Miracle-dz/UniFAR-FTUs huggingface dataset:
Coming to America: multiple origins of New World geckos

Geckos in the Western Hemisphere provide an excellent model to study faunal assembly at a continental scale. We generated a time‐calibrated phylogeny, including exemplars of all New World gecko genera, to produce a biogeographical scenario for the New World geckos. Patterns of New World gecko origins are consistent with almost every biogeographical scenario utilized by a terrestrial vertebrate with different New World lineages showing evidence of vicariance, dispersal via temporary land bridge, overseas dispersal or anthropogenic introductions. We also recovered a strong relationship between clade age and species diversity, with older New World lineages having more species than more recently arrived lineages. Our data provide the first phylogenetic hypothesis for all New World geckos and highlight the intricate origins and ongoing organization of continental faunas. The phylogenetic and biogeographical hypotheses presented here provide an historical framework to further pursue research on the diversification and assembly of the New World herpetofauna.
Sensory Innervation of the Dorsal Portion of the Lumbar Intervertebral Discs in Rats

Study Design. The levels of dorsal root ganglions (DRGs) innervating the dorsal portion of the lumbar intervertebral discs from L1–L2 to L4–L5 were investigated in rats by the retrograde transport method. The pathways and functions of nerve fibers supplying the dorsal portion of the discs were investigated by denervation and immuno-histochemistry. Objectives. To investigate the sensory innervation of the dorsal portion of the lumbar intervertebral discs in rats. Summary of Background Data. The dorsal portion of the L5–L6 disc has been reported to be innervated multisegmentally, and anesthetic blockade of the paravertebral sympathetic trunks and the L2 spinal nerve can relieve discogenic low back pain. However, sensory innervation of the dorsal portion of the lumbar discs at other levels has not been clarified. Methods. A retrograde transport of Fluoro-Gold was used. We studied a nonsympathectomy group (n = 44) and a sympathectomy group (n = 50) in which paravertebral sympathetic trunks were resected from L1 to L5 levels. Using a ventral approach, Fluoro-Gold crystals were inserted into the dorsal portion of the L1–L2, L2–L3, L3–L4, and L4–L5 discs. Seven days after surgery, Fluoro-Gold-labeled neurons were counted in the bilateral dorsal root ganglions from T10 to L6. Results. Fluoro-Gold-labeled neurons were distributed in dorsal root ganglions from T11 to L5 levels in the nonsympathectomy group. However, in the sympathectomy group the number of labeled neurons was less than that of the nonsympathectomy group in T11, T12, and T13 dorsal root ganglions of the L1–L2 disc group, in T12, T13, and L1 dorsal root ganglions of the L2–L3 disc group, in T12, T13, L1, and L2 dorsal root ganglions of the L3–L4 disc group, and in T12, T13, L1, and L2 dorsal root ganglions of the L4–L5 disc group. Conclusion. The dorsal portion of the lumbar discs from L1–L2 to L4–L5 is multisegmentally innervated by the T11 through L5 dorsal root ganglions. Sensory fibers from the upper dorsal root ganglions innervate the dorsal portion of the discs via the paravertebral sympathetic trunks, although those from the lower dorsal root ganglions innervate via the sinuvertebral nerves. Furthermore, sensory nerve fibers enter the paravertebral sympathetic trunks through the corresponding ramus communicans and reach the dorsal root ganglions via each ramus communicans at the L2 and/or more cranial levels.
Temperature effects on metabolic rate of juvenile Pacific bluefin tuna Thunnus orientalis

SUMMARY Pacific bluefin tuna inhabit a wide range of thermal environments across the Pacific ocean. To examine how metabolism varies across this thermal range, we studied the effect of ambient water temperature on metabolic rate of juvenile Pacific bluefin tuna, Thunnus thynnus, swimming in a swim tunnel. Rate of oxygen consumption (ṀO2) was measured at ambient temperatures of 8–25°C and swimming speeds of 0.75–1.75 body lengths (BL) s–1. Pacific bluefin swimming at 1 BL s–1 per second exhibited a U-shaped curve of metabolic rate vs ambient temperature, with a thermal minimum zone between 15°C to 20°C. Minimum ṀO2 of 175±29 mg kg–1 h–1 was recorded at 15°C, while both cold and warm temperatures resulted in increased metabolic rates of 331±62 mg kg–1 h–1 at 8°C and 256±19 mg kg–1 h–1 at 25°C. Tailbeat frequencies were negatively correlated with ambient temperature. Additional experiments indicated that the increase in ṀO2 at low temperature occurred only at low swimming speeds. Ambient water temperature data from electronic tags implanted in wild fish indicate that Pacific bluefin of similar size to the experimental fish used in the swim tunnel spend most of their time in ambient temperatures in the metabolic thermal minimum zone.
Clusters of microembolic signals: a new form of cerebral microembolism presentation in a patient with middle cerebral artery stenosis.

BACKGROUND Middle cerebral artery (MCA) stenosis is a rare occlusive disease in western populations, with a high risk of stroke recurrence. An artery-to-artery embolic mechanism has been argued. We report the detection of a new pattern of microembolic signals (MES) in the MCA poststenotic segment in a patient with multiple recurrent transient ischemic attacks. CASE DESCRIPTION A 75-year-old man was admitted to our hospital with a transient leg monoparesis on the left side. Right MCA stenosis was detected by transcranial Doppler ultrasonography (TCD). In spite of aspirin treatment, the patient had a recurrent right hemispheric transient ischemic attack, and anticoagulant therapy was started. A new, similar event happened after correct anticoagulation. The bigated TCD monitoring study of both MCAs disclosed clusters of MES at the poststenotic MCA segment. Each cluster contained between 12 and 45 embolic signals. The patient became asymptomatic and clusters of MES disappeared, coinciding with the combination of ticlopidine and oral anticoagulants. CONCLUSIONS We describe a new presentation of MES, ie, grouped in clusters of signals, that may be associated with a high risk of stroke recurrence.
Studies on ubiquinone. Demonstration of the total biosynthesis of ubiquinone-9 in rat liver mitochondria.

Abstract The total biosynthesis of ubiquinone-9 from p-hydroxy[U-14C]benzoate has been demonstrated in mitochondria isolated from rat liver slices preincubated with mevalonic acid. Two partial reactions were also demonstrated. These were the conversion of p-hydroxybenzoate to 5-demethoxyubiquinone-9 and sequentially, the conversion of 5-demethoxyubiquinone-9 to ubiquinone-9. Furthermore, these reactions were found to be catalyzed by the inner membrane of the mitochondrion. It appeared that the only external requirements for this mitochondrial system are ATP, p-hydroxybenzoate, and a source of isopentenyl pyrophosphate. Conversion of 5-demethoxyubiquinone-9 to ubiquinone-9, which involves one hydroxylation and one methylation, is dependent upon molecular oxygen, S-adenosylmethionine, and reducing equivalents as indicated by a preference for succinate over malate. The over-all reaction is inhibited by CO but not by KCN. External ATP was essential for the conversion of p-hydroxybenzoate to 5-demethoxyubiquinone-9, but not for the conversion of 5-demethoxyubiquinone-9 to ubiquinone-9. These data suggest that the inner membrane of liver mitochondria is capable of the hydroxylation and methylation of aromatic precursors of ubiquinone.
Effects of Bioactive Peptide, Valyl-Prolyl-Proline (VPP), and Lactobacillus helveticus Fermented Milk Containing VPP on Bone Loss in Ovariectomized Rats

Background: Valyl-prolyl-proline (VPP), a bioactive peptide formed during the fermentation with Lactobacillus helveticus LBK-16H (L. helveticus), has been shown to increase bone formation in vitro. The aim of the study was to determine whether VPP and L. helveticus fermented milk prevent bone loss in ovariectomized (OVX) rats. Methods: During the 12-week intervention study, the OVX rats received VPP in water or L. helveticus fermented milk, containing VPP. Sham-operated rats receiving water acted as controls. The trabecular and cortical bone mineral density were determined by peripheral quantitative computed tomography before the operation and at 4 and 12 weeks. The mechanical testing and ash weight analysis as well as the static and dynamic histomorphometrical parameters were assessed at the end of the intervention. Results: VPP given in water showed no clear effect on bone loss. L. helveticus fermented milk prevented bone loss by decreasing bone turnover and increasing the bone mineral density. Ovariectomycaused a 57% loss in the trabecular bone, which was attenuated by 16% in the L. helveticus group. Conclusions: VPP peptide did not prevent ovariectomy-induced bone loss, which could be due to the poor bioavailability of VPP from water solution. L. helveticus fermented milk prevented bone loss, whether this is due to the VPP peptide cannot be concluded.
Bilingual corpus for AVASR using multiple sensors and depth information

In this paper we present the Bilingual Audio-Visual Corpus with Depth information (BAVCD). The database contains utterances of connected digits, spoken by 15 subjects in English and 6 subjects in Greek, and collected employing multiple audio-visual sensors. Among them, of particular interest is the use of the Microsoft Kinect device, which is able to capture facial depth images using the structured light technique in addition to the traditional RGB video. The database allows conducting research on multiple aspects of small-vocabulary audio-visual automatic speech recognition, such as the use of visual depth information for speechreading, fusion of multiple video and audio streams, and language dependencies of the task. Preliminary results on the corpus are also presented.
System identification approach to genetic programming

Introduces a new approach to genetic programming (GP), based on a system identification technique, which integrates a GP-based adaptive search of tree structures and a local parameter tuning mechanism employing a statistical search. In Proc. 5th Int. Joint Conf. on Genetic Algorithms (1993), we introduced our adaptive program called STROGANOFF ("STructured Representation On Genetic Algorithms for NOnlinear Function Fitting"), which integrated a multiple regression analysis method and a GA-based search strategy. The effectiveness of STROGANOFF was demonstrated by solving several system identification (numerical) problems. This paper extends STROGANOFF to symbolic (non-numerical) reasoning, by introducing multiple types of nodes, using a modified minimum description length (MDL) based selection criterion, and a pruning of the resultant trees. The effectiveness of this system-identification approach to GP is demonstrated by successful application to Boolean concept formation and to symbolic regression problems. <<ETX>>
Multi-variable Extremum Seeking Control for Mini-split Air-conditioning System

In this study, a multi-variable extremum seeking control (ESC) scheme is proposed for a variable-speed mini-split air-conditioning system. The control inputs are the evaporator and condenser fan speeds, respectively. While the total power consumption is used as the feedback. The multi-variable ESC can optimize the control inputs for each channel in real-time, without relying on the accurate model of the system. This nearly model free feature makes the system more easily to be designed and deployed. First, the multi-variable ESC algorithm is deployed on a Dymola-based ASHP model to show its effectiveness in searching the optimal working point. Then, an experiment set-up is built to further demonstrate the promising performance in improving the efficiency of the mini-split AC system via multi-variable ESC.
Computational study of peptide permeation through membrane: searching for hidden slow variables

Atomically detailed molecular dynamics trajectories in conjunction with Milestoning are used to analyse the different contributions of coarse variables to the permeation process of a small peptide (N-acetyl-l-tryptophanamide, NATA) through a 1,2-dioleoyl-sn-glycero-3-phosphocholine membrane. The peptide reverses its overall orientation as it permeates through the biological bilayer. The large change in orientation is investigated explicitly but is shown to impact the free energy landscape and permeation time only moderately. Nevertheless, a significant difference in permeation properties of the two halves of the membrane suggests the presence of other hidden slow variables. We speculate, based on calculation of the potential of mean force, that a conformational transition of NATA makes significant contribution to these differences. Other candidates for hidden slow variables may include water permeation and collective motions of phospholipids.
The complexity and cost of drug regimens of older patients hospitalized with heart failure in the United States, 1998-2001.

BACKGROUND Polypharmacy-the concurrent prescription of multiple medications-is a salient consideration in the care of older patients with heart failure. Little is known, however, about the complexity and financial burden of medical therapy in this population. METHODS This is a study of the chronic medications prescribed at hospital discharge to patients 65 years or older hospitalized for heart failure in 2 cohorts separated by 27 months (April 1998-March 1999, n = 31 602; July 2000-June 2001, n = 30,774). Three utilization measures were assessed: the number of drugs, the estimated number of doses per day, and the estimated annual costs using the same cost standard (2003 average wholesale prices) for both samples. Utilization associated with population characteristics and between time frames was assessed in multivariable models. RESULTS In 1998-1999, the mean number of drugs was 6.8, representing 10.1 doses daily at a cost of 3142 dollars/y, increasing to 7.5 drugs, 11.1 doses daily and 3823 dollars/y in 2000-2001 (P<.001 for all comparisons). After adjustment, the number of drugs increased by 12% and costs by 24% between samples. Factors associated with greater complexity and cost included diabetes (1.6 additional drugs and 1094 dollars/y additional cost), prior revascularization (1.3 drugs, 1154 dollars/y), and chronic lung disease (1.2 drugs, 814 dollars/y). Younger age and white race were also associated with more drugs and higher costs. CONCLUSIONS The drug treatment of older patients with heart failure is characterized by rapidly increasing complexity and cost. Efforts should be directed toward optimizing the complex drug regimens of elderly patients with heart failure and multiple comorbidities.
GENETIC EVIDENCE FROM MITOCHONDRIAL, NUCLEAR, AND ENDOSYMBIONT MARKERS FOR THE EVOLUTION OF HOST PLANT ASSOCIATED SPECIES IN THE APHID GENUS HYALOPTERUS (HEMIPTERA: APHIDIDAE)

Abstract Over the past several decades biologists' fascination with plant–herbivore interactions has generated intensive research into the implications of these interactions for insect diversification. The study of closely related phytophagous insect species or populations from an evolutionary perspective can help illuminate ecological and selective forces that drive these interactions. Here we present such an analysis for aphids in the genus Hyalopterus (Hemiptera: Aphididae), a cosmopolitan group that feeds on plants in the genus Prunus (Rosaceae). Hyalopterus currently contains two recognized species associated with different Prunus species, although the taxonomy and evolutionary history of the group is poorly understood. Using mitochondrial COI sequences, 16S rDNA sequences from the aphid endosymbiont Buchnera aphidicola, and nine microsatellite loci we investigated population structure in Hyalopterus from the most commonly used Prunus host species throughout the Mediterranean as well as in California, where the species H. pruni is an invasive pest. We found three deeply divergent lineages structured in large part by specific associations with plum, almond, and peach trees. There was no evidence that geographic or temporal barriers could explain the overall diversity in the genus. Levels of genetic differentiation are consistent with that typically attributed to aphid species and indicate divergence times older than the domestication of Prunus for agriculture. Interestingly, in addition to their typical hosts, aphids from each of the three lineages were frequently found on apricot trees. Apricot also appears to act as a resource mediated hybrid zone for plum and almond associated lineages. Together, results suggest that host plants have played a role in maintaining host-associated differentiation in Hyalopterus for as long as several million years, despite worldwide movement of host plants and the potential for ongoing hybridization.
Rôle du complexe de cohésion sur la ligature d'extrémités d'ADN non homologues et la stabilité du génome

Au cours de la replication, la reparation des cassures double brin (CDB) par recombinaison homologue (RH), basee sur la synthese d’ADN a partir de la chromatide sœur, permet le maintien de la stabilite du genome. La religature d’extremites (EJ) eloignees de CDB peut quant a elle generer des rearrangements menacant son integrite. Nous avons etudie le mecanisme de reparation par EJ en fonction de la distance separant deux cassures double brin. En utilisant des substrats intra-chromosomiques permettant la mesure de l’efficacite et de la fidelite du EJ apres ligature d’extremites eloignees ou proximales, nous avons mis en evidence l’implication du complexe de cohesion dans l’inhibition du EJ d’extremites distales. Le complexe de cohesion joue donc un role central dans l’interface replication/reparation ; la cohesion des chromatides sœurs favorise la reparation par RH et permet l’inhibition specifique du EJ d’extremites eloignees, probablement en limitant la mobilite de la chromatine endommagee et la formation d’une synapse propice au rapprochement des extremites. La religature d’extremites eloignees est egalement necessaire aux mecanismes de diversification des genes des immunoglobulines tels que la recombinaison V(D)J et la commutation de classe. L’etude de souris Rad21+/- a egalement demontre une implication du complexe de cohesion dans ces mecanismes essentiels a la diversite de l’information genetique. Le complexe de cohesion etant implique dans ces mecanismes et dans l’inhibition des rearrangements complexes tels que les translocations et insertions il est un acteur essentiel de la diversite et de la stabilite genomique.
Antiproteinuric and anti‐inflammatory effects of thiazolidinedione (Review Article)

SUMMARY: Type 2 diabetes is the most common cause of chronic renal failure worldwide. Only a few oral antidiabetic drugs can be used for treating type 2 diabetes in patients with renal failure. Among them is thiazolidinedione, which is the agonist of peroxisome proliferator‐activated receptor (PPAR)‐γ. PPAR‐γ receptors are expressed in many tissues including the kidney. Recently, beneficial effects of PPAR‐γ agonists on several aspects related to renal function have been reported. These drugs have been shown to have favourable haemodynamic and anti‐inflammatory effects on the kidneys. On the other hand, there is a rising concern on the association between thiazolidinedione treatment and the risk of cardiovascular disease. In the present paper, we review the recent studies that evaluated these potential effects of thiazolidinedione in patients with kidney diseases.
Immune factors in corneal graft rejection.

This panorama of the immune factors in corneal graft rejection covers a spectrum of mechanisms which play a role in the opacification of corneal grafts. Great emphasis has been accorded to the role of transplantation immunity. The clinical and experimental evidence implicating transplantation immunity in the rejection of corneal grafts has been critically reviewed. In addition, evidence is presented indicating that some immune mechanisms which result in inflammatory sequelas other than classical transplantation immunity can lead to rejection of corneal grafts. Evidence also suggests that certain well-described pseudoimmune or immunomimetic reactions, which are devoid of the classic criteria required for hypersensitivity reactions, contribute to rejection of corneal grafts.
IP‐10 predicts viral response and therapeutic outcome in difficult‐to‐treat patients with HCV genotype 1 infection

Plasma from 173 patients with HCV genotype 1 infection was analyzed for IP‐10 levels prior to treatment with pegylated interferon‐α‐2a and ribavirin. Significantly lower IP‐10 levels were observed in patients achieving a rapid viral response (RVR) (P < .0001), even in those with body mass index (BMI) ≥ 25 kg/m2 (P = .004) and with baseline viral load ≥ 2 million IU/mL (P = .001). Similarly, significantly lower IP‐10 levels were observed in patients obtaining a sustained viral response (SVR) (P = .0002), including those having higher BMI (P < .05), higher viral load (P = .0005), and both higher BMI and viral load (P < .03). In multivariate logistic regression analyses, a low IP‐10 value was independently predictive of both RVR and SVR. A baseline cutoff IP‐10 value of 600 pg/mL yielded a negative predictive value (NPV) of 79% (19/24) for all genotype 1–infected patients, which was comparable with that observed using a reduction in HCV‐RNA by at least 2 logs after 12 weeks of therapy (NPV 86%; 19/22); by combining the two, 30 of 38 patients (NPV 79%) potentially could have been spared unnecessary therapy. In patients having both higher BMI and viral load, cut‐off levels of 150 and 600 pg/mL yielded a positive predictive value (PPV) of 71% and NPV of 100%, respectively. In conclusion, pretreatment IP‐10 levels predict RVR and SVR in patients infected with HCV genotype 1, even in those with higher BMI and viral load. A substantial proportion of the latter patients may achieve SVR in spite of unfavorable baseline characteristics if their pretreatment IP‐10 level is low. Thus, pretreatment IP‐10 analysis may prove helpful in decision‐making regarding pharmaceutical intervention. (HEPATOLOGY 2006;44:1617–1625.)
Croissance de la productivite, transfert de parts de marche et restructuration dans le secteur canadien de la fabrication

Il y a mouvement lorsque des entreprises gagnent et perdent des parts de marche dans le cadre de la lutte concurrentielle. La reaffectation des parts de marche d'un groupe a un autre est associee a un gain de productivite puisque les entreprises moins productives perdent des parts et que celles dont la productivite est superieure en gagnent. Le present document examine la mesure dans laquelle la productivite s'est trouvee amelioree par le mouvement des entreprises depuis les 20 dernieresannees. Il s'interesse particulierement a la mesure dans laquelle ce processus a evolue durant les annees 1980 et contribue, de fait, au ralentissement du secteur de la fabrication