Miracle-dz/UniFAR-FTUs huggingface dataset:
Analysis of gut microbial regulation of host gene expression along the length of the gut and regulation of gut microbial ecology through MyD88

Background The gut microbiota has profound effects on host physiology but local host–microbial interactions in the gut are only poorly characterised and are likely to vary from the sparsely colonised duodenum to the densely colonised colon. Microorganisms are recognised by pattern recognition receptors such as Toll-like receptors, which signal through the adaptor molecule MyD88. Methods To identify host responses induced by gut microbiota along the length of the gut and whether these required MyD88, transcriptional profiles of duodenum, jejunum, ileum and colon were compared from germ-free and conventionally raised wild-type and Myd88−/− mice. The gut microbial ecology was assessed by 454-based pyrosequencing and viruses were analysed by PCR. Results The gut microbiota modulated the expression of a large set of genes in the small intestine and fewer genes in the colon but surprisingly few microbiota-regulated genes required MyD88 signalling. However, MyD88 was essential for microbiota-induced colonic expression of the antimicrobial genes Reg3β and Reg3γ in the epithelium, and Myd88 deficiency was associated with both a shift in bacterial diversity and a greater proportion of segmented filamentous bacteria in the small intestine. In addition, conventionally raised Myd88−/− mice had increased expression of antiviral genes in the colon, which correlated with norovirus infection in the colonic epithelium. Conclusion This study provides a detailed description of tissue-specific host transcriptional responses to the normal gut microbiota along the length of the gut and demonstrates that the absence of MyD88 alters gut microbial ecology.
Mcp3 is a novel mitochondrial outer membrane protein that follows a unique IMP‐dependent biogenesis pathway

The authors noticed an error in Appendix Fig S1 as follows: In the original publication, we show the same panel for SG-Leu medium at both 30°C and 37°C, although this panel represents only 30°C, and another panel should have been shown for 37°C. In the corrected Appendix Fig S1, we fixed this error and present the correct panel for 37°C. This mistake does not alter the scientific conclusion from this figure, namely that the over-expression of Mcp3 does not influence the growth of yeast cells under these conditions. We would like to apologize for this mistake and any inconvenience it may have caused.
Characteristic of Malocclusion among Saudi Special Need Group Children.

INTRODUCTION The present study analyzed the characteristics of malocclusions, occlusal traits among Special Health care Needs (SHCN) children with Down syndrome (DS) and autism disorder (AD) in Riyadh City, Kingdom of Saudi Arabia. MATERIALS AND METHODS A total of 100 DS and 100 AD children from five rehabilitation centers in and around Riyadh, Kingdom of Saudi Arabia, were included in the study. Any children with history of ongoing medical treatment, extraction, or orthodontic treatment were excluded from the study. Out of the 200 patients examined, 131 were males and 69 were females and the age of the children ranged from 6 to 14 years. The children were examined for malocclusion characteristics using the Angle's classification of malocclusion, and also other occlusal traits, such as overjet, overbite, cross bite, and open bite were also determined. The data obtained were analyzed using Statistical Package for the Social Sciences, version 16 to generate descriptive statistics for each variable. RESULTS The analyzed data of the right and left permanent molar relation showed higher incidence of class III malocclusion (66%) in DS children as compared with (3-4%) AD children. The AD children presented with higher percentage of class I malocclu-sion (40-41%) as compared with (10-14%) DS children. During examination of the primary molars, the analyzed data showed that left primary molar had more mesial shift in AD children as compared with DS children. CONCLUSION Down syndrome children had high incidence of class III malocclusion and autistic children had high incidence of class I malocclusion. Overall, the DS children were more prone to malocclusion. CLINICAL SIGNIFICANCE This study provides database for health professionals in Saudi Arabia in regard to malocclusion of autis-tics and DS patients.
Postdischarge growth assessment in very low birth weight infants

Purpose The goal of nutritional support for very-low-birth-weight (VLBW) infants from birth to term is to match the in utero growth rates; however, this is rarely achieved. Methods We evaluated postdischarge growth patterns and growth failure in 81 Korean VLBW infants through a retrospective study. Weight and height were measured and calculated based on age percentile distribution every 3 months until age 24 months. Growth failure was defined as weight and height below the 10th percentile at 24 months. For the subgroup analysis, small-for-gestational age (SGA) and extremely low birth weight (ELBW) infants were evaluated. The growth patterns based on the Korean, World Health Organization (WHO), or Centers for Disease Control and Prevention (CDC) standard were serially compared over time. Results At postconception age (PCA) 40 weeks, 47 (58%) and 45 infants (55%) showed growth failure in terms of weight and height, respectively. At PCA 24 months, 20 infants (24%) showed growth failure for weight and 14 (18%) for height. Growth failure rates were higher for the SGA infants than for the appropriate-weight-for-gestational age infants at PCA 24 months (P=0.045 for weight and P=0.038 for height). Growth failure rates were higher for the ELBW infants than for the non-ELBW infants at PCA 24 months (P<0.001 for weight and P=0.003 for height). Significant differences were found among the WHO, CDC, and Korean standards (P<0.001). Conclusion Advancements in neonatal care have improved the catch-up growth of VLBW infants, but this is insufficient. Careful observation and aggressive interventions, especially in SGA and ELBW infants, are needed.
Performance Analysis of Multilevel Bus Networks for Hierarchical Multiprocessors

A multiple bus system provides more bandwidth and a high degree of fault tolerance than a single bus system. But such a system becomes very expensive for a large number of processors and memory modules, due to the requirement of too many connections (switches). Lang (1983) proposed a different bus-based system, known as the partial multiple bus system, which requires a lower number of connections than a multiple bus system, but with a slight degradation in system performance. This paper presents a new type of bus-based system, called the multilevel bus system. Such a bus architecture can be used to design hierarchical multiprocessors. This bus-based system requires significantly less connections than multiple and partial multiple bus systems. This system is very cost-effective, as compared to multiple and partial multiple bus systems, when there exists some locality in the computations. Analytical and simulation models have been developed to determine the performance of both synchronous and asynchronous multilevel bus systems. The results obtained from the analysis show that a multilevel bus system performs fairly close to other bus-based systems for the hierarchical reference (HR) model. In the HR model, a processor accesses its nearest memory modules more frequently than other memory modules. >
Selenium in Bone Health: Roles in Antioxidant Protection and Cell Proliferation

Selenium (Se) is an essential trace element for humans and animals, and several findings suggest that dietary Se intake may be necessary for bone health. Such findings may relate to roles of Se in antioxidant protection, enhanced immune surveillance and modulation of cell proliferation. Elucidation of the mechanisms by which Se supports these cellular processes can lead to a better understanding of the role of this nutrient in normal bone metabolism. This article reviews the current knowledge concerning the molecular functions of Se relevant to bone health.
Comparison of Molecular and Conventional Methods for Estimating Parasitism Level in the Pomegranate Aphid Aphis punicae (Hemiptera: Aphididae)

Abstract Aphidiinae (Braconidae: Aphidiinae) is a subfamily of endoparasitic wasps specialized in parasitizing aphids. Although, to date, different methods have been used to measure parasitism level, obtaining an accurate estimate remains challenging due to several limiting factors. This study was set to: 1) Compare efficiency of conventional and molecular-based methods in estimating parasitism level of the pomegranate aphid Aphis punicae (Passerini; Hemiptera: Aphididae), and 2) Estimate seasonal activity of the Aphidiinae parasitoids of the pomegranate aphid. The molecular approach (polymerase chain reaction [PCR]) detected the presence of three main parasitoids Lysiphlebus fabarum (Marshal; Hymenoptra: Braconidae), Binodoxys angelicae (Haliday; Hymenoptra: Braconidae), and Ephedrus persicae (Frogatt; Hymenoptra: Braconidae). The presence of hyperparasitoid and aphid DNAs did not interfere with the outcome, indicating specificity of the selected primers. Minimum concentrations of DNA needed for successful amplifications were 16.33, 28.65, and 22.65 ng µl−1, for L. fabarum, B. angelicae, and E. persicae, respectively. The level of parasitism was significantly higher in spring (28.42%) than both summer and fall; parasitism level during summer (11.89%) and fall (5.86%) formed a homogeneous statistical subset. Although the overall level of parasitism estimated by PCR (22.7%) was more than twofold higher than those estimated by a conventional counting method (10.5%), there was a strong positive correlation between the two approaches. Provided the potential limitations of either method, simultaneous use of both methods was recommended for an objective estimate of the effectiveness of the Aphidiinae parasitoids as biological control agents of A. punicae.
Clonal Population Structure and Antimicrobial Resistance of Campylobacter jejuni in Chicken Meat from Belgium

ABSTRACT Campylobacter jejuni is one of the most important causes of human diarrhea worldwide. In the present work, multilocus sequence typing was used to study the genotypic diversity of 145 C. jejuni isolates from 135 chicken meat preparations sampled across Belgium. Isolates were further typed by pulsed-field gel electrophoresis, and their susceptibilities to six antimicrobials were determined. Fifty-seven sequence types (STs) were identified; 26.8% of the total typed isolates were ST-50, ST-45, or ST-257, belonging to clonal complex CC-21, CC-45, or CC-257, respectively. One clonal group comprised 22% (32/145) of all isolates, originating from five different companies and isolated over seven sampling months. Additionally, 53.1% of C. jejuni isolates were resistant to ciprofloxacin, and 48.2% were resistant to tetracycline; 28.9% (42/145) of all isolates were resistant to both ciprofloxacin and tetracycline. The correlation between certain C. jejuni clonal groups and resistance to ciprofloxacin and tetracycline was notable. C. jejuni isolates assigned to CC-21 (n = 35) were frequently resistant to ciprofloxacin (65.7%) and tetracycline (40%); however, 90% (18/20) of the isolates assigned to CC-45 were pansusceptible. The present study demonstrates that certain C. jejuni genotypes recur frequently in the chicken meat supply. The results of molecular typing, combined with data on sample sources, indicate a possible dissemination of C. jejuni clones with high resistance to ciprofloxacin and/or tetracycline. Whether certain clonal groups are common in the environment and repeatedly infect Belgian broiler flocks or whether they have the potential to persist on farms or in slaughterhouses needs further investigation.
A gaze-based study for investigating the perception of visual realism in simulated scenes

Visual realism has been a major objective of computer graphics since the inception of the field. However, the perception of visual realism is not a well-understood process and is usually attributed to a combination of visual cues and image features that are difficult to define or measure. For highly complex images, the problem is even more involved. The purpose of this paper is to present a study based on eye tracking for investigating the perception of visual realism of static images with different visual qualities. The eye-fixation clusters helped to define salient image features corresponding to 3D surface details and light transfer properties that attract observers' attention. This enabled the definition and categorization of image attributes affecting the perception of photorealism. The dynamics of the visual behavior of different observer groups were examined by analyzing saccadic eye movements. We also demonstrated how the different image categories used in the experiments were perceived with varying degrees of visual realism. The results presented can be used as a basis for investigating the impact of individual image features on the perception of visual realism. This study suggests that post-recall or simple abstraction of visual experience is not accurate and the use of eye tracking provides an effective way of determining relevant features that affect visual realism, thus allowing for improved rendering techniques that target these features.
Packet classification using multidimensional cutting

This paper introduces a classification algorithm called phHyperCuts. Like the previously best known algorithm, HiCuts, HyperCuts is based on a decision tree structure. Unlike HiCuts, however, in which each node in the decision tree represents a hyperplane, each node in the HyperCuts decision tree represents a k--dimensional hypercube. Using this extra degree of freedom and a new set of heuristics to find optimal hypercubes for a given amount of storage, HyperCuts can provide an order of magnitude improvement over existing classification algorithms. HyperCuts uses 2 to 10 times less memory than HiCuts optimized for memory, while the worst case search time of HyperCuts is 50--500% better than that of HiCuts optimized for speed. Compared with another recent scheme, EGT-PC, HyperCuts uses 1.8--7 times less memory space while the worst case search time is up to 5 times smaller. More importantly, unlike EGT-PC, HyperCuts can be fully pipelined to provide one classification result every packet arrival time, and also allows fast updates.
A Substrate Isolated CMOS SPAD Enabling Wide Spectral Response and Low Electrical Crosstalk

In this work we present a substrate isolated single photon avalanche diode designed and fabricated in 180 nm CMOS technology. Substrate isolation is ensured by design to enable lower electrical crosstalk and to ease circuit integration. The presented device achieves wide spectral sensitivity enabling greater than 40% photon detection probability from 440 to 620 nm wavelength at 10 V excess bias. For a 12 μm active diameter, the dark count rate of the device is 17 Hz and 1.45 kHz at 2 and 10 V excess bias, respectively, while the after pulsing probability is less than 0.3% with 300 ns dead time at 10 V excess bias, and timing jitter was 70 ps (full width at half maximum) when using 405 nm wavelength laser.
Mental health in the oil industry: a comparative study of onshore and offshore employees

Synopsis Few empirical studies have examined the mental health of workers on North Sea oil and gas installations, and it is unclear from the available literature whether offshore employees show impaired mental health relative to their onshore counterparts. The present study was intended to clarify this issue by direct comparison of the General Health Questionnaire (GHQ) scores of onshore and offshore personnel engaged in similar work. As compared with published data, only the onshore group showed low GHQ-12 scores, although both groups were low in neuroticism. Analysis of GHQ subscale scores demonstrated that anxiety was significantly higher among offshore workers than among those working onshore, but there were no significant differences in somatic symptoms or social dysfunction. Regression analyses showed that this result was not affected by control for age, job level, and neuroticism, although there was a significant interaction between job level and neuroticism in predicting anxiety. The nature of the offshore environment, and the factors which may play a causal role in elevated anxiety among offshore workers, are discussed.
Digital subtraction angiography-guided foam sclerotherapy of peripheral venous malformations.

OBJECTIVE The purpose of this article is to describe a modified technique of using digital subtraction angiography guidance combined with the double-needle technique and the filling-defects technique for foam sclerotherapy of peripheral venous malformations. The short-term efficacy and safety of the technique were evaluated. MATERIALS AND METHODS Fourteen patients with peripheral venous malformations were treated with foam sclerotherapy. Sclerosing foam was prepared using the Tessari method to mix room air with 5% sodium morrhuate in a 4:1 ratio. Percutaneous foam sclerotherapy of venous malformations under digital subtraction angiography guidance was performed using a combined technique modified with the double-needle technique and the filling-defects technique. Follow-up clinical and radiologic assessment and evaluation of patient satisfaction were performed to evaluate the end result. RESULTS At a mean of 9.3 months (range, 6-12 months) after the last session, the overall outcome was rated as excellent improvement (i.e., clinical obliteration and asymptomatic) in four (28.6%) of 14 patients, good improvement (i.e., substantial improvement in size and symptoms of > 50%) in nine patients (64.3%), or moderate improvement (i.e., significant decrease in size and symptoms of </= 50%) in one patient (7.1%). No major complications occurred. CONCLUSION Digital subtraction angiography-guided percutaneous foam sclerotherapy modified with the double-needle technique and the filling-defects technique is an alternative method with favorable short-term results for treating peripheral venous malformations.
CHANNELS IN THE VISUAL NERVOUS SYSTEM : NEUROPHYSIOLOGY , PSYCHOPHYSICS AND MODELS

Spatial vision research during the 1970s was dominated by the spatial frequency channel paradigm of Campbell and Robson (1968). This article summarizes some research and current views on spatial frequency channels. By channels, we mean an array of medium bandwidth mechanisms, similar to the simple cells that are commonly found in the visual system. The viewpoint presented here provides a useful perspective, slightly different from that found in Graham's excellent book (1989). Spatial frequency channels play a central role in enabling us to discriminate small, complex objects with our constantly moving eyes. Given an image that is constantly moving on the retina, it is of great value to recode the information from the position domain to the relative position (size) domain to remove the effects of image motion.
The effect of indocyanine green-mediated photodynamic therapy as an adjunct to scaling and root planing in the treatment of chronic periodontitis: A comparative split-mouth randomized clinical trial

Objective: The aim of this study was to assess the effect of adjunctive photodynamic therapy (PDT) (using 810 nm diode laser and Indocyanine green as photosensitizer) in chronic periodontitis. Materials and Methods: Patients with untreated chronic periodontitis were included. Treatment was done according to a split mouth design. All sites received periodontal treatment comprising scaling and root-planing (SRP). Test group were additionally treated with PDT. Plaque Index (PI), Gingival Index (GI), Probing Pocket Depth (PPD) and Relative Attachment Level (RAL) were evaluated at baseline, 1 month and 3 months. Results: Mean baseline values for PI, GI, PPD and RAL were not different in the test group and control group. Statistical significant difference in PPD and RAL, 3 months after treatment was seen in test group as compared to the control group. Conclusions: In patients with chronic periodontitis, clinical outcomes of conventional SRP can be improved by adjunctive PDT.
Biofuncationalized microfiber Bragg grating for acid-based sensing

We demonstrate an acid-based sensor from the biofuncationalized microfiber Bragg grating. By electrostatic selfassembly layer-by-layer technique, the film consisting of sodium alginate which has hygroscopic response to the potential of hydrogen is coated on the fiber surface. Consequently, the refractive index variation of the sensing film caused by water absorption can be measured by mFBG’s higher order mode peak which can be translated into pH value information. The sensitivity of the sensor is received as high as 265pm/pH.
Recombinant human interleukin-6 induces a rapid and reversible anemia in cancer patients.

Initial studies have shown that recombinant human interleukin-6 (rhIL-6) induces anemia. Until now, the pathophysiologic mechanism of this induced anemia has been unknown. To unravel the underlying mechanism, we examined 15 cancer patients receiving rhIL-6 as an antitumor immunotherapy in a phase II study. rhIL-6 was administered subcutaneously at 150 micrograms once daily for 6 consecutive weeks. Various hematologic and biochemical parameters were measured weekly during rhIL-6 treatment and 4 weeks after rhIL-6 discontinuation. To determine plasma volume and red blood cell (RBC) volume, radioisotope dilution assays with labeled autologous RBCs and with human serum albumin were performed before rhIL-6 administration and on day 8 of rhIL-6 therapy. Hemoglobin levels decreased (mean change +/- SE) 7% +/- 1.5% within 3 days after the start of rhIL-6 therapy (P < .0001) and 19% +/- 2% at week 4. Levels had normalized at follow-up. The plasma volume increased 18% +/- 5% during the first week of rhIL-6 administration (P < .003), whereas RBC volume remained unaffected. The mean RBC corpuscular volume remained unchanged for 2 weeks and then began to decrease slowly, reaching its nadir at week 6 (5% +/- 1%; P < .01). Serum iron levels decreased 65% +/- 12% at week 4 (P < .002) and then returned to initial baseline values. Erythropoietin levels increased rapidly up to 68% at week 3 (P < .0001) and had normalized 4 weeks after rhIL-6 therapy. Levels of serum albumin, prealbumin, and transferrin decreased (P < .0001, P < .003, and P < .0001, respectively), whereas levels of serum amyloid A (P < .003), C-reactive protein, haptoglobin, and alpha-1-antitrypsin (P < .0001) increased during rhIL-6 treatment. All levels returned to pretreatment values after discontinuation of rhIL-6. No alterations in reticulocyte counts, serum lactic dehydrogenase levels, and bilirubin levels were observed. A 6-week regimen of subcutaneous rhIL-6 results in a rapid dilution anemia, caused by an acute and significant increase in plasma volume and followed by hypoferremia. This anemia is reversible after the cessation of rhIL-6 treatment.
Learning multi-faceted representations of individuals from heterogeneous evidence using neural networks

Inferring latent attributes of people online is an important social computing task, but requires integrating the many heterogeneous sources of information available on the web. We propose learning individual representations of people using neural nets to integrate rich linguistic and network evidence gathered from social media. The algorithm is able to combine diverse cues, such as the text a person writes, their attributes (e.g. gender, employer, education, location) and social relations to other people. We show that by integrating both textual and network evidence, these representations offer improved performance at four important tasks in social media inference on Twitter: predicting (1) gender, (2) occupation, (3) location, and (4) friendships for users. Our approach scales to large datasets and the learned representations can be used as general features in and have the potential to benefit a large number of downstream tasks including link prediction, community detection, or probabilistic reasoning over social networks.