Miracle-dz/UniFAR-FTUs huggingface dataset:
Function of the human T-cell leukemia virus type 1 21-base-pair repeats in basal transcription

The human T-cell leukemia virus type 1 (HTLV-1) promoter contains three copies of an imperfect 21-bp repeat called Tax-responsive element (TRE1). To examine the role of individual TRE1 sequences in basal transcription of the HTLV-1 promoter, site-directed mutations were generated in all possible combinations of one, two, or all three TRE1 elements in the viral long terminal repeat (LTR) and tested in vivo for transcriptional activity. Mutation of the middle TRE1 resulted in the greatest reduction in basal activity. Electrophoretic mobility shift analysis demonstrated that the protein complexes bound to each of the three TRE1 sequences were not identical. The complexes formed with the TATA-distal and middle TRE1s were dependent on the core cyclic AMP response element (CRE) found in all three TRE1s, while the cellular transcription factor Sp1 bound the TATA-proximal TRE1 in a CRE-independent manner. Sp1 binding produced a footprint on the viral LTR which covered the 5' region of the proximal TRE1. Mixing experiments demonstrated that the bindings of CREB and Sp1 to the proximal TRE1 were mutually exclusive. Sp1 was able to activate transcription both from the complete LTR and from the proximal TRE1 alone. These studies demonstrate that the TRE1 elements in the HTLV-1 LTR are functionally nonequivalent and suggest that Sp1 can influence HTLV-1 basal transcription.
Drift, not selection, shapes toll‐like receptor variation among oceanic island populations

Understanding the relative role of different evolutionary forces in shaping the level and distribution of functional genetic diversity among natural populations is a key issue in evolutionary and conservation biology. To do so accurately genetic data must be analysed in conjunction with an unambiguous understanding of the historical processes that have acted upon the populations. Here, we focused on diversity at toll‐like receptor (TLR) loci, which play a key role in the vertebrate innate immune system and, therefore, are expected to be under pathogen‐mediated selection. We assessed TLR variation within and among 13 island populations (grouped into three archipelagos) of Berthelot's pipit, Anthus berthelotii, for which detailed population history has previously been ascertained. We also compared the variation observed with that found in its widespread sister species, the tawny pipit, Anthus campestris. We found strong evidence for positive selection at specific codons in TLR1LA, TLR3 and TLR4. Despite this, we found that at the allele frequency level, demographic history has played the major role in shaping patterns of TLR variation in Berthelot's pipit. Levels of diversity and differentiation within and across archipelagos at all TLR loci corresponded very closely with neutral microsatellite variation and with the severity of the bottlenecks that occurred during colonization. Our study shows that despite the importance of TLRs in combating pathogens, demography can be the main driver of immune gene variation within and across populations, resulting in patterns of functional variation that can persist over evolutionary timescales.
HIV RNA level in early infection is predicted by viral load in the transmission source

Objective:HIV-1 viral load in early infection predicts the risk of subsequent disease progression but the factors responsible for the differences between individuals in viral load during this period have not been fully identified. We sought to determine the relationship between HIV-1 RNA levels in the source partner and recently infected recipient partners within transmission pairs. Methods:We recruited donor partners of persons who presented with acute or recent (<6 months) HIV infection. Transmission was confirmed by phylogenetic comparison of virus sequence in the donor and recipient partners. We compared viral load in the donor partner and the recipient in the first 6 months of HIV infection. Results:We identified 24 transmission pairs. The median estimated time from infection to evaluation in acutely/recently infected recipient individuals was 72 days. The viral load in the donor was closely associated with viral load at presentation in the recipient case (r = 0.55, P = 0.006). Conclusion:The strong correlation between HIV-1 RNA levels within HIV transmission pairs indicates that virus characteristics are an important determinant of viral load in early HIV infection.
Selfish Behavior in Network-Based Games

It is a well known principle of economics that when members of society do not coordinate and instead act independently in a self-interested fashion, the resulting outcome typically does not achieve the maximum possible total social welfare. Thus, there is often a cost to competitive behavior. This phenomenon, often referred to as the "Tragedy of the Commons", can explain the underlying cause of many diverse problems, including industrial over-pollution, nuclear proliferation, and over-fishing. In all these settings, decentralized and selfish behavior leads to suboptimal outcomes in which all parties suffer. In this thesis, we explore the extent to which a similar lack of centralized control in the design, formation, and operation of the Internet might likewise lead to an inefficient, unreliable, and needlessly expensive network. To study such scenarios, we apply the tools of game theory. This branch of mathematics allows us to formally describe these competitive environments, which we call games. Self-interested agents are represented as players, who seek to maximize their own private welfare. The stable solutions reached by these competing players are called Nash equilibria. In this thesis, we consider a number of games which model various aspects of competition in the Internet, and seek to quantify the extent to which the lack of centralized control decreases social welfare. In particular, we study games that model the competitive creation of networks and the pricing of network services, and we examine how collusion can make matters even worse. Our primary goal is to compare the quality of Nash equilibria to that of centrally designed solutions. We first introduce a game that models network formation. We show that while worst case selfish behavior is very costly, in a broad class of games, the best stable solutions are just as good as those that are designed centrally. In other words, for a large class of network creation games, selfish behavior need not lessen social welfare. We then consider the computational complexity of finding such stable outcomes. We also explore how minor restrictions on players' choices can lead to dramatically better outcomes. In particular, we show that by enforcing a certain degree of "fairness" in our network formation game, the cost of solutions reached through selfish play improves dramatically. We next consider a game in which players set prices for network services, and compete with each other for customers. We provide conditions under which Nash equilibria are guaranteed to exist, and show that for a broader class of games, equilibria are always close to optimal. Lastly, we propose a framework to model the formation of coalitions, and study these coalitions in the context of a simple load-balancing game. We show that despite the apparent increase in the level of coordination, limited collusion can actually decrease the quality of solutions that are reachable through selfish play. However, we prove that for a large class of games, this increase is always small.
Hegemony on a shoestring: indirect rule and access to agricultural land

Abstract In their efforts to govern African colonies through traditional rulers and customary law, British officials founded colonial administration on contested terrain. By committing themselves to uphold ‘native law and custom’ colonial officials linked the definition of Africans' legal rights with their social identities, which were, in turn, subject to conflicting interpretations. As agricultural growth and commercialisation intensified demand for land, competition for access to land and control over agricultural income gave rise to disputes over customary jurisdictions and structures of authority. Using evidence from colonial Nigeria, the Gold Coast, Kenya and Northern Rhodesia, this article argues that, under indirect rule, the commercialisation of transactions in rights to rural land was accompanied by, and served to promote, unresolved debate over their meaning. Résumé En s'efforçcant de gouverner les colonies africaines à travers les dirigeants traditionnels et le droit en usage, les représentants ofnciels britanniques ont fondé l'administration coloniale sur un terrain contentieux. En choisissant de maintenir ‘le droit et la coutume indigènes’, les représentants coloniaux ont lié la définition des droits légaux des africains à leurs identités sociales, qui à leur tour, étaient sujettes à des interprétations contradictoires. Comme le développement de l'agriculture et de la commercialisation ont intensiné la demande d'acquisition de terres, la concurrence pour accéder a la propriété et contrôler le revenu agricole ont engendré des controverses sur les juridictions usuelles et les structures de l'autorité. En prenant les exemples des colonies du Nigéria, de la Côte-d'Or, du Kenya et de la Rhodésie du Nord, cet article soutient que sous une représentation indirecte, la commercialisation des opérations dans les droits fonciers ruraux a contribué à engendrer un débat non résolu sur leur sens.
Natural Resources, Wage Growth and Institutions – A Panel Approach

This paper examines the effect of natural resource export dependence and fiscal responsibility on wage growth, which is derived from the labour first‐order condition and estimated using a panel growth‐accounting framework. Using annual data, the study accounts for the variability of resource revenues, one of the major difficulties of managing these resources. The control variables include the most crucial growth factors. Due to insufficient annual data, human capital is only considered inside wages as in many endogenous growth models. We estimate the influence on real wage growth arising from the growth‐impacts of natural resources through labour and capital efficiency while controlling for fiscal responsibility, which proves a suitable proxy for policies and institutions in a single‐panel case. The results show that responsible fiscal policy, assessed by the budget balance, prevents (variable) diffuse and point‐source resources from hindering real wage growth (through labour efficiency), a result also significant in a sub‐sample of un‐free countries. The hypothesis of a resource curse working through institutions and reflected on real wage growth holds for resource export shares, but not adjusting for re‐exportation. Overall, resource effects are jointly insignificant, even though point‐source resources show a positive impact through capital efficiency.
Variable returns to scale, urban unemployment and welfare

The proposition that free trade is superior to no trade has a classical ancestry. Adam Smith and Ricardo were amongst the first proponents of free trade. Samuelson [26] proved, and it is held by economists today, that free trade is the optimal policy in the presence of standard Paretoconditions. It is also generally agreed amongst economists that lower trade intervention is superior to higher trade intervention, given competitive conditions in a small country. These propositions do not hold, however, in the presence of factor market imperfections such as wage differentials in a small country and therefore production or wage subsidies improves social welfare. The two models which are generally used to investigate the positive as well as normative aspects of trade theory in the presence of unemployment, are the uniform real minimum wage model which is based on the assumption of general rigidity of real wage in one or two sectors of production and the sector-specific minimum wage model which focuses on the phenomenon of rural-urban migration in the face of large scale urban unemployment. These two models are commonly utilized by trade theorists to analyze trade and unemployment. Specifically, studies by Haberler [13], Johnson [16], Batra and Seth [3], Findlay [12] and Brecher [6; 7] investigate the consequences of rigid factor prices for a small country, whereas the normative as well as positive aspects of sector specific unemployment have been explored by Harris and Todaro [15], Bhagwati and Srinivasan [4; 5] and more recently by Batra and Naqvi [2], Das [10] and Kahn [19]. It has been correctly observed that the introduction of an exogenously specified real minimum wage among other things generates unorthodox results concerning unemployment and gains from trade. A large body of research has also been concerned with the welfare implications of different commercial policies in the context of variable returns to scale. ' Kemp and Negishi [20] have pointed out the beneficial effects of trade in the presence of variable returns to scale, production subsidy and consumption taxes. Eaton and Panagariya [11] have analyzed the question of gains from trade in the presence of variable returns to scale and in the context of Pareto welfare criterion, whereas Choi and Yu [8] have examined the welfare implications of tariffs and consumption taxes as well as the welfare rankings of these policies under variable returns to scale, while Panagariya and Succar [25] have modified the necessary and sufficient conditions for stability under increasing returns to scale in urban sector.
Depletion of Anaphase-promoting Complex or Cyclosome (APC/C) Subunit Homolog APC1 or CDC27 of Trypanosoma brucei Arrests the Procyclic Form in Metaphase but the Bloodstream Form in Anaphase*

The anaphase-promoting complex or cyclosome (APC/C) is a multiprotein subunit E3 ubiquitin ligase complex that controls segregation of chromosomes and exit from mitosis in eukaryotes. It triggers elimination of key cell cycle regulators such as securin and mitotic cyclins during mitosis by polyubiquitinating them for proteasome degradation. Seven core subunit homologs of APC/C (APC1, APC2, APC11, CDC16, CDC23, CDC27, and DOC1) were identified in the Trypanosoma brucei genome data base. Expression of six of them was individually ablated by RNA interference in both the procyclic and bloodstream forms of T. brucei. Only the CDC27- and APC1-depleted cells were enriched in the G2/M phase with inhibited growth. Further studies indicated that T. brucei APC1 and CDC27 failed to complement the corresponding deletion mutants of budding yeast. However, their depletion from procyclic-form T. brucei enriched cells with two kinetoplasts and an enlarged nucleus possessing short metaphase-like mitotic spindles, suggesting that APC1 and CDC27 may play essential roles in promoting anaphase in the procyclic form. Their depletion from the bloodstream form, however, enriched cells with two kinetoplasts and two nuclei connected through a microtubule bundle, suggesting a late anaphase arrest. This is the first time functional APC/C subunit homologs were identified in T. brucei. The apparent differential activities of this putative APC/C in two distinct developmental stages suggest an unusual function. The apparent lack of functional involvement of some of the other individual structural subunit homologs of APC/C may indicate the structural uniqueness of T. brucei APC/C.
The era of comparable life expectancy between thalassaemia major and intermedia: Is it time to revisit the major‐intermedia dichotomy?

In the last few decades, the life expectancy of regularly transfused β‐thalassaemia major (TM) patients has dramatically improved following the introduction of safe transfusion practices, iron chelation therapy, aggressive treatment of infections and improved management of cardiac complications. How such changes, especially those attributed to the introduction of iron chelation therapy, improved the survival of TM patients to approach those with β‐thalassaemia intermedia (TI) remains unknown. Three hundred and seventy‐nine patients with TM (n = 284, dead 40) and TI (n = 95, dead 13) were followed retrospectively since birth until 30 June 2015 or death. Kaplan‐Meir curves showed statistically significant differences in TM and TI survival (P < 0·0001) before the introduction of iron chelation in 1965, which were no longer apparent after that date (P = 0·086), reducing the Hazard Ratio of death in TM compared to TI from 6·8 [95% confidence interval (CI) 2·6–17·5] before 1965 to 2·8 (95% CI 0·8–9·2). These findings suggest that, in the era of iron chelation therapy and improved survival for TM, the major‐intermedia dichotomy needs to be revisited alongside future directions in general management and prevention for both conditions.
Rational Manipulation by Large Shareholders: The Hijacking of an Election

We develop a model where a manager bases value-affecting decisions on observed price patterns. This introduces the possibility of price manipulation by shareholders to induce a manager to take decisions he would not otherwise. We show that manipulation can be supported as a rational expectations equilibrium as long as there is some divergence in the objectives of the manager and shareholders, the decision is value enhancing for shareholders, and they retain an inventory in the firms stock. Providing evidence in support of manipulation is problematic because prices are forward looking making it difficult to distinguish whether prices are affecting real decisions or anticipating them. However, the Indian General Election of 2004 provides a rare opportunity. The election unexpectedly brought a new coalition into power. When the new coalition announced its leader to be the next prime minister, markets tumbled a record 11% in one day. The drop was confined only to the Indian markets and occurred in spite of abnormally low liquidity. By day-end the candidate withdrew. While supporters were dismayed, markets quickly recovered and climbed to record levels less than a year later. Apparently, through a drastic drop, markets were able to induce a change of decision that turned out to be quite favorable for business.
A restricted complete sharing policy for a stochastic knapsack problem in B-ISDN

Consider a circuit switched broadband ISDN network that support a variety of traffic classes (e.g., data, voice, video, facsimile), each of which has its own traffic requirement and reward function. We address the problem of dynamically allocating the capacity of each circuit among the traffic classes. As an optimal allocation policy is extremely hard to find, we apply a different methodology by which we bound from above the optimal expected reward, and propose a specific threshold policy-the restricted complete sharing (RCS)-that yields a reward sufficiently close to this bound. The initial parameters of the threshold policy are found with the aid of our bounding technique, and are improved by two iterative procedures. The quality of our policy is demonstrated by several numerical examples. >
A Mixed Index Approach to Identifying Hedonic Price Models

Recent literature suggests identifying house price hedonic regressions by using instrumental variables, spatial statistics, the borders approach, panel data, and other techniques. We present an empirical application of a mixed index model, first proposed by Bowden [Bowden, R.J., 1992. Competitive selection and market data: the mixed-index problem. The Review of Economic Studies 59(3):625-633. ] to identify hedonic price regressions. We compare the performance of the mixed index model to a traditional hedonic model and to a hedonic model that includes characteristics of the buyer of each house. We find the mixed index model outperforms the other models based on bootstrap distributions of predicted housing values, prediction variance, and predicted policy effects. The mixed index model distributions are less skewed and kurtotic than the other models, suggesting it more closely satisfies the classical linear regression assumption of normally distributed errors. Compared to the mixed index model, the traditional hedonic overstates the importance of lot size and school quality to house price and understates the importance of environmental quality.
Shoulder impingement syndrome: influence of shoulder position on rotator cuff impingement--an anatomic study.

OBJECTIVE The purpose of the study was to investigate the relationship of the distal supraspinatus tendon to the coracoacromial arch on radiographs and MR imaging at various shoulder positions. MATERIALS AND METHODS Radiopaque and gadolinium-impregnated markers were sutured to the distal aspect of the supraspinatus tendon and along the coracoacromial ligament in three cadavers. While varying positions of the shoulder, we obtained gross anatomic visualization, radiographs, and MR images. RESULTS Impingement of the distal aspect of the supraspinatus tendon between the acromion and the greater tuberosity of the humerus was well visualized during forward flexion and abduction of more than 30 degrees. Shoulder impingement was best seen at 60 degrees forward flexion, 60 degrees abduction, and internal rotation. CONCLUSION MR imaging of different shoulder positions may help reveal the pathogenesis of shoulder impingement syndrome.
Vertical Integration and Valuation of International Oil Companies

This paper studies financial statement information from the 50 largest international oil and gas companies during 1992 to 2011 and evaluates their relation to market values. In particular, we examine how this relationship is affected by accounting method choice (successful efforts versus full cost accounting) and vertical integration. We find that net income is more value relevant for full cost companies compared to companies that use the successful efforts accounting method. Furthermore, the value relevance of oil and gas reserves is different among successful efforts and full cost companies. Larger reserves among successful efforts companies are awarded a premium by stock markets. The value relevance of book value is significantly lower for integrated companies than for pure upstream companies. We also find that the value relevance of oil and gas reserves is different for upstream and integrated companies.
State Political Culture, Higher Education Spending Indicators, and Undergraduate Graduation Outcomes

Issues concerning higher education today (e.g., rising costs, declining public trust, changing state economics) have created new demands for postsecondary institutions to demonstrate their productivity. We examine whether differences in states’ political cultures (i.e., underlying traditions, values, and public policy choices) are reflected in variability between state finance policy indicators and institutional variables that explain undergraduate graduation rates. To test our proposed model, we use longitudinal data on state indicators and institutional variables that explain differences in graduation rates compiled over an 11-year period. Our findings suggest that differences in political culture represent mediating factors between states’ economic contexts and higher education appropriations, which help explain variation in their graduation rates over time.