Miracle-dz/UniFAR-FTUs huggingface dataset:
Faecal Metaproteomic Analysis Reveals a Personalized and Stable Functional Microbiome and Limited Effects of a Probiotic Intervention in Adults

Recent metagenomic studies have demonstrated that the overall functional potential of the intestinal microbiome is rather conserved between healthy individuals. Here we assessed the biological processes undertaken in-vivo by microbes and the host in the intestinal tract by conducting a metaproteome analysis from a total of 48 faecal samples of 16 healthy adults participating in a placebo-controlled probiotic intervention trial. Half of the subjects received placebo and the other half consumed Lactobacillus rhamnosus GG for three weeks (1010 cfu per day). Faecal samples were collected just before and at the end of the consumption phase as well as after a three-week follow-up period, and were processed for microbial composition and metaproteome analysis. A common core of shared microbial protein functions could be identified in all subjects. Furthermore, we observed marked differences in expressed proteins between subjects that resulted in the definition of a stable and personalized microbiome both at the mass-spectrometry-based proteome level and the functional level based on the KEGG pathway analysis. No significant changes in the metaproteome were attributable to the probiotic intervention. A detailed taxonomic assignment of peptides and comparison to phylogenetic microarray data made it possible to evaluate the activity of the main phyla as well as key species, including Faecalibacterium prausnitzii. Several correlations were identified between human and bacterial proteins. Proteins of the human host accounted for approximately 14% of the identified metaproteome and displayed variations both between and within individuals. The individually different human intestinal proteomes point to personalized host-microbiota interactions. Our findings indicate that analysis of the intestinal metaproteome can complement gene-based analysis and contributes to a thorough understanding of the activities of the microbiome and the relevant pathways in health and disease.
GibbsNet: Iterative Adversarial Inference for Deep Graphical Models

Directed latent variable models that formulate the joint distribution as $p(x,z) = p(z) p(x \mid z)$ have the advantage of fast and exact sampling. However, these models have the weakness of needing to specify $p(z)$, often with a simple fixed prior that limits the expressiveness of the model. Undirected latent variable models discard the requirement that $p(z)$ be specified with a prior, yet sampling from them generally requires an iterative procedure such as blocked Gibbs-sampling that may require many steps to draw samples from the joint distribution $p(x, z)$. We propose a novel approach to learning the joint distribution between the data and a latent code which uses an adversarially learned iterative procedure to gradually refine the joint distribution, $p(x, z)$, to better match with the data distribution on each step. GibbsNet is the best of both worlds both in theory and in practice. Achieving the speed and simplicity of a directed latent variable model, it is guaranteed (assuming the adversarial game reaches the virtual training criteria global minimum) to produce samples from $p(x, z)$ with only a few sampling iterations. Achieving the expressiveness and flexibility of an undirected latent variable model, GibbsNet does away with the need for an explicit $p(z)$ and has the ability to do attribute prediction, class-conditional generation, and joint image-attribute modeling in a single model which is not trained for any of these specific tasks. We show empirically that GibbsNet is able to learn a more complex $p(z)$ and show that this leads to improved inpainting and iterative refinement of $p(x, z)$ for dozens of steps and stable generation without collapse for thousands of steps, despite being trained on only a few steps.
Modeling of Force Sensing and Validation of Disturbance Observer for Force Control

Controlling robots in contact with the environment is an important problem in industry applications. Generally, a force sensor is used for sensing the external force. It is well known that information of a force sensor has much noise. Furthermore, unstable state is also caused by the narrow bandwidth of force information by a force sensor. This paper shows that stable contact with the environment is difficult when a force sensor is used because of its soft mechanical structure and narrow bandwidth of force sensing. In order to solve the instability of force control, the disturbance observer is implemented instead of the force sensor. The disturbance observer can observe the external force without force sensors. When the disturbance observer is implemented in a robot, a force control system does not include a soft mechanism between a robot and the environment. Since a robot can detect the environmental information directly, a wide bandwidth of force sensing is attained. In this way, this paper solves the problems of force control by considering the force sensing method without changing the control architecture, and the ability of force control is improved. Experimental results show viability of the proposed method
How to Compare Two Quantities? A Computational Model of Flutter Discrimination

A task that has been intensively studied at the neural level is f lutter discrimination. I argue that f lutter discrimination entails a combination of a temporal assignment problem and a quantity comparison problem, and propose a neural network model of how these problems are solved. The network combines unsupervised and one-layer supervised training. The unsupervised part clusters input features (stimulus + time window) and the supervised part categorizes the resulting clusters. After training, the model shows a good fit with both neural and behavioral properties. New predictions are outlined and links with other cognitive domains are pointed out.
New Robust 3-D Phase Unwrapping Algorithms: Application to Magnetic Field Mapping and Undistorting Echoplanar Images

The phase, as well as the magnitude, of MRI images can carry useful information. It may be used to encode flow or temperature, or to map the magnetic field for the undistorting of EPIs and automated shimming. In all cases, we measure the extra spin given to nuclei. Unfortunately, we can only measure the final phase of the spins: the rotation is wrapped into the range [-pi, +pi], and to obtain a measure of the parameter of interest the missing multiples of 2pi must be replaced--a process known as phase unwrapping. While simple in principle, standard phase unwrapping algorithms fail catastrophically in the presence of even small amounts of noise. Here we present a new algorithm for robust three-dimensional phase unwrapping, in which unwrapping is guided, so that it initially works on less noisy regions. We test the algorithm on simulated phase data, and on maps of magnetic field, which were then used to successfully undistort EPI images. The unwrapping algorithm could be directly applied to other kinds of phase data.
Over-drainage and persistent shunt-dependency in patients with idiopathic intracranial hypertension treated with shunts and bariatric surgery

Background: Idiopathic intracranial hypertension (IIH) may lead to visual impairment. Shunt surgery is indicated for refractory IIH-related symptoms that persist despite medical treatment, or those presenting with significant visual decline. Obesity is a risk factor for IIH; a reduction in weight has been shown to improve papilledema. Bariatric surgery (BS) has been suggested for treating IIH associated with morbid obesity. In this study, we describe a high rate of over-drainage (OD) seen in patients following shunts and BS. Methods: The study cohort includes 13 patients with IIH that underwent shunt surgery for treatment of the IIH-related symptoms. Six patients underwent BS in addition to the shunt surgery (but not concomitantly). Seven patients had only shunt surgeries with no BS. Data were collected retrospectively. Results: BS effectively led to weight reduction (body mass index decreasing from 43 ± 4 to 28 ± 5). Patients undergoing BS had 1–6 (2.5 ± 1.9) shunt revisions for OD following BS, as opposed to 0–3 (1.4 ± 1.1) revisions prior to BS over similar time spans (statistically insignificant difference), and 0–6 (1.6 ± 2.5) revisions among the non-BS patients over a longer time span (statistically insignificant difference). Two patients in the BS group underwent shunt externalization and closure; however, they proved to be shunt-dependent. Conclusions: Patients with IIH that undergo shunt surgery and BS (not concomitantly) may suffer from OD symptoms, necessitating multiple shunt revisions, and valve upgrades. Despite BS being a valid primary treatment for some patients with IIH, among shunted patients, BS may not lead to resolution of IIH-related symptoms and patients may remain shunt-dependent.
Regulatory Network Connecting Two Glucose Signal Transduction Pathways in Saccharomyces cerevisiae

ABSTRACT The yeast Saccharomyces cerevisiae senses glucose, its preferred carbon source, through multiple signal transduction pathways. In one pathway, glucose represses the expression of many genes through the Mig1 transcriptional repressor, which is regulated by the Snf1 protein kinase. In another pathway, glucose induces the expression of HXT genes encoding glucose transporters through two glucose sensors on the cell surface that generate an intracellular signal that affects function of the Rgt1 transcription factor. We profiled the yeast transcriptome to determine the range of genes targeted by this second pathway. Candidate target genes were verified by testing for Rgt1 binding to their promoters by chromatin immunoprecipitation and by measuring the regulation of the expression of promoter lacZ fusions. Relatively few genes could be validated as targets of this pathway, suggesting that this pathway is primarily dedicated to regulating the expression of HXT genes. Among the genes regulated by this glucose signaling pathway are several genes involved in the glucose induction and glucose repression pathways. The Snf3/Rgt2-Rgt1 glucose induction pathway contributes to glucose repression by inducing the transcription of MIG2, which encodes a repressor of glucose-repressed genes, and regulates itself by inducing the expression of STD1, which encodes a regulator of the Rgt1 transcription factor. The Snf1-Mig1 glucose repression pathway contributes to glucose induction by repressing the expression of SNF3 and MTH1, which encodes another regulator of Rgt1, and also regulates itself by repressing the transcription of MIG1. Thus, these two glucose signaling pathways are intertwined in a regulatory network that serves to integrate the different glucose signals operating in these two pathways.
Procalcitonin in pediatric emergency departments for the early diagnosis of invasive bacterial infections in febrile infants: results of a multicenter study and utility of a rapid qualitative test for this marker.

BACKGROUND Procalcitonin (PCT) is a potentially useful marker in pediatric Emergency Departments (ED). The basic objectives of this study were to assess the diagnostic performance of PCT for distinguishing between viral and bacterial infections and for the early detection of invasive bacterial infections in febrile children between 1 and 36 months old comparing it with C-reactive protein (CRP) and to evaluate the utility of a qualitative rapid test for PCT in ED. METHODS Prospective, observational and multicenter study that included 445 children who were treated for fever in pediatric ED. Quantitative and qualitative plasma values of PCT and CRP were correlated with the final diagnosis. To obtain the qualitative level of PCT the BRAHMS PCT-Q rapid test was used. RESULTS Mean PCT and CRP values in viral infections were 0.26 ng/ml and 15.5 mg/l, respectively. The area under the curve obtained for PCT in distinguishing between viral and bacterial infections was 0.82 (sensitivity, 65.5%; specificity, 94.3%; optimum cutoff, 0.53 ng/ml), whereas for CRP it was 0.78 (sensitivity, 63.5%; specificity, 84.2%; optimum cutoff, 27.5 mg/l). PCT and CRP values in invasive infections (PCT, 24.3 ng/ml; CRP 96.5 mg/l) were significantly higher than those for noninvasive infections (PCT, 0.32 ng/ml; CRP, 23.4 mg/l). The area under the curve for PCT was 0.95 (sensitivity, 91.3%; specificity, 93.5%; optimum cutoff, 0.59 ng/ml), significantly higher (P < 0.001) than that obtained for CRP (0.81). The optimum cutoff value for CRP was >27.5 mg/l with sensitivity and specificity of 78 and 75%, respectively. In infants in whom the evolution of fever was <12 h (n = 104), the diagnostic performance of PCT was also greater than that of CRP (area under the curve, 0.93 for PCT and 0.69 for CRP; P < 0.001). A good correlation between the quantitative values for PCT and the PCT-Q test was obtained in 87% of cases (kappa index, 0.8). The sensitivity of the PCT-Q test (cutoff >0.5 ng/ml) for detecting invasive infections and differentiating them from noninvasive infections was 90.6%, with a specificity of 83.6%. CONCLUSIONS PCT offers better specificity than CRP for differentiating between the viral and bacterial etiology of the fever with similar sensitivity. PCT offers better sensibility and specificity than CRP to differentiate between invasive and noninvasive infection. PCT is confirmed as an excellent marker in detecting invasive infections in ED and can even make early detection possible of invasive infections if the evolution of the fever is <12 h. The PCT-Q test has a good correlation with the quantitative values of the marker.
Proton MR spectroscopic and diffusion tensor brain MR imaging in X-linked adrenoleukodystrophy: initial experience.

PURPOSE To compare conventional magnetic resonance (MR) imaging, proton MR spectroscopic imaging, and diffusion tensor (DT) MR imaging findings in patients with X chromosome-linked adrenoleukodystrophy (X-ALD). MATERIALS AND METHODS Multisection proton MR spectroscopy and DT imaging were performed in 11 patients with X-ALD and in 11 healthy control subjects. Quantitative measures of N-acetylaspartate (NAA), choline, and creatine values and of isotropic apparent diffusion coefficient (IADC) and fractional anisotropy (FA) were obtained from coregistered regions of interest. DT imaging and metabolic parameters were compared by using regression analysis. In addition, differences in DT imaging and metabolite measurements between normal- and abnormal-appearing white matter on conventional MR images were evaluated by using a nonparametric (Mann-Whitney) test. RESULTS A strong logarithmic relationship between NAA value and FA (r = 0.64, P <.001) and an inverse logarithmic relationship were found between NAA value and IADC (r = -0.69, P <.001). Creatine and choline values correlated poorly with IADC and FA. In the normal-appearing white matter of asymptomatic patients, the NAA value was 17% lower than that in the healthy control subjects (P =.016), whereas no significant difference in DT imaging measures was seen in these regions. CONCLUSION In patients with X-ALD, MR spectroscopic imaging can depict abnormalities in white matter that have a normal appearance on both conventional MR and DT images; this finding suggests that it may be the most sensitive technique for detecting early abnormalities of demyelination or axonal loss in patients with X-ALD.
Hepatic growth hormone resistance during sepsis is associated with increased suppressors of cytokine signaling expression and impaired growth hormone signaling

Objective:During sepsis, a two- to four-fold increase in circulating growth hormone (GH) is seen with 40–50% reductions in plasma insulin-like growth factor (IGF)-I. The suppressors of cytokine signaling (SOCS), inhibitors of cytokine, and growth factor signaling via the janus kinase (JAK)/signal transducer and activator of transcription (STAT) pathway have been implicated in the development of hepatic GH resistance. In this study we examine the effects of sepsis on GH-induced IGF-I expression and potential mechanisms for GH resistance. Design:Prospective experimental study. Setting:University research laboratory. Subjects:Male Sprague-Dawley rats. Interventions:Rats were randomized to laparotomy alone (control) or implantation of fecal agar pellets inoculated with Escherichia coli and Bacteroides fragilis (sepsis). GH was injected intravenously to assess hepatic IGF-I synthesis and GH signaling. Measurements and Main Results:Plasma IGF-I was measured in both groups at baseline (4 hrs postoperatively) and then again at 12 hrs and 24 hrs after GH administration. Basal IGF-I levels were similar in both groups, but controls had a 35% increase in IGF-I at 12 hrs, whereas septic rats demonstrated reductions in circulating IGF-I at 12 and 24 hrs after GH. Hepatic expression of SOCS-1, -2, -3, and cytokine-inducible SH2-containing protein (CIS) were determined at 1, 4, 8, and 24 hrs in septic and control rats by Northern blot. SOCS-1, SOCS-3, and CIS messenger RNA in liver were increased from 4 to 8 hrs after the induction of sepsis (p < .05 for SOCS-1 and -3). Total GH receptor (GHR), JAK2, and STAT5 signaling proteins and the time course of STAT5 activation were also measured in liver after recombinant human GH administration by immunoblot and electrophoretic mobility shift analysis. Levels of total GHR, JAK2, and STAT5 were unaltered in liver from septic rats. However, phosphorylated STAT5 and STAT5 DNA binding were significantly reduced 30 mins after GH administration in liver from septic rats. Conclusions:Sepsis diminished STAT5 phosphorylation and activity in liver as well as plasma IGF-I following GH administration. Hepatic messenger RNA expression of SOCS-1, SOCS-3, and CIS was transiently increased during abdominal sepsis and temporally associated with the development of hepatic GH resistance.
Explicit conditions for stabilization over noisy channels subject to SNR constraints

In this paper, we analyze the stability of networked control systems when parallel additive white noise (AWN) channels are considered. We assume that the parallel AWN channels are individually constrained in its signal to noise ratio (SNR). We obtain explicit conditions on the minimum requirements on the channel SNRs necessary for stability for a set of particular plant structures. Our results show explicitly the role played by the unstable plant pole directions in the stability of NCSs. We also show that, when state feedback control is used, a simple characterization on the channel SNRs for stability can be given.
Sensation and Signaling of α-Ketoglutarate and Adenylylate Energy Charge by the Escherichia coli PII Signal Transduction Protein Require Cooperation of the Three Ligand-Binding Sites within the PII Trimer†

PII proteins are sensors of α-ketoglutarate and adenylylate energy charge that regulate signal transduction proteins, metabolic enzymes, and permeases involved in nitrogen assimilation. Here, purified Escherichia coli PII and two of its receptors, ATase and NRII, were used to study the mechanisms of sensation by PII. We assembled heterotrimeric forms of PII from wild-type and mutant subunits, which allowed us to assess the role of the three binding sites for α-ketoglutarate and adenylylate nucleotide in the PII trimer. Signaling of α-ketoglutarate and adenylylate energy charge by these heterotrimeric PII proteins required multiple binding sites for these effectors, and the ligand-binding sites on different subunits could influence the function of a single subunit interacting with a receptor, implying communication between PII subunits. Wild-type and heterotrimeric forms of PII were also used to examine the effects of α-ketoglutarate and ADP on PII activation of the adenylyltransferase (AT) activity of ATase. Previous work showed that when ATP was the sole adenylylate nucleotide, α-ketoglutarate controlled the extent of PII activation but did not alter the PII activation constant (Kact). We show that ADP affected both the PII Kact and the extent of activation by PII. When ATP was present, ADP dramatically reduced the Kact for wild-type PII, and this effect was antagonized by α-ketoglutarate. Consequently, when ATP was present, the antagonism between ADP and α-ketoglutarate allowed each of these effectors to influence the PII Kact for activation of ATase. A study of heterotrimeric forms of PII suggested that the major part of the ability of ADP to improve the binding of PII to ATase required multiple nucleotide binding sites and intersubunit communication. We also used nondenaturing gel electrophoresis to investigate the effect of ADP and α-ketoglutarate on the binding of PII to ATase and NRII. These studies showed that ATase and NRII differ in their requirements for interaction with PII, and that under the appropriate conditions, the antagonism between α-ketoglutarate and ADP allowed each of these effectors to influence the binding of PII to receptors.
The impact of diurnal variations of air traffic on contrail radiative forcing

We combined high resolution aircraft flight data from the EU Fifth Framework Programme project AERO2k with analysis data from the ECMWF's integrated forecast system to calculate diurnally resolved 3-D contrail cover. We scaled the contrail cover in order to match observational data for the Bakan area (eastern-Atlantic/western-Europe). We found that less than 40% of the global distance travelled by aircraft is due to flights during local night time. Yet, due to the cancellation of shortwave and longwave effects during daytime, night time flights contribute a disproportional 60% to the global annual mean forcing. Under clear sky conditions the night flights contribute even more disproportionally at 76%. There are pronounced regional variations in night flying and the associated radiative forcing. Over parts of the North Atlantic flight corridor 75% of air traffic and 84% of the forcing occurs during local night, whereas only 35% of flights are during local night in South-East Asia, yet these contribute 68% of the radiative forcing. In general, regions with a significant local contrail radiative forcing are also regions for which night time flights amount to less than half of the daily total of flights. Therefore, neglecting diurnal variations in air traffic/contrail cover by assuming a diurnal mean contrail cover can over-estimate the global mean radiative forcing by up to 30%.
Improvement of NaNO2-Oxidizing Activity in Nitrobacter vulgaris by Coentrapment in Polyacrylamide Containing Polydimethylsiloxane Copolymer and DEAE-Sephadex

ABSTRACT Removal of nitrite and nitrate from drinking water has attracted great attention in recent years because of the human health risk induced by the exposure to contaminated groundwater and surface water. We have therefore tested a model nitrite oxidation system by coentrapping the NaNO2 oxidizer Nitrobacter vulgaris with polydimethylsiloxane (PDMS) copolymer and DEAE-Sephadex in a polyacrylamide gel. The copolymer and the anion exchanger facilitate the diffusion of oxygen and NaNO2, respectively, into the gel matrix. To test the nitrite-oxidizing activity, the entrapped cells were coupled to a thermal sensor. Coentrapment of 5% (wt/vol) DEAE-Sephadex with Nitrobacter vulgaris increased the nitrite-oxidizing activity by a factor of 3.7 compared to entrapped cells alone, and by the addition of 0.86% (wt/vol) artificial oxygen carrier PDMS copolymer increased the activity further to 4.3 times higher. Operational and storage stability of the coentrapped N.vulgaris also improved. This suggests that this enhanced immobilized cell system can also be used for nitrite oxidation to nitrate in drinking water as an on-line thermally monitored bioreactor.