Miracle-dz/UniFAR-FTUs huggingface dataset:
The evolution of dosage‐compensation mechanisms

Dosage compensation is the process by which the expression levels of sex‐linked genes are altered in one sex to offset a difference in sex‐chromosome number between females and males of a heterogametic species. Degeneration of a sex‐limited chromosome to produce heterogamety is a common, perhaps unavoidable, feature of sex‐chromosome evolution. Selective pressure to equalize sex‐linked gene expression in the two sexes accompanies degeneration, thereby driving the evolution of dosage‐compensation mechanisms. Studies of model species indicate that what appear to be very different mechanisms have evolved in different lineages: the male X chromosome is hypertranscribed in drosophilid flies, both hermaphrodite X chromosomes are downregulated in the nematode Caenorhabditis elegans, and one X is inactivated in mammalian females. Moreover, comparative genomic studies demonstrate that the trans‐acting factors (proteins and non‐coding RNAs) that have been shown to mediate dosage compensation are unrelated among the three lineages. Some tantalizing similarities in the fly and mammalian mechanisms, however, remain to be explained. BioEssays 22:1106–1114, 2000. © 2000 John Wiley & Sons, Inc.
Zooming into an Instagram City: Reading the local through social media

How are users’ experiences of production, sharing, and interaction with the media they create mediated by the interfaces of particular social media platforms? How can we use computational analysis and visualizations of the content of visual social media ( e.g. , user photos, as opposed to upload dates, locations, tags and other metadata) to study social and cultural patterns? How can we visualize this media on multiple spatial and temporal scales? In this paper, we examine these questions through the analysis of the popular mobile photo–sharing application Instagram. First, we analyze the affordances provided by the Instagram interface and the ways this interface and the application’s tools structure users’ understanding and use of the “Instagram medium. ” Next, we compare the visual signatures of 13 different global cities using 2.3 million Instagram photos from these cities. Finally, we use spatio–temporal visualizations of over 200,000 Instagram photos uploaded in Tel Aviv, Israel over three months to show how they can offer social, cultural and political insights about people’s activities in particular locations and time periods.
Quantification of skin penetration of antioxidants of varying lipophilicity

Antioxidants play a vital role in protecting the skin from environmental distress. As the skin is constantly exposed to harmful UV radiation, endogenous antioxidants present in the superficial layers of the skin neutralize reactive oxygen species. Over time, antioxidants become depleted and loss their protective effect on the skin. Therefore, supplementing skin with topical antioxidant can help replenish this loss and fight the oxidative stress. The objective of this study was to deliver antioxidants topically and quantify the amount permeated in the stratum corneum and underlying skin. Polyphenols (catechin, resveratrol and curcumin) and vitamin (retinol) with various lipophilic properties were delivered via porcine ear skin, using propylene glycol as a vehicle. The amount in the stratum corneum and underlying skin was quantified using tape stripping and skin extraction methods, respectively, and samples were analysed via HPLC. All four antioxidants permeated into the skin from the propylene glycol vehicle. The order of the amount of antioxidant in the stratum corneum was catechin > resveratrol~ retinol> curcumin, whereas that in the underlying skin was retinol > catechin~ resveratrol~ curcumin. Of the total amount of polyphenols in the skin, approximately 90% was retained in the stratum corneum whereas 10% was quantified in the underlying skin. In contrast, 10% of retinol was retained in the stratum corneum whereas 90% permeated in the underlying skin. Polyphenols (catechin, resveratrol and curcumin) showed high concentration in the stratum corneum whereas retinol showed high accumulation in the underlying layers of the skin.
Big Data: Astronomical or Genomical?

Genomics is a Big Data science and is going to get much bigger, very soon, but it is not known whether the needs of genomics will exceed other Big Data domains. Projecting to the year 2025, we compared genomics with three other major generators of Big Data: astronomy, YouTube, and Twitter. Our estimates show that genomics is a “four-headed beast”—it is either on par with or the most demanding of the domains analyzed here in terms of data acquisition, storage, distribution, and analysis. We discuss aspects of new technologies that will need to be developed to rise up and meet the computational challenges that genomics poses for the near future. Now is the time for concerted, community-wide planning for the “genomical” challenges of the next decade.
Optical solutions for system-level interconnect

Throughput, power consumption, signal integrity, pin count and routing complexity are all increasingly important interconnect issues that the system designer must deal with. Recent advances in integrated optical devices may deliver alternative interconnect solutions enabling drastically enhanced performance. This paper begins by outlining some of the more pressing issues in interconnect design, and goes on to describe system-level optical interconnect for inter- and intra-chip applications. Inter-chip optical interconnect, now a relatively mature technology, can enable greater connectivity for parallel computing for example through the use of optical I/O pads and wavelength division multiplexing. Intra-chip optical interconnect, technologically challenging and requiring new design methods, is presented through a proposal for heterogeneous integration of a photonic "above-IC" layer followed by a design methodology for on-chip optical links. Design technology issues are highlighted and the paper concludes with examples of the use of optical links in clock distribution (with quantitative comparisons of dissipated power between electrical and optical clock distribution networks) and for novel network on chip architectures.
MR imaging of the postoperative knee: a pictorial essay.

Magnetic resonance (MR) imaging of the postoperative knee has become more common because more arthroscopic repair procedures are being performed. The most common procedures include partial meniscectomy and meniscal repair, anterior cruciate ligament (ACL) reconstruction, and cartilage repair procedures. Specific findings of a retorn meniscus following meniscal repair or partial meniscectomy are increased signal intensity extending through the site of repair on T2-weighted images, displaced meniscal fragments, and abnormal signal intensity at a site distant from the repair. Findings of ACL graft disruption on T2-weighted MR images include absence of intact graft fibers and increased signal intensity similar to that of fluid within the expected region of the graft. Partial tears of the graft appear as areas of increased signal intensity affecting a portion of the graft with some intact fibers still present. An impinged ACL graft may appear to be draped over the anterior inferior edge of the intercondylar roof or be posteriorly bowed. Localized anterior arthrofibrosis appears on T1-weighted MR images as a focal nodular lesion of low signal intensity that is anterior to the ACL graft in the intercondylar notch and is indistinguishable from adjacent joint fluid. On T2-weighted images, the nodule is well differentiated from high-signal-intensity joint fluid. Finally, MR imaging has been shown to be accurate in the evaluation of cartilage repair tissue. Knowledge of the normal MR imaging appearance of the knee after the more common repair procedures will allow radiologists to recognize complications associated with such procedures.
Efficiency and Completeness of the Set of Support Strategy in Theorem Proving

One of the major problems in mechanical theorem proving is the generation of a plethora of redundant and irrelevant information. To use computers effectively for obtaining proofs, it is necessary to find strategies which will materially impede the generation of irrelevant inferences. One strategy wilich achieves this end is the set of support strategy. With any such strategy two questions of primary interest are that of its efficiency and that of its logical completeness. Evidence of the efficiency of this strategy is presented, and a theorem giving sufficient conditions for its logical completeness is proved.
A protocol family approach to survivable storage infrastructures

A protocol family supports a variety of fault models with a single client-server protocol and a single server implementation. Protocol families shift the decision of which types of faults to tolerate from system design time to data creation time. With a protocol family based on a common survivable storage infrastructure, each data-item can be protected from different types and numbers of faults. Thus, a single implementation can be deployed in different environments. Moreover, a single deployment can satisfy the specific survivability requirements of different data for costs commensurate with its requirements.
Hypertension among older adults in low- and middle-income countries: prevalence, awareness and control

Background This study uses data from the World Health Organization’s Study on Global Ageing and Adult Health (SAGE) to examine patterns of hypertension prevalence, awareness, treatment and control for people aged 50 years and over in China, Ghana, India, Mexico, the Russian Federation and South Africa. Methods The SAGE sample comprises of 35 125 people aged 50 years and older, selected randomly. Hypertension was defined as ≥140 mmHg (systolic blood pressure) or ≥90 mmHg (diastolic blood pressure) or by currently taking antihypertensives. Control of hypertension was defined as blood pressure below 140/90 mmHg on treatment. A person was defined as aware if he/she was hypertensive and self-reported the condition. Results Prevalence rates in all countries are broadly comparable to those of developed countries (52.9%; range 32.3% in India to 77.9% in South Africa). Hypertension was associated with overweight/obesity and was more common in women, those in the lowest wealth quintile and in heavy alcohol consumers. Awareness was found to be low for all countries, albeit with substantial national variations (48.3%; range 23.3% in Ghana to 72.1% in the Russian Federation). This was also the case for control (10.2%; range 4.1% in Ghana to 14.1% India) and treatment efficacy (26.3%; range 17.4% in the Russian Federation to 55.2% in India). Awareness was associated with increasing age, being female and being overweight or obese. Effective control of hypertension was more likely in older people, women and in the richest quintile. Obesity was associated with poorer control. Conclusions The high rates of hypertension in low- and middle-income countries are striking. Levels of treatment and control are inadequate despite half those sampled being aware of their condition. Since cardiovascular disease is by far the largest cause of years of life lost in these settings, these findings emphasize the need for new approaches towards control of this major risk factor.
Uncontrollability for Linear Autonomous Multi-input Dynamical Systems Depending on Parameters

Linear multi-input dynamical systems smoothly depending on parameters are considered. A set of parameter values corresponding to uncontrollable systems (an uncontrollability set) is studied. The typical (generic) structure of the uncontrollability set is described. A constructive method of perturbation analysis of the uncontrollability set is developed. Formulae of first-order approximations for the uncontrollability set and generalized eigenvalues (uncontrollable modes) are derived and used for numerical construction of the uncontrollability set. The method is based on the versal deformation theory for matrix pairs under feedback equivalence. As an example, the uncontrollability set is found for a three-parameter two-degree-of-freedom mechanical system.
Instruction-set modelling for ASIP code generation

A main objective in code generation for ASIPs is to develop retargetable compilers in order to permit exploration of different architectural alternatives within short turnaround time. Retargetability requires that the compiler is supplied with a formal description of the target processor. This description is usually transformed into an internal instruction set model, on which the actual code generation operates. In this contribution we analyze the demands on instruction set models for retargetable code generation, and we present a formal instruction set model which meets these demands. Compared to previous work, it covers a broad range of instruction formats and includes a detailed view of inter-instruction restrictions.
Graph Abstraction in Real-time Heuristic Search

Real-time heuristic search methods are used by situated agents in applications that require the amount of planning per move to be independent of the problem size. Such agents plan only a few actions at a time in a local search space and avoid getting trapped in local minima by improving their heuristic function over time. We extend a wide class of real-time search algorithms with automatically-built state abstraction and prove completeness and convergence of the resulting family of algorithms. We then analyze the impact of abstraction in an extensive empirical study in real-time pathfinding. Abstraction is found to improve efficiency by providing better trading offs between planning time, learning speed and other negatively correlated performance measures.
Remobilization of Heavy Metals Retained as Oxyhydroxides or Silicates by Bacillus subtilis Cells

The stability of heavy metals bound as either silicates or oxyhydroxides by the surfaces of Bacillus subtilis with changes in pH and presence of competing cations and EDTA was studied. Wall-bound silicate was very stable. Of all conditions, a pH of 3.0 (by HNO3) promoted the greatest release of Cd (87% [wt/wt]), Pb (77%), or Cu (54%). Bacterial Pb resisted extraction by EDTA, and Cd that was included in bacterial-silicates proved difficult to remobilize.
Public policy implications of HIV/AIDS in adolescents.

Prevention of the further spread of human immunodeficiency virus (HIV) and acquired immunodeficiency syndrome (AIDS) among US adolescents requires collaboration between the health and education sectors as well as partnerships at the local state and federal levels. The effectiveness of current school-based programs has been compromised by their emphasis on sexual abstinence and refusal to acknowledge adolescent sexuality; moreover many adolescents have already begun to engage in high-risk behaviors by the time an HIV prevention curriculum is introduced. Although 34% of US middle and senior high school students have been exposed to school-based AIDS education only 8% live in communities with youth-oriented condom availability programs. The basic challenge is to enable health care professionals and educators to work together to provide comprehensive services with categorical funding streams. Recommended are five policy initiatives: 1) authorization of the Department of Health and Human Services to coordinate--through its new Office of Adolescent Health--personnel and resources for HIV prevention; 2) establishment of a network of State Offices of Adolescent HIV/AIDS Prevention to maximize coordination of resources across the health and education sectors and promote interdisciplinary approaches; 3) establishment on the state level of a per capita funding system for HIV prevention education at all grade levels to ensure program quality; 4) creation by state education departments of a Health/Education Collaborative Committee to coordinate program development; and 5) establishment by school systems of a health and education HIV/AIDS advisory committee that includes school administrators and public and private sector health professionals.
Nutritional supplementation for stable chronic obstructive pulmonary disease.

BACKGROUND Low body weight in patients with chronic obstructive pulmonary disease (COPD) is associated with an impaired pulmonary status, reduced diaphragmatic mass, lower exercise capacity and higher mortality rate when compared to adequately nourished individuals with this disease. Nutritional support may therefore be a useful part of their comprehensive care. OBJECTIVES To conduct a systematic review of randomized controlled trials (RCTs) to clarify whether nutritional supplementation (caloric supplementation for at least 2 weeks) improved anthropometric measures, pulmonary function, respiratory muscle strength and functional exercise capacity in patients with stable COPD. SEARCH STRATEGY Randomized controlled trials (RCTs) were identified from the Cochrane Airways Group register of RCTs, a hand-search of abstracts presented at international meetings and consultation with experts. SELECTION CRITERIA Two reviewers independently selected trials for inclusion, assessed quality and extracted the data. DATA COLLECTION AND ANALYSIS Within each trial and for each outcome, we calculated an effect size. The effect sizes were then pooled by a random-effects model. Homogeneity among the effect sizes was also tested. MAIN RESULTS From 272 references, nine RCTs were ultimately included. Six papers were considered as high quality and only two studies were double-blinded. For each of the outcomes studied, the effect of nutritional support was small: the 95% confidence intervals around the pooled effect sizes all included zero. The effect of nutritional support was homogeneous across studies. An additional search conducted in August 2001 did not identify further studies. REVIEWER'S CONCLUSIONS Nutritional support had no significant effect on anthropometric measures, lung function or exercise capacity in patients with stable COPD.
Active power filter with model based predictive current control in natural and dq frame

In this paper, a model based predictive current control scheme for active power filters is presented. The proposed method is based on common control schemes, but is only related with a low computational effort. For the predictive control, an inverse model of the voltage source inverter is used. For calculating the inverse model, a future value of the reference current is needed. In the steady state, the load current and thereby the reference current are periodic with the fundamental period, meaning that a future value is equal to a corresponding past value. Thus, this past value can be used. The proposed method is applied to a three-phase four-wire system with control in natural frame and to a three-phase three-wire system with control in the synchronous dq frame. With focus on the predictive control, the general advantages and disadvantages of the different setups are discussed. Simulation and measurement results compensating the distortion current of a non-linear load are presented and the performance of both setups is compared.
A Spiking Neural Repesentation for XCSF

This paper presents a Learning Classifier System (LCS) where each classifier condition is represented by a spiking neural network. Adaptive behavior is realized through the use of self-adaptive parameters and neural constructivism, providing the system with a flexible knowledge representation. The approach allows for the evolution of networks of appropriate complexity to solve a continuous maze environment, here using discrete-valued actions. It is shown that the neural LCS is capable of developing optimal solutions to the reinforcement learning task presented in this paper.
Synthesis and receptor binding of IgG1 peptides derived from the IgG Fc region

The IgG binding Fcγ receptors (FcγRs) play a key role in defence against pathogens by linking humoral and cell‐mediated immune responses. Impaired expression and/or function of FcγR may result in the development of pathological autoimmunity. Considering the functions of FcγRs, they are potential target molecules for drug design to aim at developing novel anti‐inflammatory and immunomodulatory therapies. Previous data mostly obtained by X‐ray analysis of ligand–receptor complexes indicate the profound role of the CH2 domain in binding to various FcγRs. Our aim was to localize linear segments, which are able to bind and also to modulate the function of the low affinity FcγRs, like FcγRIIb and FcγRIIIa. To this end a set of overlapping octapeptides was prepared corresponding to the 231–298 sequence of IgG1 CH2 domain and tested for binding to human recombinant soluble FcγRIIb. Based on these results, a second group of peptides was synthesized and their binding properties to recombinant soluble FcγRIIb, as well as to FcγRs expressed on the cell surface, was investigated. Here we report that peptide representing the Arg255–Ser267 sequence of IgG1 is implicated in the binding to FcγRIIb. In addition we found that peptides corresponding to the Arg255–Ser267, Lys288–Ser298 or Pro230–Val240 when presented in a multimeric form conjugated to branched chain polypeptide in uniformly oriented copies induced the release of TNFα, a pro‐inflammatory cytokine from MonoMac monocyte cell line. These findings indicate that these conjugated peptides are able to cluster the activating FcγRs, and mediate FcγR dependent function. Peptide Arg255–Ser267 can also be considered as a lead for further functional studies. Copyright © 2004 John Wiley & Sons, Ltd.
Tissue Tropism and Target Cells of NSs-Deleted Rift Valley Fever Virus in Live Immunodeficient Mice

Background Rift Valley fever virus (RVFV) causes disease in livestock and humans. It can be transmitted by mosquitoes, inhalation or physical contact with the body fluids of infected animals. Severe clinical cases are characterized by acute hepatitis with hemorrhage, meningoencephalitis and/or retinitis. The dynamics of RVFV infection and the cell types infected in vivo are poorly understood. Methodology/Principal Findings RVFV strains expressing humanized Renilla luciferase (hRLuc) or green fluorescent protein (GFP) were generated and inoculated to susceptible Ifnar1-deficient mice. We investigated the tissue tropism in these mice and the nature of the target cells in vivo using whole-organ imaging and flow cytometry. After intraperitoneal inoculation, hRLuc signal was observed primarily in the thymus, spleen and liver. Macrophages infiltrating various tissues, in particular the adipose tissue surrounding the pancreas also expressed the virus. The liver rapidly turned into the major luminescent organ and the mice succumbed to severe hepatitis. The brain remained weakly luminescent throughout infection. FACS analysis in RVFV-GFP-infected mice showed that the macrophages, dendritic cells and granulocytes were main target cells for RVFV. The crucial role of cells of the monocyte/macrophage/dendritic lineage during RVFV infection was confirmed by the slower viral dissemination, decrease in RVFV titers in blood, and prolonged survival of macrophage- and dendritic cell-depleted mice following treatment with clodronate liposomes. Upon dermal and nasal inoculations, the viral dissemination was primarily observed in the lymph node draining the injected ear and in the lungs respectively, with a significant increase in survival time. Conclusions/Significance These findings reveal the high levels of phagocytic cells harboring RVFV during viral infection in Ifnar1-deficient mice. They demonstrate that bioluminescent and fluorescent viruses can shed new light into the pathogenesis of RVFV infection.