Miracle-dz/UniFAR-FTUs huggingface dataset:
Synteny between Arabidopsis thaliana and rice at the genome level: a tool to identify conservation in the ongoing rice genome sequencing project.

BLASTX alignment between 189.5 Mb of rice genomic sequence and translated Arabidopsis thaliana annotated coding sequences (CDS) identified 60 syntenic regions involving 4-22 rice orthologs covering < or =3.2 cM (centiMorgan). Most regions are <3 cM in length. A detailed and updated version of a table representing these regions is available on our web site. Thirty-five rice loci match two distinct A.thaliana loci, as expected from the duplicated nature of the A.thaliana genome. One A.thaliana locus matches two distinct rice regions, suggesting that rice chromosomal sequence duplications exist. A high level of rearrangement characterizing the 60 syntenic regions illustrates the ancient nature of the speciation between A.thaliana and rice. The apparent reduced level of microcollinearity implies the dispersion to new genomic locations, via transposon activity, of single or small clusters of genes in the rice genome, which represents a significant additional effector of plant genome evolution.
Libration-induced mean flow in a spherical shell

Abstract We investigate the flow in a spherical shell subject to a time harmonic oscillation of its rotation rate, also called longitudinal libration, when the oscillation frequency is larger than twice the mean rotation rate. In this frequency regime, no inertial waves are directly excited by harmonic forcing. We show, however, that, through nonlinear interactions in the Ekman layers, it can generate a strong mean zonal flow in the interior. An analytical theory is developed using a perturbative approach in the limit of small libration amplitude $\varepsilon $ and small Ekman number $E$ . The mean flow is found to be at leading order an azimuthal flow that scales as the square of the libration amplitude and depends only on the cylindrical radius coordinate. The mean flow also exhibits a discontinuity across the cylinder tangent to the inner sphere. We show that this discontinuity can be smoothed through multi-scale Stewartson layers. The mean flow is also found to possess a weak axial flow that scales as $O({\varepsilon }^{2} {E}^{5/ 42} )$ in the Stewartson layers. The analytical solution is compared to axisymmetric numerical simulations, and a good agreement is demonstrated.
Measuring laryngealization in running speech: interaction with contrastive tones in yalálag zapotec

Abstract The study of glottalization is usually based on methods whose limited reliability in the analysis of non sustained phonation is widely acknowledged. In this study we propose a method to measure the degree of glottalization which is robust to variation of fundamental frequency and which, applied to the electroglottographic signal, does not depend on changes in vocal tract resonances. The method, based on an original variant of recurrence analysis, is used to study the interaction between phonological glottalization of vowels and contrastive tones in Yalalag Zapotec. In this American Indian language, both modal and laryngeal vowels can occur with three different contrastive tones (low, high and falling). However, the rapid modulation of fundamental frequency needed for the production of contrastive tones is expected to be strongly limited by the presence of laryngealization. We study how speakers resolve the competition between the constraints on the articulation of these two features of Zapotec phonology. Through wavelet based functional mixed regression we could model the changes in the degree of glottalization over the duration of both modal and laryngealized vowels produced with the three different tones.
pH and protease control of acrosomal content stasis and release during the guinea pig sperm acrosome reaction.

The purpose of this study was to examine how trypsin inhibitors affect the guinea pig sperm acrosome reaction in vitro. Using spermatozoa pretreated with lysophosphatidyl choline, we found that both naturally occurring high molecular weight and the smaller synthetic trypsin inhibitor p-aminobenzamidine (PAB) delayed the onset of the acrosome reaction as monitored by light microscopy. Examination with electron microscopy revealed that acrosomal matrix dispersal rather than membrane fusion was affected. Despite the morphologic delay in acrosomal content release, PAB unexpectedly permitted 96% of soluble acrosomal antigen to be released into the supernatant. In addition, total acrosin release in the presence of PAB was 74% of control, with the vast majority as latent rather than active enzyme. A morphologically intact but membrane-free target of acrosomal matrix (AM), which is sensitive to trypsin inhibitor, was partially purified using Triton-x-100 at pH 5.2. AM remained morphologically stable at pH 5.2; however, shift up to pH 7 resulted in rapid dissolution within several minutes as monitored by light and electron microscopy and light scattering. Trypsin inhibitor prevented dispersion of AM at pH 7. The results suggest that, during the acrosome reaction, one distinct region of the acrosomal contents disperses after membrane vesiculation in a pH and trypsin inhibitor-insensitive fashion while a pH sensitive trypsin-like activity (acrosin? ) disperses another discrete region of acrosomal matrix.
Active Disturbance Rejection Control for a Flywheel Energy Storage System

This paper presents the application of the Active Disturbance Rejection Control Technique (ADRCT) to improve the performance of a Flywheel Energy Storage System (FESS). The FESS is designed for the DC MicroGrid (MG) application. It mainly consists of a flywheel with a coaxial BrushLess DC (BLDC) machine, a three-phase full-bridge circuit, and a bidirectional Buck-Boost converter. A model-independent controller based on the ADRCT, which can estimate and compensate model uncertainties and unknown disturbances in real time, is designed for the bidirectional Buck-Boost converter control in the FESS. Simulations and experiments are conducted in both charge and discharge mode to verify the performance of the proposed controller by comparison with a traditional double loop PI controller. Results show that the new controller is more robust and more adaptive. It has a better anti-disturbance capability and a higher dynamic performance than the PI controller. Moreover, to adapt to different applications and operating conditions, the charging process of the FESS is further improved. Strategies on maximum torque control and power limiting control are developed and realized on the experimental platform.
Trypanosoma congolense infections: MHC class II‐restricted immune responses mediate either protection or disease, depending on IL‐10 function

BALB/c mice are highly susceptible and C57BL/6 relatively resistant to Trypanosoma congolense infections. Here we show that relatively resistant wild‐type B6 mice infected with T. congolense survive significantly longer (> 200 days) than infected major histocompatibility complex (MHC) class II‐deficient B6 mice (∼50 days). We also show that blocking of the interleukin‐10 (IL‐10) receptor induces early death of wild‐type B6 mice infected with T. congolense (∼10 days), but does not affect the survival of infected MHC class II‐deficient B6 mice. We conclude that MHC class II‐restricted immune responses mediate protection and, when IL‐10 function is impaired, MHC class II‐restricted immune responses mediate early mortality in otherwise resistant B6 mice. Thus, in T. congolense infections, MHC class II‐restricted immune responses mediate either protection or disease, depending on IL‐10 function.
A class of permutational and multinomial tests arising in epidemiological research.

Suppose that, in a population of size N, for subgroup a of size Na (a = 1, . , c), R. individuals develop disease. Let Xa0n be a measure, perhaps one related to the geographical separation between the subgroups, designed to help detect a specified form of departure from randomness in the occurrence of the disease. If the XaEs measure is summed over all pairs of cases of the disease, summary measures Z and W are
Trypanosoma cruzi Evades the Complement System as an Efficient Strategy to Survive in the Mammalian Host: The Specific Roles of Host/Parasite Molecules and Trypanosoma cruzi Calreticulin

American Trypanosomiasis is an important neglected reemerging tropical parasitism, infecting about 8 million people worldwide. Its agent, Trypanosoma cruzi, exhibits multiple mechanisms to evade the host immune response and infect host cells. An important immune evasion strategy of T. cruzi infective stages is its capacity to inhibit the complement system activation on the parasite surface, avoiding opsonizing, immune stimulating and lytic effects. Epimastigotes, the non-infective form of the parasite, present in triatomine arthropod vectors, are highly susceptible to complement-mediated lysis while trypomastigotes, the infective form, present in host bloodstream, are resistant. Thus T. cruzi susceptibility to complement varies depending on the parasite stage (amastigote, trypomastigotes or epimastigote) and on the T. cruzi strain. To avoid complement-mediated lysis, T. cruzi trypomastigotes express on the parasite surface a variety of complement regulatory proteins, such as glycoprotein 58/68 (gp58/68), T. cruzi complement regulatory protein (TcCRP), trypomastigote decay-accelerating factor (T-DAF), C2 receptor inhibitor trispanning (CRIT) and T. cruzi calreticulin (TcCRT). Alternatively, or concomitantly, the parasite captures components with complement regulatory activity from the host bloodstream, such as factor H (FH) and plasma membrane-derived vesicles (PMVs). All these proteins inhibit different steps of the classical (CP), alternative (AP) or lectin pathways (LP). Thus, TcCRP inhibits the CP C3 convertase assembling, gp58/68 inhibits the AP C3 convertase, T-DAF interferes with the CP and AP convertases assembling, TcCRT inhibits the CP and LP, CRIT confers ability to resist the CP and LP, FH is used by trypomastigotes to inhibit the AP convertases and PMVs inhibit the CP and LP C3 convertases. Many of these proteins have similar molecular inhibitory mechanisms. Our laboratory has contributed to elucidate the role of TcCRT in the host-parasite interplay. Thus, we have proposed that TcCRT is a pleiotropic molecule, present not only in the parasite endoplasmic reticulum, but also on the trypomastigote surface, participating in key processes to establish T. cruzi infection, such as inhibition of the complement system and serving as an important virulence factor. Additionally, TcCRT interaction with key complement components, participates as an anti-angiogenic and anti-tumor molecule, inhibiting at least in important part, tumor growth in infected animals.
Predictors of Four Functional Tasks in Patients with Osteoarthritis of the Knee

Purpose: The purpose of this study was to identify predictors of performance on four functional tasks in adults with osteoarthritis (OA) of the knee. Design: Descriptive correlation Methods: A voluntary sample of 78 community dwelling adults who reported knee pain and were previously diagnosed with osteoarthritis of the knee were timed while they performed the functional tasks of going down and getting up off of the floor and ascending and descending a flight of stairs as quickly as possible. Subjects were also evaluated for their joint pain while performing these activities, their leg strength, perceptions of joint pain, stiffness, functional ability, and other health status information. Findings: This study indicates that knee extension strength (quadriceps), joint pain during the activity, perceptions of functional ability and body weight combined can predict between 39% and 56% of the variance in the time to perform four functional tasks in adults with OA of the knee. Conclusion: Interventions that improve quadriceps strength and reduce joint pain and body weight along with facilitating perceptions of functional ability may have a positive impact upon the ability to get down to and rise up off of the floor and ascend/descend stairs in adults with OA of the knee.
Relationship between nasopharyngeal colonization and the development of otitis media in children. Tonawanda/Williamsville Pediatrics.

Streptococcus pneumoniae, nontypeable Haemophilus influenzae, and Moraxella catarrhalis are the predominant bacteria associated with otitis media. A cohort of 306 infants was followed from birth through 12 months to determine frequency and duration of colonization and risk of acute otitis media (AOM) and otitis media with effusion (OME). M. catarrhalis was the most common bacterium isolated. Infants colonized at < or = 3 months of age were at increased risk of AOM and OME. Early colonization with M. catarrhalis revealed the greatest risk (relative risk [RR] = 1.24), especially for OME (RR = 1.57). There was a strong relationship between the frequency of colonization and OM (r = .37, P < .001,) for each pathogen. Although S. pneumoniae, nontypeable H. influenzae, and M. catarrhalis are part of the normal nasopharyngeal flora during infancy, an increased rate of colonization may identify a subpopulation of children that is at increased risk of OM.
COST-EFFECTIVENESS OF INTERFERON BETA-1B IN SLOWING MULTIPLE SCLEROSIS DISABILITY PROGRESSION

Objective: To estimate the cost-effectiveness (CE) of interferon beta-1b (IFNβ-1b) in slowing disability progression in persons with relapsing-remitting multiple sclerosis (RRMS). Methods: Treatment program costs and health outcomes are modeled for cohorts of 1,000 females and 1,000 males followed 40 years from onset. Fifteen scenarios model MS natural history progression, treatment efficacy, direct treatment costs, and MS healthcare costs. A single randomized placebo-controlled trial of IFNβ-1b found reduced disease activity by MRI, reduced frequency and severity of exacerbations, and a tendency toward slower disability progression. Disability years avoided are modeled as the primary health outcome analyzed. A ministry of health (MOH) perspective is adopted, using Nova Scotia population-based data. Annual IFNβ-1b direct treatment costs (Can $16,685) are high relative to both MOH healthcare costs per person with MS (Can $2,000) and estimated MOH costs avoided. Results: Given “reference case” assumptions for women with RRMS, treatment reduces lifetime disability years by 10%. Cost per disability year avoided before discounting is Can $189,230 (US $124,892), and Can $274,842 (US $181,395) after discounting at 5%. Estimates for alternative scenarios vary greatly, leaving main findings unchanged. Conclusions: Using the Expanded Disability Status Scale, cost per disability year avoided due to interferon beta-1b treatment in RRMS is quite high. Comparable CE estimates, using MS-specific or generic health-related quality-of-life outcome measures, are even higher. Further research is required to better measure treatment effects, modification of MS natural history, and net societal costs of IFNβ-1b in RRMS.
Growth and function of thirty-four human benign and malignant thyroid xenografts in untreated nude mice.

Tissue was taken from 16 patients with benign thyroid lesions (10 nontoxic nodular colloid goiter, two follicular adenoma, one autonomous adenoma, one iodine-induced thyrotoxicosis, 2 Graves' disease) and 18 patients with malignant thyroid tumors [seven papillary, five follicular, five undifferentiated (anaplastic), and one medullalry carcinoma] and was xenotransplanted into the flanks of 124 syngeneic female BALB/c-nu/nu mice 6 weeks of age. Subsequently, without any further treatment, serum levels of thyroglobulin (TG), T3, T4, and thyroid-stimulating hormone were determined by radioimmunoassay at 4 or 5 weeks posttransplantation and at the end of the experimental time period of 4 months. All animals were autopsied. The grafts were examined by light microscopy and TG immunohistochemistry. Morphologically, the grafts of benign and malignant thyroid tumors showed features overall identical to the original tissue. Conversely, nontoxic nodular colloid goiter and Graves' disease grafts revealed a transformation to normofollicular structures. All benign thyroid grafts showed a stationary growth, as did most differentiated thyroid carcinomas. Tumor take rates in differentiated and in medullary carcinoma were 15%, and in undifferentiated carcinomas, 100%. In the cancer grafts, a correlation between resting phase (period until progressive tumor growth) and survival time of the corresponding patients was disclosed. All patients whose tumors were not taken by nude mice are still alive and show no signs of progressive tumor growth at 9 to 34 months after surgery. All but one patient with tumors revealing positive tumor take died within 3 months (resting phase, 3 weeks) or one year (resting phase, 7 to 14 weeks) after surgery. Integrity of hormonal function in benign and malignant xenografts at 4 months posttransplantation could be shown by significantly higher T3 and T4 serum concentrations in animals with benign thyroid tissues (T3, 1.69 +/- 0.13 nmol/liter; T4, 45.69 +/- 2.09 nmol/liter; S.E.) as compared to controls without grafted tissue [T3, 1.29 +/- 0.10 nmol/liter (p less than 0.05); T4, 33.39 +/- 2.71 nmol/liter (p less than 0.05)] and by increased TG serum concentrations in animals receiving benign (TG, 2.70 +/- 1.39 ng/ml) or malignant (e.g., TG in follicular carcinoma, 34.44 +/- 13.83 ng/ml; controls, 0.30 +/- 0.02 ng/ml) thyroid tissue. Thus, we conclude that benign and malignant thyroid xenografts in the nude mouse maintain full morphological and, regarding T3, T4, and TG serum levels, functional integrity for at least 4 months after transplantation.
Metabolic Syndrome in the Pregnant Mare

Metabolic syndrome is a term drawing together a seemingly disparate set of clinical findings in human patients, these including insulin resistance, hyperinsulinemia, dyslipidemia, hypertension, and atherosclerosis. Obesity is a common but not consistent finding. The term has been subsequently applied to horses with obesity, insulin resistance, hyperinsulinemia, and dyslipidemia. A chronic pro-inflammatory condition is thought to exist in metabolic syndrome, the most important sequelae of the condition in the horse being laminitic. The effects on pregnancy in the mare have not been elucidated; however, in humans, gestational diabetes, abortion, and fetal compromise have been shown to result. Author’s address: Rood and Riddle Equine Hospital, PO Box 12070, Lexington, KY 40580; e-mail: pmorresey@roodandriddle.com © 2012 AAEP.
Intracellular interleukin-2 expression by T-cell subsets in B-cell chronic lymphocytic leukemia.

Intracellular A three-color ﬂow cytometry technique was used to deter- mine interleukin-2 expression by T-cell subsets - CD3 + /CD4 + and CD3 + /CD8 + cells in patients with newly diagnosed, untreated B-cell chronic lymphocytic leukemia (B-CLL) and in a control group. The detected statistically signiﬁcant higher percentage of CD3 + /CD8 + /IL2 + cells in patients than in con-trols may indicate the activation of T-lymphocytes, in partic- ular CD8 + cells, in early stages of B-CLL. Changes in the cytokine network between malignant cells and T-lymphocytes may be responsible for accumulation of the malignant cell clone in B-cell chronic lymphocytic leukemia (B- CLL). 1 Among such cytokines, interleukin-2 (IL-2) acts as a pleiotropic mediator within the immune system having a vari- ety of effects on proliferation of T- and B-cells, macrophages and large granular lymphocytes. It has been indicated that in B-CLL IL-2 may be involved in the induction and regulation of malignant cell proliferation, 2 and can also prevent malignant cells from programmed cell death. 3 To broaden knowledge about the role of this cytokine in B-CLL we tried to determine whether the IL-2 production capacity of T-cell subsets was altered in B-CLL patients in comparison within healthy individuals. Twenty-two patients with newly diagnosed, untreated B-CLL and 12 healthy individuals were studied. Peripheral blood lym- phocytes were isolated and stimulated by PMA and ionomycin in the presence of the intracellular protein transport inhibitor brefeldin A. Combined membrane and intracytoplasmic tional capacity of T-lymphocytes to produce IL-2. In view of reports regarding T-cell abnormalities in B-CLL, that may be an indicator of the activation state of T-lymphocytes. It may sug- gest that the activated immune system in early stages of the dis-ease tries to act against malignant cells (all analyzed patients were in stages 0-II). On the other hand, the higher number of T-cells expressing IL-2 in B-CLL patients may support the described role of IL-2 regulating proliferation and apoptosis of malignant cells.
Functional Interaction of CD154 Protein with α5β1 Integrin Is Totally Independent from Its Binding to αIIbβ3 Integrin and CD40 Molecules*

Background: CD154, an immuno-inflammatory molecule, binds to four receptors. Results: CD154 differentially binds its various receptors and is capable of simultaneously interacting with multiple ones, inducing synergistic responses in monocytes. Conclusion: The simultaneous engagement of CD154 receptors can create a cross-talk between them. Significance: Concomitant binding of CD154 to multiple receptors is greatly significant in therapies of CD154-related diseases. In addition to its classical CD40 receptor, CD154 also binds to αIIbβ3, α5β1, and αMβ2 integrins. Binding of CD154 to these receptors seems to play a key role in the pathogenic processes of chronic inflammation. This investigation was aimed at analyzing the functional interaction of CD154 with CD40, αIIbβ3, and α5β1 receptors. We found that the binding affinity of CD154 for αIIbβ3 is ∼4-fold higher than for α5β1. We also describe the generation of sCD154 mutants that lost their ability to bind CD40 or αIIbβ3 and show that CD154 residues involved in its binding to CD40 or αIIbβ3 are distinct from those implicated in its interaction to α5β1, suggesting that sCD154 may bind simultaneously to different receptors. Indeed, sCD154 can bind simultaneously to CD40 and α5β1 and biologically activate human monocytic U937 cells expressing both receptors. The simultaneous engagement of CD40 and α5β1 activates the mitogen-activated protein kinases, p38, and extracellular signal-related kinases 1/2 and synergizes in the release of inflammatory mediators MMP-2 and -9, suggesting a cross-talk between these receptors.
Large intrauterine haematomata in threatened miscarriage. Frequency and clinical consequences

Summary. Previously we described intrauterine haematomata seen with ultrasound in patients with threatened miscarriage and we suggested that a haematoma of ≥50 ml might represent a risk to the pregnancy. We have now investigated 566 patients with vaginal bleeding in the first half of pregnancy and followed up 23 (4%) who had a haematoma of ≥50ml (mean 71 ml, range 50–150) at between 12 and 20 weeks gestation. One patient had a miscarriage and two had a preterm delivery, so that, contrary to our original suggestion, these large haematomata do not seem to represent any serious threat to the pregnancy.