Miracle-dz/UniFAR-FTUs huggingface dataset:
Bacteria of the human gut microbiome catabolize red seaweed glycans with carbohydrate-active enzyme updates from extrinsic microbes

Humans host an intestinal population of microbes—collectively referred to as the gut microbiome—which encode the carbohydrate active enzymes, or CAZymes, that are absent from the human genome. These CAZymes help to extract energy from recalcitrant polysaccharides. The question then arises as to if and how the microbiome adapts to new carbohydrate sources when modern humans change eating habits. Recent metagenome analysis of microbiomes from healthy American, Japanese, and Spanish populations identified putative CAZymes obtained by horizontal gene transfer from marine bacteria, which suggested that human gut bacteria evolved to degrade algal carbohydrates—for example, consumed in form of sushi. We approached this hypothesis by studying such a polysaccharide utilization locus (PUL) obtained by horizontal gene transfer by the gut bacterium Bacteroides plebeius. Transcriptomic and growth experiments revealed that the PUL responds to the polysaccharide porphyran from red algae, enabling growth on this carbohydrate but not related substrates like agarose and carrageenan. The X-ray crystallographic and biochemical analysis of two proteins encoded by this PUL, BACPLE_01689 and BACPLE_01693, showed that they are β-porphyranases belonging to glycoside hydrolase families 16 and 86, respectively. The product complex of the GH86 at 1.3 Å resolution highlights the molecular details of porphyran hydrolysis by this new porphyranase. Combined, these data establish experimental support for the argument that CAZymes and associated genes obtained from extrinsic microbes add new catabolic functions to the human gut microbiome.
Computed tomography colonography in acromegaly.

INTRODUCTION AND AIM Acromegalic patients have an increased risk for the development of colorectal cancer. For this reason, since 1996, screening colonoscopy has been recommended in all patients with acromegaly. The aim of our study was to assess the feasibility and to evaluate the results of computed tomography (CT)-colonography in acromegaly. PATIENTS AND METHODS We examined 23 acromegalic patients with no history of colorectal cancer (11 females and 12 males; age range 18-79 yr; disease duration range 1-15 yr) with CT-colonography. Twenty of them underwent traditional colonoscopy after the CT-colonography. RESULTS CT-colonography examination results were adequate in 17 of 23 cases (73%). CT-colonography found 12 polyps in eight patients, 95% confirmed by traditional colonoscopy. One polyp was a sigmoid cancer, and the diagnosis was confirmed at surgery. There were no polyps found by traditional colonoscopy that CT-colonography was not able to identify. The lesions were located in right colon (two), transversum (three), left colon (five), and sigmoid colon (two). Patient acceptance of the technique was good in 65%, medium in 20%, and poor in 15%. CONCLUSION For the first time we have demonstrated that CT-colonography has the potential ability to replace traditional colonoscopy in acromegalic patients. CT-colonography could be used as a screening modality for colon cancer in acromegaly.
Spontaneously Formed Spheroids from Mouse Compact Bone-Derived Cells Retain Highly Potent Stem Cells with Enhanced Differentiation Capability

The results from our recent study showed the presence of two distinct spheroid-forming mechanisms, i.e., spontaneous and mechanical. In this study, we focused on the spontaneously formed spheroids, and the character of spontaneously formed spheroids from mouse compact bone-derived cells (CBDCs) was explored. Cells from (C57BL/6J) mouse leg bones were isolated, and compact bone-derived cells were cultured after enzymatic digestion. Spontaneous spheroid formation was achieved on a culture plate with specific water contact angle as reported. The expression levels of embryonic stem cell markers were analyzed using immunofluorescence and quantitative reverse transcription polymerase chain reaction. Then, the cells from spheroids were induced into osteogenic and neurogenic lineages. The spontaneously formed spheroids from CBDCs were positive for ES cell markers such as SSEA1, Sox2, Oct4, and Nanog. Additionally, the expressions of fucosyltransferase 4/FUT4 (SSEA1), Sox2, and Nanog were significantly higher than those in monolayer cultured cells. The gene expression of mesenchymal stem cell markers was almost identical in both spheroids and monolayer-cultured cells, but the expression of Sca-1 was higher in spheroids. Spheroid-derived cells showed significantly higher osteogenic and neurogenic marker expression than monolayer-cultured cells after induction. Spontaneously formed spheroids expressed stem cell markers and showed enhanced osteogenic and neurogenic differentiation capabilities than cells from the conventional monolayer culture, which supports the superior stemness.
Characterization of the trunk neural crest in the bamboo shark, Chiloscyllium punctatum

The neural crest is a population of mesenchymal cells that after migrating from the neural tube gives rise to structure and cell types: the jaw, part of the peripheral ganglia, and melanocytes. Although much is known about neural crest development in jawed vertebrates, a clear picture of trunk neural crest development for elasmobranchs is yet to be developed. Here we present a detailed study of trunk neural crest development in the bamboo shark, Chiloscyllium punctatum. Vital labeling with dioctadecyl tetramethylindocarbocyanine perchlorate (DiI) and in situ hybridization using cloned Sox8 and Sox9 probes demonstrated that trunk neural crest cells follow a pattern similar to the migratory paths already described in zebrafish and amphibians. We found shark trunk neural crest along the rostral side of the somites, the ventromedial pathway, the branchial arches, the gut, the sensory ganglia, and the nerves. Interestingly, C. punctatum Sox8 and Sox9 sequences aligned with vertebrate SoxE genes, but appeared to be more ancient than the corresponding vertebrate paralogs. The expression of these two SoxE genes in trunk neural crest cells, especially Sox9, matched the Sox10 migratory patterns observed in teleosts. Also of interest, we observed DiI cells and Sox9 labeling along the lateral line, suggesting that in C. punctatum, glial cells in the lateral line are likely of neural crest origin. Although this has been observed in other vertebrates, we are the first to show that the pattern is present in cartilaginous fishes. These findings demonstrate that trunk neural crest cell development in C. punctatum follows the same highly conserved migratory pattern observed in jawed vertebrates. J. Comp. Neurol. 521:3303–3320, 2013. © 2013 Wiley Periodicals, Inc.
The impact of monetary policy on economic growth and price stability in Kenya: 1992-2013

The government of Kenya’s economic blueprint dubbed ‘Kenya Vision 2030’ acknowledges the importance of maintaining a stable macro-economic environment. Despite Kenya implementing monetary policy aimed at achieving stable prices and fostering economic growth, the economy has been reporting low economic growth and high rates of inflation. These implies there is still a point of disconnect between what Central bank of Kenya Pursues and the outcome of the objectives. In this study, structural vector autoregresion (SVAR) model is estimatedto trace the effects of monetary policy shocks on economic growth and prices in Kenya. Three alternative monetary policy instruments were put into use i.e. broad money supply (M3), interbank lending rate (ILR) and the real effective exchange rate (REER). The study found evidence that monetary policy innovations carried out on the quantity-based nominal anchor (M3) has modest effects on economic growth and prices with a very fast speed of adjustment. Innovations on the price-based nominal anchors (ILR and REER) have relative and fleeting effects on real GDP. The study recommended that Central Bank of Kenya should place more emphasis on the use of the quantity-based nominal anchor rather than the price-based nominal anchor.
Unconventional Political Participation in a Middle-Income Developing Country

In many inner city communities in Jamaica, there is the perception that the dons (ad hoc community leaders) are able to provide security, financial assistance and a social safety network, which was once the role of the state. The failure of successive governments to provide those important services, in particular security means that there is a high degree of mistrust of the state in rightfully carrying out its roles. The dons have filled the void created by the state, and people have come to rely on them precisely because of the repeated failures of successive governments. The mistrust has become so pervasive, that such a low level of trust for government leads to a rise in unorthodox political participation. This study examines the role that mistrust in government plays in unconventional political participation, and it revealed that Jamaicans who mistrust government are 2.4 times more likely to become involved in unorthodox activities compared to those who do trust government. Those activities now include protests, demonstrations, barricading a community, firing at the security forces, blogging, and using the social commentaries on talk radio. While firing at the security forces extends beyond unconventional political participation - and this aspect is not covered in the present manuscript - it is clearly an unorthodox method employed by some groups within a society.
Alteration of rat hepatic glycogen phosphorylase and phosphoenolpyruvate carboxykinase activities by Satureja khuzestanica Jamzad essential oil.

PURPOSE Regarding reported antidiabetic effect of Satureja khuzestanica essential oil (SKEO) and important role of liver on body glucose metabolism by glycogenolysis and gluconeogenesis, we were interested to examine effect of SKEO treatment on rat hepatic key enzymes of glycogenolysis and gluconeogenesis in vivo. METHODS Effective antidiabetic dose of SKEO (1000 ppm) was administered to rats through drinking water for 2 weeks. After 18 hours fasting post treatment under general anesthesia, the liver was removed by transverse abdominal incision and perfused with cold 0.9% saline and kept frozen at -70 degrees C until homogenized. The activities of the key enzymes glycogen phosphorylase (GP) and phosphoenolpyruvate carboxykinase (PEPKC) were analyzed in the homogenate. Blood sample was taken by cardiac puncture for glucose assay. RESULTS SKEO treatment did not affect blood glucose concentrations but decreased hepatic PEPCK activity by 26% (P<0.01) of control and increased hepatic GP by 24% (P<0.01) of control. CONCLUSION Disturbance of hepatic glucose metabolism is proposed as a mechanism of antidiabetic action of SKEO which could be in relation with antioxidant property of this plant.
Symbol synchronization of the Alamouti space-time block code with the Gardner algorithm

A digital communications receiver requires precise symbol synchronization before the transmitted information can be recovered. Gardner's algorithm is a synchronizer that can acquire and track timing with only two samples per symbol, and it does not require prior carrier synchronization. In this paper, a feed-forward, all-digital version of Gardner's algorithm is presented. It is shown that this synchronizer is effective when used in a wireless Alamouti space-time coded system. Besides retaining its immunity to carrier frequency offset, the algorithm does not require knowledge of the channel gains. Simulation results are presented along with mean-square estimates of the timing error for different values of signal to noise ratio and for staggered and non-staggered pulses.
A Systematic Review on the Prevalence, Etiology, and Pathophysiology of Intrinsic Pain in Dermal Scar Tissue.

BACKGROUND Scars can cause pain, even without symptoms of underlying nerve damage. A lack of knowledge on intrinsic scar pain hampers effective treatment of these complaints. OBJECTIVE Aggregate current knowledge on the prevalence, etiology, and pathophysiology of intrinsic pain in dermal scars. STUDY DESIGN Systematic review. SETTING University Medical Center. METHODS We searched the Embase, Medline, Cochrane central, CINAHL, Web-of-Science, and Pubmed databases with search terms: scar, skin, pain, and etiology/pathology, adding all synonyms of these terms. Relevant papers were selected and analyzed by 3 reviewers. RESULTS Intrinsic pain in scars has a low prevalence. However, pathologic scars and burns regularly cause pain of high intensity. The etiology is multifactorial, the extent of trauma was an important predicting factor. Nerve fiber density did not explain the intrinsic pain when pan-neuronal markers were used, while a correlation with an increased number of C-fiber subtypes seems plausible. Nerve growth factor (that stimulate these C-fibers) plays an important role in wound healing. Thereby, it also sensitizes neurons and promotes inflammation, releasing even more neurotrophic factors. Central sensitization causes a long-lasting effect even after wounds are healed. Furthermore, the opioid-system, that influences inflammation and healing and possible systemic sensory alterations after injury, is discussed. LIMITATIONS Liberal selection criteria challenged the systematic selection of papers. CONCLUSIONS Burn and pathologic scars often lead to high intensity pain symptoms. This pain has many characteristics of neuropathic pain that could be caused by an imbalance of C-fibers subtypes. The scar tissue itself may alter the nerve fiber distribution; the imbalance results in ongoing neuro-inflammation and pain symptoms. Key words: Systematic review, scar, pain, epidermal innervation, prevalence, neuro inflammatory response, peptidergic fibers.
The Role of Conserved N-Linked Glycans on Ebola Virus Glycoprotein 2.

BACKGROUND N-linked glycosylation is a common posttranslational modification found on viral glycoproteins (GPs) and involved in promoting expression, cellular attachment, protection from proteases, and antibody evasion. The GP subunit GP2 of filoviruses contains 2 completely conserved N-linked glycosylation sites (NGSs) at N563 and N618, suggesting that they have been maintained through selective pressures. METHODS We assessed mutants lacking these glycans for expression and function to understand the role of these sites during Ebola virus entry. RESULTS Elimination of either GP2 glycan individually had a modest effect on GP expression and no impact on antibody neutralization of vesicular stomatitis virus pseudotyped with Ebola virus GP. However, loss of the N563 glycan enhanced entry by 2-fold and eliminated GP detection by a well-characterized monoclonal antibody KZ52. Loss of both sites dramatically decreased GP expression and abolished entry. Surprisingly, a GP that retained a single NGS at N563, eliminating the remaining 16 NGSs from GP1 and GP2, had detectable expression, a modest increase in entry, and pronounced sensitivity to antibody neutralization. CONCLUSIONS Our findings support the importance of the GP2 glycans in GP expression/structure, transduction efficiency, and antibody neutralization, particularly when N-linked glycans are also removed from GP1.
Bacteroides vulgatus outer membrane antigens associated with carrageenan-induced colitis in guinea pigs

Previous experiments with the carrageenan model for ulcerative colitis demonstrated that the inflammatory response in guinea pigs can be enhanced by immunization with Bacteroides vulgatus and subsequent feeding of this organism to experimental animals. The studies reported here show that antigens extractable from the bacterial outer membrane by EDTA are responsible for this effect. Sodium dodecyl sulfate-polyacrylamide gel electrophoresis was used to analyze the outer membrane proteins from various strains as well as the lipopolysaccharides (LPS) extractable by the phenol-water method. Although the observed pattern of outer membrane proteins was complex, the strains could be divided into two electrophoretic types (phenons) on the basis of immunoblotting against a panel of antisera. Cross-absorbed antisera used in immunoblotting experiments identified four outer membrane proteins uniquely associated with the phenon capable of enhancing the colitis inflammatory response. These proteins had molecular weights of 100,000, 57,000, 34,000, and 21,000 when measured in 8% to 12% acrylamide gradient sodium dodecyl sulfate gels. Other antigens identified included at least one type of smooth LPS, three types of rough LPS, and a common antigen of 30,000 molecular weight among the strains of B. vulgatus tested. The outer membrane preparations were used in animal immunization and challenge experiments, and the severity of colitis was correlated with one electrophoresis type. The potential role of membrane proteins in the enhancement of colitis is discussed.
Estimating and projecting the populations of urban communities.

"The author describes a model for estimating and projecting the populations of communities living in small areas within cities. The model provides a means of updating the demographic inputs needed for projection between censuses and means of developing scenarios of demographic change and housing development. The method for estimating small-area populations between censuses is evaluated with recently published 1991 [U.K.] Census data. Single-year age-group detail is provided and the associated databases are embedded in a flexible user interface. Illustrative projections are discussed and interpreted for the northern English city of Bradford. The model, although particular to districts of West Yorkshire, has been specified in a general way and could be adapted for use with any British district. "
The Influence of Natural Surface Microtopographies on Fouling

Multiple antifouling strategies of marine organisms may consist of combinations of physical, chemical and mechanical mechanisms. In this study, the role of surface microtopography ( < 500 μm) of different marine organisms, such as Cancer pagurus, Mytilus edulis, Ophiura texturata and the eggcase of Scyliorhinus canicula, has been investigated as a possible component of their defence systems. High resolution resin replicates of these natural surface structures were exposed to natural fouling in field experiments. Abundances of recruits were determined and compared to those on untextured, but otherwise identical, control surfaces to quantify the influence of the different microtopographies on fouling rates. Antifouling effects of microtopographies varied with type of microtopography and coloniser species. The surface microtopography of C. pagurus significantly rejected macrofoulers. The surface structures of the eggcase and O. texturata had repellent effects on microfoulers. Barnacle settlement was temporarily reduced on surface microtopographies of M. edulis and the eggcase. These results emphasise the promising non-toxic antifouling properties of microtextured surfaces.
Uterine blood flow responses to ICI 182 780 in ovariectomized oestradiol‐17β‐treated, intact follicular and pregnant sheep

Oestrogen dramatically increases uterine blood flow (UBF) in ovariectomized (Ovx) ewes. Both the follicular phase and pregnancy are normal physiological states with elevated levels of circulating oestrogen. ICI 182 780 is a pure steroidal oestrogen receptor (ER) antagonist that blocks oestrogenic actions in oestrogen‐responsive tissue. We hypothesized that an ER‐mediated mechanism is responsible for in vivo rises in UBF in physiological states of high oestrogen. The purpose of the study was to examine the effect of an ER antagonist on exogenous and endogenous oestradiol‐17β (E2β)‐mediated elevations in UBF. Sheep were surgically instrumented with bilateral uterine artery blood flow transducers, and uterine and femoral artery catheters. Ovx animals (n= 8) were infused with vehicle (35% ethanol) or ICI 182 780 (0.1–3.0 μg min−1) into one uterine artery for 10 min before and 50 min after E2β was given (1 μg kg−1i.v. bolus) and UBF was recorded for an additional hour. Intact, cycling sheep were synchronized to the follicular phase using progesterone, prostaglandin F2α(PGF2α) and pregnant mare serum gonadotrophin (PMSG). When peri‐ovulatory rises in UBF reached near peak levels, ICI 182 780 (1 or 2 μg (ml uterine blood flow)−1) was infused unilaterally (n= 4 sheep). Ewes in the last stages of pregnancy (late pregnant ewes) were also given ICI 182 780 (0.23–2.0 μg (ml uterine blood flow)−1; 60 min infusion) into one uterine artery (n= 8 sheep). In Ovx sheep, local infusion of ICI 182 780 did not alter systemic cardiovascular parameters, such as mean arterial blood pressure or heart rate; however, it maximally decreased ipsilateral, but not contralateral, UBF vasodilatory responses to exogenous E2β by ∼55–60% (P < 0.01). In two models of elevated endogenous E2β, local ICI 182 780 infusion inhibited the elevated UBF seen in follicular phase and late pregnant ewes in a time‐dependent manner by ∼60% and 37%, respectively; ipsilateral ≫ contralateral effects (P < 0.01). In late pregnant sheep ICI 182 780 also mildly and acutely (for 5–30 min) elevated mean arterial pressure and heart rate (P < 0.05). We conclude that exogenous E2β‐induced increases in UBF in the Ovx animal and endogenous E2β‐mediated elevations of UBF during the follicular phase and late pregnancy are partially mediated by ER‐dependent mechanisms.
The dynamic implications of energy-intensive capital accumulation

We study the implications of assuming diff erent energy intensities for physical capital accumulation and fi nal good production in an overlapping generations (OLG) resource economy. Diff ering from the standard OLG literature, but consistently with the empirical evidence, physical capital accumulation is assumed to be relatively more energy-intensive than consumption. Focusing on exhaustible resources, we fi nd that OLG equilibria can exhibit a "non-classical behaviour": our model can generate complex dynamics where extraction may increase during some periods and decrease afterwards. As a consequence, in contrast to the classical response predicted by the standard approach, resource prices may not increase monotonically. This result points out the importance of the assumptions about energy intensity considered in the literature.
Differential Interpretation of Information and Trade in Speculative Markets

Most models of trade in speculative markets make the assumption that agents interpret public information identically. We provide empirical evidence that this assumption is overly restrictive. We begin by investigating the relation between the volume of trade and stock returns (NYSE, AMEX and NASDAQ-listed stocks) around anticipated public announcements, and find that there is a significant abnormal volume even when prices do not change in response to the announcement. We argue that this is likely due to the differences in interpretation of public information by investors. We then develop a model of trade which incorporates differential interpretations and show that its predictions are consistent with the observed volume-return relation. We go on to present a simple model of beliefs revision, which underlies our and many other models of trade and test it on the stock brokerage research analyst's earning forecasts taken from the I/B/E/S Detail Tape. The hypothesis that agents use the same model to interpret public announcements is inconsistent with the forecast revisions in this data.