Miracle-dz/UniFAR-FTUs huggingface dataset:
Evaluation of Mode Dependent Fluid Damping in a High Frequency Drumhead Microresonator

Design of high quality factor (Q) micromechanical resonators depends critically on our understanding of energy losses in their oscillations. The Q of such structures depends on process induced prestress in the structural geometry, interaction with the external environment, and the encapsulation method. We study the dominant fluid interaction related losses, namely, the squeeze film damping and acoustic radiation losses in a drumhead microresonator subjected to different prestress levels, operated in air, to predict its Q in various modes of oscillation. We present a detailed research of the acoustic radiation losses, associated with the 15 transverse vibration modes of the resonator using a hybrid analytical-computational approach. The prestressed squeeze film computation is based on the standard established numerical procedure. Our technique of computing acoustic damping based quality factor Qac includes calculation of the exact prestressed modes. We find that acoustic losses result in a non-monotonic variation of Qac in lower unstressed modes. Such non-monotonic variation disappears with the increase in the prestress levels. Although squeeze film damping dominates the net Q at lower frequencies, acoustic radiation losses dominate at higher frequencies. The combined computed losses correctly predict the experimentally measured Q of the resonator over a large range of resonant frequencies.
Manual therapy for asthma.

BACKGROUND A variety of manual therapies with similar postulated biologic mechanisms of action are commonly used to treat patients with asthma. Manual therapy practitioners are also varied, including physiotherapists, respiratory therapists, chiropractic and osteopathic physicians. A systematic review across disciplines is warranted. OBJECTIVES To evaluate the evidence for the effects of manual therapies for treatment of patients with bronchial asthma. SEARCH STRATEGY Trials were searched in computerized general (EMBASE, CINAHL and MEDLINE) and specialized databases (Cochrane Complementary Medicine Field, Cochrane Rehabilitation Field, ICL, and MANTIS). In addition, bibliographies from included studies were assessed, and authors of known studies were contacted for additional information about published and unpublished trials. Date of most recent search: December 1998. SELECTION CRITERIA Trials were included if they: (1) were randomised; (2) included asthmatic children or adults; (3) examined one or more types of manual therapy; and (4) included clinical outcomes. DATA COLLECTION AND ANALYSIS All three reviewers independently extracted data and assessed trial quality using a standard form. MAIN RESULTS From an initial 316 unique citations, 48 full text articles were retrieved and evaluated, which resulted in nine citations to five RCTs (290 patients) suitable for inclusion. Trials could not be pooled statistically because studies that addressed similar interventions used disparate patient groups or outcomes. The methodological quality of one of two trials examining chiropractic manipulation was good and neither trial found significant differences between chiropractic spinal manipulation and a sham manoeuvre on any of the outcomes measured. Quality of the remaining three trials was poor. One small trial compared massage therapy with a relaxation control group and found significant differences in many of the lung function measures obtained. However, this trial had poor reporting characteristics and the data have yet to be confirmed. One small trial compared chest physiotherapy to placebo and one small trial compared footzone therapy to a no treatment control. Neither trial found differences in lung function between groups. REVIEWER'S CONCLUSIONS There is insufficient evidence to support the use of manual therapies for patients with asthma. There is a need to conduct adequately-sized RCTs that examine the effects of manual therapies on clinically relevant outcomes. Future trials should maintain observer blinding for outcome assessments, and report on the costs of care and adverse events. Currently, there is insufficient evidence to support or refute the use of manual therapy for patients with asthma.
Mature CD11c+ cells are enhanced in hypersensitivity pneumonitis

The present study verified the hypothesis that enhanced maturation of antigen-presenting CD11c+ cells could explain the viral-induced exacerbated immune response to Saccharopolyspora rectivirgula (SR), the main antigen responsible for farmer’s lung, a classic form of hypersensitivity pneumonitis (HP). Four groups of mice were studied: group 1 received intranasal instillations of saline; group 2 received instillations of SR for 12 weeks; group 3 received instillations of saline and a single infection with Sendai virus on week 3; and group 4 received instillations of SR for 12 weeks with a single administration of Sendai virus on week 3. On week 13, mice were sacrificed and bronchoalveolar lavage was performed. Lungs were harvested, digested with enzymes, and CD11c+ cells were analysed in flow cytometry with anti-CD11c, anti-CD86 and anti-major histocompatibility complex class II markers. Immunofluorescence studies were also performed with the same cell surface markers. Both flow cytometry and immunofluorescence results demonstrate that mature CD11c+ cells are significantly enhanced in SR-challenged mice simultaneously infected with Sendai virus, compared with other groups. These CD11c+ cells persist in the lung for 9 weeks after the virus infection. Maturation of CD11c+ cells could explain, at least in part, the virus-induced increased immune response to SR antigens in this model of HP, but mechanisms have still to be elucidated.
Improving the Quality of Alerts with Correlation in Intrusion Detection

Summary With the growing deployment of networks and the Internet, the importance of network security has increased. Recently, however, systems that detect intrusions, which are important in security countermeasures, have been unable to provide proper analysis or an effective defense mechanism. Instead, they have overwhelmed human operators with a large volume of intrusion detection alerts. In this paper, we present an alert correlation technique based on causal relationships between alerts. The goal of the proposed technique is not only to group alerts together, but also to represent the correlated alerts in a way that they reflect the corresponding attack scenarios.
High performance clock routing in X-architecture

As a promising approach to mitigate the challenge of interconnect limit, X-architecture allows routings along diagonal directions in addition to rectilinear directions. It can reduce routing wire length and vias number compared with conventional Manhattan routing. Although Steiner minimum tree and signal routing algorithms have been developed for X-architecture, clock routing has not been addressed to the best of our knowledge. However, wire length reduction is even more compelling for clock net, as wire is a major power consumer and power supply noise generator. In addition, X-architecture is very effective for interconnect delay and clock skew optimization. In this paper, we investigate the layout embedding technique for clock routing in X-architecture and integrate it with the deferred-merge embedding (DME) algorithm. To alleviate the inaccuracy of the Elmore delay (ED) model, a more accurate fitted Elmore delay (FED) model is employed. Experimental results on benchmarks exhibit encouraging results
CD44 Plays a Critical Role in Regulating Diet-Induced Adipose Inflammation, Hepatic Steatosis, and Insulin Resistance

CD44 is a multifunctional membrane receptor implicated in the regulation of several biological processes, including inflammation. CD44 expression is elevated in liver and white adipose tissue (WAT) during obesity suggesting a possible regulatory role for CD44 in metabolic syndrome. To study this hypothesis, we examined the effect of the loss of CD44 expression on the development of various features of metabolic syndrome using CD44 null mice. Our study demonstrates that CD44-deficient mice (CD44KO) exhibit a significantly reduced susceptibility to the development of high fat-diet (HFD)-induced hepatic steatosis, WAT-associated inflammation, and insulin resistance. The decreased expression of genes involved in fatty acid synthesis and transport (Fasn and Cd36), de novo triglyceride synthesis (Mogat1), and triglyceride accumulation (Cidea, Cidec) appears in part responsible for the reduced hepatic lipid accumulation in CD44KO(HFD) mice. In addition, the expression of various inflammatory and cell matrix genes, including several chemokines and its receptors, osteopontin, and several matrix metalloproteinases and collagen genes was greatly diminished in CD44KO(HFD) liver consistent with reduced inflammation and fibrogenesis. In contrast, lipid accumulation was significantly increased in CD44KO(HFD) WAT, whereas inflammation as indicated by the reduced infiltration of macrophages and expression of macrophage marker genes, was significantly diminished in WAT of CD44KO(HFD) mice compared to WT(HFD) mice. CD44KO(HFD) mice remained considerably more insulin sensitive and glucose tolerant than WT(HFD) mice and exhibited lower blood insulin levels. Our study indicates that CD44 plays a critical role in regulating several aspects of metabolic syndrome and may provide a new therapeutic target in the management of insulin resistance.
Alternative activation of macrophages in human peritoneum: implications for peritoneal fibrosis.

BACKGROUND Depending on the cytokine microenvironment, macrophages (Mϕ) can adopt a proinflammatory (M1) or a profibrotic (M2) phenotype characterized by the expression of cell surface proteins such as CD206 and CD163 and soluble factors such as CC chemokine ligand 18 (CCL18). A key role for Mϕ in fibrosis has been observed in diverse organ settings. We studied the Mϕ population in a human model of peritoneal dialysis in which continuous stress due to dialysis fluids and recurrent peritonitis represent a risk for peritoneal membrane dysfunction reflected as ultrafiltration failure (UFF) and peritoneal fibrosis. METHODS We used flow cytometry and quantitative reverse transcription-polymerase chain reaction to analyse the phenotype of peritoneal effluent Mϕ and tested their ability to stimulate the proliferation of human fibroblasts. Mϕ from non-infected patients were compared with those from patients with active peritonitis. Cytokine production was evaluated by enzyme-linked immunosorbent assay (ELISA) in spent dialysates and cell culture supernatants. RESULTS CD206(+) and CD163(+) M2 were found within peritoneal effluents by flow cytometry analysis, with increased frequencies of CD163(+) cells during peritonitis (P = 0.003). TGFB1, MMP9 and CCL18 messenger RNA (mRNA) levels in peritoneal macrophages (pMϕ) were similar to those found in M2 cells differentiated in vitro. The ability of pMϕ to stimulate fibroblast proliferation correlated with CCL18 mRNA levels (r = 0.924, P = 0.016). CCL18 production by pMϕ was confirmed by immunostaining of cytospin samples and ELISA. Moreover, CCL18 effluent concentrations correlated with decreased peritoneal function, which was evaluated as dialysate to plasma ratio of creatinine (r = 0.724, P < 0.0001), and were significantly higher in patients with UFF (P = 0.0025) and in those who later developed sclerosing peritonitis (P = 0.024). CONCLUSIONS M2 may participate in human peritoneal fibrosis through the stimulation of fibroblast cell growth and CCL18 production as high concentrations of CCL18 are associated with functional deficiency and fibrosis of the peritoneal membrane.
Cone Viability Is Affected by Disruption of Melatonin Receptors Signaling

Purpose Previous studies have demonstrated that melatonin has an important role in the modulation of photoreceptor viability during aging and may be involved in the pathogenesis of age-related macular degeneration.This hormone exerts its influence by binding to G-protein coupled receptors named melatonin receptor 1 (MT1) and 2 (MT2). Melatonin receptors 1 and 2 activate a wide variety of signaling pathways. Methods Melatonin-proficient mice (C3H/f+/+) and melatonin-proficient mice lacking MT1 or MT2 receptors (MT1−/− and MT2−/−) were used in this study. Mice were killed at the ages of 3 and 18 months, and photoreceptor viability was determined by counting nuclei number in the outer nuclear layer (ONL). Cones were identified by immunohistochemistry using peanut agglutinin (PNA) and green/red and blue opsin antibodies. Protein kinase B (AKT) and forkhead box O (FOXO1) were assessed by Western blotting and immunohistochemistry. Results The number of nuclei in the ONL was significantly reduced in C3Hf+/+, MT1−/−, and MT2−/− mice at 18 months of age with respect to 3-month-old animals. In 18-month-old MT1−/− and MT2−/− mice, but not in C3H/f+/+, the number of cones was significantly reduced with respect to young MT1−/− and MT2−/− mice or age-matched C3H/f+/+. In C3H/f+/+, activation of the AKT-FOXO1 pathway in the photoreceptors showed a significant difference between night and day. Conclusions Our data indicate that disruption of MT1/MT2 heteromer signaling induces a reduction in the number of photoreceptors during aging and also suggest that the AKT-FOXO1 survival pathway may be involved in the mechanism by which melatonin protects photoreceptors.
High accuracy prediction of β‐turns and their types using propensities and multiple alignments

We have developed a method that predicts both the presence and the type of β‐turns, using a straightforward approach based on propensities and multiple alignments. The propensities were calculated classically, but the way to use them for prediction was completely new: starting from a tetrapeptide sequence on which one wants to evaluate the presence of a β‐turn, the propensity for a given residue is modified by taking into account all the residues present in the multiple alignment at this position. The evaluation of a score is then done by weighting these propensities by the use of Position‐specific score matrices generated by PSI‐BLAST. The introduction of secondary structure information predicted by PSIPRED or SSPRO2 as well as taking into account the flanking residues around the tetrapeptide improved the accuracy greatly. This latter evaluated on a database of 426 reference proteins (previously used on other studies) by a sevenfold crossvalidation gave very good results with a Matthews Correlation Coefficient (MCC) of 0.42 and an overall prediction accuracy of 74.8%; this places our method among the best ones. A jackknife test was also done, which gave results within the same range. This shows that it is possible to reach neural networks accuracy with considerably less computional cost and complexity. Furthermore, propensities remain excellent descriptors of amino acid tendencies to belong to β‐turns, which can be useful for peptide or protein engineering and design. For β‐turn type prediction, we reached the best accuracy ever published in terms of MCC (except for the irregular type IV) in the range of 0.25–0.30 for types I, II, and I′ and 0.13–0.15 for types VIII, II′, and IV. To our knowledge, our method is the only one available on the Web that predicts types I′ and II′. The accuracy evaluated on two larger databases of 547 and 823 proteins was not improved significantly. All of this was implemented into a Web server called COUDES (French acronym for: Chercher Où Une Déviation Existe Sûrement), which is available at the following URL: http://bioserv.rpbs. jussieu.fr/Coudes/index.html within the new bioinformatics platform RPBS. Proteins 2005;59. © 2005 Wiley‐Liss, Inc.
Reduced Functional Connectivity of Prefrontal Regions and Amygdala Within Affect and Working Memory Networks in Pediatric Bipolar Disorder

This study examined whether adolescents with pediatric bipolar disorder (PBD) have abnormal regional functional connectivity in distributed brain networks during an affective working memory task. Adolescents with PBD (n=41) and healthy controls (HC; n=16) performed a two-back functional magnetic resonance imaging working memory task with blocks of either angry or neutral faces. Independent component analysis methodology identified two temporally independent and functionally connected brain networks that showed differential functional connectivity in PBD and HC. Within a network for "affect evaluation and regulation," PBD showed decreased functional connectivity relative to HC in regions involved in emotion processing such as the right amygdala, and in emotion regulation regions such as the right ventrolateral prefrontal cortex (VLPFC), while functional connectivity was increased in emotion evaluation regions such as the bilateral medial PFC. Furthermore, in an "Affective Working Memory Network," PBD exhibited greater connectivity relative to HC in left dorsolateral PFC (DLPFC), caudate, and right VLPFC; and simultaneously reduced connectivity in emotion processing regions, such as the right amygdala, bilateral temporal regions, and the junction of DLPFC/VLPFC, which interfaces affective and cognitive processes. Dysfunction in network engagement in PBD patients illustrates that they are expending greater effort in face emotion evaluation, while being less able to engage affect regulation regions.
Edinburgh Research Explorer Identification of novel loci associated with gastrointestinal parasite resistance in a Red Maasai x Dorper backcross population

Gastrointestinal (GI) parasitic infection is the main health constraint for small ruminant production, causing loss of weight and/or death. Red Maasai sheep have adapted to a tropical environment where extreme parasite exposure is a constant, especially with highly pathogenic Haemonchus contortus . This breed has been reported to be resistant to gastrointestinal parasite infection, hence it is considered an invaluable resource to study associations between host genetics and resistance. The aim of this study was to identify polymorphisms strongly associated with host resistance in a double backcross population derived from Red Maasai and Dorper sheep using a SNP-based GWAS analysis. The animals that were genotyped represented the most resistant and susceptible individuals based on the tails of phenotypic distribution (10% each) for average faecal egg counts (AVFEC). AVFEC, packed cell volume (AVPCV), and live weight (AVLWT) were adjusted for fixed effects and co-vari-ables, and an association analysis was run using EMMAX. Revised significance levels were calculated using 100,000 permutation tests. The top five significant SNP markers with - log10 p-values > 3.794 were observed on five different chromosomes for AVFEC, and BLUPPf90/PostGSf90 results confirmed EMMAX significant regions for this trait. One of these regions included a cluster of significant SNP on chromosome (Chr) 6 not in linkage disequilibrium to each other. This genomic location contains annotated genes involved in cytokine signalling, haemostasis and mucus biosynthesis. Only one association detected on Chr 7 was significant for both AVPCV and AVLWT. The results generated here reveal candidate immune variants for genes involved in differential response to infection and provide additional SNP marker information that has potential to aid selection of resistance to gastrointestinal parasites in sheep of a similar genetic background to the double backcross population.
Auctions versus Negotiations in Procurement : An Empirical Analysis . ∗

Should the buyer of a customized good use competitive bidding or negotiation to select a contractor? To shed light on this question, we consider several possible determinants that may influence the choice of auctions versus negotiations. We then examine a comprehensive data set of private sector building contracts awarded in Northern California during the years 1995-2000. The analysis suggests a number of possible limitations to the use of auctions. Auctions may perform poorly when projects are complex, contractual design is incomplete and there are few available bidders. Furthermore, auctions may stifle communication between buyers and sellers, preventing the buyer from utilizing the contractor’s expertise when designing the project. Some implications of these results for procurement in the public sector are discussed. JEL classifications: D23, D82, H57, L14, L22, L74. ∗We thank Susan Athey, Tim Bresnahan, Jeremy Bulow, Igal Hendel, Matt Kahn, Pueo Keffer, Jon Levin, Scott Masten, John McMillan, Paul Milgrom, Aviv Nevo, Peter Reiss, Ilya Segal, Pablo Spiller, Bob Tatum and Oliver Williamson for helpful discussions. Pablo Spiller and two anonymous referees offered fabulous comments. This research has been supported by the National Science Foundation, grants SES0112106 and SES0122747 (Bajari), and SES–0079876 (Tadelis) and by the Stanford Institute for Economic Policy Research. Email: bajari@econ.umn. edu and stadelis@haas.berkeley. edu.
Adolescent friendships predict later resilient functioning across psychosocial domains in a healthy community cohort

Background Adolescence is a key time period for the emergence of psychosocial and mental health difficulties. To promote adolescent adaptive (‘resilient’) psychosocial functioning (PSF), appropriate conceptualisation and quantification of such functioning and its predictors is a crucial first step. Here, we quantify resilient functioning as the degree to which an individual functions better or worse than expected given their self-reported childhood family experiences, and relate this to adolescent family and friendship support. Method We used Principal Component and regression analyses to investigate the relationship between childhood family experiences and PSF (psychiatric symptomatology, personality traits and mental wellbeing) in healthy adolescents (the Neuroscience in Psychiatry Network; N = 2389; ages 14–24). Residuals from the relation between childhood family experiences and PSF reflect resilient functioning; the degree to which an individual is functioning better, or worse, than expected given their childhood family experiences. Next, we relate family and friendship support with resilient functioning both cross-sectionally and 1 year later. Results Friendship and family support were positive predictors of immediate resilient PSF, with friendship support being the strongest predictor. However, whereas friendship support was a significant positive predictor of later resilient functioning, family support had a negative relationship with later resilient PSF. Conclusions We show that friendship support, but not family support, is an important positive predictor of both immediate and later resilient PSF in adolescence and early adulthood. Interventions that promote the skills needed to acquire and sustain adolescent friendships may be crucial in increasing adolescent resilient PSF.