Miracle-dz/UniFAR-FTUs huggingface dataset:
112 Structurally distinct ubiquitin- and SUMO-modified PCNA: implications for their distinct roles in the DNA damage response

SUMMARY Proliferating cell nuclear antigen (PCNA) is a pivotal replication protein, which also controls cellular responses to DNA damage. Posttranslational modification of PCNA by SUMO and ubiquitin modulate these responses. How the modifiers alter PCNAdependent DNA repair and damage tolerance pathways is largely unknown. We used hybrid methods to identify atomic models of PCNAK107-Ub and PCNAK164-SUMO consistent with small-angle X-ray scattering data of these complexes in solution. We show that SUMO and ubiquitin have distinct modes of association to PCNA. Ubiquitin adopts discrete docked binding positions. By contrast, SUMO associates by simple tethering and adopts extended flexible conformations. These structural differences are the result of the opposite electrostatic potentials of SUMO and Ub. The unexpected contrast in conformational behavior of Ub-PCNA and SUMO-PCNA has implications for interactions with partner proteins, interacting surfaces accessibility, and access points for pathway regulation.
Turcot sendromu: (olgu sunumu)

Turcot sendromu; genetik gecisli, kolonda familyal adenomatozpolipozisle beraber, santral sinir sisteminin noroepitelialtumorunun birlikteligi ile olan bir sendromdur.Bu sendromda; glial tumorler ve medulloblastomalar santralsinir sisteminde en sik gorulen tumorlerdir. Bu olgu sunumunda;kolon tumoru nedeniyle opere edilen ve takibenglioblastoma multiforme tanisi alarak opere edilengenc bir Turcot sendromu hastasi sunularak; norosirurjikalonemi olan bu sendrom literatur bilgileri isigi altinda tartisilmistir.
Transmission of Kaposi sarcoma-associated herpesvirus in sub-Saharan Africa.

Kaposi sarcoma-associated herpesvirus (KSHV, also called human herpesvirus 8; HHV8) is a necessary, but insufficient, cause of Kaposi sarcoma (KS) [1]. KS is endemic in parts of Africa and also occurs opportunistically among individuals with AIDS [2]. In HIV-negative, KSHV-seropositive adults from the Mediterranean area over the age of 50 years, approximately one in 3000 men and less than half as many women develop KS per year [3]. In contrast, one in 30 HIV-positive, KSHV-seropositive men who have sex with men (MSM) develop KS per year [4]. This 100-fold increased risk of KS with HIV has amplified the incidence of KS in many populations of sub-Saharan Africa, where KSHV was endemic before the AIDS epidemic. In South Africa, one in three adults are KSHV seropositive [5] and the risk of KS is increased more than 20-fold with HIV infection [6]. With the HIV epidemic, KS has thus become the commonest cancer in children, women and men in many sub-Saharan African countries [7,8]. Abating this KS epidemic will require concerted efforts to treat individuals with HIV/AIDS and to reduce HIV and KSHV transmission.
Janela 3D: uma ferramenta de telecomunicação visual sensível ao ponto de vista do usuário.

Teleconference and telepresence systems are increasingly common. Based on the existence of a high capacity communication channel, it is aimed to provide user's point of view sensible realistic 3D visualization without physical distortion or any prior knowledge about the structure of the scene, using stereo cameras. Pairs of temporally coherent images ares used toh generate intermediary view of the target scene so that a tracked user will have the illusion of posing in front os the real scene. The implemented system is based on high visual quality components on the side of views generation and tries to maximize ease of use in the visualization part by using comodity components and beeing free os complex calibration procedures. keywords: telepresence. teleconference. epipolar geometry. stereo vision. immersive telecommunication
Stereo Matching Based on Efficient Image-Guided Cost Aggregation

SUMMARY Cost aggregation is one of the most important steps in lo-cal stereo matching, while it is di ﬃ cult to fulﬁll both accuracy and speed. In this letter, a novel cost aggregation, consisting of guidance image, fast aggregation function and simpliﬁed scan-line optimization, is developed. Experiments demonstrate that the proposed algorithm has competitive performance compared with the state-of-art aggregation methods on 32 Mid-dlebury stereo datasets in both accuracy and speed.
Modification of fos proteins: phosphorylation of c-fos, but not v-fos, is stimulated by 12-tetradecanoyl-phorbol-13-acetate and serum

We have investigated the covalent modification of the proteins encoded by the murine fos proto-oncogene (c-fos) and that of the corresponding gene product of FBJ murine osteosarcoma virus (v-fos). Both proteins are posttranslationally processed in the cell, resulting in forms with lower electrophoretic mobilities than that of the initial translation product on sodium dodecyl sulfate-polyacrylamide gels. Treatment with alkaline phosphatase indicates that most, if not all, of this electrophoretic shift is due to phosphoesterification of both proteins. These phosphoryl groups stoichiometrically modify the v-fos and c-fos proteins on serine residues and turn over rapidly in vivo in the presence of protein kinase inhibitors (half-life, less than 15 min). Direct quantitative comparison of steady-state labeling studies with L-[35S]methionine and [32P]phosphate reveals that the c-fos protein is four- to fivefold more highly phosphorylated than the v-fos protein is. Comparison of tryptic fragments from [32P]phosphate-labeled proteins indicates that although the two proteins have several tryptic phosphopeptides in common, the c-fos protein contains unique major tryptic phosphopeptides that the v-fos protein lacks. These unique sites of c-fos phosphorylation have been tentatively localized to the carboxy-terminal 20 amino acid residues of the protein. Phosphorylation of the c-fos protein, but not the v-fos protein, can be stimulated at least fivefold in vivo by the addition of either 12-tetradecanoyl-phorbol-13-acetate or serum. This increase in the steady-state degree of phosphorylation of c-fos appears to be independent of protein kinase C since phosphorylation is Ca2+ and diacylglycerol independent. The possible role of phosphorylation of these proteins in cellular transformation is discussed.
Gene Expression Analysis Using RNA-Seq from Organisms Lacking Substantial Genomic Resources

Development of massively parallel “next generation” sequencing technology (NGS) has dramatically revolutionized biological studies. Among the many applications of NGS, RNASeq is one of the most important uses of this technology. RNA-Seq enables investigators to accurately probe the current state of a transcriptome and assess many biologically important issues, such as; gene expression levels, differential splicing events, and allele-specific gene expression. Compared with previous technologies (e.g., microarrays, etc.) NGS has the clear advantage of not being limited to experimental systems having well characterized genomes or transcript sequence libraries. This positions RNA-seq approaches as important and versatile techniques for experimental systems and species where specific genetic information may be limited or altogether lacking. A major goal of most transcriptomic studies is the identification and characterization of all transcripts within a developmental stage or specific tissue. NGS techniques have made the massive amount of data required to carry out such studies both inexpensive and available to an unprecedented extent. Clever computer algorithms have made the assembly of these massive data sets the work of one or two people with reasonably powerful workstations or a moderate analytical server. Once a reference transcriptome has been assembled, analyses can be carried out that involve several steps, such as; mapping short sequence reads to transcriptome, quantifying the abundance of genes or gene sets, and comparing differential expression patterns among all samples. Herein we outline the processes from obtaining raw short read data to advanced comparative gene expression analysis and we review bioinformatic programs currently available, such as Tophat, Cufflinks, DESeq, that are specifically designed to address each of the above steps. We will discuss both accuracy and ease of use of these tools by biologists beginning to pursue these types of analyses. In addition to individual programs, we will also discuss integration of multiple programs into pipelines for more rapid and complete expression analyses. Overall, the future applications of RNA-Seq will open new avenues for transcriptome analyses of less well-studied and/or wild caught species that could not have previously been approached. This will yield a wealth of new comparative data highlighting the many ways plants and animals have developed to survive in this rapidly changing environment.
Degeneracy, as opposed to specificity, in immunotherapy.

While it could be argued that Jenner, with his discovery of vaccination, ushered in the field of immunotherapy, manipulation of the human immune system to treat inflammatory diseases is only now coming of age. The mechanism behind immune specificity, the basic premise of vaccination, was largely solved with appreciation of how the MHC presents antigen, and with crystallization of the MHC/T cell receptor complex. However, as has only recently been appreciated, while a given T cell receptor may ordinarily exhibit exquisite specificity, binding to some antigenic sequences can effect a conformational change to the receptor, allowing it to recognize MHC class II/peptide complexes in a highly degenerate fashion. This capacity may represent a fundamental mechanism of autoimmune disease, since it allows microbial antigens to trigger the T cell receptors of autoreactive T cells. Indeed, as discussed below, the activation of these T cells probably occurs both indirectly, by means of the innate immune system, and directly, through T cell receptor stimulation (1). Fortunately, the T cell receptor’s degeneracy may be key to therapies, with advantages not seen with antigen-specific approaches. A recent series of publications offers new insights into how this aspect of the cellular immune response might be used to treat human autoimmune disease. One well-established but still only incompletely understood reagent that may work through such a mechanism is glatiramer acetate (GA) (Copaxone, registered trademark of Teva Pharmaceutical Industries Ltd.), discussed by Karandikar et al. in this issue of the JCI (2).
Aspects of the bionomics of Phlebotomus sergenti sandflies from an endemic area of anthroponotic cutaneous leishmaniasis in Aleppo Governorate, Syria

Aspects of the bionomics of phlebotomine sandflies (Diptera: Psychodidae) were studied from June to November 2005 in three foci of anthroponotic cutaneous leishmaniasis (ACL) in Aleppo Governorate, Syria, where the agent Leishmania tropica (Wright) (Kinetoplastida: Trypanosomatidae) is transmitted by Phlebotomus sergenti Parrot. Syria has been designated by the World Health Organization as one of four countries in the Old World where cutaneous leishmaniasis is hyperendemic, but little is known about the biology of local vector populations. Standard collections by sticky traps showed two peaks in density, in June and late August. In total, 1840 sandflies were caught, comprising five species: Phlebotomus papatasi (Scopoli) (68.0%); P. sergenti (25.4%); Sergentomyia minuta (Rondani) (6.4%); Phlebotomus tobbi Adler & Theodor (0.1%), and Phlebotomus mascittii canaaniticus Adler & Theodor (0.1%). Similar numbers of P. sergenti were caught indoors (246 specimens) and outdoors (222), whereas P. papatasi was significantly more abundant indoors (1096 specimens) than outdoors (156) (χ2 = 241, P < 0.01). In total, 212 blood‐fed females were tested for host blood determination, of which 176 (83.0%) reacted with anti‐species reagent. Results from 20 P. sergenti suggest that this species is an opportunistic feeder, imbibing human, ovine, avian, bovine and feline blood, although more bloodmeals were taken from humans and cattle than expected in relation to the relative proportions of potential hosts present (the forage ratio, FR). The bionomics of P. sergenti are discussed in relation to the inefficacy of control campaigns based on indoor spraying with residual insecticides that have been implemented by the Syrian Ministry of Health to control the epidemics of ACL in the Aleppo Governorate.
Economic assessment in the management of non-Hodgkin’s lymphoma

An increasing need for economic evaluations of non-Hodgkin’s lymphoma (NHL) treatments exists. We performed a literature review on the currently available NHL economic evaluations, using PubMed and the Cochrane database. English and Dutch language papers on treatment in adults were selected. A total of 88 publications were found, 44 of which were included. Of these, 6 economic evaluation-specific methodological items are evaluated (study perspective, overhead costs, data sources, charges or prices, sensitivity analysis, presentations of resource use and unit costs), enabling readers to judge the value of these studies. The 11 subjects covered by the economic evaluations are discussed. Many NHL treatments remain to be studied in economic evaluations. Future publications should report on the six methodological items in more detail, and preferably tackle them in the recommended way.
The essential fatty acids.

In animal and human tissues, there are four families of fatty acids that are derived from the precursors palmitoleic, oleic, linoleic, and linolenic acids. Of these, linoleic and linolenic acids are essential dietary elements for humans and all higher animals. The four precursor fatty acids are metabolized (through desaturation and chain elongation) to form the long-chain polyunsaturated fatty acids. The principal fatty acids derived from linoleic acid are arachidonic acid, which contains four double bonds (tetraene) and dihomogamma linolenic acid, whereas products formed from linolenic acid are eicosapentaenoic acid and docosahexaenoic acid. The major products from palmitoleic and oleic acids are the 20 carbon fatty acids with three double bonds (triene). In the presence of adequate dietary amounts of essential fatty acids, tetraene products predominate in plasma. When the intakes of both linoleic and linolenic acids are low, triene formation is high and hence the triene/tetraene ratio in plasma is used to assess the index of essential fatty acid deficiency. The polyunsaturated fatty acids derived from essential fatty acids serve as cellular membrane phospholipid components which can influence the physicochemical characteristics of the lipid bilayer. Changes in membrane lipids can modify the mobility and function of a variety of membrane proteins which may result in altered cell/organ functions. Linoleic acid is specifically required in the skin to maintain the integrity of epidermal water barrier. The dihomogamma linolenic acid, arachidonic acid, and eicosapentaenoic acid are the precursors of eicosanoids which influence many cell processes and organ functions. (ABSTRACT TRUNCATED AT 250 WORDS)
How Do Product Users Influence Corporate Invention?

The extensive academic literature on innovation has long recognized product users as a potentially important source of ideas. Although prior work has primarily focused on understanding the unique motivations and knowledge that allow users to generate their own innovations, we extend existing theory to investigate the contribution of users to corporate invention. We draw on the knowledge-based view of the firm, evolutionary theory, and the user innovation literature to theorize that corporate inventions that integrate user knowledge will be of greater importance, contribute to a broader set of follow-on technologies, and occur earlier in the product life cycle than other corporate inventions do. We test these propositions with a large data set of medical device inventions. We find support for our predictions and discuss the implications of our results for the theoretical and empirical literature on organizational innovation.
Potential future studies on the nutritional status among indigenous peoples in Alaska and the Russian Far East: preliminary assessment of the Social Transition in the North data set

Objective. The purpose of this assessment is to examine the nutrition-related health data collected during the Social Transitions of the North (STN) study for understanding cultural differences between nations and the impact on nutritional status. Methods. The nutrition data in the STN study was collected in two regions of Alaska (Northwest Arctic and the Aleutian Islands) and in two regions of the Russian Far East (Kamchatka and Chukotka). The health questionnaire explored several factors that may contribute to identifying the nutritional status of the study populations. These factors were appetite, weight, subsistence food consumption, vitamin or mineral supplements use self-perception of health, special diets, and number of meals consumed with relatives. Results. US populations were heavier than the Russian population (p = 0.0001). Both the Alaskan and Russian populations are frequent users of subsistence foods. The US respondents reported consuming 75% or more of the total protein as subsistence protein more often (40%) than the Russian respondents (25%). Conclusion. US respondents perceive themselves as healthier than their Russian counterparts. The US respondents consumed greater amounts of subsistence foods in general, and more of their diet over the year is made up of Native protein.
Apodemus Species Mice Are Reservoir Hosts of Borrelia garinii OspA Serotype 4 in Switzerland

ABSTRACT Among Borrelia burgdorferi sensu lato isolates, seven outer surface protein A (OspA) serotypes have been described: serotypes 1 and 2 correspond to B. burgdorferi sensu stricto and Borrelia afzelii, respectively, and serotypes 3 to 7 correspond to Borrelia garinii. In Europe, serotype 4 has never been isolated from Ixodes ricinus ticks until recently, although this serotype has been frequently isolated from cerebrospinal fluid from patients. In Europe, B. afzelii and B. burgdorferi sensu stricto were found associated with rodents and B. garinii was found associated with birds. In this study, the reservoir role of Apodemus mice for B. garinii OspA serotype 4 was demonstrated by xenodiagnosis. Apodemus mice are the first identified reservoir hosts for B. garinii OspA serotype 4.
Minimization of Cogging Force in a Novel Linear Permanent-Magnet Motor for Artificial Hearts

This paper proposes a novel linear permanent-magnet (PM) motor, termed as double-stator tubular PM (DSTPM) motor, for artificial hearts. The key of the proposed DSTPM motor is to design the appropriate size of the inner and the outer stators so that the inner and the outer cogging forces can be counteracted by each other, thus minimizing the motor cogging force. To achieve this purpose, two stators are designed to have a special angle difference of 90 electrical degrees. Since one stator is located inside the mover, the inner space is fully used. Hence, the thrust density is enhanced and the axial direction length is reduced. Also, the PMs and the redundant windings are set in the stators, and the moving parts have only solid-iron salient poles. The electromagnetic characteristics of the proposed motor are analyzed by using the time-stepping finite-element method, confirming the validity of the proposed motor.
THE NATIONAL CHOLESTEROL EDUCATION PROGRAM ADULT TREATMENT PANEL III — HOW DO WOMEN FIT IN ? —

The National Cholesterol Education Program (NCEP) Adult Treatment Panel (ATP) released initial guidelines in 1988 (ATP I), followed by ATP II in 1993 and ATP III in 2001. In ATP I and II, treatment recommendations and goals of therapy for secondary prevention are similar. However, ATP III established a more aggressive approach for both secondary prevention and higher risk primary-prevention patients and included the introduction of a new coronary heart disease (CHD) risk equivalent category, an in-depth discussion of the metabolic syndrome, the establishment of non-high density lipoprotein (HDL) goals, and use of the Framingham Heart Study risk projections to identify higher risk primary-prevention patients. Patients with CHD risk equivalents are to be treated as aggressively as those patients with established CHD. In ATP III, the presence of the metabolic syndrome—characterized by the lipid triad of elevated triglycerides, low HDL cholesterol, and small, dense, low-density lipoprotein (LDL) cholesterol—is associated with an increased risk of cardiovascular events and is a secondary target of therapy. Another secondary target of therapy is non-high-density lipoprotein cholesterol (non-HDL-C), the difference between total cholesterol and HDL-C. Graded risk factors based upon the Framingham Heart Study projections are included to estimate 10-year risk of CHD. Based upon the more stringent guidelines of ATP III, as compared to ATP II, a more aggressive treatment strategy is warranted in dyslipidemic patients. (Advanced Studies in Medicine 2001;2(11):409-415)
Patient Number Calculations

Modern medical research is performed on selected groups of people, e.g., participants in randomized clinical trials, observational cohort and case-control studies, and cross-sectional surveys. The conclusions of this research, however, do not remain with the examined subjects: they are generalized to all of us. This is, at least, the aim of research. It is well known that inferences based on a sample can lead to erroneous conclusions. Some of the possible errors are known as sampling errors, others as non-sampling errors. This note concerns sampling errors. We will return to non-sampling errors later.
Bronchodilators and diuretics in children with bronchopulmonary dysplasia

Pulmonary function tests (PFT) were obtained during the course of a selfcontrolled study of six children aged 5 to 43 months who had moderate to severe bronchopulmonary dysplasia (BPD). Changes after the administration of intravenous (IV) furosemide (2 mg/kg), inhaled isoproterenol (0.2 cc, 1:200), inhaled atropine sulfate (0.05 mg/kg), and a placebo were assessed. The study indicated the furosemide and atropine significantly (P < 0.05) increased dynamic compliance (CL) for the group. A decrease in total pulmonary resistance (RL) and work of breathing (W) was observed after isoproterenol, although the responses were not significant (P = 0.08 and P = 0.09, respectively). It was speculated that pulmonary edema and increased vagal tone may contribute to small airway dysfunction in children who have BPD.
[Surgical treatment of gastric cancer: results in 423 cases].

BACKGROUND Gastric cancer is the second cause of cancer death worldwide and the first cause in Chile. Management of this pathology is controversial. AIM To report the results on morbidity, mortality, and long-term survival rates of surgical treatment of gastric cancer, and compare them with those reported in the literature. MATERIAL AND METHODS Follow up of 423 patients (aged 16 to 88 years, 271 males) operated for a gastric adenocarcinoma between 1996 and 2002. Patients were staged with the 5th edition of TNM staging system, and the 2nd edition in English of the Japanese Classification of Gastric Cancer. Morbidity was assessed using the classification of the Memorial Kettering Cancer Center group. Kapplan-Meier method was used to assay survival, and Log rank Test to compare long-term survivals. RESULTS Resectability of the lesions was 70.4%, and 88% of them corresponded to a curative-intended surgery. Seventy percent of patients were in stage TNM IIIA or higher at the moment of surgery. Mortality in curative intended operated patients was 4.2%, and morbidity was 33.7%. Overall five years survival rate was 33%: In the group with curative intended surgery it was 52%. Two years survival rate in the non intended curative group was 3.4%. CONCLUSIONS The reported incidence of complications in our series is similar to that reported in the literature. Five year survival rates, morbidity and mortality were comparable to those reported abroad.