Miracle-dz/UniFAR-FTUs huggingface dataset:
State–time spectrum of signal transduction logic models

Despite the current wealth of high-throughput data, our understanding of signal transduction is still incomplete. Mathematical modeling can be a tool to gain an insight into such processes. Detailed biochemical modeling provides deep understanding, but does not scale well above relatively a few proteins. In contrast, logic modeling can be used where the biochemical knowledge of the system is sparse and, because it is parameter free (or, at most, uses relatively a few parameters), it scales well to large networks that can be derived by manual curation or retrieved from public databases. Here, we present an overview of logic modeling formalisms in the context of training logic models to data, and specifically the different approaches to modeling qualitative to quantitative data (state) and dynamics (time) of signal transduction. We use a toy model of signal transduction to illustrate how different logic formalisms (Boolean, fuzzy logic and differential equations) treat state and time. Different formalisms allow for different features of the data to be captured, at the cost of extra requirements in terms of computational power and data quality and quantity. Through this demonstration, the assumptions behind each formalism are discussed, as well as their advantages and disadvantages and possible future developments.
The Representation of Uniform Motion in Vision

For veridical detection of object motion any moving detecting system must allocate motion appropriately between itself and objects in space. A model for such allocation is developed for simplified situations (points of light in uniform motion in a frontoparallel plane). It is proposed that motion of objects is registered and represented successively at four levels within frames of reference that are defined by the detectors themselves or by their movements. The four levels are referred to as retinocentric, orbitocentric, egocentric, and geocentric. Thus the retinocentric signal is combined with that for eye rotation to give an orbitocentric signal, and the left and right orbitocentric signals are combined to give an egocentric representation. Up to the egocentric level, motion representation is angular rather than three-dimensional. The egocentric signal is combined with signals for head and body movement and for egocentric distance to give a geocentric representation. It is argued that although motion perception is always geocentric, relevant registrations also occur at the three earlier levels. The model is applied to various veridical and nonveridical motion phenomena.
Of Bugs and Men: Antigen-Fortified Lactoccoccus lactis for Type 1 Diabetes Immunotherapy

One of the hurdles encountered by immunotherapy attempts for type 1 diabetes (T1D) is the delicate ethical issue of minimizing risks for a disease with a normal life expectancy in many patients. For this reason, antigen (Ag)-specific immunotherapies are attractive in view of their selectivity and favorable safety profile (1). However, they have not met expectations in therapeutic trials using insulin (2–4) and GAD (5). These trials face several technical difficulties: the need to produce and administer proteins of suitable quality and quantity; bioavailability issues, as prolonged delivery of small Ag amounts may be more effective at restoring long-term immune tolerance; routes of administration, with the noninvasive oral route being more tolerogenic but suffering considerable Ag degradation; and Ag delivery in a noninflammatory environment to avoid unwanted immunogenic outcomes. The most important issue is the timing of immune intervention, with a panoply of agents effective at preventing disease even in the reductionist NOD mouse model, but only a handful working at reversing established disease, which is the preferred setting for human trials. In this issue, Robert et al. (6) bring Ag-specific therapies into a new dimension by letting genetically modified Lactococcus lactis do the job. L. lactis is a nonpathogenic, noncolonizing, commensal bacterium with a long safety record in the dairy industry. Biological containment of genetically modified strains to avoid environmental propagation can be obtained …
A Study of Surface Modification of Poly(lactic-co-glycolic) Acid Using Argon Ion Irradiation

The effect of Argon ion irradiation to the surface properties of poly(lactic-co-glycolic) acid (PLGA) was studied. A beam of 170 keV Argon ions was implanted at different fluencies (1 × 1012, 1 × 1013, 1 × 1014, and 1 × 1015 ions/cm2). X-ray photoelectron spectroscopy (XPS) was used to analyze the evolution of the bonding microstructure of PLGA due to irradiation. Surface morphology was monitored using atomic force microscopy (AFM). AFM analysis shows that film roughness increased to maximum at the dose of 1 × 1014 ions/cm2 where the formations of hillocks were also detected. Hydrophilicity of PLGA is important for their applications in biomedicine such as bioscaffolds. Hydrophilicity was monitored using water contact angle measurements for both unmodified and ion-modified PLGA. It was observed that hydrophilicity of PLGA changes with the ion irradiation. This demonstrates that ion irradiation can be an alternative approach to control hydrophilicity of PLGA. PLGA scaffolds modified with ion irradiation could therefore be more suitable for the biomedical applications.
First Isolation of Streptococcus gallolyticus subsp. pasteurianus from a Korean Patient with Severe Septic Shock.

First Isolation of Streptococcus gallolyticus subsp. pasteurianus from a Korean Patient with Severe Septic Shock Seri Jeong, Ji Yeon Park, Sang Hoon Han, Yangsoon Lee, Dongeun Yong, Kyungwon Lee, Yunsop Chong Department of Laboratory Medicine and Research Institute of Bacterial Resistance, Department of Internal Medicine, Yonsei University College of Medicine, Seoul, Department of Laboratory Medicine, National Health Insurance Corporation Ilsan Hospital, Goyang, Korea
Monoclonal γ-Globulins in Ferrets with Lymphoproliferative Lesions.∗

Summary Electrophoretic analyses of sera from 92 ferrets revealed 38 to have gamma globulin values above 20%, 27 above 30%, and 12 above 40%. Sixteen of the ferrets with hypergammaglobulmemia were necrop-sied and found to have systemic plasmacellu-lar infiltrates with lymph node and frequent thymic hypertrophy. Seven of the ferrets had a monoclonal type of hypergammaglobulin-emia.
The Action Spectrum for Generation of the Primary Intermediate Revealed by Ultrafast Absorption Spectroscopy Studies of Pheomelanin¶

Abstract The observation that fair-skinned individuals are more susceptible to skin cancers is commonly explained by invoking an enhanced photoreactivity of the red melanin, pheomelanin compared with the black melanin, eumelanin. For the wavelength range from 500 to 1000 nm, pump-probe spectroscopic measurements reveal the photoexcitation of pheomelanin by UVA light that generates an immediate (<100 fs) transient absorption centered at 780 nm. Using a tunable femtosecond excitation source, the action spectrum between 300 and 390 nm for generation of the primary intermediate was measured. Similar action spectra are found for the sample with molecular weight (MW) between 1000 and 10 000 and the one with MW > 10 000 fractions of pheomelanin, indicating that the reactive chromophore has a low MW but is present and its photophysics is similar in the aggregated pigment. The shape of the action spectrum differs from the absorption spectrum of bulk melanin and mass-selected fractions but resembles reported absorption spectrum of benzothiazines, oxidation products of 5-S-cysteinyl-dopa, which are formed along the biosynthetic pathway of pheomelanin.
Regionalism Does Matter but Nationalism Prevails. A Comparative Analysis of Career Patterns in Western Multi-Level Democracies

The processes of regionalization and federalization are unquestionable trends in Europe considering the flow of powers from states to subnational levels. In multi-level systems, the patterns of regional and national careers have responded to this structural evolution. In the literature, two positions oppose each other about the effects of regionalism. Some authors argue that it does affect career patterns while other scholars found little evidence of the regionalism hypothesis. Unclear results in the literature are partly due to the limited number of comparative research across country and across time, choice in case selection, and bias of the unit of analysis. This paper seeks to address these three issues based on an original dataset of 4.991 regional and national careers in Belgium (Flanders, Wallonia, and Brussels), Canada (Ontario and Quebec), Spain (Catalonia and Castilla-La-Mancha), and the UK (Wales and Scotland). The intranational and international comparison proves that regionalism does matter – regional politics attract more professionalized MPs where regionalism is stronger – but the national parliament remains ultimately the most attractive political arena across regions.
The Epstein-Barr Virus BZLF1 Protein Inhibits Tumor Necrosis Factor Receptor 1 Expression through Effects on Cellular C/EBP Proteins

ABSTRACT The Epstein-Barr virus immediate-early protein, BZLF1 (Z), initiates the switch between latent and lytic infection and plays an essential role in mediating viral replication. Z also inhibits expression of the major receptor for tumor necrosis factor (TNF), TNFR1, thus repressing TNF cytokine signaling, but the mechanism for this effect is unknown. Here, we demonstrate that Z prevents both C/EBPα- and C/EBPβ-mediated activation of the TNFR1 promoter (TNFR1p) by interacting directly with both C/EBP family members. We show that Z interacts directly with C/EBPα and C/EBPβ in vivo and that a Z mutant altered at alanine residue 204 in the bZIP domain is impaired for the ability to interact with both C/EBP proteins. Furthermore, we find that the Z(A204D) mutant is attenuated in the ability to inhibit the TNFR1p but mediates lytic viral reactivation and replication in vitro in 293 cells as well as wild-type Z. Although Z does not bind directly to the TNFR1p in EMSA studies, chromatin immunoprecipitation studies indicate that Z is complexed with this promoter in vivo. The Z(A204D) mutant has reduced interaction with the TNFR1p in vivo but is similar to wild-type Z in its ability to complex with the IL-8 promoter. Finally, we show that the effect of Z on C/EBPα- and C/EBPβ-mediated activation is promoter dependent. These results indicate that Z modulates the effects of C/EBPα and C/EBPβ in a promoter-specific manner and that in some cases (including that of the TNFR1p), Z inhibits C/EBPα- and C/EBPβ-mediated activation.
Suppressor Mutations in the Chloroplast-encoded Large Subunit Improve the Thermal Stability of Wild-type Ribulose-1,5-bisphosphate Carboxylase/Oxygenase*

A temperature-conditional, photosynthesis-deficient mutant of the green alga Chlamydomonas reinhardtii, previously recovered by genetic screening, results from a leucine 290 to phenylalanine (L290F) substitution in the chloroplast-encoded large subunit of ribulose-1,5-bisphosphate carboxylase/oxygenase (Rubisco, EC 4.1.1.39). Rubisco purified from mutant cells grown at 25 °C has a reduction in CO2/O2 specificity and is inactivated at lower temperatures than those that inactivate the wild-type enzyme. Second-site alanine 222 to threonine (A222T) or valine 262 to leucine (V262L) substitutions were previously isolated via genetic selection for photosynthetic ability at the 35 °C restrictive temperature. These intragenic suppressors improve the CO2/O2specificity and thermal stability of L290F Rubisco in vivoand in vitro. In the present study, directed mutagenesis and chloroplast transformation were used to create the A222T and V262L substitutions in an otherwise wild-type enzyme. Although neither substitution improves the CO2/O2 specificity above the wild-type value, both improve the thermal stability of wild-type Rubisco in vitro. Based on the x-ray crystal structure of spinach Rubisco, large subunit residues 222, 262, and 290 are far from the active site. They surround a loop of residues in the nuclear-encoded small subunit. Interactions at this subunit interface may substantially contribute to the thermal stability of the Rubisco holoenzyme.
Vis-NIR Spectroscopy and PLS Regression with Waveband Selection for Estimating the Total C and N of Paddy Soils in Madagascar

Visible and near-infrared (Vis-NIR) diffuse reflectance spectroscopy with partial least squares (PLS) regression is a quick, cost-effective, and promising technology for predicting soil properties. The advantage of PLS regression is that all available wavebands can be incorporated in the model, while earlier studies indicate that PLS models include redundant wavelengths, and selecting specific wavebands can refine PLS analyses. This study evaluated the performance of PLS regression with waveband selection using Vis-NIR reflectance spectra to estimate the total carbon (TC) and total nitrogen (TN) in soils collected mainly from the surface of upland and lowland rice fields in Madagascar (n = 59; after outliers were removed). We used iterative stepwise elimination-based PLS (ISE-PLS) to estimate soil TC and TN and compared the predictive ability with standard full-spectrum PLS (FS-PLS). The predictive abilities were assessed using the coefficient of determination (R2), the root mean squared error of cross-validation (RMSECV), and the residual predictive deviation (RPD). Overall, ISE-PLS using first derivative reflectance (FDR) showed a better predictive accuracy than ISE-PLS for both TC (R2 = 0.972, RMSECV = 0.194, RPD = 5.995) and TN (R2 = 0.949, RMSECV = 0.019, RPD = 4.416) in the soil of Madagascar. The important wavebands for estimating TC (12.59% of all wavebands) and TN (3.55% of all wavebands) were selected from all 2001 wavebands over the 400–2400 nm range using ISE-PLS. These findings suggest that ISE-PLS based on Vis-NIR diffuse reflectance spectra can be used to estimate soil TC and TN contents in Madagascar with an improved predictive accuracy.
Association of intracerebral bone fragments and epilepsy in missile head injuries

Twenty young adults sustained missile injuries in the Lebanese war. They underwent repeated clinical electroencephalographical (EEG), computerised tomography scanning (CT‐scan) and polysomnographic (PSG) examinations during a 6–year period. All the patients were young adult males with an average age of 23, previously healthy according to their army profiles. Three of 20 developed between 3 to 14 months following injury generalised tonic‐clonic convulsions. The unique common epileptogenic feature characterising the 3 epileptics was the presence of bone fragments in lacerated brain tissue. The possible causal relationship between the presence of the bone fragments and epileptogenesis is discussed.
Vascular tolerance to nitroglycerin in ascorbate deficiency: results are in favour of an important role of oxidative stress in nitrate tolerance.

In their recent article ‘Vascular tolerance to nitroglycerin (GTN) in ascorbate deficiency' Wolkart et al. demonstrated an impaired vasodilator potency of GTN in ascorbate-deficient guinea pigs.1 The authors also conclude from the lack of an effect of polyethylene-glycolated superoxide dismutase (PEG-SOD) and catalase (PEG-catalase), that the impairment of GTN vasodilator potency induced by ascorbate deficiency is not mediated by induction of oxidative stress (their Figure 3 ). Although these data are interesting, especially in the context of the previous literature suggesting a role of oxidative stress in the development of nitrate tolerance, we believe that several points deserve further discussion. Recent research emphasizes the role of mitochondria in the bioactivation of organic nitrates and in triggering the processes that mediate their clinical implications, including release of a nitric oxide (NO)-containing vasodilator, induction of ischaemic preconditioning, and tolerance.2–6 A number of studies, using antioxidants of different type and different affinity, show that …
An ‘endless struggle’: a qualitative study of general practitioners’ and practice nurses’ experiences of managing multimorbidity in socio-economically deprived areas of Scotland

Objectives: To understand general practitioners’ (GPs) and practice nurses’ (PNs) experiences of managing multimorbidity in deprived areas and elicit views on what might help. Methods: Qualitative interviews with 19 GPs and PNs in four practices with a high percentage of patients living in the top 15% most deprived areas of Scotland. Data were analysed using constant comparison. Results: Professionals’ discussions of how they managed multimorbidity captured: (1) definitions of multimorbidity that included multiple social, psychological, and health problems associated with deprivation; (2) descriptions of the ‘endless struggle’ of patients trying to manage illnesses in the midst of chaotic lives with limited personal, social, and material resources; (3) accounts of the ongoing struggle of professionals trying to manage, with personal consequences for some; and (4) ideas on what might help, including ‘whole person’ approaches. Discussion: Professionals’ discussions of the difficulties that they face personally and attempt to help those most in need reflect both the continuing existence of the ‘inverse care law’ and the need for whole system changes to enhance the effectiveness of primary care for patients with multimorbidity in deprived areas.
Neurological manifestations of falciparum malaria

Plasmodium falciparum remains one of the most common causes of central nervous system infection worldwide. Recently, differences between the pathophysiology of cerebral malaria in African children and nonimmune adults have been discovered, new syndromes occurring after malaria infection described, and mechanisms for the pathogenesis proposed. In addition, new antimalarial agents have been examined worldwide and initial studies on supportive studies conducted. This paper reviews these new advances, putting them into the perspective of the more established knowledge.
The impact of dietary intervention on the cognitive development of Kenyan school children.

Previous observational studies in developing countries have suggested that diet quality, particularly increased animal source food (ASF) consumption, is positively associated with child cognitive development. This report presents findings from a study in rural Kenya, designed to test the impact of three different diets on the cognitive development of school children. Twelve schools with a total of 555 Standard 1 children (equivalent to U.S. Grade 1) were randomized to one of four feeding interventions: Meat, Milk, Energy or Control (no feeding). Feeding continued for seven school terms (21 mo), and cognitive tests were administered before the commencement of feeding and during every other term of feeding. Hierarchical linear random effects models and associated methods were used to examine the effects of treatment group on changes in cognitive performance over time. Analyses revealed that children receiving supplemental food with meat significantly outperformed all other children on the Raven's Progressive Matrices. Children supplemented with meat, and children supplemented with energy, outperformed children in the Control group on tests of arithmetic ability. There were no group differences on tests of verbal comprehension. Results suggest that supplementation with animal source food has positive effects on Kenyan children's cognitive performance. However, these effects are not equivalent across all domains of cognitive functioning, nor did different forms of animal source foods produce the same beneficial effects. Implications of these findings for supplementation programs in developing countries are discussed.
Intravenous Injection of Trauma-Hemorrhagic Shock Mesenteric Lymph Causes Lung Injury That Is Dependent Upon Activation of the Inducible Nitric Oxide Synthase Pathway

Objective:To test the hypothesis that gut-derived factors carried in trauma-hemorrhagic shock (T/HS) lymph is sufficient to induce lung injury. Additionally, because our previous studies showed that T/HS-induced nitric oxide production was associated with lung injury, we examined whether T/HS lymph-induced lung injury occurs via an inducible nitric oxide synthase (iNOS)-dependent pathway. Background:We have previously shown that T/HS-induced lung injury is mediated by gut-derived humoral factors carried in the mesenteric lymph. However, it remains unclear whether T/HS lymph itself is sufficient to induce lung injury, or requires the activation of other factors during the T/HS period to exert its effect. Methods:Mesenteric lymph collected from T/HS or trauma-sham shock (T/SS) animals was injected intravenously into male rats at a rate of 1 mL/h for 3 hours. At the end of infusion, lung injury was assessed by lung permeability and lung histology. The effect of iNOS inhibition on T/HS lymph-induced lung injury was studied and this was further confirmed in iNOS knockout mice. Finally, iNOS immunohistochemistry was performed to identify the cells of origin of iNOS. Results:The injection of T/HS lymph, but not sham shock lymph, caused lung injury. This was associated with increased plasma nitrite/nitrate levels as well as induction of iNOS protein in the lung, liver, and gut. Treatment with the selective iNOS inhibitor aminoguanidine prevented T/HS lymph-induced lung injury. iNOS knockout mice, but not their wild-type controls, were resistant to T/HS lymph-induced lung injury. By immunohistochemistry, neutrophils and macrophages, rather than parenchymal cells, were the source of T/HS lymph-induced lung iNOS. Conclusions:These results indicate that T/HS lymph is sufficient to induce acute lung injury and that lymph-induced lung injury occurs via an iNOS-dependent pathway.
Sentence Retrieval with Sentiment-specific Topical Anchoring for Review Summarization

We propose Topic Anchoring-based Review Summarization (TARS), a two-step extractive summarization method, which creates review summaries from the sentences that represent the most important aspects of a review. In the first step, the proposed method utilizes Topic Aspect Sentiment Model (TASM), a novel sentiment-topic model, to identify aspects of sentiment-specific topics in a collection of reviews. The output of TASM is utilized in the second step of TARS to rank review sentences based on how representative of the most important review aspects their words are. Qualitative and quantitative evaluation of review summaries using two collections indicate the effectiveness of structuring review summaries around aspects of sentiment-specific topics.
New technique to drive the central frequency and to improve bandwidth of EBG structures

In this paper, a parametric study was done to find out the superstrat influence on locating the central frequency of the band gap. The present work compares the standard mushroom like with the EBG structures which are located between the substrate and the superstrat. The main motivation is to present a theoretical contribution by comparing the equations describing the central frequency of the band gap. In that way, this work investigates a new proposed design to shift the central frequency of the forbidden band to a low frequency, by inserting meandered lines to connect each part of the unit cell, which give an added capacitance to the EBG structures, in order to reach a low profile and lightweight EBG structure. The band gap was recognized by computing the transmission coefficient S21 resorting to the suspended line method (SLM).
A software tool for the diagnosis of melanomas

Early detection of melanoma is one of the greatest challenges of dermatologic practice today. A new diagnostic method, the “ELM 7 point checklist”, defines a set of seven features, based on colour and texture parameters, which describe the malignancy of a lesion. It has been presented as faster and with the same accuracy than the traditional ABCD criteria in the diagnosis of melanoma. In this paper a new system for automated diagnosis of melanocytic skin lesions, based on ELM 7 point checklist, is introduced.