Miracle-dz/UniFAR-FTUs huggingface dataset:
Determining the Importance of a Specific rom Mutation in Plasmid Exclusion of pBR 322 During pUC 19 Co-Transformation

Co-transformation of the plasmids pBR322 and pUC19 has been shown to result in exclusion of pBR322 from transformed cells. The underlying mechanism for this exclusion is believed to be due to differences between the two plasmids including size, genetic mutations, and the presence or absence of specific genes. One such gene of potential importance is the rom gene, which has been shown to stabilize an interaction between RNAI and RNAII, inhibiting DNA replication in pBR322. This study investigates a derivative of the plasmid pBR322 with a specific mutation in the ribosome binding site of rom, pIK054, and compares it to pUC19 and pBR322 in co-transformation studies. It was expected that because of the mutation to the rom ribosome binding sequence, the rom gene product would not be formed and replication would increase in pIK054. It was found that despite this mutation, pIK054 did not outcompete pBR322 directly, and was still excluded during co-transformation with pUC19. The data suggests either that additional changes to the pBR322 plasmid are necessary to account for the improved replication of pUC19, or that the mutation to the ribosome binding site did not inhibit translation of the rom gene product. Future studies can investigate the presence of the rom gene product or the relative affinities of the ribosome to the ribosome binding site of the rom gene. In addition, a future study can systematically investigate the regions of pBR322 (or pIK054) that can improve replication.
Research, part of a Special Feature on Resilience and Vulnerability of Arid and Semi-Arid Social Ecological Systems China's Grassland Contract Policy and its Impacts on Herder Ability to Benefit in Inner Mongolia: Tragic Feedbacks

Northern China's grasslands have been losing productivity since the 1980s, when a policy known as the "grassland contracting policy" allocated commonly used grazing lands to individual herder households. Examined here is the connection between implementation of the grassland contracting policy and the loss of grassland production using the analytic concepts of ability to benefit and community failure. A gacha (village) of the Sunite Left Banner of the Xilingol League in Inner Mongolia is used as a case study to compare herder ability to benefit from rangeland resources during adverse climate events before and after policy implementation. Social-ecological resilience, access to social and ecological assets, and institutions supporting crisis relief have been affected. We find that the privatization of grassland use rights has weakened pastoralist ability to benefit from rangelands by weakening or dismantling what are identified as the rights-, structure-, and relations-based abilities that enabled pastoralists to cope with nonequilibrium conditions. This has led to a community failure that engenders feedbacks of increased impoverishment and environmental deterioration. The inflexible boundaries of quasi-private household property rights have caused the pastoral system to lose capacity to respond to drought and weather events through the flexibility of "otor" and other forms of herd movement, increasing vulnerability to environmental change.
Whole-exome sequencing and clinical interpretation of formalin-fixed , paraffin-embedded tumor samples to guide precision cancer medicine

682 VOLUME 20 | NUMBER 6 | JUNE 2014 naTuRe medicine Translating whole-exome sequencing (WES) for prospective clinical use may have an impact on the care of patients with cancer; however, multiple innovations are necessary for clinical implementation. These include rapid and robust WES of DNA derived from formalin-fixed, paraffin-embedded tumor tissue, analytical output similar to data from frozen samples and clinical interpretation of WES data for prospective use. Here, we describe a prospective clinical WES platform for archival formalin-fixed, paraffin-embedded tumor samples. The platform employs computational methods for effective clinical analysis and interpretation of WES data. When applied retrospectively to 511 exomes, the interpretative framework revealed a ‘long tail’ of somatic alterations in clinically important genes. Prospective application of this approach identified clinically relevant alterations in 15 out of 16 patients. In one patient, previously undetected findings guided clinical trial enrollment, leading to an objective clinical response. Overall, this methodology may inform the widespread implementation of precision cancer medicine.
Local Farmers' Organisations: A Space for Peer-to-Peer Learning? The Case of Milk Collection Cooperatives in Morocco

Abstract Purpose: The study investigated to what extent local farmers' organisations are spaces where farmers discuss, learn and innovate. Design/methodology/approach: Two milk collection cooperatives in Morocco were studied. The study analysed the discussion networks, their impacts on farmers' knowledge and innovation, and the performance of collective action at cooperative level. Findings: In both cooperatives, only two-thirds of the farmers regularly discussed dairy practices with other farmers. Most leaders of one cooperative were acknowledged to be experienced farmers and played key roles as advisors on dairy farming. Farmers' involvement in dialogue networks in this cooperative improved their capacity to innovate in dairy farming, even though their knowledge on some issues related to cattle, health and nutrition was not improved. In the other cooperative, experienced farmers did not share their knowledge and farmers' involvement in dialogue networks at cooperative level had no impact on their knowledge and practices. Dialogue networks and collective action were found to influence each other, since in the first cooperative, collective action was considered by members to be efficient, whereas in the second collective action was limited to milk collection. Practical implications: The study enabled identification of stumbling blocks which need to be addressed to get local farmers’ organisations involved in farmer capacity-building. Originality/value: While the importance of local discussion networks for knowledge creation and diffusion is widely acknowledged, taking such networks into account in farmers' capacity-building programmes in developing countries has been hindered by their informality. Combining the analysis of dialogue networks and collective action proved to be a productive way to assess the potentialities of working with farmers' organisations with the aim of establishing a connection with local discussion networks.
Size and Equal Opportunity in the Democratic Process: The Effect of the Danish Local Government Reform on Inequality in Internal Political Efficacy

A classic issue in political science is how the size of political entities affects democracy. We argue that municipal size may affect local internal political efficacy negatively in two ways: first, as existing studies show, greater distance between citizens and politicians in large municipalities may diminish citizens’ belief in their ability to influence politics. Second, it may cause greater inequality in internal political efficacy for different social groups. We use the comprehensive Danish structural reform of 2007 to examine the latter issue in a way that solves various methodological problems associated with cross sectional analysis of size effects. It turns out that there is no unequivocal development in the inequality of different social groups’ sense of efficacy. Hence, although increased size leads to decreased internal political efficacy generally, it does not systematically increase inequality.
Massive pulsating stars observed by BRITE-Constellation - I. The triple system β Centauri (Agena)

This paper aims to precisely determine the masses and detect pulsation modes in the two massive components of Beta Cen with BRITE-Constellation photometry. In addition, seismic models for the components are considered and the effects of fast rotation are discussed. This is done to test the limitations of seismic modeling for this very difficult case. A simultaneous fit of visual and spectroscopic orbits is used to self-consistently derive the orbital parameters, and subsequently the masses, of the components. The derived masses are equal to 12.02 +/- 0.13 and 10.58 +/- 0.18 M_Sun. The parameters of the wider, A - B system, presently approaching periastron passage, are constrained. Analysis of the combined blue- and red-filter BRITE-Constellation photometric data of the system revealed the presence of 19 periodic terms, of which eight are likely g modes, nine are p modes, and the remaining two are combination terms. It cannot be excluded that one or two low-frequency terms are rotational frequencies. It is possible that both components of Beta Cen are Beta Cep/SPB hybrids. An attempt to use the apparent changes of frequency to distinguish which modes originate in which component did not succeed, but there is potential for using this method when more BRITE data become available. Agena seems to be one of very few rapidly rotating massive objects with rich p- and g-mode spectra, and precisely known masses. It can therefore be used to gain a better understanding of the excitation of pulsations in relatively rapidly rotating stars and their seismic modeling. Finally, this case illustrates the potential of BRITE-Constellation data for the detection of rich-frequency spectra of small-amplitude modes in massive pulsating stars.
Environmental Policy and Technical Change : Pollution Taxes , Access to Finance , and Firm Absorptive Capacity ∗

Firms respond to higher taxes on air pollution by increasing R&D and hence their capacity to absorb new technology. The R&D response to pollution taxation only appears after the taxes are introduced and is concentrated in sectors with higher pollution intensity and relatively immobile production technologies, suggesting a causal linkage. However, the R&D response is substantially weaker in the firms most likely to face financing constraints; small firms only adjust R&D when they have demonstrated access to external financing. Taxing activities with high environmental costs can encourage technical change, but these policies have heterogeneous effects across different types of firms.
The Restoration of Phytophagous Beetles in Species‐Rich Chalk Grasslands

This study focuses on the restoration of chalk grasslands over a 6‐year period and tests the efficacy of two management practices, hay spreading and soil disturbance, in promoting this process for phytophagous beetles. Restoration success for the beetles, measured as similarity to target species–rich chalk grassland, was not found to be influenced by either management practice. In contrast, restoration success for the plants did increase in response to hay spreading management. Although the presence of suitable host plants was considered to dictate the earliest point at which phytophagous beetles could successfully colonized, few beetle species colonized as soon as their host plants became established. Morphological characteristics and feeding habits of 27 phytophagous beetle species were therefore tested to identify factors that limited their colonization and persistence. The lag time between host plant establishment and colonization was greatest for flightless beetles. Beetles with foliage‐feeding larvae both colonized at slower rates than seed‐, stem‐, or root‐feeding species and persisted within the swards for shorter periods. Although the use of hay spreading may benefit plant communities during chalk grassland restoration, it did not directly benefit phytophagous beetles. Without techniques for overcoming colonization limitation for invertebrate taxa, short‐term success of restoration may be limited to the plants only.
On Thabit ibn Kurrah’s formula for amicable numbers

This note describes some methods for deriving explicit formulas for amicable numbers which are similar to Thabit's famous rule. The search for new amnicable pairs by suchrules consists merely in primality tests for certain big numbers. Only two new pairs are actually given, demonstrating the usefulness of the results and simultaneously illustrating the quite strange form of pairs obtained by this new method. It is proposed to use a computer in order to get more solutions. 1. The numbers 220, 284 seem to have been known already to Pythagoras as the smallest pair of amicable numbers, They represent the case n = 2 of the following formula due to Thabit ibn Kurrah, an Arabian mathematician of the 9th century: If p = 3 * 2` - 1, q = 3*2" - 1, and r 9.22? 21 - 1 are primes and n 2 2, then 2rpq and 2nr are amicable numbers (4). This theorem was rediscovered by Fermat (1636) and Descartes (1638) and gen- eralized by Euler: 2"pq and 2"r arg amicable numbers, if the three integers p = 2`'f -I q = 2f - I, and r = 22-mf2 - I are primes, where n > m > I and f = 2m + 1. Thabit's rule yields amicable numbers for n = 2, 4, 7, but for no other value n < 200. With Euler's generalization, there is still one more solution: m = 7, n = 8 (Legendre, Tchebychev). Whether there are any further solutions is not known. * Jn particular, it is an open question, whether there is an infinity of amicable pairs of numbers, each having at most three distinct prime divisors (but cf. (6)). Apparently it has not been noticed up to now, that various rules can be found which are quite analogous to Thabit's. They arise naturally on considering the question whether there exists an infinity of amicable pairs with a given number of distinct prime 2. By a "Thabit-ibn-Kurrah-rule" or "Thabit-rule" T(bk, b2, p,' F1, F2), with given natural numbers b1, b2, a prime p, and polynomials F'(X), F2(X) E Z(X), we mean a statement of the form:
Migrant farmers as information brokers: agroecosystem management in the transition zone of Ghana

Environmentally induced farmer migration is an important livelihood strategy, yet little is known of the effects on the destination region agroecosystem information networks and management practices. In the forest-savanna transition zone (Brong Ahafo Region) of Ghana, where migration from northern regions (migrant) and from neighboring regions (settler) is active, we chart the role of migrant famers and the type of agroecosystem management practices embedded in information networks using a social networks approach. Based on empirical network data from 44 respondents across three communities, we illustrate a diffuse information network, with variable tie frequency between settlement categories (local, settler, or migrant) of farmers. The cohesion of this network is dependent on a few strategic bridging ties initiated by migrant farmers, who are thus centrally positioned to exchange agroecosystem management practices between geographically and socially distant groups. At the individual level, migrant and settler farmers are more likely: (1) to have larger networks with more ties between members of their networks, (2) to be brokers positioned between non-migrant farmers, and (3) to tend (although not statistically significantly) to use pro-environmental management regimes, including agroforestry practices, new planting methods, and plot-scale weeding. We conceptualize this phenomenon as extended social and environmental experience and the deployment of social-ecological memory, with migrant farmers as potential agents of innovation and adaptive management.
Natural Resources and Violent Conflict: Resource Abundance, Dependence and the Onset of Civil Wars

In this paper we examine the claim that natural resources invite civil conflict, and challenge the main stylized facts in this literature. We find that the nature of causation between resource dependence and civil war is opposite to conventional wisdom. In particular, (i) civil war creates dependence on primary sector exports, but the reverse is not true, and (ii) resource abundance is associated with a reduced probability of the onset of war. These results are robust to a range of specifications and, considering the conflict channel, we conclude there is no reason to regard resources as a general curse to development.
Factors Associated with Travel Time and Survival of Migrant Yearling Chinook Salmon and Steelhead in the Lower Snake River

Abstract Simple and multiple linear regressions were used to evaluate factors associated with travel time and survival of yearling chinook salmon Oncorhynchus tshawytscha and steelhead O. mykiss migrating in the lower Snake River. Factors were release date and environmental variables measuring river discharge (flow), water temperature, and the percentage of total flow passed over spillways at dams. Data were collected from migrant salmonids tagged with passive integrated transponder (PIT) tags from 1995 through 1999. The greatest distance over which survival could be estimated during all 5 years was from the Lower Granite Dam tailrace to the McNary Dam tailrace (225 river km encompassing four dams and reservoirs). Release groups consisted of PIT-tagged fish leaving Lower Granite Dam daily. Data from more than 451,000 PIT-tagged yearling chinook salmon and 204,000 PIT-tagged steelhead were analyzed. For each daily group, indices of exposure to environmental factors were calculated as the average value for .
Diameter and Density of Dentinal Tubule in Human Primary Teeth

The aim of this study was to investigate dentinal tubule diameter and dentinal tubule density in primary teeth and to compare those values between each tooth type at electron microscope level. Thirty freshly extracted primary teeth were included in this experiment and categorized into six groups according to their tooth types and dental arches. All samples were first sectioned longitudinally, and then sectioned perpendicular to the direction of dentinal tubules which directed from the pulpal horn at three levels represented outer, middle and inner dentin. The result revealed that the diameter and density of dentinal tubule increased from outer dentin toward the pulp. The mean±SD of tubule diameter was largest in maxillary molar (1.44±0.24μm) and smallest in mandibular incisor (1.15±0.18μm). The density of dentinal tubules was greatest in mandibular incisor (58,080.33 tubules/mm) and lowest in maxillary molar (27,476.26 tubules/mm). The diameter of dentinal tubules tended to increase from anterior to posterior teeth, while, conversely, tubule density decreased from anterior to posterior teeth.
Combination of Field Monitoring and Laboratory Bioassays for the Assessment of TBT Pollution in Ria de Aveiro

Despite the use of tributyltin (TBT) antifouling paints had been under regulatory restrictions in Portugal since the 90’s, the persistence of this compound in sediments may cause a slow decline in pollution levels over time. In this work, an historical perspective of TBT pollution in Ria de Aveiro is given by both imposex surveys as well as chemical monitoring of TBT in sediments. Additionally, a laboratory bioassay was performed for the assessment of the bioavailability of TBT in sediments: the gastropod Nassarius reticulatus was exposed to several sediments collected in Ria de Aveiro and imposex development was used as endpoint. Results of imposex levels and chemical analysis show that TBT pollution decreased in Ria de Aveiro over the last years due to the European Union (EU) ban of TBT antifouling paints in 2003 but TBT levels in the environment are above the quality standards, being still a matter of concern. The laboratory bioassay performed in the current work proved to be an effective tool for the assessment of TBT pollution and should be regarded as a valid option for monitoring programmes in near future.
Safe Haven Currencies: A Portfolio Perspective

Currency portfolios exhibit asymmetric correlations: during periods of bear, volatile world equity markets, currency portfolios provide different hedging benefits than in bull markets. I show how these time-varying hedging benefits depend on currency characteristics. This paper also illustrates how the presence of regime shifts in financial markets affects optimal portfolio choice across currency portfolios: during bear markets, investors are better off by unwinding carry trade positions, and by following currency momentum. Also, diversification benefits increase by holding undervalued currencies and currencies of countries with strong current accounts and international investment positions.
Antidiabetic potentials of Syzygium guineense methanol leaf extract

This study examines the effects of a methanol extract of Syzygium guineense leaves in streptozotocin (STZ) - induced diabetes, evaluates its effect on alpha glucosidase and 2, 2-diphenyl-1-picrylhydrazyl radical. Diabetes was induced in rats by a single intraperitoneal injection of streptozotocin (60 mg/kg). An oral glucose tolerance test was performed after diabetes induction and repeated after 14 days of treatment with the extract. The extract elicited antihyperglycemic action in diabetic rats evidenced by an improved oral glucose tolerance. A dose of 250 mg/kg of extract significantly (P<0.01, 0.001) enhanced glucose clearance at the end of treatment period and was comparable with metformin, the group also showed increase in hepatic glycogen content by 33.9% relative to the diabetic control. Serum biochemical analysis showed that the extract improved indices of renal and hepatic function by reduction in serum albumin, creatinine, liver enzymes, total and direct bilirubin. Similarly, the extract reduced serum cholesterol, triglycerides and high density lipoprotein (HDL) in a non-dose dependent manner; treatment with 250 mg/kg extract caused significant (P<0.05) reduction of HDL. Groups which received 250 and 500 mg/kg of extract showed reversal of glomerular damage compared with the diabetic untreated group. The extract also exhibited concentration-dependent antioxidant activity (EC50= 0.2 mg/ml) and statistically significant (P<0.01, 0.001) alpha glucosidase inhibitory effect (IC50= 6.15 mg/ml). These findings show the antidiabetic potential of S. guineense leaf extract, likely mediated through its ability to inhibit alpha glucosidase, scavenge free radicals and increase intrahepatic glucose uptake and storage.
Prosody and information structure in a tone language: an investigation of Mandarin Chinese

Prosody conveys discourse-level information, but the extent to which prosodic cues distinguish different kinds of information-structural concepts remains unclear. The prosodic encoding of information structure is even more complicated in tone languages, where acoustic cues such as F0, intensity and duration also distinguish lexical items (e.g. Mandarin). Prior work on Mandarin led to divergent findings regarding whether and what prosodic cues mark the distinctions between information-structural types. We conducted a production study on Mandarin to investigate whether (1) the presence/absence of corrective focus and (2) the distinction between new/given information are encoded prosodically. Our results show that correctiveness was reflected in all three acoustic parameters: corrective words had longer durations, larger F0 ranges and larger intensity ranges than non-corrective words. The new-given distinction was reflected only in lengthening and F0 range expansion, and only in the absence of correction (correctiveness-by-givenness interaction). This suggests that new information is encoded differently from corrective focus in Mandarin: only corrective focus is associated with intensity range expansion. Our results provide further evidence for the multi-functionality of acoustic-prosodic dimensions. Even in a language with lexical tones, which differ in F0, intensity and duration, all these dimensions also encode information structure. Furthermore, not only can prosodic cues indicate discourse importance, they also distinguish different types of information structure in Mandarin. Our findings highlight the fine-grained ability of the language production system to utilise different aspects of acoustic dimensions with great efficiency.