Miracle-dz/UniFAR-FTUs huggingface dataset:
Computing over the Reals: Foundations for Scientific Computing

We give a detailed treatment of the ``bit-model'' of computability and complexity of real functions and subsets of R^n, and argue that this is a good way to formalize many problems of scientific computation. In the introduction we also discuss the alternative Blum-Shub-Smale model. In the final section we discuss the issue of whether physical systems could defeat the Church-Turing Thesis.
T-bet Controls Autoaggressive CD8 Lymphocyte Responses in Type 1 Diabetes

The T-box transcription factor T-bet is known to control lineage commitment and interferon-γ production by T helper 1 (Th1) CD4 lymphocytes. We report here that T-bet is essential for development of CD8 lymphocyte-dependent autoimmune diabetes (type 1 diabetes [T1D]) in the rat insulin promoter–lymphocytic choriomeningitis virus (LCMV) transgenic model for virally induced T1D. In the absence of T-bet, autoaggressive (anti-LCMV) CD8 lymphocytes were reduced in number and produced less IFN-γ, but increased IL-2 compared with controls. Further analysis showed that T-bet intrinsically controls the generation, but not apoptosis, maintenance, or secondary expansion of antiviral effector/memory CD8 lymphocytes. This observation points toward a therapeutic opportunity for the treatment of T1D and other autoimmune disorders.
Synthesis and Differential Turnover of the CYS3 Regulatory Protein of Neurospora crassa Are Subject to Sulfur Control

ABSTRACT The transcription factor CYS3 of Neurospora crassa is a positive regulator of the sulfur regulatory circuit which contains many structural genes involved in sulfur metabolism. Expression and degradation of the CYS3 protein are precisely regulated in a sulfur-dependent manner. cys-3 expression was found to be fully repressed by high concentrations of methionine or inorganic sulfate present in the culture medium and to be derepressed when these favored sulfur sources were limited. cys-3 transcripts could be readily detected within 2 h after derepression, whereas the CYS3 protein was not found until after 4 h. CYS3 is stable, with a half-life greater than 4 h under low-sulfur conditions when it is required for cell growth. However, it is degraded relatively quickly when methionine or inorganic sulfate becomes available. Upon sulfur repression, cys-3 transcripts disappeared within 30 min with an estimated half-life of 5 min whereas CYS3 protein almost entirely disappeared in 1 h with a half-life of approximately 10 min. These results suggest that a selective elimination of CYS3 is a highly regulated process. Site-directed mutagenesis showed that Lys-105 of CYS3 is important for its instability. The change of this single residue from lysine to glutamine resulted in a prolonged half life of CYS3 and impaired responsiveness of CYS3 degradation to sulfur level changes.
The pattern of neural elements in the islets of normal and diseased pancreas and in isolated islets.

CONTEXT The association between islet cells and neural elements, the so-called "neuro-insular complex", has been known for centuries. OBJECTIVE We examined the expression of beta-III tubulin, in normal pancreases from organ donors, surgical specimens of chronic pancreatitis, surgical specimens of ductal type carcinoma, isolated and purified islets of a 57-year-old male and the pancreases of adult Syrian golden hamsters by immunohistochemistry using a monoclonal antibody to beta-tubulin. RESULTS In the normal pancreas of humans and hamsters, beta-III tubulin was expressed in alpha- and beta-cells, but not in PP cells, neural fibers and gangliae. Occasionally, intra-and peri-insular neural elements were also found. In chronic pancreatitis and pancreatic cancer samples, the number of beta-cells and the immunoreactivity of the beta-III tubulin antibody in islet cells were decreased in most cases. In cultured human islets, devoid of neural elements, no correlation was found between the expression of beta-III tubulin and islet cell hormones. CONCLUSION Beta-III tubulin is only expressed in the islets derived from the dorsal pancreas and in neural elements. In chronic pancreatitis and pancreatic cancer swelling of intra- and peri-insular nerves occurs, possibly in response to the loss of beta-cells. The secretion of insulin and the expression of beta-tubulin seem to be regulated by nerves.
In vivo Near-Infrared Fluorescence Imaging of Integrin αvβ3 in Brain Tumor Xenografts

Noninvasive visualization of cell adhesion molecule αvβ3 integrin expression in vivo has been well studied by using the radionuclide imaging modalities in various preclinical tumor models. A literature survey indicated no previous use of cyanine dyes as contrast agents for in vivo optical detection of tumor integrin. Herein, we report the integrin receptor specificity of novel peptide-dye conjugate arginine-glycine-aspartic acid (RGD)-Cy5.5 as a contrast agent in vitro, in vivo, and ex vivo. The RGD-Cy5.5 exhibited intermediate affinity for αvβ3 integrin (IC50 = 58.1 ± 5.6 nmol/L). The conjugate led to elevated cell-associated fluorescence on integrin-expressing tumor cells and endothelial cells and produced minimal cell fluorescence when coincubated with c(RGDyK). In vivo imaging with a prototype three-dimensional small-animal imaging system visualized subcutaneous U87MG glioblastoma xenograft with a broad range of concentrations of fluorescent probe administered via the tail vein. The intermediate dose (0.5 nmol) produces better tumor contrast than high dose (3 nmol) and low dose (0.1 nmol) during 30 minutes to 24 hours postinjection, because of partial self-inhibition of receptor-specific tumor uptake at high dose and the presence of significant amount of background fluorescence at low dose, respectively. The tumor contrast was also dependent on the mouse viewing angles. Tumor uptake of RGD-Cy5.5 was blocked by unlabeled c(RGDyK). This study suggests that the combination of the specificity of RGD peptide/integrin interaction with near-infrared fluorescence detection may be applied to noninvasive imaging of integrin expression and monitoring anti-integrin treatment efficacy providing near real-time measurements.
“Wrong Way Up”: Temporal and Spatial Dynamics of the Networks for Body Motion Processing at 9.4 T

Abstract Body motion delivers a wealth of socially relevant information. Yet display inversion severely impedes biological motion (BM) processing. It is largely unknown how the brain circuits for BM are affected by display inversion. As upright and upside‐down point‐light BM displays are similar, we addressed this issue by using ultrahigh field functional MRI at 9.4 T providing for high sensitivity and spatial resolution. Whole‐brain analysis along with exploration of the temporal dynamics of the blood‐oxygen‐level‐dependent response reveals that in the left hemisphere, inverted BM activates anterior networks likely engaged in decision making and cognitive control, whereas readily recognizable upright BM activates posterior areas solely. In the right hemisphere, multiple networks are activated in response to upright BM as compared with scarce activation to inversion. With identical visual input with display inversion, a large‐scale network in the right hemisphere is detected in perceivers who do not constantly interpret displays as shown the “wrong way up. ” For the first time, we uncover (1) (multi)functional involvement of each region in the networks underpinning BM processing and (2) large‐scale ensembles of regions playing in unison with distinct temporal dynamics. The outcome sheds light on the neural circuits underlying BM processing as an essential part of the social brain.
Micromechanical modeling of microtubules

Microtubules serve as one of the structural components of the cell and take place in some of the important cellular functions such as mitosis and vesicular transport. Microtubules comprise of tubulin subunits tubulin dimers arranged in a cylindrical beta and formed by alpha hollow tube structure with a diameter of 20nm. They are typically comprised of 13 or 14 protofilaments arranged in spiral configurations. The longitudinal bonds between the tubulin dimers are much stiffer and stronger than the lateral bonds. This implies the anisotropic structure and properties of the microtubule. In this work, the aim is to define a complete set of elastic properties that capture the atomistic behavior and track the deformation of the microtubules under different loading conditions. A seamless microtubule wall is represented as a two dimensional triangulated lattice of dimers from which a representative volume element can be defined. A harmonic potential is adapted for the dimer–dimer interactions. Estimating the lattice elastic constants and following the methodology from the analysis of the mechanical behavior of triangulated spectrin network of the red blood cell membrane (Arslan and Boyce, 2006); a general continuum level constitutive model of the mechanical behavior of the microtubule lattice wall is developed. The model together with the experimental data given in the literature provides an insight to defining the parameters required for the discrete numerical model created in finite element analysis medium. The three point bending simulations for a microtubule modeled using shell elements, give tube bending stiffness values that are in accordance with the experimental bending stiffness values. The micrographs also show that shrinking ends of microtubules (due to microtubule instabilities) curl out. This implies the existence of prestress. A “connector model” is proposed to include the effect of the prestress and to capture the dynamic instabilities of microtubules.
Physical comorbidities affect physical activity in chronic obstructive pulmonary disease: A prospective cohort study

The prevalence of physical comorbidities such as obesity, musculoskeletal or neurological conditions in people with chronic obstructive pulmonary disease (COPD) is high, yet little is known about the impact of these physical comorbidities on physical activity. The primary aim of the study was to compare the physical activity levels of people with COPD with physical comorbidities (COPD + PC) to people with COPD without physical comorbidities (COPD) and healthy age‐matched volunteers (control group).
Choline Protects Against Intestinal Failure–Associated Liver Disease in Parenteral Nutrition–Fed Immature Rats

BACKGROUND Deficiency of choline, a required nutrient, is related to intestinal failure-associated liver disease (IFALD). Therefore, we aimed to investigate the effects of choline supplementation on IFALD and the underlying mechanisms. METHODS Male Sprague-Dawley rats (4 weeks old) were fed AIN-93G chow and administered intravenous 0.9% saline (control), parenteral nutrition (PN), or PN plus intravenous choline (600 mg/kg) for 7 days. We evaluated body weight, hepatic histology, biochemical indicators, triglycerides, oxidative status, methylation levels of peroxisomal proliferator-activated receptor alpha (PPARα) gene promoter, expression of PPARα and carnitine palmitoyltransferase 1 (CPT1), and levels of choline metabolites. RESULTS The PN + choline group exhibited improved body weight compared with the PN group. PN impaired hepatic function, increased hepatic triglycerides, induced dyslipidemia, enhanced reactive oxygen species and malondialdehyde, and reduced total antioxidant capacity. The PN group had higher pathologic scores than the control group. These results were prevented by choline administration. Compared with the control group, PN increased PPARα promoter methylation and hepatic betaine concentration, reduced hepatic choline and phosphatidylcholine (PC) levels, decreased plasma choline and betaine concentrations, and downregulated PPARα and CPT1 mRNA and protein expression. Choline supplementation elevated hepatic choline and PC levels and enhanced plasma choline, betaine, and PC concentrations but reduced hepatic betaine level, reversed PPARα promoter hypermethylation, and upregulated PPARα and CPT1 mRNA and protein expression in PN-fed rats, compared with rats receiving PN alone. CONCLUSION Choline addition to PN may prevent IFALD by reducing oxidative stress, enhancing hepatic fat export, and promoting fatty acid catabolism in immature rats receiving PN.
The Structure of Collaborative Tagging Systems

Collaborative tagging describes the process by which many users add metadata in the form of keywords to shared content. Recently, collaborative tagging has grown in popularity on the web, on sites that allow users to tag bookmarks, photographs and other content. In this paper we analyze the structure of collaborative tagging systems as well as their dynamical aspects. Specifically, we discovered regularities in user activity, tag frequencies, kinds of tags used, bursts of popularity in bookmarking and a remarkable stability in the relative proportions of tags within a given url. We also present a dynamical model of collaborative tagging that predicts these stable patterns and relates them to imitation and shared knowledge.
A reliable ex vivo invasion assay of human reticulocytes by Plasmodium vivax

Currently, there are no reliable RBC invasion assays to guide the discovery of vaccines against Plasmodium vivax, the most prevalent malaria parasite in Asia and South America. Here we describe a protocol for an ex vivo P vivax invasion assay that can be easily deployed in laboratories located in endemic countries. The assay is based on mixing enriched cord blood reticulocytes with matured, trypsin-treated P vivax schizonts concentrated from clinical isolates. The reliability of this assay was demonstrated using a large panel of P vivax isolates freshly collected from patients in Thailand.
Development of the body condition score system in Murrah buffaloes: validation through ultrasonic assessment of body fat reserves

The body condition score (BCS) system is a subjective scoring method of evaluating the energy reserves of dairy animals to provide better understanding of biological relationships between body fat, milk production and reproduction. This method helps in adopting the optimum management practices to derive maximum production and maintain optimum health of the livestock. In this study, a new BCS system was developed for Murrah buffaloes. The skeletal check points were identified by studying the anatomical features and amount of fat reserves in slaughtered animals. The scores were assigned from 1 to 5 based on the amount of fat reserves in slaughtered animals. A score of 1 represents least and 5 represents most amount of fat. The skeletal check points identified were ordered based on the amount of carcass fat reserves and scores assigned to prepare a preliminary BCS chart on a 1 to 5 scale at 0.25 increments. The BCS chart was further modified by eliminating the skeletal check points at which the fat reserves were less evident on palpation in most of the buffaloes and a new BCS chart on a 1 to 5 scale at 0.5 increments examining eight skeletal check points was developed. The new BCS system developed was tested for precision in 10 buffaloes for each point of the 1-5 scale by ultrasonographic measurements of body fat reserves. Ultrasonographic measurements showed that as the BCS increased, the amount of fat reserves also increased (p < 0.01), indicating that the BCS adequately reflected the amount of actual fat reserves. BCS was significantly correlated (r = 0.860) with the carcass fat reserves as well as the ultrasonographic fat reserves (r = 0.854).
The role of the RE1 element in activation of the NR1 promoter during neuronal differentiation

To understand the genetic mechanism controlling the expression of the NMDA subtype of glutamate receptors during neuronal differentiation, we studied activation of the N‐methyl‐D‐aspartate receptor subunit 1 (NR1) gene and the role of the repressor element‐1 (RE1) element in NR1 promoter activation. Following neuronal differentiation of P19 embryonic carcinoma cells, the NR1 transcription rate and mRNA level were significantly increased, while the nuclear level of the repressor RE1 silencing transcription factor (REST)/neuron‐restriction silencer factor (NRSF) was reduced. Nuclear REST/NRSF from undifferentiated cells formed a large complex with the NR1 RE1 element. While this complex was significantly reduced after the differentiation, REST/NRSF from differentiated cells formed a new, faster migrating complex. In transient transfections, deletion of the RE1 element increased activity of the 5.4‐kb NR1 promoter sixfold in undifferentiated cells, but only induced approximately 1.4‐fold increase in differentiated cells. Forced expression of REST/NRSF in differentiated cells suppressed the promoter, while forced expression of a dominant‐negative REST/NRSF induced promoter activity as well as the mRNA of the NR1 gene in undifferentiated cells. In stable transfectants, the wild‐type promoter showed a robust increase in activity following differentiation in a pattern similar to the NR1 mRNA increase. Conversely, the promoter lacking the RE1 element showed only a moderate increase. Our data suggest that the NR1 gene up‐regulation during neuronal differentiation is controlled by its promoter activation, which is largely determined by the interaction between the RE1 element and the repressor REST/NRSF.
Deliberative automated negotiators using fuzzy similarities

Automated agents are autonomous entities which de cide for themselves what when and under what con ditions their actions should be performed Since agents have no direct control over others they must persuade others to act in a particular manner The type of per suasion we consider in this paper is negotiation which we de ne as a process by which a joint decision is made by two or more parties The parties rst verbalise con tradictory demands and then move towards agreements Pruitt For negotiation agents must be provided with the ca pability to represent and reason about within their in formation and resource bounds both their internal and their external world and with the capacity to interact according to a normative protocol It is this individual agent modelling which has been the central focus of the work reported in this paper This paper extends our previous work reported in Faratin Sierra Jennings on negotiation mod els in the following way The agent architecture has been updated from a purely responsive mechanisms to include new higher level deliberative mechanisms in volving the generation of trade o s and the manipula tion of the set of issues under negotiation by means of a fuzzy similarity measure This paper advances the state of the art in negotiation by designing components of a negotiation architecture which allows agents to be both responsive and deliberative and thus participate in more varied types of negotiation processes The deliberative component of the individual agent architecture is expanded on which describe evaluation and o er generation mechanisms An example of a real world scenario is then introduced to clarify the con cepts introduced in the model Finally we present the conclusions reached and future avenues of research
Food-Web Structure of Seagrass Communities across Different Spatial Scales and Human Impacts

Seagrass beds provide important habitat for a wide range of marine species but are threatened by multiple human impacts in coastal waters. Although seagrass communities have been well-studied in the field, a quantification of their food-web structure and functioning, and how these change across space and human impacts has been lacking. Motivated by extensive field surveys and literature information, we analyzed the structural features of food webs associated with Zostera marina across 16 study sites in 3 provinces in Atlantic Canada. Our goals were to (i) quantify differences in food-web structure across local and regional scales and human impacts, (ii) assess the robustness of seagrass webs to simulated species loss, and (iii) compare food-web structure in temperate Atlantic seagrass beds with those of other aquatic ecosystems. We constructed individual food webs for each study site and cumulative webs for each province and the entire region based on presence/absence of species, and calculated 16 structural properties for each web. Our results indicate that food-web structure was similar among low impact sites across regions. With increasing human impacts associated with eutrophication, however, food-web structure show evidence of degradation as indicated by fewer trophic groups, lower maximum trophic level of the highest top predator, fewer trophic links connecting top to basal species, higher fractions of herbivores and intermediate consumers, and higher number of prey per species. These structural changes translate into functional changes with impacted sites being less robust to simulated species loss. Temperate Atlantic seagrass webs are similar to a tropical seagrass web, yet differed from other aquatic webs, suggesting consistent food-web characteristics across seagrass ecosystems in different regions. Our study illustrates that food-web structure and functioning of seagrass habitats change with human impacts and that the spatial scale of food-web analysis is critical for determining results.
Effects of Ratio of CFRP Plate Length to Shear Span and End Anchorage on Flexural Behavior of SCC RC Beams

The aim of this experimental investigation is to study the effect of the ratio of carbon fiber-reinforced polymer (CFRP) precured laminate length to shear span and different end plate anchorage systems on the flexural behavior of reinforced concrete (RC) beams cast with self-consolidating concrete (SCC). SCC with a grade of 54 MPa has been used throughout this research to ensure consistent high quality and high concrete compressive strength in all beams and to eliminate the need of any compaction. Ten RC beams strengthened with CFRP plate lengths to shear span ratio of 0, 25, 70, and 85% with and without end anchorages, were tested under monotonic loading. In particular, a single layer of U-wrap sheet and two layers of U-wrap sheets with one layer in the longitudinal direction and the other in the transverse direction were used as end anchorages (double wrap). The results were compared with each other and with those of the same test conducted on an unstrengthened control beam specimen. The load-deflection.