles are one type of extracellular vesicles (EVs) which can be produced by all types of cells under physiological or pathological conditions. The diameter of MVs ranges from 100 nm to 1000 nm. MVs are different from exosomes which are smaller (20 nm 100 nm) and originate from multivescular bodies [1]. MV biogenesis is always associated with cell growth, activation or apoptosis. The process involves direct budding of plasma membrane and a wide range of external signals can stimulate cells to produce MVs. The stimulator can be physical stress (such as, shear, hypoxia and oxidative stress), physiological agonists (such as, thrombin and TNFα) or non-physiological activators (such as, phorbol myristate acetate and calcium ionophore). MV generation process is complex and multiples mechanisms have been employed by cells, including caspase activation, lipid rafts, cytoskeletal reorganization and so on [2]. MVs are heterogeneous with respect to their surface marker expression, membrane phospholipid composition, and internal protein and RNA repertoires even when they are produced by the same parent cells but with different stimulations [2].
Corrigendum to: Spatial Topography of Individual-Specific Cortical Networks Predicts Human Cognition, Personality and Emotion.

Ru Kong1, Jingwei Li1, Csaba Orban1, Mert R. Sabuncu2, Hesheng Liu8, Alexander Schaefer1, Nanbo Sun1, Xi-Nian Zuo3,4, Avram J. Holmes5, Simon B. Eickhoff6,7 and B.T. Thomas Yeo 1,8,9,10 1Department of Electrical and Computer Engineering, ASTAR-NUS Clinical Imaging Research Centre, Singapore Institute for Neurotechnology and Memory Networks Program, National University of Singapore, Singapore, 2School of Electrical and Computer Engineering, Cornell University, Ithaca, NY, USA, 3CAS Key Laboratory of Behavioral Sciences and Research Center for Lifespan Development of Brain and Mind (CLIMB), Institute of Psychology, Beijing, China, 4University of Chinese Academy of Sciences, Beijing, China, 5Department of Psychology, Yale University, New Haven, CT, USA, 6Institute for Systems Neuroscience, Medical Faculty, Heinrich-Heine University Düsseldorf, Düsseldorf, Germany, 7Institute of Neuroscience and Medicine, Brain & Behaviour (INM-7), Research Center Jülich, Jülich, Germany, 8Martinos Center for Biomedical Imaging, Massachusetts General Hospital, Charlestown, MA, USA, 9Centre for Cognitive Neuroscience, DukeNUS Medical School, Singapore and 10NUS Graduate School for Integrative Sciences and Engineering, National University of Singapore, Singapore
Genetic structure of a patchily-distributed philopatric migrant: implications for management and conservation

The Lesser Kestrel (Falco naumanni) has suffered from both population decline and range fragmentation during the last century. In this study we used multilocus microsatellite genotypes to assess the genetic population structure of the species, with main focus on the patchily distributed populations of Central-Eastern (CE) Mediterranean. Our analysis revealed significant genetic structuring of Lesser Kestrel populations, not only at cross-continental scale, but also regionally within Central and Eastern Mediterranean where a significant correlation between genetic and geographic distance was observed. We detected signs of genetic bottlenecks in some of the peripheral populations, values of genetic differentiation among populations were rather small, albeit most of them significant, whereas gene flow levels were relatively low among the discontinuously distributed populations of CE Mediterranean region. We argue that the observed spatial genetic structure can be attributed to the combined influence of recent population declines, range fragmentation and species’ philopatric behaviour. Finally, we discuss how management strategies should focus in the maintenance of current genetic diversity levels and the avoidance of inbreeding depression through restoration of gene flow rates among peripheral populations.
Identity-by-descent refines mapping of candidate regions for preaxial polydactyly in a large Chinese pedigree

Preaxial polydactyly (PPD) is congenital hand malformation characterized by the duplication of digit. Herein, we scan the genome-wide SNPs for a large Chinese family with PPD-II/III. We employ the refined IBD algorithm to identify the identity-by-decent (IBD) segments and compare the frequency among the patients and normal relatives. A total of 72 markers of 0.01 percentile of the permutation are identified as the peak signals. Among of them, 57markers locate on chromosome 7q36 which is associated with PPD. Further analyses refine the mapping of candidate region in chromosome 7q36 into two 380 Kb fragments within LMBR1 and SHH respectively. IBD approach is a suitable method for mapping cause gene of human disease. Target-enrichment sequencing as well as functional experiments are required to illustrate the pathogenic mechanisms for PPD in the future.
Assessment of genetically modified maize GA21 for renewal of authorisation under Regulation (EC) No 1829/2003 (application EFSA‐GMO‐RX‐005)

Abstract Following the submission of application EFSA‐GMO‐RX‐005 under Regulation (EC) No 1829/2003 from Syngenta Crop Protection NV/SA, the Panel on Genetically Modified Organisms of the European Food Safety Authority (GMO Panel) was asked to deliver a scientific risk assessment on the data submitted in the context of the renewal of authorisation application of the herbicide‐tolerant genetically modified maize GA21. The data received in the context of this renewal application contained post‐market environmental monitoring reports, a systematic search and evaluation of literature, updated bioinformatics analyses, and additional documents or studies performed by or on behalf of the applicant. The GMO Panel assessed these data for possible new hazards, modified exposure or new scientific uncertainties identified during the authorisation period and not previously assessed in the context of the original application. Under the assumption that the DNA sequence of the event in maize GA21 considered for renewal is identical to the corrected sequence of the originally assessed event, the GMO Panel concludes that there is no evidence in the renewal application EFSA‐GMO‐RX‐005 for new hazards, modified exposure or scientific uncertainties that would change the conclusions of the original risk assessment on maize GA21.
Single-Cell Reprogramming of Mouse Embryo Development Through a Critical Transition State

Our work dealing with the temporal development of the genome-expression profile in single-cell mouse early embryo indicated that reprogramming occurs via a critical transition state, where the critical-regulation pattern of the zygote state disappears. In this report, we unveil the detailed mechanism of how the dynamic interaction of thermodynamic states (critical states) enables the genome system to pass through the critical transition state to achieve genome reprogramming. Self-organized criticality (SOC) control of overall expression provides a snapshot of self-organization and explains the coexistence of critical states at a certain experimental time point. The time-development of self-organization is dynamically modulated by exchanges in expression flux between critical states through the cell nucleus milieu, where sequential global perturbations involving activation-inhibition of multiple critical states occur from the early state to the late 2-cell state. Two cyclic fluxes act as feedback flow and generate critical-state coherent oscillatory dynamics. Dynamic perturbation of these cyclic flows due to vivid activation of the ensemble of low-variance expression (sub-critical state) genes allows the genome system to overcome a transition state during reprogramming. Our findings imply that a universal mechanism of long-term global RNA oscillation underlies autonomous SOC control, and the critical gene ensemble at a critical point (CP) drives genome reprogramming. Unveiling the corresponding molecular players will be essential to understand single-cell reprogramming.
A new connected word recognition algorithm based on HMM/LVQ segmentation and LVQ classification

The authors present a novel HMM/LVQ (hidden Markov model/learning vector quantization) hybrid algorithm for connected word recognition (CWR). They show that, for combining both the discriminative power of LVQ and the capability of modeling temporal variations, of speech of an HMM into a hybrid algorithm, the performance of the original HMM-based speech recognition algorithm can be improved. The proposed hybrid algorithm is especially effective in cases when the training data are not adequate to characterize the test data. Preliminary results showed that this system gave a word accuracy of 98.5% on the whole TI test set, even when only HMM was used to segment speech utterances into words and states. <<ETX>>
Channel Coding with Unequal Message Protection

Error correcting codes which allow for unequal protection of messages find diverse application in information theory and a communications more broadly. Preferential protection from noise of certain messages over others is a means of incorporating the semantics of information into code design. More concretely, unequal message protection codes are invaluable when communicating with small delay. In such settings there is less time to ‘homogenize’ the information source (e.g., by compressing the data to make all messages equally likely) and codes allowing for unequal protection of messages have a distinct advantage over traditional error correcting codes. Previous work on this topic within information theory falls into two categories: either it was studied from the asymptotic (error exponent) perspective and/or it was studied only as an intermediate step towards developing bounds for the problem of joint source-channel coding. In all of these cases the study was limited to regimes where no interesting or informative performance tradeoffs between rate and reliability of different classes of messages could be observed. This thesis considers the problem of unequal message protection as a stand-alone problem. We analyze the tradeoffs between rates of different classes of messages and the levels of error protection of these classes by generalizing previous non-asymptotic and asymptotic results from channel coding. In addition, we consider two questions related to the practical constructions of codes with unequal protection of messages. First, we study leveraging existing channel codes by prefixing the message class into a header followed by data protection using a standard code. We show that, in general, this construction is not optimal at finite code lengths. We further demonstrate that our main theoretical bounds can be obtained using coset codes, which suggests a path to implementation of tractable unequal message protection codes. Finally, we