Miracle-dz/UniFAR-FTUs huggingface dataset:
Adaptations in myosin heavy chain profile in chronically unloaded muscles.

In this review, myosin heavy chain (MHC) adaptations in response to several models of decreased neuromuscular activity (i.e. electrical activation and loading of a muscle) are evaluated. In each of these "reduced-activity" models it is important to: a) quantify the changes in electrical activation of the muscle as a result of the intervention; b) quantify the forces generated by the muscle; and c) determine whether the neuromuscular junction remains normal. Most of the models, including spaceflight, hindlimb suspension, spinal cord isolation, spinal cord transection, denervation, and limb immobilization in a shortened position, result in increases in the percentage of fast MHCs (or fast MHC mRNA) in normally slow rat muscles. It also can be inferred from histochemical data that increases in fast MHCs occur with TTX application and bed rest. The only "reduced-activity" model to consistently increase slow muscle myosin mRNA, and slow fibers is limb immobilization in a stretched position; however, this model results in at least a temporary increase in tension. It appears that the most common feature of these models that might induce MHC adaptations is the modification in loading rather than a change in the neuromuscular activity.
Ontological Anti-Realism

The basic question of ontology is “What exists? ”. The basic question of metaontology is: are there objective answers to the basic question of ontology? Here ontological realists say yes, and ontological anti-realists say no. (Compare: The basic question of ethics is “What is right? ”. The basic question of metaethics is: are there objective answers to the basic question of ethics? Here moral realists say yes, and moral anti-realists say no.) For example, the ontologist may ask: Do numbers exist? The Platonist says yes, and the nominalist says no. The metaontologist may ask: is there an objective fact of the matter about whether numbers exist? The ontological realist says yes, and the ontological anti-realist says no. Likewise, the ontologist may ask: Given two distinct entities, when does a mereological sum of those entities exist? The universalist says always, while the nihilist says never. The metaontologist may ask: is there an objective fact of the matter about whether the mereological sum of two distinct entities exists? The ontological realist says yes, and the ontological anti-realist says no. Ontological realism is often traced to Quine (1948), who held that we can determine what exists by seeing which entities are endorsed by our best scientific theory of the world. In recent years, the practice of ontology has often presupposed an ever-stronger ontological realism, and strong versions of ontological realism have received explicit statements by Fine (this volume), Sider (2001; this volume), van Inwagen (1998; this volume), and others. Ontological anti-realism is often traced to Carnap (1950), who held that there are many different ontological frameworks, holding that different sorts of entities exist, and that while some INPCers: For a 30-page version, the most important sections to read are probably 1, 2, and 5-10. For those who have read the version of this paper posted in early January, the current version (early February) has only minor changes from that version.
Ultrafast Carrier Dynamics in p-doped InGaAs Quantum Dot Amplifiers

In this paper , we measure the ultrafast gain and index dynamics of the QD ground state transition in p-doped electrically-pumped InGaAs QD optical amplifiers emitting near 1.3 mum at room temperature. A pump-probe differential transmission technique in heterodyne detection with sub-picosecond time resolution was used. The refractive index dynamics also showed noticeable differences between p-doped and undoped samples. From these data a transient and time-integrated linewidth enhancement factor has been deduced.
Aggregating time partitions

Partitions of sequential data exist either per se or as a result of sequence segmentation algorithms. It is often the case that the same timeline is partitioned in many different ways. For example, different segmentation algorithms produce different partitions of the same underlying data points. In such cases, we are interested in producing an aggregate partition, i.e., a segmentation that agrees as much as possible with the input segmentations. Each partition is defined as a set of continuous non-overlapping segments of the timeline. We show that this problem can be solved optimally in polynomial time using dynamic programming. We also propose faster greedy heuristics that work well in practice. We experiment with our algorithms and we demonstrate their utility in clustering the behavior of mobile-phone users and combining the results of different segmentation algorithms on genomic sequences.
Semi-empirical model of the ensemble-averaged differential Mueller matrix for microwave backscattering from bare soil surfaces

A semi-empirical model of the ensemble-averaged differential Mueller matrix for microwave backscattering from bare soil surfaces is presented. Based on existing scattering models and data sets measured by polarimetric scatterometers and the JPL AirSAR, the parameters of the co-polarized phase-difference probability density function, namely the degree of correlation /spl alpha/ and the co-polarized phase-difference /spl sigmav/, in addition to the backscattering coefficients /spl sigma//sub /spl nu//spl nu///sup 0/,/spl sigma//sub hh//sup 0/ and /spl sigma//sub /spl nu/h//sup 0/, are modeled empirically in terms of the volumetric soil moisture content m/sub /spl nu// and the surface roughness parameters ks and kl, where k=2/spl pi/f/c, s is the rms height and l is the correlation length. Consequently, the ensemble-averaged differential Mueller matrix (or the differential Stokes scattering operator) is specified completely by /spl sigma//sub /spl nu//spl nu///sup 0/,/spl sigma//sub hh//sup 0/,/spl sigma//sub /spl nu/h//sup 0/,/spl alpha/, and /spl zeta/.
Personality in Adults Who Were Born Very Preterm

Aim To investigate the personality in very preterm individuals (VPT; gestational age, GA, <32 weeks) at adult age in two cohorts born in 1974–76 and 1980–82, respectively, and to illuminate the effect of increased survival rates and the clinical implications of deviations in personality. Method Demographic data were extracted for all individuals born in Denmark in 1974–76 and 1980–82. From each period one index-group each comprising 150 individuals with the lowest gestational age was selected. Thereafter two control groups born at term were matched by gender, age and residential area. Personality was assessed with the short version of NEO PI-R, and psychiatric diagnoses were obtained from the Danish Psychiatric Central Research Register. Results Of all the individuals born <32 weeks of gestation in 1980–82 67% were alive in 2006 vs. 43% of those born in 1974–76 (p<0.0001). A total of 433 individuals participated in the study, 76% of the VPT groups (n = 227, mean GA = 27.9) and 69% of the control groups (n = 206). There were no significant differences on personality scores between the two VPT groups. Compared to the control groups, the combined VPT groups scored higher on neuroticism (p = 0.005) and agreeableness (p = 0.012), but lower on extraversion (p = 0.002). Psychiatric disorder was strongly associated with higher scores on neuroticism and lower scores on extraversion. Interpretation Improved survival of VPT infants was not associated with increased deviances in the personality as adults. The personality traits in VPT individuals differ moderately from those of term born controls. High scores in neuroticism and low scores in extraversion were associated with increased risk psychiatric disorders. VPT adults also showed signs of positive adaptation in the form of an agreeable and confident attitude towards others. What this paper adds The much improved survival rate in very preterm infants during the early years of active neonatology was not associated with increased risk of personality deviation. There are signs of positive adaptation in the form of increased agreeableness in young adults born very preterm.
Construction of a physical map of the chromosome of Shigella flexneri 2a and the direct assignment of nine virulence‐associated loci identified by Tn5 insertions

To establish the molecular basis of the chromosomal virulence genes of Shigella flexneri 2a (YSH6000), a Notl restriction map of the chromosome was constructed by exploiting Notl‐linking clones, partial Notl digestion and DNA probes from various genes of Escherichia coli K‐12. The map revealed at least three local differences in the placements of genes between YSH6000 and E. coli K‐12. Using the additional Notl sites introduced by Tn5 insertion, nine virulence loci Identified previously by random Tn5 insertions were physically mapped on the chromosome. To demonstrate the versatility of the Notl map in direct assignment of the virulence loci tagged by Tn5 to a known genetic region in E. coli K‐12, the major class of avirulent mutants defective in the core structure of lipopolysaccharide (LPS) was examined for the sites of Tn5 insertions. The two Notl segments created by the Tn5 insertion in the Notl fragment were analysed by Southern blotting with two DNA probes for the 5′ and 3’flanking regions of the rfa region, and shown to hybridize separately with each of them, confirming the sites of Tn5 in the rfa locus. This approach will facilitate direct comparison of genetically mapped Tn5 insertion mutations of S. flexneri with genes physically determined in E. coli K‐12.
High Sensitivity of SIRT3 Deficient Hearts to Ischemia-Reperfusion Is Associated with Mitochondrial Abnormalities

Aim: Sirtuins are NAD+-dependent deacetylases that regulate cell metabolism through protein acetylation/deacetylation, and SIRT3 is the major deacetylase among mitochondrial isoforms. Here, we elucidated the possible role of acetylation of cyclophilin D, a key regulator of the mitochondrial permeability transition pore (mPTP), in mitochondria-mediated cardiac dysfunction induced by ischemia-reperfusion (IR) in wild type (WT) and SIRT3 knockout (SIRT3-/-) mice. Materials and Methods: Isolated and Langendorff-mode perfused hearts of WT and SIRT3-/- mice were subjected to 25-min global ischemia followed by 60-min of reperfusion in the presence or absence of the mPTP inhibitor, sanglifehrin A (SfA). Results: Analysis of mitochondrial sirtuins demonstrated that SIRT3 deficiency upregulated SIRT4 with no effect on SIRT5 expression. Hearts of SIRT3-/- mice exhibited significantly less recovery of cardiac function at the end of IR compared to WT mice. Intact (non-perfused) SIRT3-/- hearts exhibited an increased rate of Ca2+-induced swelling in mitochondria as an indicator of mPTP opening. However, there was no difference in mPTP opening and cyclophilin D acetylation between WT and SIRT3-/- hearts subjected to IR injury. Ca2+-stimulated H2O2 production was significantly higher in SIRT3-/- mitochondria that was prevented by SfA. Superoxide dismutase activity was lower in SIRT3-/- heart mitochondria subjected to IR which correlated with an increase in protein carbonylation. However, mitochondrial DNA integrity was not affected in SIRT3-/- hearts after IR. Conclusion: SIRT3 deficiency exacerbates cardiac dysfunction during post-ischemic recovery, and increases mPTP opening and ROS generation without oxidative damage to mitochondrial proteins and DNA.
Serum-Derived Plasminogen Is Activated by Apoptotic Cells and Promotes Their Phagocytic Clearance

The elimination of apoptotic cells, called efferocytosis, is fundamentally important for tissue homeostasis and prevents the onset of inflammation and autoimmunity. Serum proteins are known to assist in this complex process. In the current study, we performed a multistep chromatographic fractionation of human serum and identified plasminogen, a protein involved in fibrinolysis, wound healing, and tissue remodeling, as a novel serum-derived factor promoting apoptotic cell removal. Even at levels significantly lower than its serum concentration, purified plasminogen strongly enhanced apoptotic prey cell internalization by macrophages. Plasminogen acted mainly on prey cells, whereas on macrophages no enhancement of the engulfment process was observed. We further demonstrate that the efferocytosis-promoting activity essentially required the proteolytic activation of plasminogen and was completely abrogated by the urokinase plasminogen activator inhibitor-1 and serine protease inhibitor aprotinin. Thus, our study assigns a new function to plasminogen and plasmin in apoptotic cell clearance.
Effect of iron supplementation on mild to moderate anaemia in pulmonary tuberculosis

Anaemia is a common complication of pulmonary tuberculosis. The precise mechanism of anaemia in pulmonary tuberculosis is not clearly known, but anaemia of inflammation as well as of Fe deficiency has been implicated. Both are common in developing countries. It is extremely difficult to distinguish anaemia of Fe deficiency from anaemia of inflammation with the haematological indices used routinely. Therefore, Fe preparations are usually prescribed for all anaemic patients irrespective of the aetiology. This approach has been questioned. The present study aimed to assess the effect of Fe supplementation on anaemic patients with pulmonary tuberculosis. Adult male patients 15–60 years of age with pulmonary tuberculosis and a blood haemoglobin concentration 80–110 g/l were included in the study; healthy adult males matched for age and socio-economic status were taken as controls. Blood haemoglobin concentration, total erythrocyte count (TEC), packed cell volume (PCV), mean corpuscular volume (MCV), mean corpuscular haemoglobin and serum Fe, total Fe-binding capacity and ferritin were estimated before treatment and 1, 2 and 6 months after treatment. The patients were divided randomly into three groups and during the initial 2 months of treatment were provided with one of three supplementary regimens consisting of placebo, Fe alone or Fe with other haematinics. Significant improvements in haematological indices and Fe status were noticed in all three groups. Blood haemoglobin concentration, MCV and PCV were significantly higher at 1 month in both Fe-supplemented groups than the placebo group. This difference, however, disappeared at 2 and 6 months with similar values in all three groups. The increase of other haematological indices was similar in all groups. Serum Fe and Fe saturation of transferrin were significantly higher in both Fe-supplemented groups than the placebo group up to 2 months; this effect, however, disappeared at 6 months. There was a consistent increase in TEC and decrease in ferritin values up to 6 months in all groups. Radiological and clinical improvement was similar in all three groups. These observations suggest that Fe supplementation in mild to moderate anaemia associated with pulmonary tuberculosis accelerated the normal resumption of haematopoiesis in the initial phases by increasing Fe saturation of transferrin. However, consistent improvement of haematological status was dependent only on the improvement of the disease process.
Postfracture irradiation effects on the biomechanical and histologic parameters of fracture healing

The effects of single‐dose local irradiation on the biomechanical properties of closed femoral fractures were studied in 75 mature Sprague‐Dawley rats. Ten days after fracture, the rats were irradiated with 900 rads at 250 kV to the entire fractured femur. At 2, 3, 4, 8, and 16 weeks after fracture, both fractured and contralateral intact femurs were recovered and evaluated biomechanically by testing to failure in torsion. Results were compared with those from a similar study involving fractures irradiated 3 days after fracture as well as nonirradiated control fractures. Fracture healing progressed faster when irradiation was delayed 10 days than when delayed 3 days, and control fractures healed more rapidly than after either delay. In the 10‐day delay group, fractures showed greater strength than did those in the 3‐day delay group at 8 weeks, but the strength of irradiated fractures in both groups was similarly depressed at 16 weeks, with a maximum torque well below that of control fractures. These results suggest that delaying radiation exposure of a fracture may mitigate short‐term deleterious effects on fracture repair, but that long‐term results may be similar to those associated with expeditious irradiation.
Effects of post-weld heat treatment on microstructure and mechanical properties of friction stir welded joints of 2219-O aluminium alloy

Abstract Post-weld heat treatment (PWHT) of 2219-O aluminium alloy friction stir welding joints was carried out at solution temperatures of 480, 500 and 540°C for 32 min followed by aging at 130°C for 9 h. The effects of PWHT on the microstructure and mechanical properties of the joints were investigated. Experimental results show that PWHT causes coarsening of the grains in the weld, and the coarsening degree increases with increasing solution temperature. The tensile strength of the heat treated joints increases with increasing solution temperature. The maximum tensile strength can reach 260% that of the base material at the solution temperature of 540°C. PWHT has a significant effect on the fracture locations of the joints. When the solution temperature is lower than 500°C, the joints fracture in the base material; when the temperature is higher than 500°C, the joints fracture in the weld. The change of the fracture locations of joints is attributed to the presence of precipitate free zones beside the grain boundaries and coarsening equiaxed grain structures in the weld.
2 SEM and Causality : A Brief History of Unhappy Encounters

The role of causality in SEM research is widely perceived to be, on the one hand, of pivotal methodological importance and, on the other hand, confusing, enigmatic, and controversial. The confusion is vividly portrayed, for example, in the influential report of Wilkinson and Task Force (1999), on “Statistical Methods in Psychology Journals: Guidelines and Explanations. ” In discussing SEM, the report starts with the usual warning: “Correlation does not prove causation,” but then ends with a startling conclusion: “The use of complicated causal-modeling software [read SEM] rarely yields any results that have any interpretation as causal effects. ” The implication being that the entire enterprise of causal modeling, from Sewell Wright (1921) to Blalock (1964) and Duncan (1975), the entire literature in econometric research, including modern advances in graphical and nonparametric structural models, has been misguided, for researchers have been chasing parameters that have no causal interpretation. The motives for such overstatements notwithstanding, readers may rightly ask: “If SEM methods do not ‘prove’ causation, how can they yield results that have causal interpretation? ” Put another way, if the structural coefficients that SEM researchers labor to estimate can legitimately be interpreted as causal effects, then, unless these parameters are grossly misestimated, why deny SEM researchers the honor of “establishing causation” or at least of deriving some useful claims about causation? The answer is that a huge logical gap exists between “establishing causation,” which requires careful manipulative experiments, and “interpreting parameters as causal effects,” which may be based on firm scientific knowledge or on previously conducted experiments, perhaps by other researchers. One can legitimately be in possession of a parameter that stands for a causal effect and still be unable, using statistical means alone, to determine the magnitude of that parameter given nonexperimental data. As a matter of fact, we know that no such statistical means exists; that is, causal effects in observational studies can only be
The gamma and epsilon subunits of the CD3 complex inhibit pre-Golgi degradation of newly synthesized T cell antigen receptors

The T cell receptor for antigen (TCR) is composed of six different transmembrane proteins. T cells carefully control the intracellular transport of the receptor and allow only complete receptors to reach the plasma membrane. In an attempt to understand how T cells regulate this process, we used c-DNA transfection and subunit-specific antibodies to follow the intracellular transport of five subunits (alpha beta gamma delta epsilon) of the receptor. In particular, we assessed the intracellular stability of each chain. Our results showed that the chains were markedly different in their susceptibility to intracellular degradation. TCR alpha and beta and CD3 delta were degraded rapidly, whereas CD3 gamma and epsilon were stable. An analysis of the N-linked oligosaccharides of the glycoprotein subunits suggested that the chains were unable to reach the medial Golgi during the metabolic chase. This was supported by immunofluorescence micrographs that showed both the stable CD3 gamma and unstable CD3 delta chain localized in the endoplasmic reticulum. To study the effects of subunit associations on intracellular transport we used cotransfection to reconstitute precise combinations of subunits. Associations between stable and unstable subunits expressed in the same cell led to the formation of stable complexes. These complexes were retained in or close to the endoplasmic reticulum. The results suggested that the intracellular transport of the T cell receptor could be regulated by two mechanisms. The TCR alpha and beta and CD3 delta subunits were degraded rapidly and as a consequence failed to reach the plasma membrane. CD3 gamma or epsilon were stable but were retained inside the cell. The results also demonstrated that there was an interplay between the two pathways such that the CD3 gamma and epsilon subunits were able to protect labile chains from rapid intracellular degradation. In this way, they could seed subunit assembly in or close to the endoplasmic reticulum and allow a stable receptor to form before its transport to the plasma membrane.