Miracle-dz/UniFAR-FTUs huggingface dataset:
Seawater redox variations during the deposition of the Kimmeridge Clay Formation, United Kingdom (Upper Jurassic): Evidence from molybdenum isotopes and trace metal ratios

[1] The Kimmeridge Clay Formation (KCF) and its equivalents worldwide represent one of the most prolonged periods of organic carbon accumulation of the Mesozoic. In this study, we use the molybdenum (Mo) stable isotope system in conjunction with a range of trace metal paleoredox proxies to assess how seawater redox varied both locally and globally during the deposition of the KCF. Facies with lower organic carbon contents (TOC 1–7 wt %) were deposited under mildly reducing (suboxic) conditions, while organic-rich facies (TOC >7 wt %) accumulated under more strongly reducing (anoxic or euxinic) local conditions. Trace metal abundances are closely linked to TOC content, suggesting that the intensity of reducing conditions varied repeatedly during the deposition of the KCF and may have been related to orbitally controlled climate changes. Long-term variations in δ98/95Mo are associated with the formation of organic-rich intervals and are related to third-order fluctuations in relative sea level. Differences in the mean δ98/95Mo composition of the organic-rich intervals suggest that the global distribution of reducing conditions was more extensive during the deposition of the Pectinatites wheatleyensis and lower Pectinatites hudlestoni zones than during the deposition of the upper Pectinatites hudlestoni and Pectinatites pectinatus zones. The global extent of reducing conditions during the Kimmerigidan was greater than today but was less widespread than during the Toarcian (Early Jurassic) oceanic anoxic event. This study also demonstrates that the Mo isotope system in Jurassic seawater responded to changes in redox conditions in a manner consistent with its behavior in present-day sedimentary environments.
Transcriptional control of differentiation and neurogenesis in autonomic ganglia

Autonomic neuron development is controlled by a network of transcription factors, which is induced by bone morphogenetic protein signalling in neural crest progenitor cells. This network intersects with a transcriptional program in migratory neural crest cells that pre‐specifies autonomic neuron precursor cells. Recent findings demonstrate that the transcription factors acting in the initial specification and differentiation of sympathetic neurons are also important for the proliferation of progenitors and immature neurons during neurogenesis. Elimination of Phox2b, Hand2 and Gata3 in differentiated neurons affects the expression of subtype‐specific and/or generic neuronal properties or neuron survival. Taken together, transcription factors previously shown to act in initial neuron specification and differentiation display a much broader spectrum of functions, including control of neurogenesis and the maintenance of subtype characteristics and survival of mature neurons.
Resolving Noun Compounds with Multi-Use Domain Knowledge

In this paper we describe a system for semantic interpretation of noun compounds that relies on world and domain knowledge from a knowledge base. This architecture combines domain-independent compounding rules with a task-independent knowledge representation, allowing both components to be flexibly reused. We present examples from Scientific American text, on which the system was developed, and then describe an exercise that tests the portability of the architecture to a new domain: email text on the topic of conference planning.
Perceptual Learning Induced by Short-Term Training with Visual Stimuli: Effects of Retinal Position and Stimulus Type

We investigated perceptual learning in 85 healthy adults with stereoscopic information contained in dynamic random dot stimuli or with vernier targets. Stimuli were flashed simultaneously at 8 locations at an eccentricity of 1.15° or 2.3°, and subjects had to detect a target in an “8 Alternative Forced Choice” task. For training at a given eccentricity stimuli at the other eccentricity served as a “no training” control. Viewing of visual targets for about 20 minutes resulted in a significant increase of discrimination performance only for the trained stimuli (significant interaction between training and time). Thus, learning is position specific: improved performance can be demonstrated only when test and training stimuli are presented to the same retinal areas. In combination with our earlier electrophysiological results, this study illustrates how perceptual training induces stimulus and visual field specific neural plasticity in adults.
Anesteziye Tavşanlarda Santral Serotoninin Solunum Düzenlemesindeki Rolü

Cal›ﬂmam›zda, santral eksojen serotonin'in (5-HT) normoksi ve hipokside solunum duzenlenmesi uzerindeki etkisini belirlemeyi amaclad›k. Deneyler urethane (400 mg/kg I.V) ve alpha-chloralose (40 mg/kg I.V) kar›ﬂ›m› ile anesteziye edilmiﬂ tavﬂanlarda yap›ld›. ‹ntraserebroventrikuler (ICV) 5-HT, sol lateral ventrikul icine stereotaksik yontemle yerleﬂtirilen kanul arac›l›¤› ile verildi. Soluk frekans› (f/dk), soluk hacmi (VT), solunum dakika hacmi (VE) ve sistemik arteriyel kan bas›nc› (SAB) kaydedildi ve ortalama sistemik arteriyel bas›nc (SAOB) hesapland›. ICV serotonin (20 μg/kg) f/dk ,VT ve VE de anlaml› art›ﬂlara neden oldu. Hava faz›n› takiben, tekrar ICV 5-HT injeksiyonu yap›l›p, hipoksik gaz kar›ﬂ›m› (% 8 O2-% 92 N2) solutuldu¤unda, hipokside gozlenen solunum faaliyetindeki art›ﬂ›n daha fazla oldu¤u saptand›. Tavﬂanlara ICV ketanserin (5-HT2A/2C reseptor antagonisti, 10 μg/kg) verilmesi f/dk, VT ve VE'de anlaml› azalmalara neden olurken, 5-HT'nin ventilasyonda oluﬂturdu¤u art›ﬂ› onledi. Bulgular›m›z santral ekzojen 5-HT'nin normoksik ve hipoksik ventilasyonu 5-HT2 reseptorleri arac›l›¤› ile art›rd›¤›n› goster- mektedir. Anahtar Kelimeler: Serotonin, akut hipoksi, ketanserin. Cerrahpaﬂa T›p Derg 2006; 37: 98 - 102 The Role of Central Serotonin on Respiratory Regulation in Anaesthetized Rabbits. Abstract In the present study, we aimed to investigate the effect of central exogenous serotonin (5-HT) on ventilation during normoxia and hypoxia. The experiments were performed in peripheral chemoreceptors intact rabbits anesthetized with urethane (400 mg/kg I.V) and alpha-chloralose (40 mg/kg I.V). For intracerebroventricular (ICV) administration of serotonin (5-HT), a cannula was placed intracerebroventricularly to the left lateral ventricle with stereotaxy. Respiratory frequency (f/min), tidal volume (VT), ventilation minute volume (VE) and systemic arterial blood pressure (BP) were recorded and mean arterial pressure was calculated (MAP). ICV administration of 5-HT (20 μg/kg) caused an increased in f/dk ,VT and VE. After ICV administration of 5-HT, breathing of hypoxic gas mixture (8 % O2 - 92 % N2) produced an increase in hypoxic respiratory responses. ICV ketanserin administration (5-HT2A/2C receptor antagonist, 10 (g/kg), in rabbits caused a decrease in f/min, VT, and VE. ICV ketanserin also prevented the stimulatory effect of 5-HT on ventilation during normoxia. In conclussion, the results of this study show that 5-HT increases ventilation during normoxia and hypoxia via 5-HT2 receptors. KeyWords: Serotonin, acute hypoxia, ketanserin. Cerrahpasa J Med 2006; 37: 98 - 102
Serum Immunoglobulin Response and Protection from Homologous Challenge by Proteus mirabilis in a Mouse Model of Ascending Urinary Tract Infection

ABSTRACT We tested the hypothesis that experimental Proteus mirabilis urinary tract infection in mice would protect against homologous bladder rechallenge. Despite production of serum immunoglobulin G (IgG) and IgM (median titers of 1:320 and 1:80, respectively), vaccinated (infected and antibiotic-cured) mice did not show a decrease in mortality upon rechallenge; the survivors experienced only modest protection from infection (mean log10 number of CFU of P. mirabilisNalr HI4320 per milliliter or gram in vaccinated mice versus sham-vaccinated mice: urine, 100-fold less [3.5 versus 5.5;P = 0.13]; bladder, 100-fold less [3.1 versus 5.1;P = 0.066]; kidneys, 40-fold less [2.7 versus 4.3;P = 0.016]). Western blots using protein from the wild-type strain and isogenic mutants demonstrated antibody responses to MR/P and PMF fimbriae and flagella. There was no correlation between serum IgG or IgM levels and protection from mortality or infection. There was a trend toward elevated serum IgA titers and protection from subsequent challenge (P ≥ 0.09), although only a few mice developed significant serum IgA levels. We conclude that prior infection with P. mirabilis does not protect significantly against homologous challenge.
The Plight of the U.S. Working Class

Modern capitalism, sociologist Max Weber famously observed early in the twentieth century, is based on “the rational capitalistic organization of (formally) free labor. ” But the “rationality” of the system in this sphere, as Weber was to acknowledge elsewhere, was so restrictive as to be in reality “irrational. ” Despite its formal freedom, labor under capitalism was substantively unfree. … This was in accordance with the argument advanced in Karl Marx’s Capital. Since the vast majority of individuals in the capitalist system are divorced from the means of production they have no other way to survive but to sell their labor power to those who own these means, that is, the capitalist class. … The result is a strong tendency to the polarization of income and wealth in society. The more the social productivity of labor grows the more it serves to promote the wealth and power of private capital, while at the same time increasing the relative poverty and economic dependency of the workers. This article can also be found at the Monthly Review website , where most recent articles are published in full. Click here to purchase a PDF version of this article at the Monthly Review website.
DETERMINATION OF THE GLYCAEMIC INDEX OF PREPARATIONS FOR SPORTS PERFORMANCE

Introduction: Glycaemic index (GI) of a certain quantity and type of carbohydrate affects the rate of change of glucose concentration or glucose metabolism in blood. Consumption of carbohydrates with different GI before, during and after exercise affects the athletic performance and food with a high GI is preferred. Aims: To determine GI of two commercially available recovery preparations and accordingly assess their classification in the group of training recovery products. Methods: Five healthy males, 21 – 26 years, full-time students, non–smokers, volunteered for the study. The main inclusion criteria were absence of diabetes, prediabetes or any other diagnosis that affects glycaemia and intensive physical activity in leisure time, measured through body composition (Tanita MC-180 analyzer) and a standardized physical activity questionnaire. GI determination for two commercially available recovery preparations was done according to ISO 26 642:2010 method. Results: Test sample 1 had significantly lower hedonic score (4.0 ± 1.7) and a subjective feeling of satiety (50.5 ± 3.6), while Control sample had the highest scores (2.0 or 64.8 ± 9.0). Significantly higher blood glucose was determined for both test samples as compared to Control. The area under the blood glucose curve (iAUC) was significantly higher for Test sample 1 (255.9 ± 50.7) as compared to Control (78.9 ± 8.0), and Test sample 2 (127.3 ± 12.6). GI of Test sample 1 was significantly higher than the one of Test sample 2 (317.9 ± 122.4 versus 161.6 ± 14.6, p = 0.022). Conclusions: Both samples belong into the category of high GI products, which is in accordance with their intended purpose. The results indicate differences in the mechanism of action ; i.e. influence on glucose metabolism, probably as a result of product formulations (nutritional composition). Despite the same classification of two tested products by the manufacturer, more detailed description of mechanism of action for training recovery products should be encouraged.
Impact of paediatric human immunodeficiency virus infection on children's and caregivers' daily functioning and well-being: a qualitative study.

BACKGROUND Human immunodeficiency virus (HIV) infection impacts not only upon the physical health of affected children, but also their psychosocial functions, family relationships and economical status. Caregivers are confronted with complex challenges related to the physical, emotional and financial demands of raising these children. The purpose of this study was to enhance our understanding of the impact of HIV disease on both children's and caregivers' well-being, using a qualitative inquiry approach. METHODS A total of 35 primary caregivers of HIV-infected children participated in in-depth interviews. The issues discussed included the major negative impacts on children's daily functioning and well-being, and the perceived caregiver/parental burden. Participants included parents (40%), grandparents (22.8%), other relatives (e.g. uncles, aunts) (34.3%) and one foster parent (2.8%). RESULTS Qualitative analysis revealed that the major negative impacts of HIV/AIDS included physical symptoms, school performance and relationship changes. The major negative impacts on caregivers' well-being included acceptance of the diagnosis, dealing with the financial burden and keeping the diagnosis private. CONCLUSIONS Approaches are needed to address these challenges by enhancing families' coping skills and building supportive networks.
The Mitotic Exit Network Regulates Spindle Pole Body Selection During Sporulation of Saccharomyces cerevisiae

Age-based inheritance of centrosomes in eukaryotic cells is associated with faithful chromosome distribution in asymmetric cell divisions. During Saccharomyces cerevisiae ascospore formation, such an inheritance mechanism targets the yeast centrosome equivalents, the spindle pole bodies (SPBs) at meiosis II onset. Decreased nutrient availability causes initiation of spore formation at only the younger SPBs and their associated genomes. This mechanism ensures encapsulation of nonsister genomes, which preserves genetic diversity and provides a fitness advantage at the population level. Here, by usage of an enhanced system for sporulation-induced protein depletion, we demonstrate that the core mitotic exit network (MEN) is involved in age-based SPB selection. Moreover, efficient genome inheritance requires Dbf2/20-Mob1 during a late step in spore maturation. We provide evidence that the meiotic functions of the MEN are more complex than previously thought. In contrast to mitosis, completion of the meiotic divisions does not strictly rely on the MEN whereas its activity is required at different time points during spore development. This is reminiscent of vegetative MEN functions in spindle polarity establishment, mitotic exit, and cytokinesis. In summary, our investigation contributes to the understanding of age-based SPB inheritance during sporulation of S. cerevisiae and provides general insights on network plasticity in the context of a specialized developmental program. Moreover, the improved system for a developmental-specific tool to induce protein depletion will be useful in other biological contexts.
Some criteria for the recognition of Nocardia madurae (Vincent) Blanchard.

SUMMARY: A combination of characters for the description and identification of strains of Nocardia madurae, based on the examination of 44 strains, is presented. Although nearly all the 44 strains were received from medical laboratories, a few were isolated from soil. Some of the distinguishing properties of N. madurae are compared with those of N. asteroides, N. caviae, N. brasiliensis, N. pelletieri and Streptomyces somaliensis.
Fuzzy controller design: recommendations to the user

This paper attempts to analyse and classify different methods of fuzzy control (FC) design. It aims at providing some practical recommendations on how to design a FC and how to choose the right design method. The goal is to develop a more or less systematic procedure of a FC design which can be used as a reference. The design process can be roughly divided into two stages: an initial choice of the controller structures and parameters, and their further adjustment. Recommendations are given at the first stage regarding a choice of the structure, scaling factors, rules and membership functions, though the main attention is focused on the membership functions and scaling factors. Different methodologies, such as neural networks, genetic/evolutionary algorithms, are considered at the second stage.
A comparative study of the severity of emphysema in necropsy populations in three different countries.

Paper-mounted, whole lung sections were examined from 369 random necropsies in Montreal, Canada; 920 random necropsies in Cardiff, Wales; 453 random necropsies in Malmoe, Sweden. The severity of emphysema was not only related to cigarette smoking but also to age and sex, with women having less emphysema than men when normalized for age and smoking history. Differences between the centers were slight, but in heavy smokers and ex-smokers in the eighth decade, the most emphysema occurred in the Cardiff cases and the least in the Malmoe cases. The data suggest that one can reasonably extrapolate conclusions from a hospital necropsy population to the general population.
Maintaining object-oriented software

The maintenance requirements of object-oriented software, including the ability to make changes easily and an in-depth understanding of the software's structure and behavior, are discussed. The problems encountered by a maintainer trying to understand object-oriented software by reading and statically analyzing it are described. The problems caused by dynamic binding, polymorphism, and cooperating object classes in object-oriented software maintenance are reviewed. <<ETX>>
Spatiotemporal control of epithelial remodeling by regulated myosin phosphorylation

Significance Cells in the fruit fly Drosophila require forces generated by the myosin II motor to reorganize the embryo and elongate the body axis from head to tail. It has been proposed that regulated myosin phosphorylation generates global patterns of myosin activity that shape tissues. However, the mechanisms that determine where and when forces are generated are not well understood. We show that myosin variants that evade upstream regulation by preventing or mimicking phosphorylation disrupt the spatiotemporal pattern of forces during axis elongation. Mimicking myosin phosphorylation accelerates cell rearrangements, but these rearrangements are poorly oriented and produce less efficient elongation. These results indicate that regulated myosin phosphorylation provides an instructive cue that determines where and when myosin generates force to shape multicellular tissues. Spatiotemporally regulated actomyosin contractility generates the forces that drive epithelial cell rearrangements and tissue remodeling. Phosphorylation of the myosin II regulatory light chain (RLC) promotes the assembly of myosin monomers into active contractile filaments and is an essential mechanism regulating the level of myosin activity. However, the effects of phosphorylation on myosin localization, dynamics, and function during epithelial remodeling are not well understood. In Drosophila, planar polarized myosin contractility is required for oriented cell rearrangements during elongation of the body axis. We show that regulated myosin phosphorylation influences spatial and temporal properties of contractile behavior at molecular, cellular, and tissue length scales. Expression of myosin RLC variants that prevent or mimic phosphorylation both disrupt axis elongation, but have distinct effects at the molecular and cellular levels. Unphosphorylatable RLC produces fewer, slower cell rearrangements, whereas phosphomimetic RLC accelerates rearrangement and promotes higher-order cell interactions. Quantitative live imaging and biophysical approaches reveal that both phosphovariants reduce myosin planar polarity and mechanical anisotropy, altering the orientation of cell rearrangements during axis elongation. Moreover, the localized myosin activator Rho-kinase is required for spatially regulated myosin activity, even when the requirement for phosphorylation is bypassed by the expression of phosphomimetic myosin RLC. These results indicate that myosin phosphorylation influences both the level and the spatiotemporal regulation of myosin activity, linking molecular properties of myosin activity to tissue morphogenesis.
The Hepatitis C Virus Non-structural NS5A Protein Impairs Both the Innate and Adaptive Hepatic Immune Response in Vivo*

The role of hepatitis C virus (HCV) protein non-structural (NS) 5A in HCV-associated pathogenesis is still enigmatic. To investigate the in vivo role of NS5A for viral persistence and virus-associated pathogenesis a transgenic (Tg) mouse model was established. Mice with liver-targeted NS5A transgene expression were generated using the albumin promoter. Alterations in the hepatic immune response were determined by Western blot, infection by lymphocytic choriomeningitis virus (LCMV), and using transient NS3/4A Tg mice generated by hydrodynamic injection. Cytotoxic T lymphocyte (CTL) activity was investigated by the Cr-release assay. The stable NS5A Tg mice did not reveal signs of spontaneous liver disease. The intrahepatic immunity was disrupted in the NS5A Tg mice as determined by clearance of LCMV infection or transiently NS3/4A Tg hepatocytes in vivo. This impaired immunity was explained by a reduced induction of interferon β, 2′,5′-OAS, and PKR after LCMV infection and an impairment of the CTL-mediated elimination of NS3-expressing hepatocytes. In conclusion, these data indicate that in the present transgenic mouse model, NS5A does not cause spontaneous liver disease. However, we discovered that NS5A could impair both the innate and the adaptive immune response to promote chronic HCV infection.
Functional and comparative metagenomic analysis of bile salt hydrolase activity in the human gut microbiome

Bile salt hydrolases (BSHs) catalyze the “gateway” reaction in a wider pathway of bile acid modification by the gut microbiota. Because bile acids function as signaling molecules regulating their own biosynthesis, lipid absorption, cholesterol homeostasis, and local mucosal defenses in the intestine, microbial BSH activity has the potential to greatly influence host physiology. However, the function, distribution, and abundance of BSH enzymes in the gut community are unknown. Here, we show that BSH activity is a conserved microbial adaptation to the human gut environment with a high level of redundancy in this ecosystem. Through metagenomic analyses we identified functional BSH in all major bacterial divisions and archaeal species in the gut and demonstrate that BSH is enriched in the human gut microbiome. Phylogenetic analysis illustrates that selective pressure in the form of conjugated bile acid has driven the evolution of members of the Ntn_CGH-like family of proteins toward BSH activity in gut-associated species. Furthermore, we demonstrate that BSH mediates bile tolerance in vitro and enhances survival in the murine gut in vivo. Overall, we demonstrate the use of function-driven metagenomics to identify functional anchors in complex microbial communities, and dissect the gut microbiome according to activities relevant to survival in the mammalian gastrointestinal tract.