Miracle-dz/UniFAR-FTUs huggingface dataset:
Alternate Mucosal Immune System: Organized Peyer’s Patches Are Not Required for IgA Responses in the Gastrointestinal Tract1

The progeny of mice treated with lymphotoxin (LT)-β receptor (LTβR) and Ig (LTβR-Ig) lack Peyer’s patches but not mesenteric lymph nodes (MLN). In this study, we used this approach to determine the importance of Peyer’s patches for induction of mucosal IgA Ab responses in the murine gastrointestinal tract. Immunohistochemical analysis revealed that LTβR-Ig-treated, Peyer’s patch null (PP null) mice possessed significant numbers of IgA-positive (IgA+) plasma cells in the intestinal lamina propria. Further, oral immunization of PP null mice with OVA plus cholera toxin as mucosal adjuvant resulted in Ag-specific mucosal IgA and serum IgG Ab responses. OVA-specific CD4+ T cells of the Th2 type were induced in MLN and spleen of PP null mice. In contrast, when TNF and LT-α double knockout (TNF/LT-α−/−) mice, which lack both Peyer’s patches and MLN, were orally immunized with OVA plus cholera toxin, neither mucosal IgA nor serum IgG anti-OVA Abs were induced. On the other hand, LTβR-Ig- and TNF receptor 55-Ig-treated normal adult mice elicited OVA- and cholera toxin B subunit-specific mucosal IgA responses, indicating that both LT-αβ and TNF/LT-α pathways do not contribute for class switching for IgA Ab responses. These results show that the MLN plays a more important role than had been appreciated until now for the induction of both mucosal and systemic Ab responses after oral immunization. Further, organized Peyer’s patches are not a strict requirement for induction of mucosal IgA Ab responses in the gastrointestinal tract.
Distributionally Robust Stochastic Optimization with Wasserstein Distance

Distributionally robust stochastic optimization (DRSO) is an approach to optimization under uncertainty in which, instead of assuming that there is a known true underlying probability distribution, one hedges against a chosen set of distributions. In this paper, we first point out that the set of distributions should be chosen to be appropriate for the application at hand and some of the choices that have been popular until recently are, for many applications, not good choices. We next consider sets of distributions that are within a chosen Wasserstein distance from a nominal distribution. Such a choice of sets has two advantages: (1) The resulting distributions hedged against are more reasonable than those resulting from other popular choices of sets. (2) The problem of determining the worst-case expectation over the resulting set of distributions has desirable tractability properties. We derive a strong duality reformulation of the corresponding DRSO problem and construct approximate worst-case distributions (or an exact worst-case distribution if it exists) explicitly via the first-order optimality conditions of the dual problem. Our contributions are fourfold. (i) We identify necessary and sufficient conditions for the existence of a worst-case distribution, which are naturally related to the growth rate of the objective function. (ii) We show that the worst-case distributions resulting from an appropriate Wasserstein distance have a concise structure and a clear interpretation. (iii) Using this structure, we show that data-driven DRSO problems can be approximated to any accuracy by robust optimization problems, and thereby many DRSO problems become tractable by using tools from robust optimization. (iv) Our strong duality result holds in a very general setting. As examples, we show that it can be applied to infinite dimensional process control and intensity estimation for point processes.
Abnormal lactic dehydrogenase isoenzyme patterns in ulcerative colitis with precancerous change

The isoenzyme pattern of lactic dehydrogenase was measured in rectal biopsies from six patients with ulcerative colitis in whom precancerous histological changes had been independently recognized. There was a highly significant increase in the ratio of isoenzymes IV + V to I + II. This suggests that lactic dehydrogenase isoenzyme measurement may prove a valuable addition to histology in the recognition of precancer in ulcerative colitis.
Period-Different $m$-Sequences With at Most Four-Valued Cross Correlation

This paper follows the recent work of Helleseth, Kholosha, Johansen, and Ness to study the cross correlation between an m -sequence of period 2m - 1 and the d-decimation of an m-sequence of a shorter period 2n - 1 for an even number m = 2n. Assuming that d satisfies d(2l + 1) = 2i (mod 2n - 1) for some l > 0 and i > 0, it is proved that the cross correlation takes on either exactly three or four values depending on whether I and n are coprime or not. The distribution of the cross-correlation values is also completely determined. Our results theoretically confirm the numerical data by Ness and Helleseth. It is conjectured that there are no other decimations that give at most four-valued cross correlation apart from the ones proved here.
Do we mind other minds when we mind other minds' actions? A functional magnetic resonance imaging study

Action observation engages higher motor areas, possibly reflecting an internal simulation. However, actions considered odd or unusual were found to trigger additional activity in the so‐called theory of mind (ToM) network, pointing to deliberations on the actor's mental states. In this functional magnetic resonance imaging study, the hypothesis was tested that an allocentric perspective on a normal action, and even more so the sight of the actor's face, suffices to evoke ToM activity. Subjects observed short videos of object manipulation filmed from either the egocentric or the allocentric perspective, the latter including the actor's face in half of the trials. On the basis of a regions of interest analysis using ToM coordinates, we found increased neural activity in several regions of the ToM network. First, perceiving actions from an allocentric compared with the egocentric perspective enhanced activity in the left temporoparietal junction (TPJ). Second, the presence of the actor's face enhanced activation in the TPJ bilaterally, the medial prefrontal cortex (mPFC) and posterior cingulate cortex (PCC). Finally, the mPFC and PCC showed increased responses when the actor changed with respect to the preceding trial. These findings were further corroborated by zmap findings for the latter two contrasts. Together, findings indicate that observation of normal everyday actions can engage ToM areas and that an allocentric perspective, seeing the actor's face and seeing a face switch, are effective triggers. Hum Brain Mapp, 2011. © 2011 Wiley Periodicals, Inc.
Parallel time integration with multigrid

With current trends in computer architectures leading towards systems with more, but not faster, processors, faster time‐to‐solution must come from greater parallelism. We present a family of truly multilevel approaches to parallel time integration based on multigrid reduction (MGR) principles. The resulting multigrid‐reduction‐in‐time (MGRIT) algorithms are non‐intrusive approaches, which directly use an existing time propagator and, thus, can easily exploit substantially more computational resources then standard sequential time‐stepping. Furthermore, we demonstrate that MGRIT offers excellent strong and weak parallel scaling up to thousands of processors for solving diffusion equations in two and three space dimensions. (© 2014 Wiley‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Coded caching with linear subpacketization is possible using Ruzsa-Szeméredi graphs

Coded caching is a problem where encoded broadcasts are used to satisfy users requesting popular files and having caching capabilities. Recent work by Maddah-Ali and Niesen showed that it is possible to satisfy a scaling number of users with only a constant number of broadcast transmissions by exploiting coding and caching. Unfortunately, all previous schemes required the splitting of files into an exponential number of packets before the significant coding gains of caching appeared. The question of what can be achieved with polynomial subpacketization (in the number of users) has been a central open problem in this area. We resolve this problem and present the first coded caching scheme with polynomial (in fact, linear) subpacketization. We obtain a number of transmissions that is not constant, but can be any polynomial in the number of users with an exponent arbitrarily close to zero. Our central technical tool is a direct connection between Ruzsa-Szeméredi graphs and coded caching schemes with linear file size.
Irreducible Coxeter Groups

We prove that a non-spherical irreducible Coxeter group is (directly) indecomposable and that an indefinite irreducible Coxeter group is strongly indecomposable in the sense that all its finite index subgroups are (directly) indecomposable. Let W be a Coxeter group. Write W = WX1 × ⋯ × WXb × WZ3, where WX1, … , WXb are non-spherical irreducible Coxeter groups and WZ3 is a finite one. By a classical result, known as the Krull–Remak–Schmidt theorem, the group WZ3 has a decomposition WZ3 = H1 × ⋯ × Hq as a direct product of indecomposable groups, which is unique up to a central automorphism and a permutation of the factors. Now, W = WX1 × ⋯ × WXb × H1 × ⋯ × Hq is a decomposition of W as a direct product of indecomposable subgroups. We prove that such a decomposition is unique up to a central automorphism and a permutation of the factors. Write W = WX1 × ⋯ × WXa × WZ2 × WZ3, where WX1, … , WXa are indefinite irreducible Coxeter groups, WZ2 is an affine Coxeter group whose irreducible components are all infinite, and WZ3 is a finite Coxeter group. The group WZ2 contains a finite index subgroup R isomorphic to ℤd, where d = |Z2| - b + a and b - a is the number of irreducible components of WZ2. Choose d copies R1, … , Rd of ℤ such that R = R1 × ⋯ × Rd. Then G = WX1 × ⋯ × WXa × R1 × ⋯ × Rd is a virtual decomposition of W as a direct product of strongly indecomposable subgroups. We prove that such a virtual decomposition is unique up to commensurability and a permutation of the factors.
Vascular Endothelial Growth Factor and Ki-67 Antigen Expression in Relation to Age and Gender in Oral Squamous Cell Carcinoma

Background and aims Vascular endothelial growth factor (VEGF) and Ki-67 antigen are contributing factors in this process cell proliferation and new blood vessels formation in tumor progression. This study was conducted to examine the relationship between the expression of VEGF and Ki-67 and gender and age of patients with oral squamous cell carcinoma (OSCC). Materials and methods Twenty-three archival samples of well-differentiated OSCC were examined immunohisto-chemically and assessed by obtaining Total Score (TS = proportion score × staining index). For statistical analysis, t-test and Pearson’s correlation were employed. P≤0.05 was considered statistically significant. Results The differences in VEGF expression between males and females (P = 0.43) and different ages (P = 0.88) were not significant. The differences in Ki-67 expression was between males and females (P = 0.67) and different ages (P = 0.88) were also not significant. A positive correlation of VEGF and Ki-67 expression was observed in males and females in addi-tion to ≤ 60 years age group (r = 0.22, r = 0.008, and r = 0.58, respectively; P < 0.05). The expression of VEGF had a nega-tive relation to Ki-67 in > 60 years group (r = −0.48, P < 0.05). Conclusion The expression of VEGF and Ki-67 between males and females and different ages were not significant among oral squamous cell carcinoma cases evaluated.
CD40 is required for the optimal induction of protective immunity to Mycobacterium avium

C57Bl/6 mice and mice deficient in the CD40 molecule were infected with three strains of Mycobacterium avium. Two of the M. avium strains proliferated more extensively in CD40‐deficient (CD40−/−) mice than in control mice. The increased susceptibility to infection of CD40−/− mice was associated with the generation of poorer interleukin‐12 (IL‐12) p40 and interferon‐γ (IFN‐γ) responses as compared to the controls, suggesting a role for CD40 in the development of protective immunity. In contrast, direct triggering of CD40 on infected macrophages failed to induce any anti‐mycobacterial activity in infected macrophages.
Emergent Central Pattern Generator Behavior in Gap-Junction-Coupled Hodgkin-Huxley Style Neuron Model

Most models of central pattern generators (CPGs) involve two distinct nuclei mutually inhibiting one another via synapses. Here, we present a single-nucleus model of biologically realistic Hodgkin-Huxley neurons with random gap junction coupling. Despite no explicit division of neurons into two groups, we observe a spontaneous division of neurons into two distinct firing groups. In addition, we also demonstrate this phenomenon in a simplified version of the model, highlighting the importance of afterhyperpolarization currents (I AHP) to CPGs utilizing gap junction coupling. The properties of these CPGs also appear sensitive to gap junction conductance, probability of gap junction coupling between cells, topology of gap junction coupling, and, to a lesser extent, input current into our simulated nucleus.
Pancreatic lipase inhibitory activity of taraxacum officinale in vitro and in vivo

Obesity has become a worldwide health problem. Orlistat, an inhibitor of pancreatic lipase, is currently approved as an anti-obesity drug. However, gastrointestinal side effects caused by Orlistat may limit its use. In this study the inhibitory activities of dandelion (Taraxacum officinale) against pancreatic lipase in vitro and in vivo were measured to determine its possible use as a natural anti-obesity agent. The inhibitory activities of the 95% ethanol extract of T. officinale and Orlistat were measured using 4-methylumbelliferyl oleate (4-MU oleate) as a substrate at concentrations of 250, 125, 100, 25, 12.5 and 4 µg/ml. To determine pancreatic lipase inhibitory activity in vivo, mice (n=16) were orally administered with corn oil emulsion (5 ml/kg) alone or with the 95% ethanol extract of T. officinale (400 mg/kg) following an overnight fast. Plasma triglyceride levels were measured at 0, 90, 180, and 240 min after treatment and incremental areas under the response curves (AUC) were calculated. The 95% ethanol extract of T. officinale and Orlistat, inhibited, porcine pancreatic lipase activity by 86.3% and 95.7% at a concentration of 250 µg/ml, respectively. T. officinale extract showed dose-dependent inhibition with the IC50 of 78.2 µg/ml. A single oral dose of the extract significantly inhibited increases in plasma triglyceride levels at 90 and 180 min and reduced AUC of plasma triglyceride response curve (p<0.05). The results indicate that T. officinale exhibits inhibitory activities against pancreatic lipase in vitro and in vivo. Further studies to elucidate anti-obesity effects of chronic consumption of T. officinale and to identify the active components responsible for inhibitory activity against pancreatic lipase are necessary.
Mechanism of Ribonuclease Cytotoxicity (*)

Bovine seminal ribonuclease (BS-RNase), a dimeric homolog of bovine pancreatic ribonuclease A (RNase A), is toxic to mammalian cells. In contrast to dimeric BS-RNase, monomeric BS-RNase and RNase A are not cytotoxic and are bound tightly by cytosolic ribonuclease inhibitor. To elucidate the mechanism of ribonuclease cytotoxicity, we constructed a series of hybrid and semisynthetic enzymes and examined their properties. In five hybrid enzymes, divergent residues in BS-RNase were replaced with the analogous residues of RNase A so as to diminish an interaction with a putative cellular receptor. In a semisynthetic enzyme, the disulfide bonds that cross-link the monomeric subunits of dimeric BS-RNase were replaced with thioether bonds, which can withstand the reducing environment of the cytosol. Each hybrid and semisynthetic enzyme had ribonucleolytic and cytotoxic activities comparable with those of wild-type BS-RNase. These results suggest that dimeric BS-RNase (pI = 10.3) enters cells by adsorptive rather than receptor-mediated endocytosis and then evades cytosolic ribonuclease inhibitor so as to degrade cellular RNA. This mechanism accounts for the need for a cytosolic ribonuclease inhibitor and for the cytotoxicity of other homologs of RNase A.
Comparative Genomic Analyses of the Moraxella catarrhalis Serosensitive and Seroresistant Lineages Demonstrate Their Independent Evolution

The bacterial species Moraxella catarrhalis has been hypothesized as being composed of two distinct lineages (referred to as the seroresistant [SR] and serosensitive [SS]) with separate evolutionary histories based on several molecular typing methods, whereas 16S ribotyping has suggested an additional split within the SS lineage. Previously, we characterized whole-genome sequences of 12 SR-lineage isolates, which revealed a relatively small supragenome when compared with other opportunistic nasopharyngeal pathogens, suggestive of a relatively short evolutionary history. Here, we performed whole-genome sequencing on 18 strains from both ribotypes of the SS lineage, an additional SR strain, as well as four previously identified highly divergent strains based on multilocus sequence typing analyses. All 35 strains were subjected to a battery of comparative genomic analyses which clearly show that there are three lineages—the SR, SS, and the divergent. The SR and SS lineages are closely related, but distinct from each other based on three different methods of comparison: Allelic differences observed among core genes; possession of lineage-specific sets of core and distributed genes; and by an alignment of concatenated core sequences irrespective of gene annotation. All these methods show that the SS lineage has much longer interstrain branches than the SR lineage indicating that this lineage has likely been evolving either longer or faster than the SR lineage. There is evidence of extensive horizontal gene transfer (HGT) within both of these lineages, and to a lesser degree between them. In particular, we identified very high rates of HGT between these two lineages for ß-lactamase genes. The four divergent strains are sui generis, being much more distantly related to both the SR and SS groups than these other two groups are to each other. Based on average nucleotide identities, gene content, GC content, and genome size, this group could be considered as a separate taxonomic group. The SR and SS lineages, although distinct, clearly form a single species based on multiple criteria including a large common core genome, average nucleotide identity values, GC content, and genome size. Although neither of these lineages arose from within the other based on phylogenetic analyses, the question of how and when these lineages split and then subsequently reunited in the human nasopharynx is explored.
Genetic epidemiology of mutated K-rasproto-oncogene, altered suppressor genes, and microsatellite instability in colorectal adenomas

BACKGROUND The genetic epidemiology of colorectal adenomas has not been studied prospectively in colonoscopy patients without cancer. AIMS To study genetic alterations in colorectal adenomas and correlate these with patient demographics and adenoma characteristics. METHODS Mutations and allelic deletions in 201 adenomas from 60 patients were compared with demographic features, adenoma characteristics, and family history. RESULTS The most common alteration was K-ras proto-oncogene mutation, present in 35% of adenomas and 65% of patients. Patients 65 years of age and older had a decreased probability of K-ras mutations (26% versus 45%). Overexpression of p53 gene product was present in only 6% of adenomas but was more frequent in villous or tubulovillous adenomas (19% versus 3%). Allelic loss of chromosome 18q was present in only 2% of adenomas and was significantly less frequent than p53 overexpression. DNA replication errors (RER) were present in 7% of adenomas and 15% of patients, including multiple adenomas in four patients (two with hereditary non-polyposis colorectal cancer syndrome). Only 36% of RER positive adenomas had alteration of BAT-26 alleles, none had alteration of BAT-25, and only one (8%) had mutation in the transforming growth factor β type II receptor gene. RER positive adenomas were more likely to have a K-ras mutation. In patients with multiple adenomas, there was concordance of p53 overexpression and RER but not of K-ras mutations. CONCLUSIONS Genetic progression in colorectal adenomas is heterogeneous, involving factors related to patient age and the presence of RER for the occurrence of ras mutations, but different intraindividual characteristics for the occurrence of p53 alterations and RER.
MatrixPro - A Tool for On-The-Fly Demonstration of Data Structures and Algorithms

In this paper, we introduce a new tool, MatrixPro, intended for illustrating algorithms in action. One can produce algorithm animations in terms of direct manipulation of the library data structures, the process we call visual algorithm simulation. The user does not need to code anything to build animations. Instead, he or she can graphically invoke ready-made operations available in the library data structures to simulate the working of real algorithms. Since the system understands the semantics of the operations, teachers can demonstrate the execution of algorithms on-the-fly with different input sets, or work with ”what-if” questions students ask in lectures. Such an approach lowers considerably the step to adopt algorithm visualization for regular lecture practice.
Inhibition of bradykinin B2receptor preserves microcirculation in experimental pancreatitis in rats.

The effect of B2 receptor bradykinin antagonist icatibant on postcapillary leukostasis, microcirculatory stasis, and tissue necrosis was studied in acute pancreatitis. In rats, pancreatitis was induced by intraductal injection of sodium taurocholate (ST), intravenous caerulein and intraductal infusion of glucodeoxycholic acid (GDOC), or intravenous caerulein infusion alone. Intravital pancreatic microcirculation was observed. Icatibant or vehicle was given 30 min before induction of pancreatitis. In ST pancreatitis, the number of perfused capillaries increased in icatibant-pretreated rats (77% vs. 0% for controls, P < 0.001). Capillary flow was preserved in icatibant-treated rats; total stasis was observed in controls. Mean venular leukocyte adherence decreased in icatibant-treated rats (26% vs. 74% for controls, P < 0.001), and median histopathologic score was reduced (icatibant vs. controls, 5.0 vs. 12 points, respectively; P < 0.01). Kinase II inhibitor captopril or exogenous bradykinin in addition to an otherwise effective dosage of icatibant resulted in microcirculatory stasis, extensive venular leukocyte adherence, and severe histological damage. With a 100 times greater icatibant dosage, this adverse effect was compensated. The beneficial effects of icatibant were also observed in intermediate pancreatitis (caerulein + GDOC). In ST and intermediate pancreatitis, icatibant preserved microcirculation, reduced venular leukocyte adherence, and prevented pancreatic tissue damage. B2 receptor bradykinin-mediated postcapillary leukostasis plays an important role in the pathogenesis of severe forms of acute pancreatitis.