Miracle-dz/UniFAR-FTUs huggingface dataset:
Cryptic population genetic structure: the number of inferred clusters depends on sample size

Clustering methods have been used extensively to unravel cryptic population genetic structure. We investigated the effect of the number of individuals sampled in each location on the resulting number of clusters. Our study was motivated by recent results in Arabidopsis thaliana: studies in which more than one individual was sampled per location apparently have led to a much higher number of clusters than studies where only one individual was sampled in each location, as is generally done in this species. We show, using computer simulations and microsatellite data in A. thaliana, that the number of sampled individuals indeed has a strong impact on the number of resulting clusters. This effect is smaller if the sampled populations have a hierarchical structure. In most cases, sampling 5–10 individuals per population should be enough. The results argue for abandoning the concept of ‘accessions’ in partially selfing organisms.
Distributed Charge Scheduling of Plug-In Electric Vehicles Using Inter-Aggregator Collaboration

Plug-in electric vehicles (PEVs) are emerging as an eco-friendly and cost-effective alternative to conventional vehicles driven by internal combustion engines. However, uncoordinated charging of a large number of PEVs may cause grid failure. Therefore, charge scheduling of PEVs is an important problem. However, the charge scheduling by a single aggregator does not scale well as the PEV population grows. We propose a distributed framework for efficient PEV charging with multiple aggregators in a city where a PEV raises its charging request to a specific aggregator, and each aggregator has partial information about others. The aggregators collaborate among themselves for scheduling PEVs for charging in different charging stations owned by it or others. In this paper, we formulate a bi-objective charge scheduling optimization problem that attempts to maximize the total profit of the aggregators while maximizing the total number of PEVs charged. We first prove that the problem is NP-complete. We then propose distributed offline and online algorithms to solve the problem, and present simulation results for some realistic traffic scenarios.
A cryptic sulfur cycle driven by iron below the sulfate-methane transition zone

Sediments of upwelling regions off Namibia, Peru, and Chile contain dense populations of large nitrate-storing sulfide-oxidizing bacteria, Thiomargarita, Beggiatoa, and Thioploca. Increased contents of monounsaturated C16 and C18 fatty acids have been found at all stations studied, especially when a high density of sulfide oxidizers in the sediments was observed. The distribution of lipid biomarkers attributed to sulfate reducers (10MeC16:0 fatty acid, ai-C15:0 fatty acid, and mono-O-alkyl glycerol ethers) compared to the distribution of sulfide oxidizers indicate a close association between these bacteria. As a consequence, the distributions of sulfate reducers in sediments of Namibia, Peru, and Chile are closely related to differences in the motility of the various sulfide oxidizers at the three study sites. Depth profiles of mono-O-alkyl glycerol ethers have been found to correlate best with the occurrence of large sulfide-oxidizing bacteria. This suggests a particularly close link between mono-O-alkyl glycerol ether-synthesizing sulfate reducers and sulfide oxidizers. The interaction between sulfide-oxidizing bacteria and sulfate-reducing bacteria reveals intense sulfur cycling and degradation of organic matter in different sediment depths.
Dynamic Linkages between Implied Volatility Indices of Developed and Emerging Financial Markets: An Econometric Approach

Since 2008, the financial systems around the world have been hit by a series of financial crisis from burst housing bubbles and crippling unemployment to unsustainable debt levels and volatile financial markets. An important measure to assess the market expectation of the future volatility of underlying asset is the implied volatility index (IVI). The main objective of the article is to examine the IVI linkages between developed financial markets (US, UK and Japan) and emerging financial markets (BRIC—Brazil, Russia, India and China) and to conclude about the degree of integration between these markets. The data consist of daily closing prices of stock index options between April 2010 and March 2013. The methodology involves the augmented Dickey–Fuller (ADF) test, unit root test, vector autoregressive (VAR) modelling and variance decomposition. The results of the study suggest that the US IVI has substantial impact over the variations of other IVIs, thus raising the possibility of it constituting a usable risk factor for investors internationally.
The Competence of the European Union to Adopt Measures Harmonizing the Procedural Rules Governing EC Antitrust Damages Actions

In December 2005 the European Commission published a Green Paper on Damages Actions for Breach of the EC Antitrust Rules. The Green Paper examines the conditions for bringing damages actions for breach of the EC antitrust rules and identifies obstacles to the current framework. Some of the options presented in the Green Paper that aim at facilitating private enforcement of EC competition law would require a certain level of harmonization of the national procedural rules governing EC antitrust damages actions. The objective of this working paper is to examine the competence of the EU to adopt such harmonizing measures. The paper will analyse, whether the Member States have a procedural autonomy when it comes to determining the procedural conditions governing rights conferred by Community law and the possible limitations to that autonomy. Moreover, it will examine possible legal bases for a harmonization, namely Articles 65, 83, 95 and 308 EC.
Outage Performance Analysis of Cooperative Diversity

Cooperative diversity has attracted great attention in recent years. In such a system, even single-antenna terminals can achieve spatial diversity with the help of other terminals. In this paper, we focus on the outage performance of cooperative diversity. The outage probabilities of several mean cooperative protocols are analyzed and compared. Theory analysis and simulation results show that the outage performances of these protocols vary with the channel conditions, and we may choose the appropriate cooperative protocol according to the channel conditions.
Natural killer cell‐derived large granular lymphocyte lymphoma of lung developed in a patient with hypersensitivity to mosquito bites and reactivated Epstein‐Barr virus infection

A 17‐year‐old female developed natural killer (NK) cell‐derived large granular lymphocyte (LGL) lymphoma of the lung. She had a past history of hypersensitivity to mosquito bites (HMB). After an eight‐year chronic, active Epstein‐Barr virus (EBV) infection, she developed multiple lung lesions and pleural effusion. In the effusion, 60% of the cells were LGL. They were CD2+, 3−, 16+, 56+, 57+, 45RO+/RA + weak, and possessed strong NK activity. No rearrangement of T‐cell–receptor genes was detected. From all these results, a diagnosis of NK‐LGL lymphoma of the lung was made. EB virus DNA was detected in cells infiltrating the pleural effusion. The clonality of the LGLs was determined by Southern blot hybridization with the terminal repeat sequence of EB virus as a probe, and by chromosomal abnormalities. The patient died from respiratory failure. Necropsy of the lung revealed diffuse lymphoma composed of polymorphic cells with typical angiocentric lesions. Reportedly, lymphomas of NK lineage show predominantly extranodal involvement, and primary lung lesions are rare. In the pleural effusion of the present case, abnormally high levels of soluble Fas ligand, interleukin‐10 and interferon γ were detected. This hypercytokinemia, reflecting the microenvironment of lymphoma cells, may play a role in the progression of the lymphoma and organ injury in the lung. Am. J. Hematol. 59:309–315, 1998. © 1998 Wiley‐Liss, Inc.
Xenopus U3 snoRNA GAC-Box A′ and Box A Sequences Play Distinct Functional Roles in rRNA Processing

ABSTRACT Mutations in the 5′ portion of Xenopus U3 snoRNA were tested for function in oocytes. The results revealed a new cleavage site (A0) in the 3′ region of vertebrate external transcribed spacer sequences. In addition, U3 mutagenesis uncoupled cleavage at sites 1 and 2, flanking the 5′ and 3′ ends of 18S rRNA, and generated novel intermediates: 19S and 18.5S pre-rRNAs. Furthermore, specific nucleotides in Xenopus U3 snoRNA that are required for cleavages in pre-rRNA were identified: box A is essential for site A0 cleavage, the GAC-box A′ region is necessary for site 1 cleavage, and the 3′ end of box A′ and flanking nucleotides are required for site 2 cleavage. Differences between metazoan and yeast U3 snoRNA-mediated rRNA processing are enumerated. The data support a model where metazoan U3 snoRNA acts as a bridge to draw together the 5′ and 3′ ends of the 18S rRNA coding region within pre-rRNA to coordinate their cleavage.
HIV-1 Envelope Induces Memory B Cell Responses That Correlate with Plasma Antibody Levels after Envelope gp120 Protein Vaccination or HIV-1 Infection1

Successful vaccines (i.e., tetanus and diphtheria) can induce long-lived Ab levels that are maintained by bone marrow plasma cells and plasma Ab levels do not correlate with numbers of blood memory B cells. Destruction of CD4+ T cells early in HIV-1 acute infection may result in insufficient induction of neutralizing Ab responses; thus, an HIV-1 vaccine should elicit high levels of durable Abs by long-lived plasma cells to be protective. We asked if HIV-1 envelope-specific memory responses were sustained by memory B cells in the settings of HIV-1 gp120 envelope vaccination and chronic HIV-1 infection. Levels of anti-HIV-1 envelope plasma Abs and memory B cells were found to correlate in both settings. Moreover, whereas the expected half-life of plasma Ab levels to protein vaccines was >10 years when maintained by long-lived plasma cells, anti-envelope Ab level half-lives were ∼33–81 wk in plasma from antiretroviral drug-treated HIV-1+ subjects. In contrast, anti-p55 Gag Ab level half-life was 648 wk, and Ab titers against influenza did not decay in-between yearly or biennial influenza vaccine boosts in the same patients. These data demonstrated that HIV-1 envelope induces predominantly short-lived memory B cell-dependent plasma Abs in the settings of envelope vaccination and HIV-1 infection. The inability to generate high titers of long-lived anti-envelope Abs is a major hurdle to overcome for the development of a successful HIV-1 vaccine.
[Immune tolerance and control of CNS autoimmunity: from animal models to MS patients].

INTRODUCTION Multiple sclerosis (MS) is a chronic inflammatory disease resulting in demyelination and axonal loss within the central nervous system (CNS). An autoimmune reaction directed against CNS antigens contributes to the disease process. Since the CNS has long been considered as an immune privileged site, how such an immune response can develop locally has remained enigmatic. Recent data, mostly based on the study of animal models for MS, have shown that the CNS is in fact more permissive to the development of immune responses than previously thought. This observation is counterbalanced by the fact that immune tolerance to neural antigens can be induced outside the CNS. This review focuses on the mechanisms preventing CNS autoimmunity, which act in three separate tissues. STATE OF THE ART In the thymus, expression of CNS auto-antigens promotes partial protection, notably through elimination of autoreactive T cells. In the secondary lymphoid organs, the remaining autoreactive T cells are kept under control by the thymus-derived naturally occurring regulatory T cells of the CD4(+) Foxp3(+) phenotype. In the CNS, multiple mechanisms including the local activation of regulatory T cells further limit autoimmunity. CONCLUSIONS AND PERSPECTIVES A better understanding of the induction of regulatory T cells, of their mechanisms of action, and of approaches to manipulate them in vivo may offer new therapeutic opportunities for MS patients.
High resolution molecular and histological analysis of renal disease progression in ZSF1 fa/faCP rats, a model of type 2 diabetic nephropathy

ZSF1 rats exhibit spontaneous nephropathy secondary to obesity, hypertension, and diabetes, and have gained interest as a model system with potentially high translational value to progressive human disease. To thoroughly characterize this model, and to better understand how closely it recapitulates human disease, we performed a high resolution longitudinal analysis of renal disease progression in ZSF1 rats spanning from early disease to end stage renal disease. Analyses included metabolic endpoints, renal histology and ultrastructure, evaluation of a urinary biomarker of fibrosis, and transcriptome analysis of glomerular-enriched tissue over the course of disease. Our findings support the translational value of the ZSF1 rat model, and are provided here to assist researchers in the determination of the model’s suitability for testing a particular mechanism of interest, the design of therapeutic intervention studies, and the identification of new targets and biomarkers for type 2 diabetic nephropathy.
Morphological evidence of the relevance of aromatase P 450 in autoparacrine regulation and pathology of the hypophysis REVIEW

Department of Human Anatomy and Histology, Faculty of Medicine, University of Salamanca, Spain, Laboratory of Neuroendocrinology, INCyL and IBSAL, University of Salamanca, Spain, Department of Physiology and Pharmacology, Faculty of Medicine, University of Salamanca, Spain, Faculty of Human and Social Sciences, Catholic University of Salamanca, Spain, Department of Human Anatomy and Embryology I, Faculty of Medicine, Complutense University of Madrid, Spain, Department of Human Anatomy and Embryology, Faculty of Medicine, University of Granada, Spain
The Digital Economy Act 2010 - a cause for celebration, or a cause for concern

Outside of legislation pertaining to security and counter-terrorism in the United Kingdom, such as the Terrorism Act 20001 and the Regulation of Investigatory Powers Act 2000,2 one of the more controversial Parliamentary Acts passed during the term of the Labour Government is that of the Digital Economy Act of 2010.3 Indeed, few Acts have caused as much controversy and outrage, particularly amongst internet-based communities and activist groups. Organisations such as the Open Rights Group, which states its goal as being the preservation and promotion of rights and civil liberties in the digital age, have denounced the Act as undemocratic. One such example comes in an article written by the Open Rights Group shortly after the Digital Economy Bill (a draft of the passed legislation) was announced, emotively titled “Digital Economy Bill: Dangerous and Draconian Just Got Dictatorial”. 4 The article described the proposed legislation as being arbitrary, disproportional and a threat to online rights. Another writer stated that: “The British government has brought down its long-awaited Digital Economy Bill, and it's perfectly useless and terrible. It consists almost entirely of penalties for people who do things which upset the entertainment industry. ”5 The same author wrote of the passed Act that it was an attack on privacy, on democracy and on transparency.6 In contrast, during the drafting and development of the Bill, representatives from the entertainment industry wrote of the Bill in glowing terms: “the Act's measures to reduce illegal downloading will spur on investment in new music and innovation in legal business models”,7 stated the head of the British Phonographic Industry (BPI). Yet why is this newly passed Act so divisive? Why is there little consensus on the aims and effects of the Act, even in the Parliament which assented to the Bill passing into law? In order to better understand these difficulties, it is necessary not only to look at the content of the Act, but also its development and the manner in which it was enacted. This article shall consider in depth the copyright infringement related sections of the Act, and their origins, in order to determine the effectiveness and legitimacy of this controversial piece of legislation.
Adult scoliosis surgery outcomes: a systematic review.

OBJECT Appreciation of the optimal management of skeletally mature patients with spinal deformities requires understanding of the natural history of the disease relative to expected outcomes of surgical intervention. Appropriate outcome measures are necessary to define the surgical treatment. Unfortunately, the literature lacks prospective randomized data. The majority of published series report outcomes of a particular surgical approach, procedure, or surgeon. The purpose of the current study was to systematically review the present spine deformity literature and assess the available data on clinical and radiographic outcome measurements. METHODS A systematic review of MEDLINE and PubMed databases was performed to identify articles published from 1950 to the present using the following key words: "adult scoliosis surgery," "adult spine deformity surgery," "outcomes," and "complications. " Exclusion criteria included follow-up shorter than 2 years and mean patient age younger than 18 years. Data on major curve (coronal scoliosis or lumbar lordosis Cobb angle as reported), major curve correction, Oswestry Disability Index (ODI) scores, Scoliosis Research Society (SRS) instrument scores, complications, and pseudarthroses were recorded. RESULTS Forty-nine articles were obtained and included in this review; 3299 patient data points were analyzed. The mean age was 47.7 years, and the mean follow-up period was 3.6 years. The average major curve correction was 26.6 degrees (for 2188 patients); for 2129 patients, it was possible to calculate average curve reduction as a percentage (40.7%). The mean total ODI was 41.2 (for 1289 patients), and the mean postoperative reduction in ODI was 15.7 (for 911 patients). The mean SRS-30 equivalent score was 97.1 (for 1700 patients) with a mean postoperative decrease of 23.1 (for 999 patients). There were 897 reported complications for 2175 patients (41.2%) and 319 pseudarthroses for 2469 patients (12.9%). CONCLUSIONS Surgery for adult scoliosis is associated with improvement in radiographic and clinical outcomes at a minimum 2-year follow-up. Perioperative morbidity includes an approximately 13% risk of pseudarthrosis and a greater than 40% incidence of perioperative adverse events. Incidence of perioperative complications is substantial and must be considered when deciding optimal disease management. Although the quality of published studies in this area has improved, particularly in the last few years, the current review highlights the lack of routine use of standardized outcomes measures and assessment in the adult scoliosis literature.
Outcomes for Arthroscopic Treatment of Anterior Inferior Iliac Spine (Subspine) Hip Impingement

Background: Femoroacetabular hip impingement (FAI) is now well recognized; however, anterior inferior iliac spine (AIIS; or subspine) impingement is a form of hip impingement that is underrecognized and can be an important source of hip disability and functional limitation. Purpose: To investigate the outcomes after arthroscopic treatment of AIIS/subspine-related hip impingement in the absence of FAI surgery. Study Design: Case series; Level of evidence, 4. Methods: A prospective institutional hip preservation registry was reviewed to identify patients who underwent arthroscopic AIIS decompression without concurrent treatment of FAI. Primary outcome tools captured in the registry included the modified Harris Hip Score (mHHS), the Hip Outcome Score (HOS), and the International Hip Outcome Tool–33 (iHOT-33). Patients with minimum 1-year follow-up were included. Meaningful outcome improvement was determined per minimal clinically important difference (MCID). Statistical analyses were primarily descriptive. Results: Thirty-three patients with a mean follow-up of 19.1 months (range, 12-44 months) were identified. All patients were female, with a mean ± SD age of 26.1 ± 10.3 years. All patients were found to have an associated labral tear, and the mean acetabular version was increased at 2 and 3 o’clock (14.5° and 19.8°, respectively). Mean preoperative outcome scores on the mHHS, HOS ADL (activities of daily living), HOS sport, and iHOT-33 were 57.2 ± 15.3, 66.9 ± 18.8, 43.9 ± 23.6, and 33.5 ± 18.3, respectively. At final available follow-up, mean scores on these outcome measures were 79.5 ± 19.0, 86.8 ± 15.8, 70.4 ± 32.8, and 65.0 ± 31.0, respectively. By the 1-year follow-up, MCID had been achieved in the majority of patients across all 4 tools. Conclusion: There is a paucity of outcomes evidence on AIIS/subspine-related hip impingement. This study demonstrates that isolated subspine impingement can be a cause of hip disability, even in the absence of FAI. Patients with isolated subspine impingement are more likely to be women and to present with low patient-reported outcome scores. However, meaningful outcome improvement can be achieved with arthroscopic AIIS decompression.
Influence of human activities and climate variability on green and blue water provision in the Heihe River Basin, NW China

Human activities and climate simultaneously affect water cycling and provision. Here, we study the impacts of climate variability and human activities on green and blue water provision (or the flows of both green water and blue water) in the inland Heihe River Basin as simulated by the Soil and Water Assessment Tool (SWAT). The results show that total green and blue water flow varied significantly from 1980 to 2010. Direct human activities did not significantly change the sum of green and blue water flow volumes. However, land use change led to a transformation of 206 million m3/year in the entire river basin from green to blue water flow, while farmland irrigation expansion resulted in a transformation of 66 million m3 from blue to green water flow. The synchronous climate variability, with an upward precipitation trend, caused an increase of green water flow by 469 million m3/year and an increase of blue water flow by 146 million m3/year at the river basin level over the study period. The results provide a general approach to investigate the impacts of historical human activities and climate variability on water provision at the river basin level.