Miracle-dz/UniFAR-FTUs huggingface dataset:
Sequential and differential interaction of assembly factors during nitrogenase MoFe protein maturation

Nitrogenases reduce atmospheric nitrogen, yielding the basic inorganic molecule ammonia. The nitrogenase MoFe protein contains two cofactors, a [7Fe-9S-Mo-C-homocitrate] active-site species, designated FeMo-cofactor, and a [8Fe-7S] electron-transfer mediator called P-cluster. Both cofactors are essential for molybdenum-dependent nitrogenase catalysis in the nitrogen-fixing bacterium Azotobacter vinelandii. We show here that three proteins, NafH, NifW, and NifZ, copurify with MoFe protein produced by an A. vinelandii strain deficient in both FeMo-cofactor formation and P-cluster maturation. In contrast, two different proteins, NifY and NafY, copurified with MoFe protein deficient only in FeMo-cofactor formation. We refer to proteins associated with immature MoFe protein in the following as “assembly factors. ” Copurifications of such assembly factors with MoFe protein produced in different genetic backgrounds revealed their sequential and differential interactions with MoFe protein during the maturation process. We found that these interactions occur in the order NafH, NifW, NifZ, and NafY/NifY. Interactions of NafH, NifW, and NifZ with immature forms of MoFe protein preceded completion of P-cluster maturation, whereas interaction of NafY/NifY preceded FeMo-cofactor insertion. Because each assembly factor could independently bind an immature form of MoFe protein, we propose that subpopulations of MoFe protein–assembly factor complexes represent MoFe protein captured at different stages of a sequential maturation process. This suggestion was supported by separate isolation of three such complexes, MoFe protein–NafY, MoFe protein–NifY, and MoFe protein–NifW. We conclude that factors involved in MoFe protein maturation sequentially bind and dissociate in a dynamic process involving several MoFe protein conformational states.
Development and characterization of genomic SSR markers for Anneslea fragrans (Pentaphylacaceae)

Premise of the study: The genus Anneslea (Pentaphylacaceae) contains four species and six varieties, most of which are locally endemic. Here, simple sequence repeat (SSR) markers were developed for the conservation of these species. Methods and Results: The genome of A. fragrans was sequenced and de novo assembled into 445,162 contigs, of which 30,409 SSR loci were detected. Primers for 100 SSR loci were validated with PCR amplification in three populations of A. fragrans. Seventy-nine loci successfully amplified, and 30 were polymorphic. The mean number of alleles, observed heterozygosity, and expected heterozygosity were 7.01 ± 1.60, 0.817 ± 0.241, and 0.796 ± 0.145, respectively. Most primers could be amplified in Ternstroemia gymnanthera, T. kwangtungensis, and Cleyera pachyphylla. Conclusions: Our study demonstrated that shotgun genome sequencing is an efficient way to develop genomic SSR markers for nonmodel species. These genomic SSR loci will be valuable in population genetic studies in Anneslea and its relatives.
An Assessment of Myotube Morphology, Matrix Deformation, and Myogenic mRNA Expression in Custom-Built and Commercially Available Engineered Muscle Chamber Configurations

There are several three-dimensional (3D) skeletal muscle (SkM) tissue engineered models reported in the literature. 3D SkM tissue engineering (TE) aims to recapitulate the structure and function of native (in vivo) tissue, within an in vitro environment. This requires the differentiation of myoblasts into aligned multinucleated myotubes surrounded by a biologically representative extracellular matrix (ECM). In the present work, a new commercially available 3D SkM TE culture chamber manufactured from polyether ether ketone (PEEK) that facilitates suitable development of these myotubes is presented. To assess the outcomes of the myotubes within these constructs, morphological, gene expression, and ECM remodeling parameters were compared against a previously published custom-built model. No significant differences were observed in the morphological and gene expression measures between the newly introduced and the established construct configuration, suggesting biological reproducibility irrespective of manufacturing process. However, TE SkM fabricated using the commercially available PEEK chambers displayed reduced variability in both construct attachment and matrix deformation, likely due to increased reproducibility within the manufacturing process. The mechanical differences between systems may also have contributed to such differences, however, investigation of these variables was beyond the scope of the investigation. Though more expensive than the custom-built models, these PEEK chambers are also suitable for multiple use after autoclaving. As such this would support its use over the previously published handmade culture chamber system, particularly when seeking to develop higher-throughput systems or when experimental cost is not a factor.
A new, objective radiographic classification system for the assessment of treatment results in developmental dysplasia of the hip

The new, objective radiographic classification system for the assessment of treatment results in developmental dysplasia of the hip includes three quantitative parameters: centre–edge angle of Wiberg, acetabular angle of Sharp and the centre–trochanter distance. Each parameter is divided into three subgroups and assigned a point score (0, 1 and 2) according to their previously determined values. Besides this, three corrective items on the existence of middle/posterior acetabular deficiency, secondary operation and resubluxation/redislocation are added to the classification system and in the presence of any of these items, one point for each item is extracted from the total points. A total of five or six points represents a satisfactory outcome and less than five points, an unsatisfactory outcome. The new system was found to have adequate intraobserver and interobserver agreement levels. It was also observed that, the gold standard Severin system could lead the raters to obtain somewhat more optimistic results with respect to the new system before and after skeletal maturity. It was concluded that the present system could evaluate both the final radiographic status of the hip and the success or failure of the primary treatment and could be capable of leading orthopaedic surgeons to speak the same language while assessing radiographic results in developmental dysplasia of the hip.
Arithmetical Difficulties and Low Arithmetic Achievement: Analysis of the Underlying Cognitive Functioning

Abstract This study analyzed the cognitive functioning underlying arithmetical difficulties and explored the predictors of arithmetic achievement in the last three grades of Spanish Primary Education. For this purpose, a group of 165 students was selected and divided into three groups of arithmetic competence: Mathematical Learning Disability group (MLD, n = 27), Low Achieving group (LA, n = 39), and Typical Achieving group (TA, n = 99). Students were assessed in domain-general abilities (working memory and PASS cognitive processes), and numerical competence (counting and number processing) during the last two months of the academic year. Performance of children from the MLD group was significantly poorer than that of the LA group in writing dictated Arabic numbers (d = –0.88), reading written verbal numbers (d = –0.84), transcoding written verbal numbers to Arabic numbers (–0.75) and comprehension of place value (d = –0.69), as well as in simultaneous (d = –0.62) and successive (d = –0.59) coding. In addition, a specific developmental sequence was observed in both groups, the implications of which are discussed. Hierarchical regression analysis revealed simultaneous coding (β = .47, t(155) = 6.18, p < . 001) and number processing (β = .23, t(155) = 3.07, p < . 01) as specific predictors of arithmetical performance.
Patterns of HIV and Sexually Transmitted Infection Testing Among Men Who Have Sex With Men Couples in the United States

Background Most men who have sex with men (MSM) within the United States acquire human immunodeficiency virus (HIV) while in a same-sex relationship. Few studies have examined HIV and sexually transmitted infection (STI) testing rates among MSM couples. Interestingly, the patterns that MSM test for HIV while in their relationships remain largely unknown. The current study helps fill this gap in knowledge by assessing HIV testing patterns and HIV and STI testing rates from a large convenience sample of Internet-using MSM couples. Methods The current study used a cross-sectional study design to collect dyadic data from 361 MSM couples who lived throughout the United States. A novel recruitment strategy that included placing paid targeted advertisements on Facebook enrolled both men in the couple to independently complete the confidential electronic survey. Results Nearly half of the HIV-negative men indicated either not having been tested for HIV since their relationship started or only testing if they believed they were at risk. Few men reported testing every 3 to 4 months. HIV/STI testing rates varied among the sample of couples. Few men reported having been diagnosed with a recent STI. Testing patterns and rates were mostly similar, irrespective of whether unprotected anal intercourse was practiced within and/or outside the relationship. Conclusions HIV testing and prevention services must target men who are at risk for acquiring HIV within MSM couples. To help accomplish this goal, additional research is needed to examine the specific barriers and facilitators to HIV and STI testing among MSM in couples.
Education, employment and human development: illustrations from Mexico

By applying Amartya Sen's capability approach, this article questions the functionalist idea that suggests that education can precipitate economic growth and development. It will be argued that the freedom‐centred perspective advances the concept of human capital and that it allows a deeper understanding of the relationship between higher education and human development in Mexico. This empirical‐based article shows how an educational institution contributes to expanding its graduates' basic functionings (e.g. being able to acquire knowledge, being able to get a job in a short time, being able to change jobs and thus to improve earnings, being able to search for better opportunities). However, a further enlargement of human capabilities is restrained due to the lack of social and economic opportunities which are commonly neglected in the mainstream analyses on education, employment and development. The removal of such ‘unfreedoms’ demands a renovated perspective in which education can be seen as a factor—momentous as it is—that interacts continuously with contradictory forces within complex social settings.
Multi-Task Deep Learning for Predicting Poverty From Satellite Images

Estimating economic and developmental parameters such as poverty levels of a region from satellite imagery is a challenging problem that has many applications. We propose a two step approach to predict poverty in a rural region from satellite imagery. First, we engineer a multi-task fully convolutional deep network for simultaneously predicting the material of roof, source of lighting and source of drinking water from satellite images. Second, we use the predicted developmental statistics to estimate poverty. Using full-size satellite imagery as input, and without pre-trained weights, our models are able to learn meaningful features including roads, water bodies and farm lands, and achieve a performance that is close to the optimum. In addition to speeding up the training process, the multi-task fully convolutional model is able to discern task specific and independent feature representations.
Open Space and Public Access: A Contingent Choice Application to Coastal Preservation

States and municipalities have committed over $24 billion in bond issues for land conservation in recent years, yet the structure of the land conservation industry and markets is poorly understood. Using a stated choice experiment survey, we examine the role of public access in willingness to pay (WTP) for coastal land conservation. We identify complex patterns in WTP, as related to level of access and to attitudes toward access and environmental protection. Our findings contribute to understanding market segments that may motivate heterogeneity in land conservation agents and that reveal opportunities to optimize conservation programs that serve heterogeneous populations. (JEL Q26)
Considering childbearing in the age of highly active antiretroviral therapy (HAART): Views of HIV-positive couples

Objectives: Based on a qualitative study conducted in Bulawayo, Zimbabwe, this article examines how the availability of HAART since April 2004 may impact the views and choices of HIV-positive couples on childbearing. Methods: In-depth interviews were conducted with 15 couples where at least one partner was HIV positive. All respondents were of reproductive age and had or were confronting reproductive and sexual decision-making. Results: HAART seems to have had a profound impact on the subject of childbearing among those who still desire to have children. Where hitherto individuals had only a desire for a child many are now, as a result of the availability of HAART, actively planning to have one. HAART has not only transformed their physical state but it has also transformed mostly what had been desire into intention. The impact, however, has not been uniform. Some respondents still desired to have a child but were not yet convinced about the efficacy of HAART in preventing vertical transmission. Some respondents felt that HAART may have a negative impact on the foetus and as such were against childbearing by HIV-positive people. No respondent indicated that their desire or intention to have a child had been extinguished by the advent of HAART. Conclusion: Based on the findings of the study, HAART seems to have had a differential but nonetheless significant role in the reproductive plans of HIV-positive couples. The study also notes that there is a need to make available complete and unbiased information on HAART, mother-to-child transmission risk (MTCT) and pregnancy to HIV-positive couples so as to enable them to make informed decisions.
TOPCASED Combining Formal Methods with Model-Driven Engineering

This paper briefly presents the TOPCASED project which gathers industrialists, researchers, universities and SMEs, aiming at producing a free/open-source system/software/hardware-engineering toolkit, implemented over the Eclipse platform, using only standard components. An important aspect of TOPCASED is that it enables researchers to plug in their tools easily. TOPCASED is meant to be used on actual industrial projects and may therefore be considered as an important target by researchers working on formal methods and foundations of software engineering for critical systems
Information processing on the Swiss stock market

We conduct an event study to investigate the processing of information and the existence of insider trading on the Swiss stock market. Although Swiss laws are less restrictive than those of other countries, we find the empirical evidence for systematic insider trading before the publication of information to be fairly weak. Even for information producing large positive or negative returns upon publication, no statistically significant run-up returns can be detected. Regarding the processing of information, the Swiss market appears to be rather slow in incorporating new information into stock prices. We find significantly abnormal returns for approximately four days following the date of the publication of price-relevant information. Information with a large price impact seems to be processed faster than information with a small impact. The market value of a firm seems to have only a limited impact on the processing of information. Whereas the price impact of information is larger for small firms, the speed of information processing is not.
Generalized Distributed Multi-antenna Architecture Based Location Technology for Beyond 3G Systems

In order to research mobile terminal location technology for the next generation mobile communications, this paper sums up existing location technology of current mobile communications system, and then introduces generalized distributed antenna network architecture for beyond 3G system. On this basis, this paper presents a novel mobile terminal location technology. This method is based on the multi-antenna architecture, which calculates the distance between each antenna and mobile terminal by link gain, then locates the position of mobile terminal, or its probability in this region. The simulation result and error analysis confirm that this method can provide a location technology with higher precision than other location technologies in current mobile communication system.
Does Microfinance Promote Entrepreneurship and Innovation? A Macro Analysis

Innovative entrepreneurs in Africa experience a lack of financial support and underdeveloped financial systems. Microfinance could offer a solution to this complex issue. In this respect, this research paper studies the contribution of microfinance to the innovation process through entrepreneurship. The study first reviews the effect of microfinance on opportunity-driven entrepreneurship and necessity-driven entrepreneurship. Second, it investigates the relationship between entrepreneurship and innovation. According to the literature, opportunity-driven entrepreneurship is more associated with different forms of innovation than necessity-driven entrepreneurship. Using pooled ordinary least squares (OLS) and random effects techniques on an unbalanced panel of 45 countries, our analysis supports the hypothesis that microfinance has a negative effect on necessity entrepreneurship. However, its effect on opportunity entrepreneurship depends on the socio-economic conditions of the countries. Regarding regional differences, there is strong evidence of an entrepreneurial shift from necessity to opportunity motivations in the Middle East and North Africa region and weak evidence in Sub-Saharan Africa.
Crystallographic studies on human BST-1/CD157 with ADP-ribosyl cyclase and NAD glycohydrolase activities.

cADPR is the novel second messenger that elicits calcium release from intracellular calcium stores and works independently of IP(3). In mammals, the ADP-ribosyl cyclase function is found in two membrane proteins, CD38 and BST-1/CD157. These enzymes, exposed extracellularly, bear cADPR hydrolase and NAD glycohydrolase activities. In spite of its functional importance, the structural basis of these enzymatic reactions remains elusive. We determined the crystal structures of the extracellular region of human BST-1 at atomic resolution in the free form and in complexes with five substrate analogues: nicotinamide, NMN, ATPgammaS, ethenoNADP, and ethenoNAD. The three-dimensional structural views of the reaction centre with these ligands revealed the mode of substrate binding and the catalytic mechanism of the multifunctional enzymatic reactions. In each catalytic cleft of the dimeric enzyme, substrates are recognized predominantly through van der Waals interactions with two tryptophan residues, and thereby the N-glycosidic bond of NAD is correctly exposed near a catalytic glutamate residue. Its carboxyl side-chain stabilizes the catalytic intermediate of the S(N)-1 type reaction. This conformation of the catalytic cleft also implies the mechanism of cyclization between the adenine base and the ribose. The three key residues are invariant among the sequences of BST-1, CD38, and Aplysia cyclase, and hence this substrate recognition mode and catalytic scheme appear to be common in the cyclase family.
“Hotspots” in trauma memories in the treatment of post-traumatic stress disorder: A replication

“Hotspots” refer to memories of detailed moments of peak emotional distress during a traumatic event. This study investigates hotspot frequency, and the emotions and cognitions contained in hotspots of memory for trauma, to replicate a previous study in this area (Holmes, Grey, & Young, 2005). Participants were patients receiving treatment for post-traumatic stress disorder (PTSD) at a specialist outpatient clinic after experiencing a range of traumatic events. The main finding was that, after fear, the most common emotions reported were anger and sadness. Cognitions related to psychological threat to the self were more common than those related to physical threat.
The Nature of the Firm

Economic theory has suffered in the past from a failure to state clearly its assumptions. Economists in building up a theory have often omitted to examine the foundations on which it was erected. This examination is, however, essential not only to prevent the misunderstanding and needless controversy which arise from a lack of knowledge of the assumptions on which a theory is based, but also because of the extreme importance for economics of good judgement in choosing between rival sets of assumptions. For instance, it is suggested that the use of the word “firm” in economics may be different from the use of the term by the “plain man. ”1 Since there is apparently a trend in economic theory towards starting analysis with the individual firm and not with the industry,2 it is all the more necessary not only that a clear definition of the word “firm” should be given but that its difference from a firm in the “real world,” if it exists, should be made clear. Mrs. Robinson has said that “the two questions to be asked of a set of assumptions in economics are: Are they tractable? and: Do they correspond with the real world? ”3 Though, as Mrs. Robinson points out, “more often one set will be manageable and the other realistic,” yet there may well be branches of theory where assumptions may be both manageable and realistic. It is hoped to show in the following paper that a definition of a firm may be obtained which is not only realistic in that it corresponds to what is meant by a firm in the real world, but is tractable by two of the most powerful instruments of economic analysis developed by Marshall, the idea of the margin and that of substitution, together giving the idea of substitution at the margin.
On the Use of the WRF Model to Mitigate Tropospheric Phase Delay Effects in SAR Interferograms

A method that is used to generate synthetic interferograms of the atmospheric phase delay temporal changes is presented. The Weather Research and Forecasting Model is used to forecast the spatial distribution of the main atmospheric parameters at the acquisition times of synthetic aperture radar (SAR) images. The method is applied to mitigate atmospheric artifacts in SAR interferograms. The Lisbon Region and the Pico and Faial Islands in the Azores archipelago are chosen as case studies. They are characterized by a different temporal behavior of atmospheric phase delay properties. Results are assessed by means of a statistical analysis.
Does Ownership Affect Firms' Efficiency? Panel Data Evidence on Italy

This paper provides empirical evidence on the relation between the identity of ultimate owners and technical (in)efficiency by estimating stochastic production frontiers on Italian firm level panel data for twelve manufacturing industries over the 1978–93 period. Privately-owned independent firms are used as reference group and their efficiency is assessed against three alternative forms of ownership: subsidiaries of (privately owned) national business groups, subsidiaries of foreign multinationals, and state owned firms. Even if cross-industry differences obviously exist a common pattern can however be identified. Overall, subsidiaries of foreign multinationals (state owned firms) are found to be more (less) efficient than the reference group. On the contrary, no systematic difference is found between independent firms and subsidiaries of national business groups.