Miracle-dz/UniFAR-FTUs huggingface dataset:
Four-Dimensional Microvascular Analysis Reveals That Regenerative Angiogenesis in Ischemic Muscle Produces a Flawed Microcirculation

Rationale: Angiogenesis occurs after ischemic injury to skeletal muscle, and enhancing this response has been a therapeutic goal. However, to appropriately deliver oxygen, a precisely organized and exquisitely responsive microcirculation must form. Whether these network attributes exist in a regenerated microcirculation is unknown, and methodologies for answering this have been lacking. Objective: To develop 4-dimensional methodologies for elucidating microarchitecture and function of the reconstructed microcirculation in skeletal muscle. Methods and Results: We established a model of complete microcirculatory regeneration after ischemia-induced obliteration in the mouse extensor digitorum longus muscle. Dynamic imaging of red blood cells revealed the regeneration of an extensive network of flowing neo-microvessels, which after 14 days structurally resembled that of uninjured muscle. However, the skeletal muscle remained hypoxic. Red blood cell transit analysis revealed slow and stalled flow in the regenerated capillaries and extensive arteriolar-venular shunting. Furthermore, spatial heterogeneity in capillary red cell transit was highly constrained, and red blood cell oxygen saturation was low and inappropriately variable. These abnormalities persisted to 120 days after injury. To determine whether the regenerated microcirculation could regulate flow, the muscle was subjected to local hypoxia using an oxygen-permeable membrane. Hypoxia promptly increased red cell velocity and flux in control capillaries, but in neocapillaries, the response was blunted. Three-dimensional confocal imaging revealed that neoarterioles were aberrantly covered by smooth muscle cells, with increased interprocess spacing and haphazard actin microfilament bundles. Conclusions: Despite robust neovascularization, the microcirculation formed by regenerative angiogenesis in skeletal muscle is profoundly flawed in both structure and function, with no evidence for normalizing over time. This network-level dysfunction must be recognized and overcome to advance regenerative approaches for ischemic disease.
The road to genetic selection for methane emission from ruminants - a global approach

Measuring and mitigating methane (CH4) emissions from livestock is of increasing political and economic importance. Potentially, the most sustainable way of reducing CH4 emission from ruminants is through the estimation of genomic breeding values to facilitate genetic selection. Enteric CH4 emissions are difficult and expensive to measure, thus genomic prediction could provide significant, long term economic benefits. Implementation will require global collaboration to define a suitable measure and many thousands of records to ensure valid and accurate evaluations. A number of approaches for individual measures on a large scale have been recently proposed including fixed and portable respiratory chambers, SF6 tracer gas, laser detector systems and sniffers or spot samples at milking. Some studies have also shown promising results in predicting individual animal CH4 emission from mid infra-red milk spectra data. It is currently unclear, however, how well measures between these approaches correlate. Comparison and validation of these novel phenotypes presents a huge task over the coming years. A crucial first step is to define a trait phenotype and measuring protocols to create a robust resource for the global sharing and comparison of data, and further, to measure correlations with production traits. Proposed phenotypes could be measures of “total methane emissions”, measured in grams CH4 per day, or “methane yield” measured in grams CH4 per kg dry matter intake (DMI) when DMI is available as a phenotype, or “methane intensity” measured in grams CH4 per kg of produced human edible protein. Here, we describe how two recently established entities; an ICAR Working Group and the EU COST-Action network METHAGENE are working in close collaboration to successfully address these major challenges together with the Animal Selection Genetics and Genomics Network (ASGGN) of the Livestock Research Group of the Global Research Alliance (GRA) on agricultural greenhouse gases.
On the Dynamics of a Simple Rational Planar Map

The dynamics of the map are discussed for various values of its parameters. Despite the simple algebraic structure, this map, recently introduced in the literature, is very rich in nonlinear phenomena. Multiple strange attractors, transitions to chaos via period-doubling bifurcations, quasiperiodicity as well as intermittency, interior crisis, hyperchaos are only a few. In this work, strange attractors, bifurcation diagrams, periodic windows, invariant characteristics are investigated both analytically and numerically.
Physiol Regulatory Integrative Comp Physiol

[PDF] [Full Text] [Abstract] , July 1, 2000; 279 (1): R255-R262. Am J Physiol Regulatory Integrative Comp Physiol C. L. Buck and B. M. Barnes arctic hibernator Effects of ambient temperature on metabolic rate, respiratory quotient, and torpor in an [PDF] [Full Text] [Abstract] , January 1, 2004; 89 (1): 27-38. Exp Physiol G. Recordati and T. G. Bellini thermodynamics A definition of internal constancy and homeostasis in the context of non-equilibrium [PDF] [Full Text] [Abstract] , July 1, 2004; 287 (1): R167-R173. Am J Physiol Regulatory Integrative Comp Physiol A. S. Kauffman, M. J. Paul and I. Zucker Increased heat loss affects hibernation in golden-mantled ground squirrels
Modulation of the expression of an apical plasma membrane protein of Madin-Darby canine kidney epithelial cells: cell-cell interactions control the appearance of a novel intracellular storage compartment

Experimental conditions that abolish or reduce to a minimum intercellular contacts between Madin-Darby canine kidney epithelial cells result in the appearance of an intracellular storage compartment for apical membrane proteins. Subconfluent culture, incubation in 1-5 microM Ca++, or inclusion of dissociated cells within agarose or collagen gels all caused the intracellular accumulation of a 184-kD apical membrane protein within large (0.5-5 micron) vacuoles, rich in microvilli. Influenza virus hemagglutinin, an apically targeted viral glycoprotein, is concentrated within these structures but the basolateral glycoprotein G of vesicular stomatitis virus and a cellular basolateral 63-kD membrane protein of Madin-Darby canine kidney cells were excluded. This novel epithelial organelle (VAC), which we designate the vacuolar apical compartment, may play an as yet unrecognized role in the biogenesis of the apical plasma membrane during the differentiation of normal epithelia.
Resource Sharing in Global Fixed-Priority Preemptive Multiprocessor Scheduling

In this paper we consider global fixed-priority preemptive multiprocessor scheduling of constrained-deadline sporadic tasks that share resources in a non-nested manner. We develop a novel resource-sharing protocol and a corresponding schedulability test for this system. We also develop the first schedulability analysis of priority inheritance protocol for the aforementioned system. Finally, we show that these protocols are efficient (based on the developed schedulability tests) for a class of priority-assignments called reasonable priority-assignments.
Pocket proteins critically regulate cell cycle exit of the trabecular myocardium and the ventricular conduction system

Summary During development, the ventricular conduction system (VCS) arises from the trabecular or spongy myocardium. VCS and trabecular myocytes proliferate at a significantly slower rate than compact zone myocardial cells, establishing a transmural cell cycle gradient. The molecular determinants of VCS/trabecular myocyte cell cycle arrest are not known. Given the importance of pocket proteins (Rb, p107 and p130) in mediating G0/G1 arrest in many cell types, we examined the role of this gene family in regulating cell cycle exit of the trabecular myocardium and ventricular conduction system. Using a combinatorial knockout strategy, we found that graded loss of pocket proteins results in a spectrum of heart and lung defects. p107/p130 double knockout (dKO) hearts manifest dysregulated proliferation within the compact myocardium and trabecular bases, while the remaining trabecular region cell cycle exits normally. Consequently, dKO hearts exhibit defective cardiac compaction, septal hyperplasia and biventricular outflow tract obstruction, while the VCS appears relatively normal. Loss of all three pocket proteins (3KO) is necessary to completely disrupt the transmural cell cycle gradient. 3KO hearts exhibit massive overgrowth of the trabecular myocardium and ventricular conduction system, which leads to fetal heart failure and death. Hearts carrying a single pocket protein allele are able to maintain the transmural cell cycle gradient. These results demonstrate the exquisite sensitivity of trabecular and conduction myocytes to pocket protein function during ventricular chamber development.
Piscine Orthoreovirus from Western North America Is Transmissible to Atlantic Salmon and Sockeye Salmon but Fails to Cause Heart and Skeletal Muscle Inflammation

Heart and skeletal muscle inflammation (HSMI) is a significant and often fatal disease of cultured Atlantic salmon in Norway. The consistent presence of Piscine orthoreovirus (PRV) in HSMI diseased fish along with the correlation of viral load and antigen with development of lesions has supported the supposition that PRV is the etiologic agent of this condition; yet the absence of an in vitro culture system to demonstrate disease causation and the widespread prevalence of this virus in the absence of disease continues to obfuscate the etiological role of PRV with regard to HSMI. In this study, we explore the infectivity and disease causing potential of PRV from western North America—a region now considered endemic for PRV but without manifestation of HSMI—in challenge experiments modeled upon previous reports associating PRV with HSMI. We identified that western North American PRV is highly infective by intraperitoneal injection in Atlantic salmon as well as through cohabitation of both Atlantic and Sockeye salmon. High prevalence of viral RNA in peripheral blood of infected fish persisted for as long as 59 weeks post-challenge. Nevertheless, no microscopic lesions, disease, or mortality could be attributed to the presence of PRV, and only a minor transcriptional induction of the antiviral Mx gene occurred in blood and kidney samples during log-linear replication of viral RNA. Comparative analysis of the S1 segment of PRV identified high similarity between this North American sequence and previous sequences associated with HSMI, suggesting that factors such as viral co-infection, alternate PRV strains, host condition, or specific environmental circumstances may be required to cause this disease.
The influence of socioeconomic deprivation on multimorbidity at different ages: a cross-sectional study

Background Multimorbidity occurs at a younger age in individuals in areas of high socioeconomic deprivation but little is known about the ‘typology’ of multimorbidity in different age groups and its association with socioeconomic status. Aim To characterise multimorbidity type and most common conditions in a large nationally representative primary care dataset in terms of age and deprivation. Design and setting Cross-sectional analysis of 1 272 685 adults in Scotland. Method Multimorbidity type of participants (physical-only, mental-only, mixed physical, and mental) and most common conditions were analysed according to age and deprivation. Results Multimorbidity increased with age, ranging from 8.1% in those aged 25–34 to 76.1% for those aged ≥75 years. Physical-only (56% of all multimorbidity) was the most common type of multimorbidity in those aged ≥55 years, and did not vary substantially with deprivation. Mental-only was uncommon (4% of all multimorbidity), whereas mixed physical and mental (40% of all multimorbidity) was the most common type of multimorbidity in those aged <55 years and was two- to threefold more common in the most deprived compared with the least deprived in most age groups. Ten conditions (seven physical and three mental) accounted for the top five most common conditions in people with multimorbidity in all age groups. Depression and pain featured in the top five conditions across all age groups. Deprivation was associated with a higher prevalence of depression, drugs misuse, anxiety, dyspepsia, pain, coronary heart disease, and diabetes in multimorbid patients at different ages. Conclusion Mixed physical and mental multimorbidity is common across the life-span and is exacerbated by deprivation from early adulthood onwards.
Translation initiation mediated by RNA looping

Significance “Ribosomal scanning” is the generally accepted hypothesis for explaining how eukaryotic 40S ribosomal subunits find initiation codons. Some recently described phenomena cannot be explained by the ribosomal scanning hypothesis, however. Here we show that 43S ribosomal complexes recruited to locations downstream of a reporter gene can direct translation of the reporter independent of the 5′ end, suggesting that 43S ribosomal complex recognizes the initiation codon by “RNA looping” of the intervening mRNA segment between the ribosome recruiting site and the initiation codon. Moreover, we provide a mathematical model for the RNA looping hypothesis. The RNA looping hypothesis provides a logical explanation for translational augmentation by translation-enhancing elements located upstream and/or downstream of a protein-coding region. Eukaryotic translation initiation commences at the initiation codon near the 5′ end of mRNA by a 40S ribosomal subunit, and the recruitment of a 40S ribosome to an mRNA is facilitated by translation initiation factors interacting with the m7G cap and/or poly(A) tail. The 40S ribosome recruited to an mRNA is then transferred to the AUG initiation codon with the help of translation initiation factors. To understand the mechanism by which the ribosome finds an initiation codon, we investigated the role of eIF4G in finding the translational initiation codon. An artificial polypeptide eIF4G fused with MS2 was localized downstream of the reporter gene through MS2-binding sites inserted in the 3′ UTR of the mRNA. Translation of the reporter was greatly enhanced by the eIF4G-MS2 fusion protein regardless of the presence of a cap structure. Moreover, eIF4G-MS2 tethered at the 3′ UTR enhanced translation of the second cistron of a dicistronic mRNA. The encephalomyocarditis virus internal ribosome entry site, a natural translational-enhancing element facilitating translation through an interaction with eIF4G, positioned downstream of a reporter gene, also enhanced translation of the upstream gene in a cap-independent manner. Finally, we mathematically modeled the effect of distance between the cap structure and initiation codon on the translation efficiency of mRNAs. The most plausible explanation for translational enhancement by the translational-enhancing sites is recognition of the initiation codon by the ribosome bound to the ribosome-recruiting sites through “RNA looping. ” The RNA looping hypothesis provides a logical explanation for augmentation of translation by enhancing elements located upstream and/or downstream of a protein-coding region.
Changes in reference evapotranspiration over China during 1960–2012: Attributions and relationships with atmospheric circulation

This study investigates reference evapotranspiration (ET0) trends in China from 1960 to 2012 based on the Penman–Monteith equation and gridded meteorological measurements. Under the combined impacts of factors influencing ET0 (i.e., net radiation [RN], mean temperature [TAVE], vapour pressure deficit [VPD], and wind speed [WND]), both seasonal and annual ET0 for the whole China and more than half of the grids decreased over the past 53 years. The attribution analyses suggest that for the whole China, the WND is responsible for annual and seasonal ET0 decreases (excluding summer, where RN is responsible). Across China, the annual cause of WND with the largest spatial extent (43.1% of grids) mainly derives from north of the Changjiang River Basin (CJRB), whereas VPD (RN) as a cause is dispersedly distributed (within and to the south of the CJRB). In summer, RN is dominant in more than half of the grids, but the dominance of VPD and WND accounts for approximately 90% of grids during the remaining seasons. Finally, the correlation coefficients between ET0 and the Atlantic Oscillation (AO), North AO, Indian Ocean Dipole (IOD), Pacific Decadal Oscillation (PDO), and El Niño Southern Oscillation (ENSO) indices with different lead times are calculated. For the whole China, annual and seasonal ET0 always significantly correlate with these indices (excluding the IOD) but with varied lead times. Additionally, near half of the grids show significant and maximum (i.e., the largest one between ET0 and a certain index with a lead time of 0–3 seasons) correlation coefficients of ET0 with PDO in spring and summer, ENSO in autumn, and AO in winter. This study is not only significant for understanding ET0 changes, but it also provides preliminary and fundamental reference information for ET0 prediction.
Cross-Reactivity of Porcine Immunoglobulin A Antibodies with Fecal Immunoglobulins of Wild Boar (Sus scrofa) and Other Animal Species

Fecal samples obtained from wild boar habitats are useful for the surveillance of diseases in wild boar populations; however, it is difficult to determine the species of origin of feces collected in natural habitats. In this study, a fecal IgA ELISA was evaluated as a method for identifying the porcine species from fecal samples. Both domestic pigs (Sus scrofa domestica) and wild boars (Sus scrofa coreanus) showed significantly higher levels of fecal IgA than other animal species. Additionally, age dependent changes in the level of Ig A in wild boars and domestic pigs were identified; Titers of Ig A were highest in suckling period and lowest in weanling period.
Gated audiovisual speech identification in silence vs. noise: effects on time and accuracy

This study investigated the degree to which audiovisual presentation (compared to auditory-only presentation) affected isolation point (IPs, the amount of time required for the correct identification of speech stimuli using a gating paradigm) in silence and noise conditions. The study expanded on the findings of Moradi et al. (under revision), using the same stimuli, but presented in an audiovisual instead of an auditory-only manner. The results showed that noise impeded the identification of consonants and words (i.e., delayed IPs and lowered accuracy), but not the identification of final words in sentences. In comparison with the previous study by Moradi et al., it can be concluded that the provision of visual cues expedited IPs and increased the accuracy of speech stimuli identification in both silence and noise. The implication of the results is discussed in terms of models for speech understanding.
Randomized controlled trial of neurofeedback on chemotherapy‐induced peripheral neuropathy: A pilot study

Chemotherapy‐induced peripheral neuropathy (CIPN) is a significant problem for cancer patients, and there are limited treatment options for this often debilitating condition. Neuromodulatory interventions could be a novel modality for patients trying to manage CIPN symptoms; however, they are not yet the standard of care. This study examined whether electroencephalogram (EEG) neurofeedback (NFB) could alleviate CIPN symptoms in survivors.
Effects of Dietary Levels of Calcium and Nonphytate Phosphorus in Broiler Starter Diets on Live Performance, Bone Development and Growth Plate Conditions in Male Chicks Fed a Corn-Based Diet1

A study was conducted to evaluate the effects of dietary levels of calcium, nonphytate P (NPP), phytase and 25-hydroxycholecalciferol (25-OH) on live performance and bone development in male chicks fed a wheat-based diet. Dietary treatments consisted of a 2 x 2 x 4 x 4 factorial arrangements with two levels of supplemental phytase (0 or 1200 FTU/kg), two levels of 25-OH (0 or 69 μg/kg), four levels of calcium (0.20% less than a 2:1 ratio of Ca to NPP; 2:1 ratio of Ca to NPP; 0.20% Ca greater than a 2:1 ratio of Ca to NPP; 0.40% Ca greater than a 2:1 ratio of Ca to NPP) and four levels of NPP (0.35, 0.40, 0.45 and 0.50%) for a total of 64 treatments. The primary basal diet used to mix all experimental diets was supplemented with a complete vitamin mix containing 5500 IU of cholecalciferol. Each diet was fed to two pens of six male chicks of a commercial broiler strain in electrically heated battery brooders for three consecutive trials using the same diet mix for a total of six replicates per treatment. At 18 d birds were weighed, feed consumption determined and all birds killed for bone measurements. Toes from all birds within a pen were removed and ashed. Tibiae from both legs were removed and scored for incidence and severity of tibial dyschondroplasia and for incidence of calcium or phosphorus rickets. Ca: NPP ratios and calcium levels similar or higher than NRC (1994) recommendations appear necessary for adequate bird performance. Phytase supplementation improved performance parameters such as FCR and body weight, whereas the addition of 25-OH to diets already containing 5500 IU/kg of cholecalciferol had a negative effect on FCR due to a possible hypercalcemia condition. Bone development was improved by increasing phosphorus and calcium levels. Moreover, supplementation with 25-OH and its combination with phytase were effective in enhancing bone development. Increasing Ca levels consistently reduced leg abnormalities. Addition of 25-OH helped to relieve leg problems when suboptimal calcium levels were supplied while phytase supplementation was effective for this purpose when high Ca levels were given. The addition of these additives could be seen as an strategy to alleviate problems with suboptimal Ca: NPP ratios.