Miracle-dz/UniFAR-FTUs huggingface dataset:
Oxidative Stress Mediates Physiological Costs of Begging in Magpie (Pica pica) Nestlings

Background Theoretical models predict that a cost is necessary to guarantee honesty in begging displays given by offspring to solicit food from their parents. There is evidence for begging costs in the form of a reduced growth rate and immunocompetence. Moreover, begging implies vigorous physical activity and attentiveness, which should increase metabolism and thus the releasing of pro-oxidant substances. Consequently, we predict that soliciting offspring incur a cost in terms of oxidative stress, and growth rate and immune response (processes that generate pro-oxidants substances) are reduced in order to maintain oxidative balance. Methodology/Principal Findings We test whether magpie (Pica pica) nestlings incur a cost in terms of oxidative stress when experimentally forced to beg intensively, and whether oxidative balance is maintained by reducing growth rate and immune response. Our results show that begging provokes oxidative stress, and that nestlings begging for longer bouts reduce growth and immune response, thereby maintaining their oxidative status. Conclusions/Significance These findings help explaining the physiological link between begging and its associated growth and immunocompetence costs, which seems to be mediated by oxidative stress. Our study is a unique example of the complex relationships between the intensity of a communicative display (begging), oxidative stress, and life-history traits directly linked to viability.
Investigation into Waste Tire Rubber-Filled Concrete

Over the years, there has been mounting interest in the use of recycled tire rubbers in highway construction. Tire rubber-filled concrete, a rubberized Portland cement concrete with a portion of aggregates replaced by tire rubber particles, represents an alternative of using recycled tire rubbers. It is found that rubberized concrete has very high toughness. However, its strength decreases significantly as the rubber content increases. This limits its application to secondary structural components only. Very little progress has been made in increasing the strength of rubberized concrete due to the lack of understanding of the toughing mechanism. In this study, rubberized concrete was treated as a multiphase particulate-filled composite material. A modified three-layer built-in composite model was proposed based on a previous study on ordinary concrete. Finite element analysis was conducted on the developed composite model. Cylindrical rubberized concrete samples and ordinary concrete samples were prepared and tested to provide basic physical/mechanical properties in the analysis. The effect of various design parameters on the composite strength was evaluated. The finite element analysis validated the test results.
Detection of 6 K gas in Ophiuchus D

Context. Cold cores in interstellar molecular clouds represent the very first phase in star formation. The physical conditions of these objects are studied in order to understand how molecular clouds evolve and how stellar masses are determined. Aims. The purpose of this study is to probe conditions in the dense, starless clump Ophichus D (Oph D). Methods. The ground-state (110 → 111) rotational transition of ortho-H2D + was observed with APEX towards the density peak of Oph D. Results. The width of the H2D + line indicates that the kinetic temperature in the core is about 6 K. So far, this is the most direct evidence of such cold gas in molecular clouds. The observed H2D + spectrum can be reproduced with a hydrostatic model with the temperature increasing from about 6 K in the centre to almost 10 K at the surface. The model is unstable against any increase in the external pressure, and the core is likely to form a low-mass star. Conclusions. The results suggest that an equilibrium configuration is a feasible intermediate stage of star formation even if the larger scale structure of the cloud is thought to be determined by turbulent fragmentation. In comparison with the isothermal case, the inward decrease in the temperature makes smaller, i.e. less massive, cores susceptible to externally triggered collapse.
The genetic contribution to severe post-traumatic osteoarthritis

Objective to compare the combined role of genetic variants loci associated with risk of knee or hip osteoarthritis (OA) in post-traumatic (PT) and non-traumatic (NT) cases of clinically severe OA leading to total joint replacement. Methods A total of 1590 controls, 2168 total knee replacement (TKR) cases (33.2% PT) and 1567 total hip replacement (THR) cases (8.7% PT) from 2 UK cohorts were genotyped for 12 variants previously reported to be reproducibly associated with risk of knee or hip OA. A genetic risk score was generated and the association with PT and NT TKR and THR was assessed adjusting for covariates. Results For THR, each additional genetic risk variant conferred lower risk among PT cases (OR=1.07, 95% CI 0.96 to 1.19; p=0.24) than NT cases (OR 1.11, 95% CI 1.06 to 1.17; p=1.55×10−5). In contrast, for TKR, each risk variant conferred slightly higher risk among PT cases (OR 1.12, 95% CI 1.07 to 1.19; p=1.82×10−5) than among NT cases (OR 1.08, 95% CI 1.03 to 1.1; p=0.00063). Conclusions Based on the variants reported to date PT TKR cases have at least as high a genetic contribution as NT cases.
Application of pattern reversal visual evoked potentials (PVEPS) in transient monocular blindness (resp. amaurosis fugax).

UNLABELLED We investigated 11 patients (63.1 +/- 10.9 y) after recovery (median: 3 days) from amaurosis fugax of 12.1 +/- 12.0 min duration with the method of pattern reversal visual evoked potentials (PVEPs) derived from Oz to Fz (Cz ground) after randomized monocular stimulation. SELECTION CRITERIA clear-cut cases with no hemispheric symptomatology, normal vision and normal cranial CT. The parameters were measured without knowing the affected eye and compared with age matched controls (n = 32). N80 latencies of the affected eyes were significantly prolonged (3.2 +/- 1.9 ms; p < .025) in comparison with the not affected eyes. The controls did not show such interocular difference. P100 latency behaved similarly but less prominently so (2.0 +/- 2.3 ms; p < .05; controls: p > .05). N80/P100 amplitude was reduced in 82% after stimulation of the affected side without reaching statistical significance. The 5 patients showing angiographically ipsilateral very tight stenosis of carotid artery (> 95%) behaved more prominently so in all 3 parameters. The findings indicate a damage of nerval tissue responsible for visual perception or a hemodynamic insufficiency under stimulus condition in affected eyes outlasting the clinical symptomatology for a certain period of time.
Review of neuroimaging studies of child and adolescent psychiatric disorders from the past 10 years.

OBJECTIVES To review recent neuroimaging studies of serious emotional disorders in youth and identify problems and promise of neuroimaging in clinical practice. METHOD Published reports from refereed journals are briefly described, critiqued, and synthesized into a summary of the findings to date. RESULTS Childhood-onset schizophrenia shows progressive ventricular enlargement, reduction in total brain and thalamus volume, changes in temporal lobe structures, and reductions in frontal metabolism. Autistic disorder is associated with cerebellar changes, greater total brain and lateral ventricle volume, and asymmetry. The prefrontal cortex and the basal ganglia are consistently reported as abnormal in attention-deficit/hyperactivity disorder. Patients with anorexia nervosa show enlarged CSF spaces and reductions in gray and white matter that are only partially reversible with weight recovery. CONCLUSIONS Results from neuroimaging studies of childhood-onset psychiatric disorders suggest consistency in the structures found to be abnormal, but inconsistencies in the nature of these abnormalities. Although neuroimaging technology holds great promise for neurodevelopmental research, it is not yet a diagnostic instrument.
Appendix for online publication

Table A.1 expands the balance table in the main paper for the full set of baseline covariates available and used in the treatment effects regressions.1 Column 1 reports the sample mean for each covariate, and Columns 2 to 7 report the coefficients and p values on treatment indicators from ordinary least squares (OLS) regressions of each baseline covariate on three treatment indicators (one for assignment to each treatment arm) controlling for block fixed effects. Column 8 reports the p value from a joint test of significance of the three coefficients. Finally, at the base of the table we report the p value from a test of joint significance of all covariates from an OLS regression of each treatment indicator on all covariates (including that treatment group and the control group alone).
Correlates of Household Seismic Hazard Adjustment Adoption

This study examined the relationships of self‐reported adoption of 12 seismic hazard adjustments (pre‐impact actions to reduce danger to persons and property) with respondents' demographic characteristics, perceived risk, perceived hazard knowledge, perceived protection responsibility, and perceived attributes of the hazard adjustments. Consistent with theoretical predictions, perceived attributes of the hazard adjustments differentiated among the adjustments and had stronger correlations with adoption than any of the other predictors. These results identify the adjustments and attributes that emergency managers should address to have the greatest impact on improving household adjustment to earthquake hazard.
Acute inflammation and infection maintain circulating phospholipid levels and enhance lipopolysaccharide binding to plasma lipoproteins Published, JLR Papers in Press, August 16, 2003. DOI 10.1194/jlr.M300228-JLR200

Circulating lipoproteins are thought to play an important role in the detoxification of lipopolysaccharide (LPS) by binding the bioactive lipid A portion of LPS to the lipoprotein surface. It has been assumed that hypocholesterolemia contributes to inflammation during critical illness by impairing LPS neutralization. We tested whether critical illness impaired LPS binding to lipoproteins and found, to the contrary, that LPS binding was enhanced and that LPS binding to the lipoprotein classes correlated with their phospholipid content. Whereas low serum cholesterol was almost entirely due to the loss of esterified cholesterol (a lipoprotein core component), phospholipids (the major lipoprotein surface lipid) were maintained at near normal levels and were increased in a hypertriglyceridemic subset of septic patients. The levels of phospholipids found in the LDL and VLDL fractions varied inversely with those in the HDL fraction, and LPS bound predominantly to lipoproteins in the LDL and VLDL fractions when HDL levels were low. Lipoproteins isolated from the serum of septic patients neutralized the bioactivity of the LPS that had bound to them. Our results show that the host response to acute inflammation and infection tends to maintain lipoprotein phospholipid levels and that, despite hypocholesterolemia and reduced HDL levels, circulating lipoproteins maintain their ability to bind and neutralize an important bacterial agonist, LPS.
Long-Term Maintenance of Callus Cultures from Immature Embryo of Sorghum bicolor

2 Abstract: A protocol was developed for long-term maintenance of callus cultures, induced from immature embryo of Sorghum bicolor (L.) Moench. Maintenance of callus cultures for prolonged duration in a regenerable state is one of the most important requirements for using in vitro techniques for plant improvements. In the present study calli were maintained satisfactorily on MS medium over 57 weeks and plantlets regenerated from them on transfer to light. Immature embryo was used as source material for callus initiation. The callus cultures were cultured on MS media with 1.5 mg/L of 2,4-D (2,4-dichlorophenoxy acetic acid), 10mg/L silver nitrate (AgNo ), 400mg/L casein hydrolysate (CH), 200mg/L L-proline and L-asparagine. 3 After callus initiation cultures were maintained in dark conditions and subcultured for every 3 week intervals. Greening of callus and regeneration of shoot-buds from callus occurred on transfer to MS media with 2mg/L BAP + TDZ (Thidiazuron). These shoots grew further in media with both, BAP and TDZ, Rooting of shoots occurred on media with NAA, the rooted plantlets could be transferred to autoclaved soil. Genetically uniform plantlets regenerated continuously from established callus upto 57 weeks old; thereby helping in multiplication and to facilitate the year round availability of explants and/or somatic embryos for Sorghum tissue culture and transformation.
Selenium Dependent Glutathione Peroxidase: A Physiological Regulatory System for Platelet Function

Summary In human platelets the selenoenzyme glutathione peroxidase (GSH-Px) acts as a scavenger of the peroxides generated during the burst of arachidonic acid (AA) metabolism. Such a mechanism inhibits the biosynthesis of both thromboxane A2 (TXA2) and lipoxygenase products. The same mechanism is not effective on the prostacyclin (PGI2) biosynthesis from cultured endothelial cells. In order to evaluate this effect in vivo, besides in vitro, we activated the enzyme in eight normal volunteers by increasing their daily Se intake for 8 weeks, monitoring: platelet GSH-Px activity, platelet aggregation induced by A A and U 44069, and concurrent malondialdehyde (MDA) and thromboxane B2 (TXB2) production, urinary excretion of renal and systemic TXA2 and PGI2 metabolites, platelet enzyme activities of the hexose monophosphate pathway and glutathione content, platelet adenine nucleotides, bleeding time, plasma Se concentration. We found: a) progressive platelet GSH-Px activation by Se paralleling an enhancement of platelet aggregation threshold values for AA, but not for U 44069; b) concurrent inhibition of platelet biosynthesis of TXA2 both in vitro and in vivo while the biosynthesis of systemic prostacyclin was unaffected; c) a progressive increase in the bleeding time, unmodified by aspirin. In conclusion, we believe that Se-dependent GSH-Px represents a physiological mechanism regulating the biosynthesis of prostanoids with implications in platelet function and that a Se dietary supplement might be considered in the prevention of arterial thrombosis.
Topological fluid dynamics

T opological fluid dynamics is a young mathematical discipline that studies topological features of flows with complicated trajectories and their applications to fluid motions, and develops group-theoretic and geometric points of view on various problems of hydrodynamical origin. It is situated at a crossroads of several disciplines, including Lie groups, knot theory, partial differential equations, stability theory, integrable systems, geometric inequalities, and symplectic geometry. Its main ideas can be traced back to the seminal 1966 paper [1] by V. Arnold on the Euler equation for an ideal fluid as the geodesic equation on the group of volume-preserving diffeomorphisms. One of the most intriguing observations of topological fluid dynamics is that one simple construction in Lie groups enables a unified approach to a great variety of different dynamical systems, from the simple (Euler) equation of a rotating top to the (also Euler) hydrodynamics equation, one of the most challenging equations of our time. A curious application of this theory is an explanation of why long-term dynamical weather forecasts are not reliable: Arnold’s explicit estimates related to curvatures of diffeomorphism groups show that the earth weather is essentially unpredictable after two weeks as the error in the initial condition grows by a factor of 105 for this period, that is, one loses 5 digits of accuracy. (Ironically, 15 day(! ) weather forecasts for any country in the world are now readily available online at www.accuweather. com. ) Another application is related to the Sakharov–Zeldovich problem on whether a neutron star can extinguish by “reshaping” and turning to radiation the excessive magnetic energy. In this introductory article we will touch on these and several other purely mathematical problems motivated by fluid mechanics, referring the interested reader to the book [4] for further details and the extensive bibliography.
Long-term impact of farm management and crops on soil microorganisms assessed by combined DGGE and PLFA analyses

In the present study, long-term organic and conventional managements were compared at the experimental field of Monsampolo del Tronto (Marche region, Italy) with the aim of investigating soil chemical fertility and microbial community structure. A polyphasic approach, combining soil fertility indicators with microbiological analyses (plate counts, PCR-denaturing gradient gel electrophoresis [DGGE] and phospholipid fatty acid analysis [PLFA]) was applied. Organic matter, N as well as some important macro and micronutrients (K, P, Mg, Mn, Cu, and Zn) for crop growth, were more available under organic management. Bacterial counts were higher in organic management. A significant influence of management system and management x crop interaction was observed for total mesophilic bacteria, nitrogen fixing bacteria and actinobacteria. Interestingly, cultivable fungi were not detected in all analyzed samples. PLFA biomass was higher in the organic and Gram positive bacteria dominated the microbial community in both systems. Even if fungal biomass was higher in organic management, fungal PCR-DGGE fingerprinting revealed that the two systems were very similar in terms of fungal species suggesting that 10 years were not enough to establish a new dynamic equilibrium among ecosystem components. A better knowledge of soil biota and in particular of fungal community structure will be useful for the development of sustainable management strategies.
Efficacy of Enteral Supplementation Enriched with Glutamine, Fiber, and Oligosaccharide on Mucosal Injury following Hematopoietic Stem Cell Transplantation

The combination of glutamine, fiber and oligosaccharides (GFO) is thought to be beneficial for alleviating gastrointestinal mucosal damage caused by chemotherapy. A commercial enteral supplementation product (GFO) enriched with these 3 components is available in Japan. We performed a retrospective study to test whether oral GFO decreased the severity of mucosal injury following hematopoietic stem cell transplantation (HSCT). Of 44 HSCT patients, 22 received GFO and 22 did not. Severity of diarrhea/mucositis, overall survival, weight loss, febrile illness/documented infection, intravenous hyperalimentation days/hospital days, engraftment, acute and chronic GVHD, and cumulative incidence of relapse were studied. Sex, age, performance status, diagnosis, disease status, and treatment variables were similar in both groups. There were fewer days of diarrhea grade 3-4 in patients receiving GFO than in those who did not (0.86 vs. 3.27 days); the same was true for days of mucositis grade 3-4 (3.86 vs. 6.00 days). Survival at day 100 was 100% in the GFO group, but only 77.3% for the patients not receiving GFO (p = 0.0091, log-rank test). Weight loss and the number of days of intravenous hyperalimentation were better in the GFO group (p < 0.001 and p = 0.0014, respectively). Although not significant, less gut bacterial translocation with Enterococcus species developed in the GFO group (p = 0.0728) than in the non-GFO group. Other outcomes were not affected. To the best of our knowledge, this is the first comparative clinical study of GFO supplementation to alleviate mucosal injury after allo-HSCT. We conclude that glutamine, fiber and oligosaccharide supplementation is an effective supportive therapy to decrease the severity of mucosal damage in HSCT.
Detecting malicious routers

The Internet is not a safe place. Unsecured hosts can expect to be compromised within minutes of connecting to the Internet and even well-protected hosts may be crippled with denial-of-service attacks. However, while such threats to host systems are widely understood, it is less well appreciated that the network infrastructure itself is subject to constant attack as well. Indeed, through combinations of social engineering and exploitation of weak passwords, attackers have seized control over of thousands of Internet routers. Once a router has been compromised in such a fashion, an attacker may interpose on the traffic stream and manipulate it maliciously to attack others—selectively dropping, modifying, or re-routing packets. First, we specify this problem of detecting routers with incorrect packet forwarding behavior and we explore the design space of protocols that implement such a detector. We further present two concrete protocols that differ in accuracy, completeness, and overhead—one of which is likely inexpensive enough for practical implementation at scale. We present a prototype system that implements this approach on a PC router and describe our experiences with it. We believe our work is an important step in being able to tolerate attacks on key network infrastructure components. Unfortunately, it is quite challenging to attribute a missing packet to a malicious action because normal network congestion can produce the same effect. Modern networks routinely drop packets when the load temporarily exceeds a router's buffering capacity. Previous detection protocols have tried to address this problem using a user-defined threshold. Recently, we have designed, developed and implemented a new compromised router detection protocol that dynamically infers, based on measured traffic rates and buffer sizes, the number of congestive packet losses that will occur. Once the ambiguity from congestion is removed, subsequent packet losses can be attributed to malicious actions. We have tested this protocol in Emulab and have studied its effectiveness in differentiating attacks from legitimate network behavior. We believe this protocol is the first to automatically predict congestion in a systematic manner and is necessary for making any such network fault detection practical.
Functional properties and structural characterization of rice δ1-pyrroline-5-carboxylate reductase

The majority of plant species accumulate high intracellular levels of proline to cope with hyperosmotic stress conditions. Proline synthesis from glutamate is tightly regulated at both the transcriptional and the translational levels, yet little is known about the mechanisms for post-translational regulation of the enzymatic activities involved. The gene coding in rice (Oryza sativa L.) for δ1-pyrroline-5-carboxylate (P5C) reductase, the enzyme that catalyzes the second and final step in this pathway, was isolated and expressed in Escherichia coli. The structural and functional properties of the affinity-purified protein were characterized. As for most species, rice P5C reductase was able to use in vitro either NADH or NADPH as the electron donor. However, strikingly different effects of cations and anions were found depending on the pyridine nucleotide used, namely inhibition of NADH-dependent activity and stimulation of NADPH-dependent activity. Moreover, physiological concentrations of proline and NADP+ were strongly inhibitory for the NADH-dependent reaction, whereas the NADPH-dependent activity was mildly affected. Our results suggest that only NADPH may be used in vivo and that stress-dependent variations in ion homeostasis and NADPH/NADP+ ratio could modulate enzyme activity, being functional in promoting proline accumulation and potentially also adjusting NADPH consumption during the defense against hyperosmotic stress. The apparent molecular weight of the native protein observed in size exclusion chromatography indicated a high oligomerization state. We also report the first crystal structure of a plant P5C reductase at 3.40-Å resolution, showing a decameric quaternary assembly. Based on the structure, it was possible to identify dynamic structural differences among rice, human, and bacterial enzymes.