Miracle-dz/UniFAR-FTUs huggingface dataset:
Bone Turnover, Osteoprotegerin/Rankl and Inflammation with Antiretroviral Initiation: Tenofovir versus Non-Tenofovir Regimens

Background Bone mineral density decreases with anti-retroviral therapy (ART) initiation, although the pathogenesis, including the role of tenofovir (TDF), is unclear. This study assessed changes in bone-turnover markers, osteoprotegerin (OPG), soluble receptor activator for nuclear factor-κβ ligand (sRANKL), and inflammation in subjects initiating TDF- versus non-TDF- containing regimens, and determined the relationship between bone turnover, OPG/sRANKL and inflammation. Methods This was a longitudinal observational study comparing levels of bone turnover markers (C- terminal telopeptide of type I collagen [CTX] and osteocalcin [OC]), OPG, sRANKL and inflammatory cytokines (soluble tumour necrosis factor [TNF]-α receptor [sTNFR]-I, sTNFR-II and interleukin-6) prior to ART and 6-12 months after ART initiation with a TDF- versus non-TDF-containing regimen in HIV-infected subjects 18-50 years old. Results A total of 87 subjects were enrolled (TDF n=44 and non-TDF n=43). Groups were similar except subjects on TDF had a lower CD4+ T-cell nadir (P<0.01) and were more likely to receive a protease inhibitor (PI; P=0.03). At pre-ART, 35% and 1% of subjects had CTX and OC above the normal range, respectively. Both increased with ART initiation, whereas OPG, sRANKL and inflammatory markers significantly decreased. In multivariate models, increases in OC were associated with TDF use, PI use and pre-ART levels of sTNFR-I, whereas increases in CTX were associated with CD4+ T-cell nadir <50 cell/mm3. Increases in bone markers were unrelated to pre-ART levels of OPG/sRANKL and changes in OPG/sRANKL after ART initiation. Conclusions TDF use, PI use, TNF-α activity and advanced HIV disease are associated with changes in bone turnover markers, underscoring the complicated interaction between ART, bone turnover, inflammation and immune status, which extend beyond the OPG/RANKL system.
Pulling tethers from pore-spanning bilayers: towards simultaneous determination of local bending modulus and lateral tension of membranes.

Membrane mechanics play a pivotal role in many cellular processes, such as endocytosis, exocytosis comprising the budding–fission–fusion chain of events, cell migration, and cell division. [1] A fundamental understanding of these intricate processes that involve bending deformation, shearing, and area dilatation of the plasma membrane requires detailed knowledge of mechanical parameters on various length scales ranging from the dimension of the entire cell (5–20 μm) to the mesh size of the underlying cytoskeleton (30–300 nm). However, the complicated and intrinsically heterogeneous composition of native plasma membranes that may consist of thousands of different lipids, steroids, and proteins as well as the attachment of the lipid bilayer to the underlying cytoskeleton render the accurate determination of elastic constants a difficult task. Therefore, tailored giant liposomes that allow for the control of membrane composition have been frequently used as model systems to measure mechanical parameters of lipid bilayers, such as area compressibility and bending moduli. Because lipid bilayers are extremely flexible, the bending rigidity measurements are frequently inferred indirectly from bilayer fluctuations using optical microscopy. [2] The measurements either utilize the dependence of thermally excited membrane undulations on membrane rigidity or determine directly the force needed to deform a lipid bilayer concomitant to its shape. The former approach is realized by directly observing the fluctuations through flicker spectroscopy using optical microscopy and suppressing fluctuations in the low-tension regime of a micropipette suction experiment. [2b–d] The latter—a direct determination of the bending rigidity—might be achieved by estimating the force needed to pull highly curved nanotubes (tethers) out of membranes. [1j,2a,2e,3] Formation of membrane-tethers requires work against bending and against the creation of new surface producing a constant force to further elongate the nanotube (F ≈ √ σκ ). [2f,3b] Separation of surface tension σ and bending modulus κ requires sophisticated experiments, as recently accomplished by Cuvelier et al. using a combination of micropipette manipulation and optical tweezers techniques. [2e]
Pentapeptide‐rich peptidoglycan at the Bacillus subtilis cell‐division site

Peptidoglycan (PG), the major component of the bacterial cell wall, is one large macromolecule. To allow for the different curvatures of PG at cell poles and division sites, there must be local differences in PG architecture and eventually also chemistry. Here we report such local differences in the Gram‐positive rod‐shaped model organism Bacillus subtilis. Single‐cell analysis after antibiotic treatment and labeling of the cell wall with a fluorescent analogue of vancomycin or the fluorescent D‐amino acid analogue (FDAA) HCC‐amino‐D‐alanine revealed that PG at the septum contains muropeptides with unprocessed stem peptides (pentapeptides). Whereas these pentapeptides are normally shortened after incorporation into PG, this activity is reduced at division sites indicating either a lower local degree of PG crosslinking or a difference in PG composition, which could be a topological marker for other proteins. The pentapeptides remain partially unprocessed after division when they form the new pole of a cell. The accumulation of unprocessed PG at the division site is not caused by the activity of the cell division specific penicillin‐binding protein 2B. To our knowledge, this is the first indication of local differences in the chemical composition of PG in Gram‐positive bacteria.
Genetic analyses of live-animal ultrasound and abattoir carcass traits in Australian Angus and Hereford cattle.

In order to estimate genetic parameters, abattoir carcass data on 1,713 Angus and 1,007 Hereford steers and heifers were combined with yearling live-animal ultrasound measurements on 8,196 Angus and 3,405 Hereford individuals from seedstock herds. Abattoir measures included carcass weight (CWT), percentage of retail beefyield (RBY), near-infrared measured intramuscular fat percentage (CIMF), preslaughter scanned eye muscle area (CEMA), and subcutaneous fat depth at the 12th rib (CRIB) and at the P8 site (CP8). Ultrasound scans on yearling animals included 12th-rib fat depth (SRIB), rump fat depth at the P8 site (SP8), eye muscle area (SEMA), and percentage of intramuscular fat (SIMF). Records on CWT were adjusted to 650-d slaughter age, and the remaining abattoir traits were adjusted to 300-kg CWT. Scan data were analyzed treating records on males and females as different traits. Multivariate analyses were performed on a variety of trait combinations using animal model and REML algorithm. Heritability (h2) estimates for CWT, RBY, CIMF, CP8, CRIB, and CEMA were . 31, . 68, . 43, . 44, . 28, and . 26, respectively, for Angus and . 54, . 36, . 36, . 08, . 27, . 38, respectively, for Hereford. Pooled across sexes, h2 estimates for SIMF, SP8, SRIB, and SEMA were . 33, . 55, . 51, and . 42, respectively, for Angus and . 20, . 31, . 18, and . 38, respectively, for Hereford. Genetic correlations (r(g)) between the same pair of carcass traits measured at yearling through scanning and directly at the abattoir were moderate to strongly positive, suggesting that selection using yearling ultrasound measurements of seedstock cattle should result in predictable genetic improvement for abattoir carcass characteristics. Estimates of r(g) between the scanned fat measurements and RBY were negative, ranging from -. 85 for Angus heifers to -. 05 for Hereford heifers. Also, the estimates of r(g) between SEMA and the fat records measured at the abattoir were negative and ranged from -. 94 in Hereford heifers to -. 02 in Angus heifers.
NAO signal recorded in the stable isotopes of Greenland ice cores

The winter δ18O signal is extracted from 7 Greenland ice cores covering the past ∼700 years. To filter out noise and local variations in the 7 isotope records a principal component analysis is carried out on the ice core data. A comparison between the time series of the first principal component (PC1) with 67 years of winter (December to March) temperature measurements from 3 southern Greenland synoptic stations shows highly significant correlations. Southern Greenland winter temperatures are known to be greatly influenced by the North Atlantic Oscillation (NAO). A good proxy for southern Greenland temperatures is therefore expected to reveal at least parts of the NAO signal. It is shown that the PC1 time series indeed is significantly correlated to the NAO during the winter months. The inclusion of ice core winter season δ18O time series in future multiproxy NAO reconstructions is therefore recommended.
Trends in resistance to penicillin and erythromycin of invasive pneumococci in Portugal

SUMMARY Antimicrobial resistance of pneumococci is influenced by serotypes, antimicrobial consumption and vaccine use. Serotyping of 697 out of 1331 pneumococcal isolates, recovered in Portugal from 1994 to 2004, showed that the theoretical rate of heptavalent conjugate vaccine coverage was 91·7% and 63·6% for penicillin and erythromycin non-susceptible strains, respectively, in children up to 1 year old. The use of amoxicillin and erythromycin decreased in the vaccine period 2001–2004 (P=0·04 and P<0·01, respectively) but azithromycin usage increased in the same period (P<0·01). By using linear regression models, we evaluated the role of antimicrobial and vaccine use in the trends of resistance to penicillin and erythromycin among the isolates. The models suggest that the use of macrolides was the main factor associated with an increase of penicillin and erythromycin non-susceptible isolates from adults (P<0·01) and erythromycin non-susceptible isolates among children (P=0·006). These models also suggest that heptavalent vaccine is failing to reduce antimicrobial resistance as expected, possibly due to the increased consumption of azithromycin (P=0·04). The efficient use of new antibiotics may reverse the present trends of antimicrobial resistance.
Employee Compensation: Theory, Practice, and Evidence

SummaryReinforcement, expectancy, and agency theories all focus on the fact thatbehavior -reward contingencies can shape behaviors. However, agency theory is ofparticular value in studying variable pay because of its emphasis on the risk -rewardtrade -off, an issue that needs close attention when considering variable pay plans, which cancarry significant risk. Equity theory is also very relevant because it can be applied to just aboutany pay decision, because fairness is always a key concern.Moving away from individual -level theories, life cycle and diversification -basedcontingency theories suggest that pay strategies should fit with corporate strategies. Theevolving empirical literature provides tentative support for many of the specific propositions.PAY PROGRAMSTable 2 summarizes the key features of some of the most widely used pay programs.Key dimensions include the payment method (whether increases roll into base salary or arepaid as bonuses or equity), the frequency of payouts, the nature of the performance measure,and who is typically covered under the different plans.Table 2. Comparison of Different Pay Programs
Leishmania infantum LeIF protein is an ATP‐dependent RNA helicase and an eIF4A‐like factor that inhibits translation in yeast

LeIF, a Leishmania protein similar to the eukaryotic initiation factor eIF4A, which is a prototype of the DEAD box protein family, was originally described as a Th1‐type natural adjuvant and as an antigen that induces an IL12‐mediated Th1 response in the peripheral blood mononuclear cells of leishmaniasis patients. This study aims to characterize this protein by comparative biochemical and genetic analysis with eIF4A in order to assess its potential as a target for drug development. We show that a His‐tagged, recombinant, LeIF protein of Leishmania infantum, which was purified from Escherichia coli, is both an RNA‐dependent ATPase and an ATP‐dependent RNA helicase in vitro, as described previously for other members of the DEAD box helicase protein family. In vivo experiments show that the LeIF gene cannot complement the deletion of the essential TIF1 and TIF2 genes in the yeast Saccharomyces cerevisiae that encode eIF4A. In contrast, expression of LeIF inhibits yeast growth when endogenous eIF4A is expressed off only one of its two encoding genes. Furthermore, in vitro binding assays show that LeIF interacts with yeast eIF4G. These results show an unproductive interaction of LeIF with translation initiation factors in yeast. Furthermore, the 25 amino terminal residues were shown to enhance the ability of LeIF to interfere with the translation machinery in yeast.
Caspofungin versus liposomal amphotericin B for empirical antifungal therapy in patients with persistent fever and neutropenia.

BACKGROUND Patients with persistent fever and neutropenia often receive empirical therapy with conventional or liposomal amphotericin B for the prevention and early treatment of invasive fungal infections. Caspofungin, a member of the new echinocandin class of compounds, may be an effective alternative that is better tolerated than amphotericin B. METHODS In this randomized, double-blind, multinational trial, we assessed the efficacy and safety of caspofungin as compared with liposomal amphotericin B as empirical antifungal therapy. At study entry, patients were stratified according to risk and according to whether they had previously received antifungal prophylaxis. A successful outcome was defined as the fulfillment of all components of a five-part composite end point. RESULTS Efficacy was evaluated in 1095 patients (556 receiving caspofungin and 539 receiving liposomal amphotericin B). After adjustment for strata, the overall success rates were 33.9 percent for caspofungin and 33.7 percent for liposomal amphotericin B (95.2 percent confidence interval for the difference, -5.6 to 6.0 percent), fulfilling statistical criteria for the noninferiority of caspofungin. Among patients with baseline fungal infections, a higher proportion of those treated with caspofungin had a successful outcome (51.9 percent vs. 25.9 percent, P=0.04). The proportion of patients who survived at least seven days after therapy was greater in the caspofungin group (92.6 percent vs. 89.2 percent, P=0.05). Premature study discontinuation occurred less often in the caspofungin group than in the amphotericin B group (10.3 percent vs. 14.5 percent, P=0.03). The rates of breakthrough fungal infections and resolution of fever during neutropenia were similar in the two groups. Fewer patients who received caspofungin sustained a nephrotoxic effect (2.6 percent vs. 11.5 percent, P<0.001), an infusion-related event (35.1 percent vs. 51.6 percent, P<0.001), or a drug-related adverse event or discontinued therapy because of drug-related adverse events. CONCLUSIONS Caspofungin is as effective as and generally better tolerated than liposomal amphotericin B when given as empirical antifungal therapy in patients with persistent fever and neutropenia.
An LMI approach to H∞ filtering of uncertain systems

This paper studies the H∞ filtering problem of linear uncertain systems with polytopic uncertainties. By introducing some slack matrices and using the parameter-dependent Lyapunov function approaches, sufficient conditions for the existence of such filter are expressed in terms of linear matrix inequalities (LMIs). And, a convex analysis procedure is implemented to derive the filter gain matrices. Finally, a numerical example is presented to illustrate the theoretical developments.
Structuration genetique des populations de laminaria digitata (phaeophycees) en manche : utilisation de marqueurs hypervariables

Laminaria digitata, classe des pheophycees, ordre des laminariales, est une macroalgue brune commune en manche et en atlantique. Elle forme des populations importantes le long des cotes rocheuses, en mode semi-battu ou battu, au niveau de l'etage infra-littoral. Les laminariales se distinguent par un cycle de reproduction haplodiplophasique nettement heteromorphe (sporophytes macroscopiques ; gametophytes microscopiques). Le sporophyte, thalle d'environ 1,5 m de long, est recolte (environ 60. 000 t/an, principalement en manche) pour sa forte teneur en alginate. Ces deux caracteristiques (cycle de vie, recolte), ainsi que la continuite de ses peuplements, font de cette espece un bon modele d'etude de la diversite genetique en milieu marin. Des marqueurs microsatellites, rares chez cette espece, ont ete identifies chez l. Digitata afin d'etudier son regime de reproduction ainsi que la structuration de ses populations en manche. Les individus presentent un apparentement a l'echelle du metre, provenant de la faible dispersion des gametes males. L'effectif efficace des peuplements continus est estime a 16 000 individus, soit environ un km de long. Il semble que l'allofecondation y soit la regle, signe de la dispersion des spores. La differenciation entre populations se fait selon le modele d'isolement par la distance et reflete assez bien les courants en manche, ainsi que les effets des substrats sur la structure du peuplement. Cette etude est la premiere de cette ampleur (nombre d'individus et nombre de locus) chez des especes a peuplement continu et en particulier, chez les algues. Elle a permis de mettre en evidence deux systemes de dispersion : les gametes d'une part et d'autre part les spores ou l'arrachage de fragments de thalles fertiles. De plus, elle a permis de detecter des isolements liees aux courants dans un milieu considere comme a priori homogene.
A Data-Driven, Cooperative Approach for Wind Farm Control: A Wind Tunnel Experimentation

This paper discusses a data-driven, cooperative control strategy to maximize wind farm power production. Conventionally, every wind turbine in a wind farm is operated to maximize its own power production without taking into account the interactions between the wind turbines in a wind farm. Because of wake interference, such greedy control strategy can significantly lower the power production of the downstream wind turbines and, thus, reduce the overall wind farm power production. As an alternative to the greedy control strategy, we study a cooperative wind farm control strategy that determines and executes the optimum coordinated control actions for maximizing the total wind farm power production. To determine the optimum coordinated control actions of the wind turbines, we employ a data-driven optimization method that seeks to find the optimum control actions using only the power measurement data collected from the wind turbines in a wind farm. In particular, we employ the Bayesian Ascent (BA) algorithm, a probabilistic optimization method constructed based on Gaussian Process regression and the trust region concept. Wind tunnel experiments using 6 scaled wind turbine models are conducted to assess (1) the effectiveness of the cooperative control strategy in improving the power production; and (2) the efficiency of the BA algorithm in determining the optimum control actions of the wind turbines using only the input control actions and the output power measurement data.
Modified ELISPOT assay may predict T‐cell hyporesponsiveness to non‐inherited maternal antigens

Clinical reports have suggested the existence of immunological tolerance to noninherited maternal antigens (NIMA) in human leukocyte antigen (HLA) mismatched allogeneic stem cell transplantation (allo‐SCT). We studied the T‐cell reactivity using IFN‐γ enzyme‐linked immunospot (ELISPOT) assay in three HLA fully matched allo‐SCT cases and one healthy volunteer family case. In HLA fully matched allo‐SCT cases, ELISPOT assay could detect the hyporesponsiveness of T cells from donors to the B cells from recipients. Moreover, ELISPOT assay showed that the T cells from an individual responded to B cell from his mother significantly weakly than those from an unrelated HLA‐haploidentical individual. These observations suggest that our IFN‐γ ELISPOT assay‐based method may predict the presence of immunological tolerance to NIMA.
A nucleolar AAA‐NTPase is required for parasite division

Apicomplexa division involves several distinct phases shared with other eukaryote cell cycles including a gap period (G1) prior to chromosome synthesis, although how progression through the parasite cell cycle is controlled is not understood. Here we describe a cell cycle mutant that reversibly arrests in the G1 phase. The defect in this mutant was mapped by genetic complementation to a gene encoding a novel AAA‐ATPase/CDC48 family member called TgNoAP1. TgNoAP1 is tightly regulated and expressed in the nucleolus during the G1/S phases. A tyrosine to a cysteine change upstream of the second AAA+ domain in the temperature sensitive TgNoAP1 allele leads to conditional protein instability, which is responsible for rapid cell cycle arrest and a primary defect in 28S rRNA processing as confirmed by knock‐in of the mutation back into the parent genome. The interaction of TgNoAP1 with factors of the snoRNP and R2TP complexes indicates this protein has a role in pre‐rRNA processing. This is a novel role for a cdc48‐related chaperone protein and indicates that TgNoAP1 may be part of a dynamic mechanism that senses the health of the parasite protein machinery at the initial steps of ribosome biogenesis and conveys that information to the parasite cell cycle checkpoint controls.
Resource and space use in the wild golden lion tamarin, Leontopithecus rosalia

Title of Document: RESOURCE AND SPACE USE IN THE WILD GOLDEN LION TAMARIN, LEONTOPITHECUS ROSALIA Sarah Eileen Johnson Hankerson, Doctor of Philosophy, 2008 Directed By: Dr. James M. Dietz, Professor Behavior, Ecology, Evolution, & Systematics Animals move through their environment in response to resource, competitor, and predator distribution. In this dissertation I examine resource and space use in wild golden lion tamarins (GLTs, Leontopithecus rosalia). In chapter one I present the results of a field study exploring factors predicting sleeping site selection. GLTs preferentially slept in tree holes. Each group had a few frequently used sites typically found in large, living trees on hillsides near other large trees. Topography and smallscale forest and tree variables were better than habitat-level classifications in predicting sleeping site use. In my second chapter I evaluated home range calculation methods. Using 19 years of data for 15 groups of GLTs, I calculated a yearly home range for each group with the three most commonly used methods: minimum convex polygon (MCP), grid cell, and kernel density estimates. MCP produced the largest home range estimates, grid cell the smallest, and kernel estimates were intermediary. Kernel estimates were preferred because probability of use may be calculated for any part of the home range, there is high concordance between observation spatial distribution and home range shape, and there is a lack of relationship between sample size and home range size. In my third chapter I tested three hypotheses explaining home range size in group-dwelling animals. First, I tested the dominant hypothesis, which states that home range size is determined by group energetic needs and, therefore, group size. The second and third hypotheses relate to numbers of adult females and males present in groups. More adults may increase ranging because of increased reproduction, search for breeding opportunities, or defense. I also examined how variation in predation affects population density and demography and, thus, mediates space use. I found support for all three hypotheses. Larger ranges were occupied by groups that were large, had two breeding females, and/or more potentially breeding males or adult natal males. Intense predation resulted in lower population densities, smaller groups, only one breeding female per group, and fewer adult natal males. Population density and predation had significant, negative impacts on home range size. RESOURCE AND SPACE USE IN THE WILD GOLDEN LION TAMARIN, LEONTOPITHECUS ROSALIA