Miracle-dz/UniFAR-FTUs huggingface dataset:
Analysing Network Models to Make Discoveries about Biological Mechanisms

Systems biology provides alternatives to the strategies to developing mechanistic explanations traditionally pursued in cell and molecular biology and much discussed in accounts of mechanistic explanation. Rather than starting by identifying a mechanism for a given phenomenon and decomposing it, systems biologists often start by developing cell-wide networks of detected connections between proteins or genes and construe clusters of highly interactive components as potential mechanisms. Using inference strategies such as ‘guilt-by-association’, researchers advance hypotheses about functions performed of these mechanisms. I examine several examples of research on budding yeast, first on what are taken to be enduring networks and subsequently on networks that change as cells perform different activities or respond to different external conditions. 1. Introduction2. Analysing Networks under Static Conditions 2.1. Networks constructed from structural relations between proteins2.2. Networks constructed using information about functional interactions3. Analysing Changes in Networks across Conditions 3.1. Active sub-networks3.2. Differential network biology4. Conclusion Introduction Analysing Networks under Static Conditions 2.1. Networks constructed from structural relations between proteins2.2. Networks constructed using information about functional interactions Networks constructed from structural relations between proteins Networks constructed using information about functional interactions Analysing Changes in Networks across Conditions 3.1. Active sub-networks3.2. Differential network biology Active sub-networks Differential network biology Conclusion
Supply chain management of laboratory supportive services and its potential implications on the quality of HIV diagnostic services in Tanzania

Background: Reliable supply of laboratory supportive services contributes significantly to the quality of HIV diagnostic services. This study assessed the status of supply chain management of laboratory supportive services and its potential implications on the quality of HIV diagnostic services in selected districts of Tanzania. Methods: The study was conducted in 39 health facilities (HFs) from eight districts in four regions of Tanzania, namely Iringa, Mtwara, Tabora and Tanga. Facilities with care and treatment centres for HIV/AIDS patients were purposively selected for the study. The study utilized a quantitative method of data collection. A questionnaire was administered to heads of laboratories to obtain information on laboratory supply chain management. Results: A total of 39 health facilities (HF) were included in the study. This included 23 public and 16 private facilities. In 82% of the HFs, ordering of supplies was performed by the laboratory departments. The information commonly used to forecast requirements of the laboratories included the number of tests done (74.4%; n=29), current stock levels (69.2%; n=27), average monthly consumption (64.1%, n=25) and minimum and maximum stock levels (10.2%, n=4). Emergency orders were significantly common in public than private facilities (73.9% vs. 56.3%, p=0.004). Delivery of ordered supplies took 1 to 180 days with a significantly longer mean period for public than private facilities (32.5 vs. 13.1 days, p=0.044). Most of the public HFs ordered supplies from diverse sources compared to private facilities (68.2% vs. 31.8%). Conclusion: There was a weak inventory management system and delays in delivery of supplies in the majority of HFs, which are likely to impede quality of HIV care and treatment. Strengthening capacity for data management and ensure constant supply will potentially improve the quality of HIV diagnostic
Radiation field in a semi-infinite homogeneous atmosphere with internal sources

The equation of radiative transfer in a semi-infinite homogeneous atmosphere with different internal sources is solved by the method of kernel approximation—the kernel in the equation for the Sobolev resolvent function is approximated by a Gauss–Legendre sum. Then the obtained approximate equation can be solved exactly and the solution is a weighted sum of exponentials. All the necessary coefficients of the solutions may be easily found. Since the resolvent function is closely connected with the Green function of the integral radiative transfer equation, the radiation field for different internal sources can be found by simple integration. For the considered cases the formulas for the radiation field are obtained and the respective accuracy estimated. The package of codes in Fortran-77 is given at http://www.aai. ee/ viik/homogen.for. r 2007 Elsevier Ltd. All rights reserved.
Modelling of a Hybrid UAV Using Test Flight Data

The concept of an aircraft capable of both hover as well as fast forward flight (hybrid) has recently been implemented on unmanned aerial vehicles (UAV). Hybrid UAVs combine hover capability with long range and endurance. As UAVs are often required to operate without human intervention, there is a call for autonomous guidance of hybrid UAVs. Because the dynamics in the transition region from hover to forward flight are not well known, this research focusses on the development of a longitudinal model for a hybrid UAV based on test flight data. The same approach can be used for other types of airframes as well, allowing cheap and easy modelling. Sensors were logged for nine different flights and a Kalman filter was used for state estimation. The system was excited by doublet inputs on the commanded pitch and thrust. From the input-output response a piecewise linear model was estimated. This model was verified by comparing the measured doublet input response to the simulated response based on the model, yielding a very similar result.
ASSIMILATING DATA INTO AN αΩ DYNAMO MODEL OF THE SUN: A VARIATIONAL APPROACH

We have developed a variational data assimilation technique for the Sun using a toy αΩ dynamo model. The purpose of this work is to apply modern data assimilation techniques to solar data using a physically based model. This work represents the first step toward a complete variational model of solar magnetism. We derive the adjoint αΩ dynamo code and use a minimization procedure to invert the spatial dependence of key physical ingredients of the model. We find that the variational technique is very powerful and leads to encouraging results that will be applied to a more realistic model of the solar dynamo.
Transient bacteremia caused by Atopobium vaginae after caesarean delivery: Case report

Introduction: Genital microbiome of woman is still a puzzle to this day. It consists of a large number of diff erent bacterial species and phenotypes that make up the normal genital fl ora, while in the cases of its change there is a predominance of certain, especially anaerobic species, which is the case with bacterial vaginosis. These types are mostly rare causing invasive infections, but under certain conditions can lead to severe infections, such as multiple parts of the genital tract, and to an unwanted outcome in the pregnancy. Case report: This paper presents an extremely rare case of transient bacteremia caused by Atopobium vaginae type in a patient following a cesarean section where empirical therapy gave a positive eff ect and the patient recovered and released home with healthy newborn. Conclusions: During the clinical work it is important to be aware of the diff erent anaerobic species present in the genital tract of women microbiome like Atopobium vaginae and should adjust the empirical therapy, which was the case here.
Regression between true scores

plied under this model is much less strong than the essential r-equivalence relationship. By employing this model and the split-half technique, it is shown that the estimates of the true regression coefficients and the reliability coefficients of the two tests are obtainable from nine equations. Furthermore, the results show that the absolute value of the estimated true slope is larger than or equal to the absolute value of the ordinary least squares estimate of slope, and the observed correlation coefficient between the two tests is the geometric mean of the estimated reliability coefficients for the two tests.
Numerical analysis of block stone displacements in ancient masonry structures: A new method to estimate historic ground motions

An innovative approach is presented, in which the discontinuous deformation analysis (DDA) method is used to estimate historic ground motions by back analysis of unique structural failures in archaeological sites. Two archaeological sites in Israel are investigated using this new approach and results are presented in terms of displacement evolution of selected structural elements in the studied masonry structure. The response of the structure is studied up to the point of incipient failure, in a mechanism similar to the one observed in the field. Structural response is found to be very sensitive to dynamic parameters of the loading function such as amplitude and frequency.
THE METHODS MATUSITA, KISSINGER AND OZAWA IN THE STUDY OF THE CRYSTALLIZATION OF GLASSES. THE CASE OF Ge-Sb-Te ALLOYS

Chalcogenide glasses based on Ge-Te-Sb are used in the technology of phase change optical memories. Non-isothermal crystallization for Ge15.5-xTe84.5Sbx (0.5 <x< 1.5) investigated by differential scanning calorimetry (DSC) shows two glass transition temperatures followed by two crystallization peaks and melting point at 385°C . The activation energy of crystallization has been calculated in the frame of three models: Matusita, Kissinger and Ozawa. The particularity of every model is analysed.
A Microassembly System for the Flexible Assembly of Hybrid Robotic Mems Devices

This paper presents a full 6 DOF microassembly system that features a novel remote center of motion configuration paired with advanced vision and illumination modules, as well as innovative user interaction concepts. Even though the semi-automatic design is primarily focused on the assembly of 3D bio-microrobotic devices out of individual 2.5D MEMS components, it can be configured for a large variety of assembly tasks. A gripper exchange mechanism allows reaching for parts with dimensions ranging from 5–800 µm and a micro-fabricated platform featuring a special pattern provides a structured working area. The assembly of a miniature bio-microrobot is presented to demonstrate the dexterity and powerful features of this system. The underlying microassembly station combines multiple concepts for another step towards full manipulation automation in industrial and research applications.
Dynamic Portfolio Optimization with Looping Contagion Risk

In this paper we consider a utility maximization problem with defaultable stocks and looping contagion risk. We assume that the default intensity of one company depends on the stock prices of itself and another company, and the default of the company induces an immediate drop in the stock price of the surviving company. We prove the value function is the unique continuous viscosity solution of the HJB equation. We also compare and analyse the statistical distributions of terminal wealth of log utility based on two optimal strategies, one using the full information of intensity process, the other a proxy constant intensity process. These two strategies may be considered respectively the active and passive optimal portfolio investment. Our simulation results show that, statistically, active portfolio investment is more volatile and performs either much better or much worse than the passive portfolio investment in extreme scenarios.
The Mediating Role of Basic Psychological Needs in Relation between Job Characteristics and Organizational Citizenship Behavior

Several researches administrated to investigate the relationship between organizational citizenship behaviors (OCB) with job characteristics (JCs). The results were different. One category of variables that probably cause different results is mediators like psychological needs. The aim of this research is to investigate the mediating role of basic psychological needs in relation between JCs and OBCs. Participants in this study were employees of Ferdowsi University of Mashhad. A 220 Sample of respondents was selected using quota sampling method. The study tested a model for measuring each of the three variables applying separate questionnaires for JC scale from Hackman & Oldham, citizenship behavior scale from Podsakoff; and basic psychological needs scale. Data were analyzed using path analysis. The results of Pearson correlation showed that there was a mutual correlation between some of the components of basic psychological needs and JC and OCBs. The correlations were positive and statistically significant while per posed model was fitted to data, and nondirective path was more strength and significance.
Easing transition and promoting a positive student experience within an international partnership scheme for British and Chinese teachers

This article investigates the needs and challenges of a group of Chinese secondary school teachers in their transition to postgraduate studies in the UK in the context of a British-Chinese partnership. The strategies and efforts of the host institution, local community and the Chinese students themselves to help ease the transition and promote a positive student experience are discussed. The article highlights the sociological processes of international postgraduate student transition and contributes to our understanding of the issues of student support pertinent to international partnership arrangements.
Populational approach in ecophysiological studies: the case of Plathymenia reticulata, a tree from Cerrado and Atlantic Forest

The variability of ecophysiological traits among populations can be a result of selection in response to environmental pressure and/or due to random factors, like the genetic drift. The analysis of both genetic and phenotypic variation within populations can lead to better understanding of adaptation in order to colonize different habitats. In the last years we have developed several studies with an widely ecogeographic distributed legume tree species, Plathymenia reticulata, which were focused on identifying specific morphological and physiological traits related to adaptation to the habitats of origin of each studied population. We studied populations from Atlantic Forest, Cerrado and ecotonal sites in relation to phenology, seed morphological traits and their relation with seed dispersion, seed dormancy and germination, and growth traits in a common garden experiment. In several analyzed traits we found high diversity in this species that can explain its occurrence in a broad geographical range. The existence of genetically based differences of traits in an adaptive way among savanna and forest populations suggests a degree of divergence that characterizes the existence of ecotypes from Cerrado and Atlantic Forest. We also pointed future perspectives in studies at population level in evolutionary ecophysiology and implications of these studies for flora conservation and habitat restoration.
A Reflective Study on English Language Learning and Teaching: A Comparison Between an EFL Teacher and an ELA Teacher

In this comparative self-study, two English teachers, one English as a foreign language (EFL) teacher from China and one English language arts (ELA) teacher in the United States, examined their perceptions of English language learning and instruction. Through a set of documents, i.e., reflective teaching journals, written teaching philosophies, and peer interviews and talks, the narrative study explored and revealed the two teachers’ perceptions of English learning process as a learner, English teaching process as a teacher, and how these experiences informed and affected their doctoral practices. Through their reflections on their examined experiences, the study found that the two teachers both used a theoretical lens of social constructivism to guide their perceptions or beliefs. The paper finally gave suggestions on how to improve English instruction from a sociocultural perspective.
Establishment of Brachiaria brizantha cv. Marandu, under levels of soil water availability in stages of growth of the plants

The objective of this work was to evaluate yield traits and development of palisadegrass under the influence of water deficit during the establishment period. The experiment was carried out in a greenhouse, in a completely random block statistical design in a factorial arrangement and additional treatment (3 × 3 + 1). The treatments referred to the suppression of irrigation at different phases of the establishment (sowing, germination and initial tillerring) until the soil presented water content of 75%, 50%, and 25% of the moisture related to field capacity (qFC), besides control treatment with no water restriction. Evaluations of number of grown tillers per vase, green leaves per tiller and plant height were carried out weekly, for five weeks after the first tillers appeared. Biomass sampling was carried out approximately 30 days after the end of the last applied treatment, when the soil was kept close to 100% of field capacity relative moisture. Tillering and biomass yield of palisadegrass during establishment phase are reduced when water deficit is sufficient to make soil content water reach 25% of relative moisture field capacity, regardless to the season when water shortage takes place.
On Simultaneous Data-Based Dimension Reduction and Hidden Phase Identification

A problem of simultaneous dimension reduction and identification of hidden attractive manifolds in multidimensional data with noise is considered. The problem is approached in two consecutive steps: (i) embedding the original data in a sufficiently high-dimensional extended space in a way proposed by Takens in his embedding theorem, followed by (ii) a minimization of the residual functional. The residual functional is constructed to measure the distance between the original data in extended space and their reconstruction based on a low-dimensional description. The reduced representation of the analyzed data results from projection onto a fixed number of unknown low-dimensional manifolds. Two specific forms of the residual functional are proposed, defining two different types of essential coordinates: (i) localized essential orthogonal functions (EOFs) and (ii) localized functions called principal original components (POCs). The application of the framework is exemplified both on a Lorenz attractor model with measurement noise and on historical air temperature data. It is demonstrated how the new method can be used for the elimination of noise and identification of the seasonal low-frequency components in meteorological data. An application of the proposed POCs in the context of the low-dimensional predictive models construction is presented.
Optimizing screening protocols for non-indigenous species: are currently used tools over-parameterized?

While screening-level risk assessment (SLRA) tools for non-indigenous species generally provide managers with reliable information for decision making (e.g., a proposed species introduction should be allowed or rejected), the results are affected by several sources of uncertainty. In particular, model uncertainty, related to the influence of factors/questions included in SLRA tools has rarely been addressed. Here we undertook an investigation of model uncertainty using a detailed evaluation of the contribution of questions included in the Canadian Marine Invasive Screening Tool (CMIST) and determined if the tool can be made more accurate through a series of optimization procedures. Accuracy was defined as the fit between assessment scores and the results of an expert opinion survey of risk posed by 48 marine invertebrate species known to have been introduced into Canadian coastal waters. We first measured the contribution of each question to accuracy and removed the ones that did not improve the fit. We then derived optimal weights that adjust the contribution of each question to maximize accuracy. Eight of 17 questions were found not to improve accuracy, or even decreased it; removing these questions, followed by addition of weights made the tool gradually more accurate when all species were included. However, an independent cross-validation test showed these weights to be too variable to consistently improve fit; this was probably related to the relatively small number of species included in the tests. Tools that have previously been tested using a large number of species should be used to determine if addition of optimal weights can improve independent predictions. The evidence that risk assessment tools are over-parameterized is building and we suggest that currently used tools would benefit from a detailed evaluation of the value of questions they include. Careful selection of questions and weights, based on accuracy improvement and other elements (e.g., organizational mandate) could greatly benefit SLRA tools, by providing more accurate estimations of risk and accelerating assessments.
Local regulation between formal and informal institutions: Analysis by application to the case of the town of Ksar-Hellal (Tunisia).

The purpose of this paper is to detect the relevance degrees of formal and informal institutions at the level of local regulation, as well as their effects on the local companies’ productivities. Indeed, by an analysis of the territory of the Ksar-Hellal town, we noted that informal institutions, apprehended by the trust and the collective punishment, contribute beside the formal penal institutions to channel the behaviors of the hilalian companies but with a less effectiveness. Similarly, the strong contribution of exogenous institutions in boosting productivity compared to that endogenous, states that the decision makers should improve the quality of formal regulation, and this at the expense of any form of regulation built by values commonly shared by the local community.
Otx 2 and HNF-β interactions and anterior patterning 357 Otx 2 and HNF 3 β genetically interact in anterior patterning

Patterning the developing nervous system in the mouse has been proposed to depend on two separate sources of signals, the anterior visceral endoderm (AVE) and the node or organizer. Mutation of the winged-helix gene HNF3β leads to loss of the node and its derivatives, while mutation of the homeobox gene Otx2 results in loss of head structures, apparently at least partially because of defects in the AVE. To investigate the potential genetic interactions between the two signaling centers, we crossed Otx2+/and HNF3β+/mice and found that very few Otx2+/-;HNF3β +/double heterozygous mutants survived to weaning. Normal Mendelian ratios of genotypes were observed during gestation, but more than half the double heterozygotes displayed a severe anterior patterning phenotype that would be incompatible with postnatal survival. The phenotype was characterized by varying degrees of holoprosencephaly, cyclopia with proboscis-like structures, and anterior forebrain truncations. Regional marker analysis revealed that ventral forebrain structures of Otx2+/-;HNF3β +/mutant embryos were most severely affected. Shh expression was completely absent in the anterior region of Otx2+/-;HNF3β +/embryos, suggesting that Otx2 and HNF3β genetically interact, directly or indirectly, to regulate Shh expression in the anterior midline. In addition, the forebrain truncations suggest an involvement of both genes in anterior patterning, through their overlapping expression domains in either the AVE and/or the prechordal mesoderm.