Miracle-dz/UniFAR-FTUs huggingface dataset:
Controllability in Cancer Metabolic Networks According to Drug Targets as Driver Nodes

Networks are employed to represent many nonlinear complex systems in the real world. The topological aspects and relationships between the structure and function of biological networks have been widely studied in the past few decades. However dynamic and control features of complex networks have not been widely researched, in comparison to topological network features. In this study, we explore the relationship between network controllability, topological parameters, and network medicine (metabolic drug targets). Considering the assumption that targets of approved anticancer metabolic drugs are driver nodes (which control cancer metabolic networks), we have applied topological analysis to genome-scale metabolic models of 15 normal and corresponding cancer cell types. The results show that besides primary network parameters, more complex network metrics such as motifs and clusters may also be appropriate for controlling the systems providing the controllability relationship between topological parameters and drug targets. Consequently, this study reveals the possibilities of following a set of driver nodes in network clusters instead of considering them individually according to their centralities. This outcome suggests considering distributed control systems instead of nodal control for cancer metabolic networks, leading to a new strategy in the field of network medicine.
A Unified Analysis for Conforming and Nonconforming Stabilized Finite Element Methods Using Interior Penalty

We discuss stabilized Galerkin approximations in a new framework, widening the scope from the usual dichotomy of the discontinuous Galerkin method on the one hand and Petrov--Galerkin methods such as the SUPG method on the other. The idea is to use interior penalty terms as a means of stabilizing the finite element method using conforming or nonconforming approximation, thus circumventing the need of a Petrov--Galerkin-type choice of spaces. This is made possible by adding a higher-order penalty term giving L2-control of the jumps in the gradients between adjacent elements. We consider convection-diffusion-reaction problems using piecewise linear approximations and prove optimal order a priori error estimates for two different finite element spaces, the standard H1-conforming space of piecewise linears and the nonconforming space of piecewise linear elements where the nodes are situated at the midpoint of the element sides (the Crouzeix--Raviart element). Moreover, we show how the formulation extends to discontinuous Galerkin interior penalty methods in a natural way by domain decomposition using Nitsche's method.
Translocation kinetics of plutonium oxide from the popliteal lymph nodes of beagles.

The translocation kinetics of high-fired plutonium oxide from the popliteal lymph nodes was studied in beagles with 9.2 to 39.445 of plutonium-239 oxide implanted subcutaneously in the left hind paws to simulate accidental contamination of hand wounds. The left hind paw was amputated 4 weeks after implantation to prevent continued deposition of plutonium oxide particles in the left popliteal lymph node. External in situ scintillation data showed slight clearance of plutonium from the popliteal lymph nodes of beagles monitored for 32 weeks. The estimated time for the fraction of plutonium retained at 100 days to be reduced by one-half varied from 290 to 1508 days. Treatment with DTPA did not have a measurable effect on the clearance of high-fired plutonium oxide from popliteal lymph nodes. INTRODUCTION REGIONAL lymph nodes are major repositories for plutonium in beagles after subcutaneous injections simulating contamination of hand wounds (JOHNSON e t al., 1970; WATTERS and LEBEL, 1971; LEBEL and WATTERS, 1972; BISTLINE e t al., 1972; BISTLINE, 1973). Plutonium continued to accumulate for 2-4 weeks in the left superficial cervical lymph nodes of dogs after implantation of plutonium into the left forepaw. At longer intervals, the amount of plutonium was occasionally observed to decrease in the superficial cervical lymph nodes. The kinetics of lymph node clearance were complicated by continuous plutonium translocation from the injection site to these regional lymph nodes. The influence of the superficial cervical lymph nodes on systemic deposition of plutonium from subcutaneous wounds was also difficult to assess because the * This study was performed at Colorado State University with support from the United States Atomic Energy Commission, Division of Biology and Medicine [Contract No. A.T. (1 1-1)-17871; this is report No. COO-1787-22. R. BUSCHBOM, at Battelle Pacific Northwest Laboratories, assisted in statistical evaluation. t Biology Department, Battelle Pacific Northwest Laboratories, Richland, Washington 99352. $, Division of Biomedical and Environmental Research, U.S. Atomic Energy Commission, Washington, D.C. 20545. $ Los Alamos Scientific Laboratory, Los Alamos, New Mexico 87544. number of such nodes and the route of drainage varied from animal to animal (GOMEZ, 1973). This report describes experiments designed to provide a more precise model for elucidation of the mode and kinetics of clearance of plutonium from wound sites, from lymph nodes, and from phagocytic cells.
Efficacy of Sublingual Immunotherapy with Multiple Allergens in Bronchial Asthma

Background : Specific allergen immunotherapy (SIT) involves the administration of allergen extracts to modify or abolish symptoms associated with atopic allergy. Allergen specific immunotherapy is a cornerstone in the management of respiratory allergy. The traditional subcutaneous route is burdened with the severe adverse reactions. In the present study, an attempt has been made to administer the allergen specific vaccine through oral route using multiple allergens in allergic bronchial asthma. The efficacy and safety with sublingual immunotherapy has already been demonstrated mostly in the treatment of allergic rhinitis. Setting and Design : Based on clinical history, symptoms presented for at least 3 years with set criteria for immuno-modulation for asthma, failure in allergen avoidance and moderate to severe clinical manifestations. Material and Methods : A total number of 60 patients with allergic asthma were scrutinized of which 25 were subjected for detailed physical examination family history, pulse, blood pressure. , haemoglobin, stool examination and medication Allergy skin test with various allergens were performed by using modified skin prick test method. Allergens showing reactions equivalent or more than positive control (histamine were incorporated in the formulation of immunotherapy mixture. Symptoms before and after the therapy, Peak expiratory flow rate (PEFR), skin test, side effects and medications were studied. Results and Conclusions : Our results of sublingual immunotherapy using multiple allergen showed significant reduction in symptoms, medication, and improvement in PEFR by modifying the natural history of the disease and preventing the onset of new sensitization. SLIT could be a viable alternative to SCIT, with the same rationale and indication. It could be used in association with proper pharmaco-therapy at the earlier stages of allergic bronchial asthma for optimal symptomatic relief.
Fine-Structure Molecular Typing of Irish Helicobacter pylori Isolates and Their Genetic Relatedness to Strains from Four Different Continents

ABSTRACT Genotyping of 74 Irish Helicobacter pylori isolates was performed at four different loci (vacA signal sequence and mid-region, insertion-deletion polymorphisms at the 3′ end of the cag pathogenicity island, and cagA). The predominant vacA alleles and insertion-deletion motifs suggest an ancestral relationship between Irish isolates and either specific East Asian or Northern European strains. In addition, fluorescent amplified fragment length polymorphism-PCR genotyping and phylogenetic analysis of 32 representative Irish H. pylori isolates and 22 isolates from four different continents demonstrated that the Irish H. pylori isolates examined were weakly clonal and showed some association with both European and Asian isolates. These three genotyping techniques show that Irish H. pylori isolates have distinctive features that may have evolved in this insular European population.
Essential role of p38 MAPK for activation of skeletal muscle glucose transport by lithium

Abstract Lithium increases glucose transport and glycogen synthesis in insulin-sensitive cell lines and rat skeletal muscle, and has been used as a non-selective inhibitor of glycogen synthase kinase-3 (GSK-3). However, the molecular mechanisms underlying lithium action on glucose transport in mammalian skeletal muscle are unknown. Therefore, we examined the effects of lithium on glucose transport activity, glycogen synthesis, insulin signaling elements (insulin receptor (IR), Akt, and GSK-3β), and the stress-activated p38 mitogen-activated protein kinase (p38 MAPK) in the absence or presence of insulin in isolated soleus muscle from lean Zucker rats. Lithium (10 mM LiCl) enhanced basal glucose transport by 62% (p < 0.05) and augmented net glycogen synthesis by 112% (p < 0.05). Whereas lithium did not affect basal IR tyrosine phosphorylation or Akt ser473 phosphorylation, it did enhance (41%, p < 0.05) basal GSK-3β ser9 phosphorylation. Lithium further enhanced (p < 0.05) the stimulatory effects of insulin on glucose transport (43%), glycogen synthesis (44%), and GSK-3β ser9 phosphorylation (13%). Lithium increased (p < 0.05) p38 MAPK phosphorylation both in the absence (37%) and presence (41%) of insulin. Importantly, selective inhibition of p38 MAPK (using 10 μM A304000) completely prevented the basal activation of glucose transport by lithium, and also significantly reduced (52%, p < 0.05) the lithium-induced enhancement of insulin-stimulated glucose transport. Theses results demonstrate that lithium enhances basal and insulin-stimulated glucose transport activity and glycogen synthesis in insulin-sensitive rat skeletal muscle, and that these effects are associated with a significant enhancement of GSK-3β phosphorylation. Importantly, we have documented an essential role of p38 MAPK phosphorylation in the action lithium on the glucose transport system in isolated mammalian skeletal muscle.
Greenhouse Gas Flux and Crop Productivity after 10 Years of Reduced and No Tillage in a Wheat-Maize Cropping System

Appropriate tillage plays an important role in mitigating the emissions of greenhouse gases (GHG) in regions with higher crop yields, but the emission situations of some reduced tillage systems such as subsoiling, harrow tillage and rotary tillage are not comprehensively studied. The objective of this study was to evaluate the emission characteristics of GHG (CH4 and N2O) under four reduced tillage systems from October 2007 to August 2009 based on a 10-yr tillage experiment in the North China Plain, which included no-tillage (NT) and three reduced tillage systems of subsoil tillage (ST), harrow tillage (HT) and rotary tillage (RT), with the conventional tillage (CT) as the control. The soil under the five tillage systems was an absorption sink for CH4 and an emission source for N2O. The soil temperature positive impacted on the CH4 absorption by the soils of different tillage systems, while a significant negative correlation was observed between the absorption and soil moisture. The main driving factor for increased N2O emission was not the soil temperature but the soil moisture and the content of nitrate. In the two rotation cycle of wheat-maize system (10/2007–10/2008 and 10/2008–10/2009), averaged cumulative uptake fluxes of CH4 under CT, ST, HT, RT and NT systems were approximately 1.67, 1.72, 1.63, 1.77 and 1.17 t ha−1 year−1, respectively, and meanwhile, approximately 4.43, 4.38, 4.47, 4.30 and 4.61 t ha−1 year−1 of N2O were emitted from soil of these systems, respectively. Moreover, they also gained 33.73, 34.63, 32.62, 34.56 and 27.54 t ha−1 yields during two crop-rotation periods, respectively. Based on these comparisons, the rotary tillage and subsoiling mitigated the emissions of CH4 and N2O as well as improving crop productivity of a wheat-maize cropping system.
Comparative bioavailability of ferric polymaltose and ferrous sulphate in iron‐deficient blood donors

Absolute iron deficiency is treated by correcting the causative lesion and then, traditionally, administering sufficient amounts of ferrous salt to return the haemoglobin level to normal and replenish body stores. The bioavailability of ferric compounds has been questioned and accordingly their therapeutic role remains controversial. A special problem is posed by regular blood donation, where the frequency of phlebotomy is limited by the haemoglobin level, which, in turn, requires maintenance of an adequate supply of iron from dietary sources. Since this latter situation may not always occur, it would be of practical benefit to have a form of supplementation that is effective and can be taken without side effects. These issues were prospectively examined in a consecutive series of otherwise healthy blood donors who developed absolute iron deficiency anaemia and were then randomly allocated to receive 60 mg of this metal as ferrous sulphate twice a day (Group 1: n = 51), 100 mg as chewable ferric polymaltose daily (Group 2: n = 53), or the latter product twice a day (Group 3: n = 55). Serial studies showed that 80% of patients in Groups 1 and 3 had reached normal haemoglobin levels by 12 weeks, but this figure was only 50% in Group 2. Similarly, the proportion of patients improving their percentage saturation of transferrin to within the normal range was significantly better in Groups 1 and 3 than in Group 2 (P < .01). However, body iron stores, reflected in serum ferritin level, was significantly better in Group 1 (P < .01); there was no difference in this respect between Groups 2 and 3. Toxicity was more severe in those receiving ferrous sulphate, with 20% having to discontinue participation owing to nausea and vomiting, whereas this was mild in those receiving ferric polymaltose and none withdrew from the trial for this reason. It can be concluded that the two forms of iron are equally bioavailable for hemoglobin regeneration, but at 12 weeks of study ferrous sulphate was superior in reconstituting stores, as reflected in the serum ferritin level. Since the ferric iron complex is associated with only minimal side effects, it may be useful in selected populations and, in the context of blood donors, valuable as a means of maintaining positive balance, thereby diminishing the number of donors rejected because of their having developed phlebotomy‐iron deficiency anaemia. © 1993 Wiley‐Liss, Inc.
Marine Toxins That Target Voltage-gated Sodium Channels

Eukaryotic, voltage-gated sodium (NaV) channels are large membrane proteins which underlie generation and propagation of rapid electrical signals in nerve, muscle and heart. Nine different NaV receptor sites, for natural ligands and/or drugs, have been identified, based on functional analyses and site-directed mutagenesis. In the marine ecosystem, numerous toxins have evolved to disrupt NaV channel function, either by inhibition of current flow through the channels, or by modifying the activation and inactivation gating processes by which the channels open and close. These toxins function in their native environment as offensive or defensive weapons in prey capture or deterrence of predators. In composition, they range from organic molecules of varying size and complexity to peptides consisting of ~10–70 amino acids. We review the variety of known NaV-targeted marine toxins, outlining, where known, their sites of interaction with the channel protein and their functional effects. In a number of cases, these natural ligands have the potential applications as drugs in clinical settings, or as models for drug development.
Examining a model of antecedents and consequences of perceptions of organizational politics (POPS)

Perceptions of organizational politics (POPS) have received significant attention in the literature and scholars have devoted great efforts to explore this phenomenon. Although they have recognized organizations as inherently political arenas relatively little is known about the antecedents as well as the consequences of POPS on employees and their organizations. This thesis draws on social exchange framework to describe the relationships among POPS and individual and organizational outcomes namely affective commitment, turnover intentions, organisational citizenship behaviors, and innovativeness related behavior. However, what drives employees to engage in POPS? It answers this fundamental question by examining the role of personality in the prediction of POPS. Furthermore, it explores how the mediating variables (organizational cynicism, political influence behavior, and trust) affect these relationships. A two wave study addresses these questions over a six-month period. In addition this study introduces the political skill self-efficacy (PSSE) construct and investigates its moderating impact on POPS-outcomes relationships. I developed and validated a scale of political skill self-efficacy (PSSE) to measure the proposed construct using three independently samples. Findings indicated that personality trait of neuroticism predicts POPS (T1) while POPS (T1) found to have positive significant relationship with organizational cynicism. I also found evidence that POPS (Time 1) has an impact on turnover intentions (Time 2) and affective commitment (Time 2). Specifically, increased perceptions of politics were associated to decreased affective commitment and increased turnover intentions. In addition, no support found for the mediating role of organisational cynicism, interpersonal trust and political influence behavior in the relationships among POPs (T1) and organizational outcomes (T2). Further, results partially supported the mediating role of organisational trust
Sales Promotion Effectiveness: The Impact of Culture at an Ethnic-Group Level

There is considerable interest and debate over the effectiveness of sales promotion. Previous studies have shown that sales promotions are more effective when they provide benefits that are congruent with those of the promoted product. This study explores and extends the congruency framework by analysing the impact of culture at an ethnic group level. The purpose is to investigate the popular assumption that cultural differences exist at this level and to see whether these differences have an impact on sales promotion effectiveness. A quasi-experimental design is used to test a series of hypotheses based on a sample of Anglo-Australians and Chinese-Australians. It is found that despite the existence of cultural differences at an ethnic level, culture does not appear to have a significant impact on consumer responses to sales promotion. It is also found that the congruency effects between product and promotion type are weak and may be non-existent in some cases. Finally, the study also provides evidence that further validates a scale used for the measurement of culture.
Predicting the Sentiment Polarity and Rating of Yelp Reviews

Online reviews of businesses have become increasingly important in recent years, as customers and even competitors use them to judge the quality of a business. Yelp is one of the most popular websites for users to write such reviews, and it would be useful for them to be able to predict the sentiment or even the star rating of a review. In this paper, we develop two classifiers to perform positive/negative classification and 5-star classification. We use Naive Bayes, Support Vector Machines, and Logistic Regression as models, and achieved the best accuracy with Logistic Regression: 92.90% for positive/negative classification, and 63.92% for 5-star classification. These results demonstrate the quality of the Logistic Regression model using only the text of the review, yet there is a promising opportunity for improvement with more data, more features, and perhaps different models.
Monoamine oxidase A and childhood adversity as risk factors for conduct disorder in females

Background Recent studies among males have reported a genotype–environment interaction (G×E) in which low-activity alleles at the monoamine oxidase A (MAOA) locus conferred greater sensitivity to the effects of childhood adversity on risk for conduct disorder (CD). So far, few studies of females have controlled for gene–environment correlation or used females heterozygous for this X-linked gene. Method Logistic regression analysis of a sample of 721 females ages 8–17 years from the longitudinal Virginia Twin Study of Adolescent Behavioral Development (VTSABD) assessed the additive effects of MAOA genotypes on risk for CD, together with the main effect of childhood adversity and parental antisocial personality disorder (ASP), as well as the interaction of MAOA with childhood adversity on risk for CD. Results A significant main effect of genotype on risk for CD was detected, where low-activity MAOA imparted the greatest risk to CD in girls while controlling for the significant effects of maternal ASP and childhood adversity. Significant G×E with weak effect was detected when environmental exposure was untransformed, indicating a higher sensitivity to childhood adversity in the presence of the high-activity MAOA allele. The interaction was no longer statistically significant after applying a ridit transformation to reflect the sample sizes exposed at each level of childhood adversity. Conclusions The main effect of MAOA on risk for CD in females, its absence in males and directional difference of interaction is suggestive of genotype–sex interaction. As the effect of G×E on risk for CD was weak, its inclusion is not justified.
Cryopreservation of Hepatocyte Microbeads for Clinical Transplantation

Intraperitoneal transplantation of hepatocyte microbeads is an attractive option for the management of acute liver failure. Encapsulation of hepatocytes in alginate microbeads supports their function and prevents immune attack of the cells. Establishment of banked cryopreserved hepatocyte microbeads is important for emergency use. The aim of this study was to develop an optimized protocol for cryopreservation of hepatocyte microbeads for clinical transplantation using modified freezing solutions. Four freezing solutions with potential for clinical application were investigated. Human and rat hepatocytes cryopreserved with University of Wisconsin (UW)/10% dimethyl sulfoxide (DMSO)/5% (300 mM) glucose and CryoStor CS10 showed better postthawing cell viability, attachment, and hepatocyte functions than with histidine–tryptophan–ketoglutarate/10% DMSO/5% glucose and Bambanker. The 2 freezing solutions that gave better results were studied with human and rat hepatocytes microbeads. Similar effects on cryopreserved microbead morphology (external and ultrastructural), viability, and hepatocyte-functions post thawing were observed over 7 d in culture. UW/DMSO/glucose, as a basal freezing medium, was used to investigate the additional effects of cytoprotectants: a pan-caspase inhibitor (benzyloxycarbonyl-Val-Ala-dl-Asp-fluoromethylketone [ZVAD]), an antioxidant (desferoxamine [DFO]), and a buffering and mechanical protectant (human serum albumin [HSA]) on RMBs. ZVAD (60 µM) had a beneficial effect on cell viability that was greater than with DFO (1 mM), HSA (2%), and basal freezing medium alone. Improvements in the ultrastructure of encapsulated hepatocytes and a lower degree of cell apoptosis were observed with all 3 cytoprotectants, with ZVAD tending to provide the greatest effect. Cytochrome P450 activity was significantly higher in the 3 cytoprotectant groups than with fresh microbeads. In conclusion, developing an optimized cryopreservation protocol by adding cytoprotectants such as ZVAD could improve the outcome of cryopreserved hepatocyte microbeads for future clinical use.