Miracle-dz/UniFAR-FTUs huggingface dataset:
Modular Parameter Identi(cid:28)cation of Biomolecular Networks

The increasing complexity of dynamic models in systems and synthetic biology poses computational challenges especially for the identiﬁcation of model parameters. While modularization of the corresponding optimization problems could help reduce the ”curse of dimensionality”, abundant feedback and crosstalk mechanisms prohibit a simple decomposition of most biomolecular networks into sub-networks, or modules. Drawing on ideas from network modularization and multiple-shooting optimization, we here present a modular parameter identiﬁcation approach that explicitly allows for such interdependencies. Interfaces between our modules are given by the experimentally measured molecular species. This deﬁnition allows deriving good (initial) estimates for the inter-module communication directly from the experimental data. Given these estimates, the states and parameter sensitivities of diﬀerent modules can be integrated independently. To achieve consistency between modules, we iteratively adjust the estimates for inter-module communication while optimizing the parameters. After convergence to an optimal parameter set–but not during earlier iterations–the inter-module communication as well as the individual modules’ state dynamics agree with the dynamics of the non-modularized network. Our modular parameter identiﬁcation approach allows for easy parallelization; it can reduce the computational complexity for larger networks and decrease the probability to converge to sub-optimal local minima. We demonstrate the algorithm’s performance in parameter estimation for two biomolecular networks, a synthetic genetic oscillator and a mammalian signaling pathway.
2.5. Rock in Rio’s business model: An exploratory approach

The scope of this paper is the Rock in Rio’s (RIR) Business Model (BM). The concept of creating shared value (CSV) is integrated for a better understanding of the company’s sustainability program. The main goal is the construction of RIR’s BM based on Canvas BM. The research method used was qualitative and focused on a case study. Data was collected from sixteen public interviews, with a total length of five hours, and sixteen public documents, with a total of ten pages, available in different formats (video, digital and print). Content analysis was used to process data and deliver results. The main limitation found during the research was the lack of direct information, due to untimely response to a questionnaire sent to RIR’s managers, which conditioned the enhancement of data triangulation and obtaining information related to the use of CSV in the company’s sustainability program.
How SCRAM Implements MPC using TFHE

2 Background 2 2.1 Fully Homomorphic Encryption . 2 2.2 Threshold Fully Homomorphic Encryption . 3 2.3 MPC via TFHE . 3 2.3. 1 General case . 3 2.3. 2 The specific construction of MIT SCRAM . 4 2.3. 3 Distributed Key Generation . 4 2.3. 4 Distributed Decryption . 4 2.4 Security Guarantees . 5 2.4. 1 Notation . 6 2.4. 2 Ring Learning with Errors . 6 2.4. 3 Discrete Gaussian Distribution . 6 2.4. 4 Number Theoretic Transform . 6 2.5 Potential Weaknesses . 7
Running head: CONCEPT MAPPING IN ILL-STRUCTURED DOMAINS Concept Mapping in Ill-Structured Domains: Using Cognitive Flexibility Theory to Guide Future Design CONCEPT MAPPING IN ILL-STRUCTURED DOMAINS

Concept maps are technologies which visually display the organization of knowledge. Traditional concept maps which are characterized by heretical rigidity and generalizability of concept definitions work well in knowledge construction processes in knowledge domains guided by high predictability and structure, but in knowledge domains characterized by unpredictability and whose concepts cannot be universally defined, traditional concept maps may contribute to overgeneralizations and misconceptions. Cognitive flexibility theory (CFT) is a framework for constructing knowledge in ill-structured domains. A feature of cognitive flexibility theory called context sensitive selective highlighting (CSSH) reorganizes how knowledge is conceptualized based on individual contexts rather than an abstract set of rules. I propose that concept maps integrated with the feature of CSSH is a technology that can help to reduce misconceptions and overgeneralizations of concepts in ill-structured domains and help learners develop more flexible patterns of knowledge construction in domains whose concepts are not universally operationalized across all contexts.
NANO SPRAY DRYING OF BIOACTIVE FOOD INGREDIENTS

Nano spray drying is a process for converting liquid substances into a dried submicron powder. Nanoencapsulated bioactive food ingredients (e.g. vitamins, antioxidants, oils, plant extracts, minerals, amino acids, peptides, enzymes) improve protection, ensure stability, increase shelf life and enable controlled release. This study provides an up-to-date overview of the research work on nano spray drying of bioactive food ingredients.
Nuclear staining of telogen hair roots contributes to successful forensic nDNA analysis

Telogen hairs have generally presented significant challenges to routine and advanced forensic nDNA typing techniques. Nuclear specific DAPI fluorescence staining of telogen hair roots introduced a method of determining the number of nuclei still present in the hair root. However, a simple fixation step has increased the yield of complete nDNA profiles over the unfixed telogen root and the introduction of Harris' Haematoxylin nuclear specific staining makes this technique readily available to all forensic biology laboratories.
Early patterns of recovery from disturbance in intertidal algal assemblages: consistency across regions within a marine province

Disturbance and the subsequent rate and pattern of recovery have long been recog- nised as important drivers of community structure. Community recovery is affected by processes operating at local and regional scales, yet the examination of community-level responses to a stan- dardised disturbance at regional scales (i.e. among regions under different environmental condi- tions) has seldom been attempted. Here, we mechanically disturbed rocky intertidal lower-shore algal-dominated assemblages at 3 locations within each of 3 different regions within the Lusitan- ian biogeographical province (Azores, northern Portugal and the Canary Islands). All organisms were cleared from experimental plots and succession followed over a period of 12 mo, at which time we formally compared the assemblage structure to that of unmanipulated controls. Early pat- terns of recovery of disturbed communities varied among regions and were positively influenced by temperature, but not by regional species richness. Different components of the assemblage responded differently to disturbance. Regional differences in the relative abundance and identity of species had a key influence on the overall assemblage recovery. This study highlights how regional-scale differences in environmental conditions and species pools are important determi- nants of recovery of disturbed communities.
Screening and Identification Potent Inhibitors of LAM protein involved in Mycobacterium tuberculosis

Mycobacterium tuberculosis, the etiological agent of tuberculosis, spreads by aerosol, mainly infecting alveolar macrophages, by which the bacterium is ingested. Through inhibition of macrophage functions, the bacterium modulates the host immune response. The best-characterized virulence factor of M. tuberculosis, lipoarabinomannan (LAM), is an abundant glycolipid, which is attached to the plasma membrane by a glycosylphosphatidylinositol (GPI) anchor and extends through the cell wall of the bacterium. During uptake of mycobacteria, LAM interacts with the cell membrane of the host macrophage via specific receptors, including the macrophage mannose receptor and complement receptor and can then be detected at multiple sites in the cell. The host cell exports LAM from the phagosome in an exocytosis-like manner, eliciting responses in bystander cells. Host-directed therapies for tuberculosis have been much written about lately. If such therapies are developed, their use is likely to be most significant in patients with multidrug-resistant and extensively drug-resistant tuberculosis. The current work presented in this article could point to in silico identification the inhibitors of LAM protein by molecular docking approach to development novel strategies evaluating structure-based drug designing.
Small table-top adaptive optical systems for human retinal imaging

Two generations of adaptive optical system for human retina imaging have been developed. The wavefront correcting elements are small PZT 19 and 37 element deformable mirrors (DM) with novel structure. The diameters of these DMs are 24 and 50mm respectively. By using these DMs, the size of whole optical system are rather small and can be fit on table. These systems are successfully used to correct the aberrations of living human eye. High-resolution images of microscopic structure in the scale of single photo-receptor cell and capillary in the human retina have been obtained by real-time correction of adaptive optical systems.
Abundant human β-defensin-1 expression in milk and mammary gland epithelium

Abstract Human β-defensin-1 (HBD-1) was detected in breast milk in concentrations of ~1 to 10 μg/mL. Breast tissue during lactation showed HBD-1 expression in mammary gland epithelia and within luminal secretions. The peptide demonstrated antimicrobial activity against Escherichia coli . HBD-1 may augment neonatal host defenses through antimicrobial effects or prime the adaptive immune system at mucosal surfaces. (J Pediatr 2001;138:109-12)
A Study on the Effect of Comparison with Others and Social Support on Life Satisfaction of Facebook

This study investigates the effect of Facebook users’ envy of other users and social support on life satisfaction with self-esteem as a mediating variable. The survey was conducted on 1332 female and male Facebook users in five main Korean cities. The results showed that user’s envy of other people and social support had a significant effect on life satisfaction. In addition, the greater the upward comparison with others, the lower the self-esteem, which leads to lower life satisfaction; When Facebook users upward compare themselves with others, it lowers their self-esteem which in turn reduces their life satisfaction. And when users have social support, they will have better self-esteem, which leads to higher life satisfaction Finally, the implications, discussions and limitations of this study are presented.
Peaceful and Happy Schools: How to Build Positive Learning Environments

It is very important for students and teachers to have a positive learning environment. The school that is an institution for educating children should be a peaceful and happy environment. There are principles such as love, respect, honesty, courage, empathy and kindness in the peaceful and happy schools. This study examined the concept of a “peaceful and happy school” and aimed to describe a peaceful and happy school from the point of view of primary school teachers and primary school students. It was designed with a case-study research model. A peaceful and happy school climate is the “case” of this study. The participants of the study consisted of 126 persons, 103 primary school students, and 23 primary school teachers from public schools in Turkey. Data were collected through face-to-face interviews from primary school students and teachers. Semi-structured interview form was used for both groups. At the end of the study, primary school teachers’ and students’ defini - tions of a peaceful and happy school were presented. It was understood from the findings that primary school students and teachers want to improve the same basic issues related to a peaceful and happy school.
Morphological and Molecular Comparison of Hemigrapsus crenulatus (Milne Edwards, 1837) (Brachyura: Varunidae) from New Zealand and Chile: Was Miss Rathbun Right?

Abstract The estuarine crab Hemigrapsus crenulatus (H. Milne Edwards, 1837) is a native of New Zealand, but it is also known from the coast of Chile some 8900 km eastwards across the Pacific. Mary Rathbun (1898) was the first person to call crabs from the Chilean coast, H. crenulatus, saying that they were conspecific with crabs described by Milne Edwards (1837). However, Bennett (1964) took the advice of H. Balss that the Chilean species should be known as Hemigrapsus granarius (Nicolet, 1849). No type specimens are available for either of these species. We have used mitochondrial 16S rRNA and COI sequences derived from fresh specimens to find out who was correct. There are few if any consistent morphological differences between populations from either side of the South Pacific and very few molecular differences (only 3 fixed nucleotide differences out of 1190 bp total sequenced – 0.25%). None of these differences exceed variation within either population, so we must declare Miss Rathbun the winner! The molecular data suggest that there is only one species, Hemigrapsus crenulatus, and that the two populations have been separated only recently in the last few thousand years, perhaps during the last glacial epoch. How this species colonized the coast of South America remains an open question. It does not even occur on off-shore islands near the New Zealand mainland so it probably needed assistance to cross the Pacific.
Pollinator Visits to Threatened Species Are Restored Following Invasive Plant Removal

An indirect consequence of plant invasions is the disruption of native plant-pollinator interactions. We examined effects of invasive baby’s breath (Gypsophila paniculata) and spotted knapweed (Centaurea maculosa) on floral visitors to federally threatened Pitcher’s thistle (Cirsium pitcheri) in Lake Michigan dunes. In sweep net surveys, abundances of pollinator taxa were five times higher in invaded than in naturally invader-free sites. However, plot-level G. paniculata removal treatments increased pollinator visits to C. pitcheri relative to invaded plots and restored visitation to levels found in naturally uninvaded plots. Invader removal also increased native plant species richness, which was positively correlated with pollinator visitation to C. pitcheri, suggesting an indirect effect on pollinators mediated through invader-altered plant composition. In temporary floral arrays, the rate of pollinator visitation to C. pitcheri was not affected by neighbor plant species identity. However, compared with native Monarda punctata, invasive C. maculosa attracted more total pollinators to the array but reduced the proportion of total visits that were to C. pitcheri and increased pollinator movements between plant species. While both G. paniculata and C. maculosa appear to act as magnet species by attracting more pollinators at the plot level, these invaders have the potential to reduce reproduction of C. pitcheri by decreasing pollinator visits and increasing interspecific pollen transfer.
Biochemical and chemotaxonomic characterization of Pseudomonas stutzeri genomovars

A total of 48 strains representing the seven Pseudomonas stutzeri genomovars (DNA/DNA homology groups) were studied for cellular fatty acid composition, physiological characteristics and protein profiles. All strains were found to be homogeneous with respect to their fatty acid patterns. Numerical analysis of physiological properties demonstrated a considerable phenotypic heterogeneity within the genomovars. Characterization of the individual genomic groups on the basis of biochemical tests was not possible. In a numerical study of cellular protein patterns, two main clusters were obtained, one representing genomovars 1, 6 and 7 characterized by a high G + C content (mean value > 64 mol%), the other representing genomovars 2, 3, 4 and 5 with a low G + G content (< 64 mol%). The standardized cellular protein patterns have potential for differentiation of the genomic groupings within the species Ps. stutzeri as currently circumscribed.
Mammalian activity – rest rhythms in Arctic continuous daylight

Abstract Activity – rest (circadian) rhythms were studied in two species of Arctic mammals living in Arctic continuous daylight with all human-induced regular environmental cues (zeitgebers) removed. The two Arctic species (porcupine and ground squirrel) lived outdoors in large enclosures while the Arctic summer sun circled overhead for 82 days. Would local animals maintained under natural continuous daylight demonstrate the Aschoff effect described in previously published laboratory experiments using continuous light, in which rats' circadian activity patterns changed systematically to a longer period, expressing a 26-hour day of activity and rest? The outdoor experiments reported here, however, showed that under natural continuous daylight, both species (porcupine and ground squirrel) had specific times of activity and rest on a nearly 24-hour scale, and their activity peaks did not come later each day. The daily rhythms of the two species were recorded using implanted physiological radio capsules, and from direct observation.
Engineering Rubisco to change its catalytic properties

1,5-bisphosphate (RuBP), the enzyme ribulose-1,5 bisphosphate carboxylase/oxygenase (Rubisco) catalyses three other reactions, the most important of which is the oxygenation of RuBP. Consequently, the enzyme plays a pivotal role partitioning carbon between the Calvin cycle and the photorespiratory cycle. Photo respiration is wasteful because it consumes energy and results in the loss of fixed carbon. The oxygenase reaction is probably the most important metabolic constraint on plant productivity: it can result in a loss of up to 50% of the carbon fixed by a C3 plant (Zelitch, 1973). Furthermore, Rubisco is a poor catalyst: the enzyme from higher plants has a turnover number of only 3s"1 at 25 °C. Plants thus invest heavily in Rubisco to sustain high photosynthetic rates, which represents a large invest ment of nitrogen (Rubisco accounts for up to 30% of total nitrogen in a typical C3 leaf grown with adaquate nitrogen). One approach to optimizing nitrogen use and reducing fertilizer inputs as well as increasing production per se would be to engineer an enzyme with a higher
Modelo computacional y experimental del comportamiento mecánico y biológico de fibroblastos aislados del ligamento colateral de la rodilla expuestos a estímulos biofísicos del ultrasonido

El objetivo de esta tesis fue modelar computacional y experimentalmente el comportamiento mecanico y biologico de fibroblastos del ligamento colateral de la rodilla expuestos a estimulos biofisicos del ultrasonido. Tratamiento con ultrasonido pulsatil a una frecuencia de 1.0 MHz con dos intensidades diferentes 1.0 W/cm2 (Grupo A) y 2.0 W/cm2 (Grupo B) fue aplicado cada 24 horas por cinco dias a cultivos monocapa de fibroblastos de ligamento. Un grupo control no recibio tratamiento (Grupo C). La autora midio el modulo de elasticidad celular a traves del ensayo con Microscopio de Fuerza Atomica (AFM), armonicos utilizando el Metodo de los Elementos Finitos (FEM), viabilidad a traves de la tecnica de citometria de flujo, proliferacion por medio de un ensayo colorimetrico (MTS), sintesis de colageno tipo I y III, y fibronectina mediante el Ensayo de Inmunoabsorbancia Ligado a Enzimas (ELISA), y migracion celular a traves del ensayo de lesion por raspado. Los resultados mostraron una disminucion en el modulo de elasticidad (22% y 32%, p0.05), en los armonicos (20% y 20%) y en la viabilidad celular (1% y 10%) para la baja y alta intensidad, respectivamente. La proliferacion celular fue aumentada 10% (Grupo A) y disminuida 13% (Grupo B) (p0.05). El colageno tipo I fue aumentado 100% para la alta intensidad, y no hubo expresion de colageno tipo III para la baja intensidad ni para el grupo control. La produccion de fibronectina fue aumentada 79% (Grupo A) y 61% (Grupo B). Se comprobo que la disminucion del modulo de elasticidad se produjo por una reorganizacion del citoesqueleto de la celula para 1) proliferar y migrar (aumento del 4%) a la zona de lesion ante baja intensidad de tratamiento y para 2) producir matriz extracelular en la zona de lesion y por tanto disminuir la migracion celular (11%) para el tratamiento con alta intensidad (p0.05). Estos hallazgos mostraron que baja dosis de ultrasonido puede estimular la etapa temprana o regenerativa de reparacion y alta dosis de tratamiento estimula la etapa tardia o de remodelado. Este trabajo sugiere que el ultrasonido pulsatil estimula a las celulas para mejorar el proceso de reparacion de los ligamentos.
Looks are important: parasitic assemblages of agromyzid leafminers (Diptera) in relation to mine shape and contrast

Summary 1. We test the hypothesis that leaf mine appearance can affect the risk of leafminers being discovered by parasitoids, and therefore influence parasitic assemblages, using a comparative study of parasitic complexes associated with 28 agromyzid species in Central Argentina. Analyses were based on size, structure (defined as the number of species in host-range categories) and impact (percentage parasitism) of parasitic complexes on leafminers. Mine appearance was defined in terms of shape (linear, linear-blotch, blotch) and colour (high or low contrast with the leaf lamina). 2. Irrespective of the agromyzid species involved, significant differences were found in the structure of the parasitoid complexes: specialists were more abundant and generalists rarer than expected in blotch and cryptically coloured mines. 3. There were no differences in average parasitoid species richness and parasitism rates among differently coloured or shaped galleries. However, mine appearance significantly affected parasitic assemblage structure, with shape driving generalist species richness and contrast influencing that of specialists. Mine shape also affected parasitism rates, which were highest for generalists in linear mines, and for specialists in blotch mines. The existence of a gradient of discovery from the cryptically coloured blotch mines to the most apparent highly contrasting linear ones was supported by significant correlations of this gradient with richness and parasitism rates of generalist and specialist parasitoids. 4. Taxonomic composition of parasitic complexes (analysed through parasitoid species abundance) was separated significantly according to host mine shape. An even more significant classification of assemblages was achieved when the combination of mine shape and colour was considered in the discoverability gradient. 5. Our results suggest that despite leaf mines being an ecologically homogeneous resource, their morphology might offer varying degrees of refuge against different parasitoids.