Miracle-dz/UniFAR-FTUs huggingface dataset:
Variations of Bacterial Populations in Human Feces Measured by Fluorescent In Situ Hybridization with Group-Specific 16S rRNA-Targeted Oligonucleotide Probes

ABSTRACT Six 16S rRNA-targeted oligonucleotide probes were designed, validated, and used to quantify predominant groups of anaerobic bacteria in human fecal samples. A set of two probes was specific for species of the Bacteroides fragilis group and the speciesBacteroides distasonis. Two others were designed to detect species of the Clostridium histolyticum and theClostridium lituseburense groups. Another probe was designed for the genera Streptococcus andLactococcus, and the final probe was designed for the species of the Clostridium coccoides-Eubacterium rectalegroup. The temperature of dissociation of each of the probes was determined. The specificities of the probes for a collection of target and reference organisms were tested by dot blot hybridization and fluorescent in situ hybridization (FISH). The new probes were used in initial FISH experiments to enumerate human fecal bacteria. The combination of the two Bacteroides-specific probes detected a mean of 5.4 × 1010 cells per g (dry weight) of feces; the Clostridium coccoides-Eubacterium rectalegroup-specific probe detected a mean of 7.2 × 1010cells per g (dry weight) of feces. The Clostridium histolyticum, Clostridium lituseburense, andStreptococcus-Lactococcus group-specific probes detected only numbers of cells ranging from 1 × 107 to 7 × 108 per g (dry weight) of feces. Three of the newly designed probes and three additional probes were used in further FISH experiments to study the fecal flora composition of nine volunteers over a period of 8 months. The combination of probes was able to detect at least two-thirds of the fecal flora. The normal biological variations within the fecal populations of the volunteers were determined and indicated that these variations should be considered when evaluating the effects of agents modulating the flora.
Adjustment of genomic waves in signal intensities from whole-genome SNP genotyping platforms

Whole-genome microarrays with large-insert clones designed to determine DNA copy number often show variation in hybridization intensity that is related to the genomic position of the clones. We found these ‘genomic waves’ to be present in Illumina and Affymetrix SNP genotyping arrays, confirming that they are not platform-specific. The causes of genomic waves are not well-understood, and they may prevent accurate inference of copy number variations (CNVs). By measuring DNA concentration for 1444 samples and by genotyping the same sample multiple times with varying DNA quantity, we demonstrated that DNA quantity correlates with the magnitude of waves. We further showed that wavy signal patterns correlate best with GC content, among multiple genomic features considered. To measure the magnitude of waves, we proposed a GC-wave factor (GCWF) measure, which is a reliable predictor of DNA quantity (correlation coefficient = 0.994 based on samples with serial dilution). Finally, we developed a computational approach by fitting regression models with GC content included as a predictor variable, and we show that this approach improves the accuracy of CNV detection. With the wide application of whole-genome SNP genotyping techniques, our wave adjustment method will be important for taking full advantage of genotyped samples for CNV analysis.
Design of reinforced concrete frames of limited ductility.

An experimental programme was carried out to investigate the flexural strength and ductility.of reinforced concrete columns under simulated earthquake loading. The main variable examined was the quantity of transverse reinforcement for concrete confinement. The experimental results were described and compared with theoretical studies. It was found that to achieve adequate ductility in columns, the current New Zealand concrete design code NZS3101:1982 equations for concrete confinement need to be refined. Using design charts for ductility, which were previously derived from a theory for cyclic moment-curvature behaviour, a refined design equation to replace the current code equations is proposed. The inelastic dynamic response of frames of limited ductility was examined, and compared with the response of ductile frames. The analysis indicated that non-capacity designed frames, designed for seismic forces corresponding to a limited ductility demand, performed reasonably well. Although some plastic hinges did develop in the columns, the ductility demand was acceptable and can be achieved by appropriate detailing. As a result, some suggestions for the seismic design requirements of frames ~f limited ductility are presented.
Sarcoma of the breast: an update on a rare entity

Breast sarcoma is a rare condition. It consists of a heterogeneous group of non-epithelial tumours arising from the mesenchymal tissue of the breast. It has a distinctly different natural history, treatment response and prognosis as compared with carcinoma of the breast. A different diagnostic approach and treatment strategy have to be defined for this group of tumours. Due to its rarity, the current understanding on breast sarcoma is limited and is mostly based on small retrospective case series or case reports. Hence, the management generally follows the algorithms derived from randomised control trials of soft tissue sarcomas in the extremities and chest wall. Through this review, we discuss the results of major retrospective studies on breast sarcomas including data on epidemiology, aetiology, diagnostic approach, treatment strategies and outcomes of this challenging and potentially aggressive condition.
A Comparative Study on Feature Selection Methods for Drug Discovery

Feature selection is frequently used as a preprocessing step to machine learning. The removal of irrelevant and redundant information often improves the performance of learning algorithms. This paper is a comparative study of feature selection in drug discovery. The focus is on aggressive dimensionality reduction. Five methods were evaluated, including information gain, mutual information, a chi2-test, odds ratio, and GSS coefficient. Two well-known classification algorithms, Naïve Bayesian and Support Vector Machine (SVM), were used to classify the chemical compounds. The results showed that Naïve Bayesian benefited significantly from the feature selection, while SVM performed better when all features were used. In this experiment, information gain and chi2-test were most effective feature selection methods. Using information gain with a Naïve Bayesian classifier, removal of up to 96% of the features yielded an improved classification accuracy measured by sensitivity. When information gain was used to select the features, SVM was much less sensitive to the reduction of feature space. The feature set size was reduced by 99%, while losing only a few percent in terms of sensitivity (from 58.7% to 52.5%) and specificity (from 98.4% to 97.2%). In contrast to information gain and chi2-test, mutual information had relatively poor performance due to its bias toward favoring rare features and its sensitivity to probability estimation errors.
Reducing performance non-determinism via cache-aware page allocation strategies

Performance non-determinism in computer systems complicates evaluation, use, and even development of these systems. In performance evaluation via benchmarking and simulation, non-determinism requires long executions and more complex experiment design. Real-time systems are hard to dimension and tune with non-determinism. The slower benchmarking also slows down system development, as it takes developers longer to see performance implications of their modifications. Cache-unaware physical page allocation in an operating system is believed to be a significant cause of non-determinism, but there is no published empirical study that would confirm it. We provide such a study for the Linux operating system, comparing the default cache-unaware page allocation strategy to known cache-aware strategies, page coloring and bin hopping. We have implemented a framework for page allocation strategies in the Linux kernel, employed it for these two strategies, and measured the non-determinism on a large and diverse set of benchmarks. We propose a statistical technique which allows to classify different kinds of performance non-determinism and evaluate their magnitudes. Application of our technique reveals that the two strategies do reduce performance non-determinism without significantly increasing mean response time.
Early Onset Photoreceptor Abnormalities Induced by Targeted Disruption of the Interphotoreceptor Retinoid-Binding Protein Gene

Vision in all vertebrates is dependent on an exchange of retinoids between the retinal pigment epithelium and the visual photoreceptors. It has been proposed that the interphotoreceptor retinoid-binding protein (IRBP) is essential for this intercellular exchange, and that it serves to prevent the potentially cytotoxic effects of retinoids. Although its precise function in vivo has yet to be defined, the early expression of IRBP suggests that it may also be required for normal photoreceptor development. To further assess the biological role of IRBP, we generated transgenic mice with targeted disruption of the IRBP gene (IRBP−/− mice). Specifically, homologous recombination was used to replace the first exon and promoter region of the IRBP gene with a phosphoglycerate kinase-promoted neomycin-resistant gene. Immunocytochemical and Western blot analyses demonstrated the absence of IRBP expression in theIRBP−/− mice. As early as postnatal day 11, histological examination of the retinas of IRBP−/− mice revealed a loss of photoreceptor nuclei and changes in the structural integrity of the receptor outer segments. At 30 d of age, the photoreceptor abnormalities in IRBP−/− mice were more severe, and electroretinographic recordings revealed a marked loss in photic sensitivity. In contrast, no morphological or electrophysiological changes were detected in age-matched heterozygotes. These observations indicate that normal photoreceptor development and function are highly dependent on the early expression of IRBP, and that in the absence of IRBP there is a slowly progressive degeneration of retinal photoreceptors.
The Time-Varying Networks in P300:  A Task-Evoked EEG Study

P300 is an important event-related potential that can be elicited by external visual, auditory, and somatosensory stimuli. Various cognition-related brain functions (i.e., attention, intelligence, and working memory) and multiple brain regions (i.e., prefrontal, frontal, and parietal) are reported to be involved in the elicitation of P300. However, these studies do not investigate the instant interactions across the neural cortices from the hierarchy of milliseconds. Importantly, time-varying network analysis among these brain regions can uncover the detailed and dynamic information processing in the corresponding cognition process. In the current study, we utilize the adaptive directed transfer function to construct the time-varying networks of P300 based on scalp electroencephalographs, investigating the time-varying information processing in P300 that can depict the deeper neural mechanism of P300 from the network. Our analysis found that different stages of P300 evoked different brain networks, i.e., the center area performs as the central source during the decision process stage, while the source region is transferred to the right prefrontal cortex (rPFC) in the neuronal response stage. Moreover, during the neuronal response stage, the directed information that flows from the rPFC to the parietal cortex are remarkably important. These findings indicate that the two brain hemispheres exhibit asymmetrical functions in processing related information for different P300 stages, and this work may provide new evidence for our better understanding of the neural mechanism of P300 generation.
Load Balancing Under Heavy Traffic in RPL Routing Protocol for Low Power and Lossy Networks

RPL is an IPv6 routing protocol for low-power and lossy networks (LLNs) designed to meet the requirements of a wide range of LLN applications including smart grid AMIs, industrial and environmental monitoring, and wireless sensor networks. RPL allows bi-directional end-to-end IPv6 communication on resource constrained LLN devices, leading to the concept of the Internet of Things (IoT) with thousands and millions of devices interconnected through multihop mesh networks. In this article, we investigate the load balancing and congestion problem of RPL. Specifically, we show that most of the packet losses under heavy traffic are due to congestion, and a serious load balancing problem appears in RPL in terms of routing parent selection. To overcome this problem, this article proposes a simple yet effective queue utilization based RPL (QU-RPL) that achieves load balancing and significantly improves the end-to-end packet delivery performance compared to the standard RPL. QU-RPL is designed for each node to select its parent node considering the queue utilization of its neighbor nodes as well as their hop distances to an LLN border router (LBR). Owing to its load balancing capability, QU-RPL is very effective in lowering queue losses and increasing the packet delivery ratio. We implement QU-RPL on a low-power embedded platform, and verify all of our findings through experimental measurements on a real testbed of a multihop LLN over IEEE 802.15. 4. We present the impact of each design element of QU-RPL on performance in detail, and also show that QU-RPL reduces the queue loss by up to 84 percent and improves the packet delivery ratio by up to 147 percent compared to the standard RPL.
Genome-Wide Analysis of Gene Expression during Early Arabidopsis Flower Development

Detailed information about stage-specific changes in gene expression is crucial for the understanding of the gene regulatory networks underlying development. Here, we describe the global gene expression dynamics during early flower development, a key process in the life cycle of a plant, during which floral patterning and the specification of floral organs is established. We used a novel floral induction system in Arabidopsis, which allows the isolation of a large number of synchronized floral buds, in conjunction with whole-genome microarray analysis to identify genes with differential expression at distinct stages of flower development. We found that the onset of flower formation is characterized by a massive downregulation of genes in incipient floral primordia, which is followed by a predominance of gene activation during the differentiation of floral organs. Among the genes we identified as differentially expressed in the experiment, we detected a significant enrichment of closely related members of gene families. The expression profiles of these related genes were often highly correlated, indicating similar temporal expression patterns. Moreover, we found that the majority of these genes is specifically up-regulated during certain developmental stages. Because co-expressed members of gene families in Arabidopsis frequently act in a redundant manner, these results suggest a high degree of functional redundancy during early flower development, but also that its extent may vary in a stage-specific manner.
Growth gains from selective breeding in a spruce hybrid zone do not compromise local adaptation to climate

Hybrid zones contain extensive standing genetic variation that facilitates rapid responses to selection. The Picea glauca × Picea engelmannii hybrid zone in western Canada is the focus of tree breeding programs that annually produce ~90 million reforestation seedlings. Understanding the direct and indirect effects of selective breeding on adaptive variation is necessary to implement assisted gene flow (AGF) polices in Alberta and British Columbia that match these seedlings with future climates. We decomposed relationships among hybrid ancestry, adaptive traits, and climate to understand the implications of selective breeding for climate adaptations and AGF strategies. The effects of selection on associations among hybrid index estimated from ~6,500 SNPs, adaptive traits, and provenance climates were assessed for ~2,400 common garden seedlings. Hybrid index differences between natural and selected seedlings within breeding zones were small in Alberta (average +2%), but larger and more variable in BC (average −7%, range −24% to +1%), slightly favoring P. glauca ancestry. The average height growth gain of selected seedlings over natural seedlings within breeding zones was 36% (range 12%–86%). Clines in growth with temperature‐related variables were strong, but differed little between selected and natural populations. Seedling hybrid index and growth trait associations with evapotranspiration‐related climate variables were stronger in selected than in natural seedlings, indicating possible preadaptation to drier future climates. Associations among cold hardiness, hybrid ancestry, and cold‐related climate variables dominated signals of local adaptation and were preserved in breeding populations. Strong hybrid ancestry–phenotype–climate associations suggest that AGF will be necessary to match interior spruce breeding populations with shifting future climates. The absence of antagonistic selection responses among traits and maintenance of cold adaptation in selected seedlings suggests breeding populations can be safely redeployed using AGF prescriptions similar to those of natural populations.
Increasing background ozone in surface air over the United States

The long‐term trend of background O3 in surface air over the United States from 1980 to 1998 is examined using monthly probability distributions of daily maximum 8‐hour average O3 concentrations at a large ensemble of rural sites. Ozone concentrations have decreased at the high end of the probability distribution (reflecting emission controls) but have increased at the low end. The cross‐over takes place between the 30th and 50th percentiles in May–August and between the 60th and 90th percentiles during the rest of the year. The increase is statistically significant at a 5% level in spring and fall, when it is 3–5 ppbv. The maximum increase is in the Northeast. A possible explanation is an increase in the O3 background transported from outside the United States. Better understanding of the causes of the increase is needed because of its implications for meeting O3 air quality standards.
— — – CHAPTER 1 AN ELLIPSOIDAL PARTICLE-FINITE ELEMENT METHOD FOR HYPERVELOCITY IMPACT SIMULATION

A number of coupled particle-element and hybrid particle-element methods have been developed for the simulation of hypervelocity impact problems, to avoid certain disadvantages associated with the use of pure continuum based or pure particle based methods. To date these methods have employed spherical particles. In recent work a hybrid formulation has been extended to the ellipsoidal particle case. A model formulation approach based on La-grange's equations, with particles entropies serving as generalized coordinates, avoids the angular momentum conservation problems which have been reported with ellipsoidal smooth particle hydrodynamics models.
The Left, The Better: White-Matter Brain Integrity Predicts Foreign Language Imitation Ability

Speech imitation is crucial for language acquisition and second-language learning. Interestingly, large individual differences regarding the ability in imitating foreign-language sounds have been observed. The origin of this interindividual diversity remains unknown, although it might be partially explained by structural predispositions. Here we correlated white-matter structural properties of the arcuate fasciculus (AF) with the performance of 52 German-speakers in a Hindi sentence- and word-imitation task. First, a manual reconstruction was performed, permitting us to extract the mean values along the three branches of the AF. We found that a larger lateralization of the AF volume toward the left hemisphere predicted the performance of our participants in the imitation task. Second, an automatic reconstruction was carried out, allowing us to localize the specific region within the AF that exhibited the largest correlation with foreign language imitation. Results of this reconstruction also showed a left lateralization trend: greater fractional anisotropy values in the anterior half of the left AF correlated with the performance in the Hindi-imitation task. From the best of our knowledge, this is the first time that foreign language imitation aptitude is tested using a more ecological imitation task and correlated with DTI tractography, using both a manual and an automatic method.
Effects of epimuscular myofascial force transmission on sarcomere length of passive muscles in the rat hindlimb

Results from imaging studies and finite element models suggest epimuscular myofascial effects on sarcomere lengths in series within muscle fibers. However, experimental evidence is lacking. We evaluated epimuscular myofascial effects on (1) muscle belly, fiber, and mean sarcomere length and (2) sarcomere length distribution within passive fibers of the rat tibialis anterior (TA) and soleus (SO) muscles. Hindlimbs (n = 24) were positioned in predefined knee (55°, 90°, 125°, 160°) and ankle (either 90° or 125°) angles, and fixed in a formaldehyde solution. Varying knee joint angle causes changes in muscle–tendon unit length of SO and TA's synergists, but not of SO and TA. Whole fibers were taken from SO and TA and photographed along their length. Mean sarcomere length was assessed for the entire fiber and for the proximal, intermediate, and distal thirds (fiber segments) separately. Mean sarcomere length of the fiber was not affected by knee angle, neither for SO (mean: 2.44 ± 0.03 μm and 2.19 ± 0.05 μm for ankle angles of 90° and 125°, respectively) nor for TA (mean: 2.33 ± 0.05 μm and 2.51 ± 0.07 μm for ankle angle set to 90° and 125°, respectively). Only for TA, a significant interaction between knee angle and fiber segment was found, indicating changes in the distribution of lengths of in‐series sarcomeres. Thus, while epimuscular myofascial force transmission did not cause mean sarcomere length changes within passive SO and TA, it did alter the length distribution of sarcomeres within passive TA.
LncRNA OIP5-AS1/cyrano suppresses GAK expression to control mitosis

Some long noncoding RNAs (lncRNAs) can regulate gene expression programs, in turn affecting specific cellular processes. We sought to identify the mechanism through which the lncRNA OIP5-AS1, which is abundant in the cytoplasm, suppressed cell proliferation. Silencing of OIP5-AS1 in human cervical carcinoma HeLa cells triggered the appearance of many aberrant (monopolar, multipolar, misaligned) mitotic spindles. Through a combination of approaches to pull down mRNAs bound to OIP5-AS1 and identify proteins differentially expressed when OIP5-AS1 was silenced, we identified a subset of human cell cycle regulatory proteins encoded by mRNAs that interacted with OIP5-AS1 in HeLa cells. Further analysis revealed that GAK mRNA, which encodes a cyclin G-associated kinase important for mitotic progression, associated prominently with OIP5-AS1. The interaction between these two transcripts led to a reduction in GAK mRNA stability and GAK protein abundance, as determined in cells in which OIP5-AS1 levels were increased or decreased. Importantly, the aberrant mitotic cell division seen after silencing OIP5-AS1 was partly rescued if GAK was simultaneously silenced. These findings indicate that the abnormal mitoses seen after silencing OIP5-AS1 were caused by an untimely rise in GAK levels and suggest that OIP5-AS1 suppresses cell proliferation at least in part by reducing GAK levels.