Miracle-dz/UniFAR-FTUs huggingface dataset:
Non-Pathogenic Bacteria Modulate Colonic Epithelial Gene Expression in Germ-Free Mice

Background: We established a bacterial reconstitution model to investigate epithelial cell-luminal bacteria interaction. The aim of the study was to identify the known genes directly or indirectly modulated by non-pathologic bacterial flora in the colonic epithelia of germ-free mice. Methods: Germ-free mice were orally given a bacterial suspension prepared from specific pathogen-free counterparts (bacterial reconstitution). Colonic epithelial cells were isolated, then total and poly (A) RNA were extracted. We investigated differential gene expression in colonic epithelial cells among germ-free, bacteria-reconstituted, and specific pathogen-free mice by DNA microarray. Finally, differential expression was confirmed by Northern blot or quantitative RT-PCR. Results: Thirty genes were initially selected as differentially expressed genes in DNA microarray analysis. We confirmed that genes associated with growth (Reg III #, Reg III % , guanylate nucleotide binding protein 2), apoptosis (Bcl-associated death promotor), cytoskeleton (tubulin ! 4, erythrocyte protein band 7.2), and immune response (lymphocyte antigen complex 6) were induced by bacterial reconstitution. In contrast, genes possibly participating in extracellular oxidant defence (selenoprotein P, metallothionein 1) and cellular metabolism (cytochrome P450, HMGCoA synthase 2, alcohol dehydrogenase 1 complex, aldehyde dehydrogenase family 1, carbonic anhydrase 1, glycoprotein galactosyltransferase ! 1,3) were down-regulated by bacterial challenge. Conclusion: Non-pathogenic bacteria modulated colonic gene expression in germ-free mice, suggesting that non-pathogenic bacteria possibly initiate epithelial change in genetically normal and/or abnormal hosts. The present study provides a basis for the functional study of each molecule in symbiosis with luminal bacteria in healthy and diseased colon.
Otitis Media With Effusion: An Underestimated Cause of Hearing Loss in Infants

Objective: Otitis media with effusion (OME) is the major reason for failure of neonatal hearing screening. However, little is known about the impact on hearing status of OME in infants during the first months of life. Patients: Infants who failed universal newborn hearing screening. Methods: Prospective evaluation for the presence of OME, the degree of hearing loss and the disease evolution. Results: Between 2007 and 2008, approximately 152 infants were referred because of unilateral or bilateral failure on universal newborn hearing screening with an automated auditory brainstem response device. Eighty-four (55.3%) had OME, 20 of them were lost to follow-up. The remainder 64 infants comprised 37 boys and 27 girls, with a median age of 49 days (range, 40-65 d) at admission. Auditory brainstem response thresholds were 50 dB nHL (range, 40-60) in both ears. A spontaneous resolution of OME was documented in 15 infants. In the remaining, hearing normalized after tympanocentesis or placement of ventilation tubes. Normal hearing could be ascertained in all children at a median age of 4.8 months (range, 3.3-7.8 mo). In the group of infants analyzed, no permanent hearing loss could be detected. Conclusion: OME is an important cause of transient, moderately severe hearing loss during the first months of life-a critical period for development of the auditory system. Active treatment should be considered if spontaneous resolution does not occur to prevent any delay in language acquisition and to exclude an underlying sensorineural hearing loss.
Nonlinear Effects of Nanoparticles: Biological Variability from Hormetic Doses, Small Particle Sizes, and Dynamic Adaptive Interactions

Researchers are increasingly focused on the nanoscale level of organization where biological processes take place in living systems. Nanoparticles (NPs, e.g., 1–100 nm diameter) are small forms of natural or manufactured source material whose properties differ markedly from those of the respective bulk forms of the “same” material. Certain NPs have diagnostic and therapeutic uses; some NPs exhibit low-dose toxicity; other NPs show ability to stimulate low-dose adaptive responses (hormesis). Beyond dose, size, shape, and surface charge variations of NPs evoke nonlinear responses in complex adaptive systems. NPs acquire unique size-dependent biological, chemical, thermal, optical, electromagnetic, and atom-like quantum properties. Nanoparticles exhibit high surface adsorptive capacity for other substances, enhanced bioavailability, and ability to cross otherwise impermeable cell membranes including the blood-brain barrier. With super-potent effects, nano-forms can evoke cellular stress responses or therapeutic effects not only at lower doses than their bulk forms, but also for longer periods of time. Interactions of initial effects and compensatory systemic responses can alter the impact of NPs over time. Taken together, the data suggest the need to downshift the dose-response curve of NPs from that for bulk forms in order to identify the necessarily decreased no-observed-adverse-effect-level and hormetic dose range for nanoparticles.
Association of a novel long non‐coding RNA in 8q24 with prostate cancer susceptibility

Recent genome‐wide association studies reported strong and reproducible associations of multiple genetic variants in a large “gene‐desert” region of chromosome 8q24 with susceptibility to prostate cancer (PC). However, the causative or functional variants of these 8q24 loci and their biological mechanisms associated with PC susceptibility remain unclear and should be investigated. Here, focusing on its most centromeric region (so‐called Region 2: Chr8: 128.14‐128.28 Mb) among the multiple PC loci on 8q24, we performed fine mapping and re‐sequencing of this critical region and identified SNPs (single nucleotide polymorphisms) between rs1456315 and rs7463708 (chr8: 128,173,119‐128,173,237 bp) to be most significantly associated with PC susceptibility (P = 2.00 × 10−24, OR = 1.74, 95% confidence interval = 1.56–1.93). Importantly, we show that this region was transcribed as a ∼13 kb intron‐less long non‐coding RNA (ncRNA), termed PRNCR1 (prostate cancer non‐coding RNA 1), and PRNCR1 expression was upregulated in some of the PC cells as well as precursor lesion prostatic intraepithelial neoplasia. Knockdown of PRNCR1 by siRNA attenuated the viability of PC cells and the transactivation activity of androgen receptor, which indicates that PRNCR1 could be involved in prostate carcinogenesis possibly through androgen receptor activity. These findings could provide a new insight in understanding the pathogenesis of genetic factors for PC susceptibility and prostate carcinogenesis. (Cancer Sci 2011; 102: 245–252)
Genome-Wide Association Study Identifies NBS-LRR-Encoding Genes Related with Anthracnose and Common Bacterial Blight in the Common Bean

Nucleotide-binding site and leucine-rich repeat (NBS-LRR) genes represent the largest and most important disease resistance genes in plants. The genome sequence of the common bean (Phaseolus vulgaris L.) provides valuable data for determining the genomic organization of NBS-LRR genes. However, data on the NBS-LRR genes in the common bean are limited. In total, 178 NBS-LRR-type genes and 145 partial genes (with or without a NBS) located on 11 common bean chromosomes were identified from genome sequences database. Furthermore, 30 NBS-LRR genes were classified into Toll/interleukin-1 receptor (TIR)-NBS-LRR (TNL) types, and 148 NBS-LRR genes were classified into coiled-coil (CC)-NBS-LRR (CNL) types. Moreover, the phylogenetic tree supported the division of these PvNBS genes into two obvious groups, TNL types and CNL types. We also built expression profiles of NBS genes in response to anthracnose and common bacterial blight using qRT-PCR. Finally, we detected nine disease resistance loci for anthracnose (ANT) and seven for common bacterial blight (CBB) using the developed NBS-SSR markers. Among these loci, NSSR24, NSSR73, and NSSR265 may be located at new regions for ANT resistance, while NSSR65 and NSSR260 may be located at new regions for CBB resistance. Furthermore, we validated NSSR24, NSSR65, NSSR73, NSSR260, and NSSR265 using a new natural population. Our results provide useful information regarding the function of the NBS-LRR proteins and will accelerate the functional genomics and evolutionary studies of NBS-LRR genes in food legumes. NBS-SSR markers represent a wide-reaching resource for molecular breeding in the common bean and other food legumes. Collectively, our results should be of broad interest to bean scientists and breeders.
A Laboratory Investigation of Orthodontic Elastomeric Chains

The dimensions and force/extension characteristics of 13 commercially available orthodontic chain elastomeric materials are reported. The relationship between force and extension was not linear over the range investigated and there were two definite transition points in the curves. Over the first linear part of the curve the two-loop specimens had stiffness values from 0·9 to 1·6 N/mm. Stiffness fell as the number of loops increased so that four-loop chains produced 0·6–1·1 N/mm. One hundred per cent extension produced forces in the 4–5 N range for most specimens. It is suggested that an extension of between 50 and 70 per cent would provide the most satisfactory orthodontic force.
Link Adaptation in IEEE 802.15.4-based Wireless Body Area Networks

In this paper we consider an IEEE 802.15. 4-based Wireless Body Area Network, where wearable sensor devices are distributed on a body and have to send the measured data to a coordinator. The Carrier Sense Multiple Access with Collision Avoidance algorithm defined by the standard is used as Medium Access Control protocol, whereas different modulation schemes are assumed to be available at the physical layer. We propose a novel Link Adaptation (LA) strategy, where nodes select the modulation scheme according to the experienced channel quality and level of interference. The novelty lays in the fact that in case of large Signal-to-Noise Ratio and low Signal-to-Interference Ratio nodes increase the bit rate, instead of reducing it, as largely done in the works present in the literature. The reduction of the bit rate, in fact, allows to decrease the time the channel is occupied and, therefore, the collision probability. Performance is evaluated in terms of packet error rate and results achieved with and without LA are compared. Results show that the proposed strategy improves performance.
Phase III Study of Cabozantinib in Previously Treated Metastatic Castration-Resistant Prostate Cancer: COMET-1.

PURPOSE Cabozantinib is an inhibitor of kinases, including MET and vascular endothelial growth factor receptors, and has shown activity in men with previously treated metastatic castration-resistant prostate cancer (mCRPC). This blinded phase III trial compared cabozantinib with prednisone in patients with mCRPC. PATIENTS AND METHODS Men with progressive mCRPC after docetaxel and abiraterone and/or enzalutamide were randomly assigned at a two-to-one ratio to cabozantinib 60 mg once per day or prednisone 5 mg twice per day. The primary end point was overall survival (OS). Bone scan response (BSR) at week 12 as assessed by independent review committee was the secondary end point; radiographic progression-free survival (rPFS) and effects on circulating tumor cells (CTCs), bone biomarkers, serum prostate-specific antigen (PSA), and symptomatic skeletal events (SSEs) were exploratory assessments. RESULTS A total of 1,028 patients were randomly assigned to cabozantinib (n = 682) or prednisone (n = 346). Median OS was 11.0 months with cabozantinib and 9.8 months with prednisone (hazard ratio, 0.90; 95% CI, 0.76 to 1.06; stratified log-rank P = .213). BSR at week 12 favored cabozantinib (42% v 3%; stratified Cochran-Mantel-Haenszel P < .001). rPFS was improved in the cabozantinib group (median, 5.6 v 2.8 months; hazard ratio, 0.48; 95% CI, 0.40 to 0.57; stratified log-rank P < .001). Cabozantinib was associated with improvements in CTC conversion, bone biomarkers, and post-random assignment incidence of SSEs but not PSA outcomes. Grade 3 to 4 adverse events and discontinuations because of adverse events were higher with cabozantinib than with prednisone (71% v 56% and 33% v 12%, respectively). CONCLUSION Cabozantinib did not significantly improve OS compared with prednisone in heavily treated patients with mCRPC and progressive disease after docetaxel and abiraterone and/or enzalutamide. Cabozantinib had some activity in improving BSR, rPFS, SSEs, CTC conversions, and bone biomarkers but not PSA outcomes.
Temperature changes in deep muscles of humans during ice and ultrasound therapies: an in vivo study.

Therapeutic ultrasound can be a very effective treatment modality when used correctly in the treatment of musculoskeletal conditions and wound healing. However, many protocols for the administration of ultrasound have not been scientifically tested. The purpose of this study was to measure muscle temperature changes during a frequently used protocol, ie. , preicing prior to ultrasound application. A 23-gauge hypodermic needle microprobe was inserted 5 cm deep into the medial aspect of the anesthetized triceps surae muscle of 16 subjects. Two groups consisting of eight subjects each were tested for temperature changes during: a) ultrasound treatment on precooled tissue or b) ultrasound with no preceding treatment. Each treatment consisted of 10 minutes of continuous ultrasound delivered topically at 1.5 watts/cm2. A significant difference between the two treatment methods was measured (F = 19.06, p < 0.01). Ultrasound alone increased tissue temperature an average of 4.0 +/- . 83 degrees C, whereas ultrasound preceded by 5 minutes of ice increased tissue temperature only 1.8 +/- 1.0 degrees C above original baseline level. At a depth of 5 cm, ultrasound preceded by ice treatment yielded little or no thermal benefits.
Positioning and localisation for Location-based services

Success of Location-Based Services (LBS), a subset of mobile communication services, suffers from the lack of multidisciplinary co-operation due to misunderstandings caused by deployment of unilateral development models. Here we propose the re-definition of the essential terms and processes, that results in creation of the new LBS operational model, thus allowing for the enhanced and more fruitful multidisciplinary collaboration on LBS development.
Bypassing rRNA methylation by RsmA/Dim1during ribosome maturation in the hyperthermophilic archaeon Nanoarchaeum equitans.

In all free-living organisms a late-stage checkpoint in the biogenesis of the small ribosomal subunit involves rRNA modification by an RsmA/Dim1 methyltransferase. The hyperthermophilic archaeon Nanoarchaeum equitans, whose existence is confined to the surface of a second archaeon, Ignicoccus hospitalis, lacks an RsmA/Dim1 homolog. We demonstrate here that the I. hospitalis host possesses the homolog Igni_1059, which dimethylates the N6-positions of two invariant adenosines within helix 45 of 16S rRNA in a manner identical to other RsmA/Dim1 enzymes. However, Igni_1059 is not transferred from I. hospitalis to N. equitans across their fused cell membrane structures and the corresponding nucleotides in N. equitans 16S rRNA remain unmethylated. An alternative mechanism for ribosomal subunit maturation in N. equitans is suggested by sRNA interactions that span the redundant RsmA/Dim1 site to introduce 2'-O-ribose methylations within helices 44 and 45 of the rRNA.
Effectiveness of social media text classification by utilizing the online news category

Social media text can illustrate significant information of our real social situation. It can show the direction of real-time social movement. However, it has its own characteristics such as using short text and informal language, many unstructured information and argot. This kind of text is hard to classify and difficult to analyze to extract the useful information. In this paper, we propose an effective technique to classify the social media text by utilizing the initial keywords from well-formed sources of data, such as online news. Term frequency-inverse document frequency weighting technique (TF-IDF) and Word Article Matrix (WAM) are used as main methods in this research. We use the extracted keywords from the well-formed source as a main factor to do experiment on Twitter messages. We found a set of the social media keywords can represent the essence of social events and can be used to classify the text effectively.
NADPH oxidase 4 (Nox4) is a major source of oxidative stress in the failing heart

NAD(P)H oxidases (Noxs) produce O2− and play an important role in cardiovascular pathophysiology. The Nox4 isoform is expressed primarily in the mitochondria in cardiac myocytes. To elucidate the function of endogenous Nox4 in the heart, we generated cardiac-specific Nox4−/− (c-Nox4−/−) mice. Nox4 expression was inhibited in c-Nox4−/− mice in a heart-specific manner, and there was no compensatory up-regulation in other Nox enzymes. These mice exhibited reduced levels of O2− in the heart, indicating that Nox4 is a significant source of O2− in cardiac myocytes. The baseline cardiac phenotype was normal in young c-Nox4−/− mice. In response to pressure overload (PO), however, increases in Nox4 expression and O2− production in mitochondria were abolished in c-Nox4−/− mice, and c-Nox4−/− mice exhibited significantly attenuated cardiac hypertrophy, interstitial fibrosis and apoptosis, and better cardiac function compared with WT mice. Mitochondrial swelling, cytochrome c release, and decreases in both mitochondrial DNA and aconitase activity in response to PO were attenuated in c-Nox4−/− mice. On the other hand, overexpression of Nox4 in mouse hearts exacerbated cardiac dysfunction, fibrosis, and apoptosis in response to PO. These results suggest that Nox4 in cardiac myocytes is a major source of mitochondrial oxidative stress, thereby mediating mitochondrial and cardiac dysfunction during PO.
Is whole grain intake associated with reduced total and cause-specific death rates in older women? The Iowa Women's Health Study.

OBJECTIVES This study sought to determine whether nutrient-rich whole grains reduce mortality risk. METHODS The study included 38,740 Iowa women, aged 55 to 69 years. A food frequency questionnaire was used to obtain data on grain intake. RESULTS Median whole grain intake quintiles ranged from a median of 0.2 to more than 3 servings per day. Women with higher intakes had healthier lifestyles and less baseline disease. The total death rate decreased in increasing quintiles, and the pattern repeated for cancer, cardiovascular disease, and other causes combined. Adjusted for lifestyle and baseline disease, the relative hazard rate ratio for total death was about 0.85 in daily consumers of whole grain. Findings persisted in strata of baseline healthy and diseased and were not explained by dietary fiber. Rates of total mortality, but not cardiovascular disease mortality, were higher among frequent consumers of refined grain. CONCLUSIONS Total mortality risk was inversely associated with whole grain intake and positively associated with refined grain intake. Refined grains contributed more than 20% of energy intake, and whole grains contributed 1%. Substitution of whole for refined grain may reduce chronic disease risk in the United States.
Hemodynamics and the vascular endothelium.

The endothelium, once thought to be a passive, non-thrombogenic barrier, is now recognized as being a dynamic participant in vascular biology and pathobiology. Part of its dynamic nature is due to the influence of the mechanical environment imposed by the hemodynamics of the vascular system. Over the past two decades much has been learned about the influence of hemodynamics on the vascular endothelium. This has been in part through in vivo experiments; however, in the past 15 years a number of laboratories have turned to the application of in vitro cell culture systems to investigate the influence of flow and cyclic stretch on the biology of vascular endothelium. Taken together these studies demonstrate that flow and the associated shear stress modulate both endothelial cell structure and function. Cell culture studies employing cyclic stretch provide similar evidence. Furthermore, these effects of mechanical environment extend to the gene expression level, with there being a differential regulation of mRNA. A critical question is how does an endothelial cell recognize the mechanical environment in which it resides and, having done so, how is this transduced into the changes in structure and function observed? Although our knowledge of the recognition events remains limited, studies on signal transduction in response to a mechanical stimulus indicate that many of the second messengers known to be triggered by chemical agonists also are involved in transducing a mechanical signal. (ABSTRACT TRUNCATED AT 250 WORDS)
Evidence for suppressor cells in Lewis rats' experimental allergic encephalomyelitis

In this work we demonstrate a suppressive activity on the induction of experimental allergic encephalomyelitis (EAE) in Lewis rats, transferable to syngeneic animals, challenged with encephalitogenic mixture (myelin basic protein, complete Freund's adjuvant plus Bordetella pertussis organisms) 24 h later. This activity is probably effected by T cells and not by (an) inhibitory serum factor(s). The induction of this specific protection could be due to the penetration of the myelin basic protein antigen into the thymus where we first found suppressive cells. From the thymus, suppressor cells could then emigrate to spleen (on day 15) and to nondraining lymph nodes (on day 17). In the course of normal EAE in Lewis rats and especially at the time of self cure, this suppression is not demonstrated, but possible.
Parallel Algorithms for Dynamic Programming Recurrences with More than O(1) Dependency

We study the parallel computation of dynamic programming. We consider four important dynamic programming problems which have wide application, and that have been studied extensively in sequential computation: (1) the 1D problem, (2) the gap problem, (3) the parenthesis problem, and (4) the RNA problem. The parenthesis problem has fast parallel algorithms; almost no work has been done for parallelizing the other three. We present a unifying framework for the parallel computation of dynamic programming recurrences with more than O(1) dependency. We use two well-known methods, the closure method and the matrix product method, as general paradigms for developing parallel algorithms. Combined with various techniques, they lead to a number of new results. Our main results are optimal sublinear-time algorithms for the 1D, parenthesis, and RNA problems.
Effect of a visual-based sensory motor task on muscle tuning during a dynamic balance task

In this research, we explored visually-based sensory motor learning when a transformation was applied to the trajectory used to move and track a visual target in a virtual environment. The virtual task was controlled by the subject's center of foot pressure (COP), where the COP position was mapped to an on-screen cursor. Target balloons appeared randomly on the screen; the subject was instructed to move the COP-controlled cursor to intersect and burst the balloons. A transformation was applied to the movement trajectory, which rotated the on-screen cursor counter-clockwise by 60°. The transformation required the subjects to update their spatial reference coordinates between the physical COP position and the on-screen cursor. To investigate learning during the transformation, electromyogram (EMG) data was recorded from the tibialis anterior and peroneus longus muscles. The muscle activity, calculated as the root mean square (RMS) of the EMG data, was calculated for each muscle as a function of the movement direction during movement initiation. The preferred direction (PD) for each muscle was then determined as the directional sum of the RMS values. The results showed a shift in the preferred direction (PD) of the muscles with learning.