Miracle-dz/UniFAR-FTUs huggingface dataset:
In vivo cleavage of transgene donors promotes nuclease‐mediated targeted integration

Targeted DNA integration is commonly used to eliminate position effects on transgene expression. Integration can be targeted to specific sites in the genome via both homology‐based and homology‐independent processes. Both pathways start the integration process with a site‐specific break in the chromosome, typically from a zinc‐finger nuclease (ZFN). We previously described an efficient homology‐independent targeted integration technique that captures short (<100 bp) pieces of DNA at chromosomal breaks created by ZFNs. We show here that inclusion of a nuclease target site on the donor plasmid followed by in vivo nuclease cleavage of both the donor and the chromosome results in efficient integration of large, transgene‐sized DNA molecules into the chromosomal double‐strand break. Successful targeted integration via in vivo donor linearization is demonstrated at five distinct loci in two mammalian cell types, highlighting the generality of the approach. Finally, we show that CHO cells, a cell type recalcitrant to homology‐based integration, are proficient at capture of in vivo‐linearized transgene donors. Moreover, we demonstrate knockout of the hamster FUT8 gene via the simultaneous ZFN‐ or TALE nuclease‐mediated integration of an antibody cassette. Our results enable efficient targeted transgene addition to cells and organisms that fare poorly with traditional homology‐driven approaches. Biotechnol. Bioeng. 2013; 110: 871–880. © 2012 Wiley Periodicals, Inc.
Failure to achieve reduction in the incidence of human immunodeficiency virus among men who have sex with men: A worrisome global concern

Sir, Over the years, the trends of surveillance have time and again suggested that men who have sex with men (MSM) have a higher risk of acquiring the infection by human immunodeficiency virus (HIV) than the general population. [1,2] In‐fact, the MSM has almost 20 times additional risk of being infected with HIV in comparison with the general population, especially in low and middle income nations. [2] Further, it is important to note that even though a decline in the incidence of HIV across the world has been observed, the scenario among MSM is altogether different, as either incidence of HIV has remained same or even increased in nations like the United States. [1,2] It is really worrisome that despite the existence of various behavioral prevention initiatives such as measures to enhance the access and utilization of condoms and lubricant, facilities for early diagnosis of infection, the existence of a mechanism to ensure quick linkage with sustained care and supportive services, and availability of an effective antiretroviral therapy (ART), the scenario is not as expected. [1,3]
Which came first, people or pollution? Assessing the disparate siting and post-siting demographic change hypotheses of environmental injustice

Although a large body of quantitative environmental justice research exists, only a handful of studies have examined the processes by which racial and socioeconomic disparities in the location of polluting industrial facilities can occur. These studies have had mixed results, we contend, principally because of methodological differences, that is, the use of the unit-hazard coincidence method as compared to distance-based methods. This study is the first national-level environmental justice study to conduct longitudinal analyses using distance-based methods. Our purposes are to: (1) determine whether disparate siting, post-siting demographic change, or a combination of the two created present-day disparities; (2) test related explanations; and (3) determine whether the application of distance-based methods helps resolve the inconsistent findings of previous research. We used a national database of commercial hazardous waste facilities sited from 1966 to 1995 and examined the demographic composition of host neighborhoods around the time of siting and demographic changes that occurred after siting. We found strong evidence of disparate siting for facilities sited in all time periods. Although we found some evidence of post-siting demographic changes, they were mostly a continuation of changes that occurred in the decade or two prior to siting, suggesting that neighborhood transition serves to attract noxious facilities rather than the facilities themselves attracting people of color and low income populations. Our findings help resolve inconsistencies among the longitudinal studies and builds on the evidence from other subnational studies that used distance-based methods. We conclude that racial discrimination and sociopolitical explanations (i.e., the proposition that siting decisions follow the ‘path of least resistance’) best explain present-day inequities.
Comparative Analysis of the Río Balsas and Tehuacán Models for the Origin of Maize

This paper examines the archaeological and biological evidence for shifts in human subsistence strategies during the transition from hunting and foraging to maize agriculture as posited in the Río Balsas, or lowland origin of maize, model and the Tehuacán, or highland origin of maize, model. These are two different interpretations of the genetic evidence for the ancestry of maize, the archaeological evidence for plant exploitation, and the ecological evidence for paleoenvironments and climate change in the two regions. In contrast to Panama, where there is good evidence for progressive intensification of human forest disturbance by 10,000 B.P., horticultural forest clearing by 8000 B.P., and slash-and-burn agriculture by 6000 B.P., the evidence for Mesoamerica, where maize agriculture originated, fits a different picture of biocultural evolution. The lowland regions of Mexico, Guatemala, Belize, and probably Honduras, were apparently undisturbed, semi-evergreen forests around 10,000 B.P. New findings from experimental maize genetics, combined with the comprehensive archaeological picture from Tehucán, Oaxaca, Tamaulipas, and the Valley of Mexico, support a highland Mesoamerican origin of maize.
Host specificity of insect herbivores in tropical forests

Studies of host specificity in tropical insect herbivores are evolving from a focus on insect distribution data obtained by canopy fogging and other mass collecting methods, to a focus on obtaining data on insect rearing and experimentally verified feeding patterns. We review this transition and identify persisting methodological problems. Replicated quantitative surveys of plant–herbivore food webs, based on sampling efforts of an order of magnitude greater than is customary at present, may be cost-effectively achieved by small research teams supported by local assistants. Survey designs that separate historical and ecological determinants of host specificity by studying herbivores feeding on the same plant species exposed to different environmental or experimental conditions are rare. Further, we advocate the use of host‐specificity measures based on plant phylogeny. Existing data suggest that a minority of species in herbivore communities feed on a single plant species when alternative congeneric hosts are available. Thus, host plant range limits tend to coincide with those of plant genera, rather than species or suprageneric taxa. Host specificity among tropical herbivore guilds decreases in the sequence: granivores>leaf-miners>fructivores>leaf-chewers=sap-suckers>xylophages>root-feeders, thus paralleling patterns observed in temperate forests. Differences in host specificity between temperate and tropical forests are difficult to assess since data on tropical herbivores originate from recent field studies, whereas their temperate counterparts derive from regional host species lists, assembled over many years. No major increase in host specificity from temperate to tropical communities is evident. This conclusion, together with the recent downward revisions of extremely high estimates of tropical species richness, suggest that tropical ecosystems may not be as biodiverse as previously thought.
INFLUÊNCIA DA ESTRUTURA DE CAPITAL NO DESEMPENHO ECONÔMICO DAS EMPRESAS BRASILEIRAS DE TECNOLOGIA

O objetivo do estudo foi verificar a influencia das determinantes da estrutura de capital no desempenho economico de empresas brasileiras de tecnologia. A pesquisa caracteriza-se como descritiva, documental e quantitativa. A amostra foi composta por 21 empresas, referentes aos setores de comunicacoes, telecomunicacoes e industria digital definidos conforme a base de dados da Revista Exame. Os dados coletados compreendem ao periodo de 2009 a 2013, do qual foram analisados por meio de regressao linear multipla, tendo como variaveis dependentes o Retorno dos Ativos e o Retorno do Patrimonio Liquido e como variaveis independentes as determinantes da estrutura de capital, sendo o Endividamento Geral, o Tamanho da empresa medido pelo volume de vendas e numero de empregados, a Taxa de crescimento das vendas, o Tipo de capital e o Tipo de controle. Os resultados indicam que o Retorno dos Ativos foi influenciado positivamente pela Taxa de Vendas no ano de 2009, no ano de 2011 e no ano de 2013. O Retorno do Patrimonio Liquido demostrou-se influenciado positivamente pelo Endividamento Geral no ano de 2010, assim como pela Taxa de Vendas no ano de 2009 e 2013 e no ano de 2013 o tipo de capital apontou significância negativa quanto ao retorno do patrimonio liquido. Os achados revelam que o desempenho economico das empresas de tecnologia e principalmente determinado pela taxa de crescimento das vendas, em virtude de que quanto maior as vendas do ano atual em relacao ao ano anterior melhor o retorno dos ativos e do patrimonio das organizacoes.
Lymphoscintigraphic Visualization of Internal Mammary Nodes With Subtumoral Injection of Radiocolloid in Patients With Breast Cancer

ObjectiveTo determine whether subtumoral injection of radiocolloid is useful for lymphoscintigraphic visualization of the internal mammary node and in sentinel lymph node (SLN) biopsy of the axilla in breast cancer patients. Summary Background DataThe presence of retromammary lymphatics connecting to the axillary and internal mammary basins has been demonstrated by early anatomic studies. Thus, it is hypothesized that some lymph, especially that from the parenchyma under the tumor, may drain into both the axillary and internal mammary basins. MethodsPatients (n = 196) with T1-2, N0 breast cancer underwent preoperative lymphoscintigraphy with radiocolloid (technetium 99m tin colloid) injection into various sites of the breast, followed by SLN biopsy using the combined method with blue dye. Patients were divided into four groups: group A (n = 41), peritumoral injection of both radiocolloid and blue dye; group B (n = 70), periareolar radiocolloid and peritumoral blue dye; group C (n = 45), intradermal radiocolloid and periareolar blue dye; and group D (n = 40), subtumoral radiocolloid and intradermal blue dye. A retrospective analysis of 1,297 breast cancer patients who underwent extended radical mastectomy with internal mammary node dissection was also conducted to determine the relationship between vertical tumor location (superficial or deep) and frequency of axillary and internal mammary node metastases. ResultsOne patient (2%) in group A, 3 (4%) in group B, 0 (0%) in group C, and 15 (38%) in group D exhibited hot spots in the internal mammary region on lymphoscintigraphy (P < .001, group D vs. the other groups). The concordance rate of radiocolloid and blue dye methods in detection of SLNs in the axillary basin was significantly lower in group D than in the other groups. In contrast, the mismatch rate (some SLNs were identified by radiocolloid and other SLNs were identified by blue dye, but no SLN was identified by both in the same patient) was significantly higher in group D than in the other groups. In patients treated with extended radical mastectomy, positivity of axillary and internal mammary metastases was significantly higher in patients (n = 215) with deep tumors than those (n = 368) with superficial tumors. ConclusionsThese results suggest the presence of a retromammary lymphatic pathway from the deep portion of the breast to both axillary and internal mammary basins, which is distinct from the superficial pathway. Therefore, SLN biopsy with a combination of subtumoral and other (peritumoral, dermal, or areolar) injections of radiocolloid will improve both axillary and internal mammary nodal staging.
Mlc1p promotes septum closure during cytokinesis via the IQ motifs of the vesicle motor Myo2p

Little is known about the molecular machinery that directs secretory vesicles to the site of cell separation during cytokinesis. We show that in Saccharomyces cerevisiae, the class V myosin Myo2p and the Rab/Ypt Sec4p, that are required for vesicle polarization processes at all stages of the cell cycle, form a complex with each other and with a myosin light chain, Mlc1p, that is required for actomyosin ring assembly and cytokinesis. Mlc1p travels on secretory vesicles and forms a complex(es) with Myo2p and/or Sec4p. Its functional interaction with Myo2p is essential during cytokinesis to target secretory vesicles to fill the mother bud neck. The role of Mlc1p in actomyosin ring assembly instead is dispensable for this process. Therefore, in yeast, as recently shown in mammals, class V myosins associate with vesicles via the formation of a complex with Rab/Ypt proteins. Further more, myosin light chains, via their ability to be transported by secretory vesicles and to interact with class V myosin IQ motifs, can regulate vesicle polarization processes at a specific location and stage of the cell cycle.
Drug‐Induced Hypersensitivity Syndrome Associated with Human Herpesvirus 6 and Cytomegalovirus Reactivation

We describe a patient with drug‐induced hypersensitivity syndrome (DIHS) associated with human herpesvirus 6 (HHV‐6) and cytomegalovirus (CMV) infection induced by sulfasalazine. Two weeks after starting sulfasalazine to treat a rectal ulcer, the patient developed disseminated macular erythema accompanied by fever, liver injury, and lymphadenopathy. Seroconversion of antibodies to HHV‐6 was observed. Systemic steroid treatment was not effective against the eruptions. Five months after the onset, he presented with an acute febrile disease. The detection of CMV antigen on peripheral blood leukocytes and positive staining for CMV on cutaneous endothelium indicated active CMV infection. Furthermore, he developed a bacteremia of methicillin resistant Staphylococcus aureus. An associatiation the CMV reactivation with DIHS was suggested, although there remains the possibility that the systemic steroid treatment precipitated CMV reactivation. Recently, HHV‐6 has been documented to have immunomodulating effects and to be associated with CMV reactivation. Therefore, we should pay attention to the possibility of CMV reactivation in patients with DIHS in whom the immunomodulating virus of HHV‐6 has been reactivated.
Dexmedetomidine: new insights

Dexmedetomidine is a potent alpha-2-adrenergic agonist, more selective than clonidine, with widespread actions on the mammalian brain that include sedation, anaesthetic-sparing, analgesia and sympatholytic properties. A large body of recent work supports its favourable profile in improving outcome and long-term brain function in the critically ill. The source of these benefits may lie in the neuroprotective properties that are seen in experimental models and in the clinical setting, in which it can attenuate delirium, preserve sleep architecture, preserve ventilatory drive and decrease sympathetic tone and inflammatory response. Dexmedetomidine may also be a valuable adjuvant when regional anaesthesia is used. Future research should aim at establishing the risk/benefit ratio when used at the bedside.
[State of the art treatment of progressive or refractory multiple myeloma].

UNLABELLED Multiple myeloma (MM) is with an incidence of 4-6/100 000 inhabitants a fairly frequent malignancy of B cells. The incidence increases markedly with age. In this review changes in the treatment of relapsed / refractory myeloma during the last decade have been analysed. The present standard of care in the progressive or refractory myeloma was elaborated by the working group "Refractory Multiple Myeloma" using an extensive literature search for studies published between 2003 and 2013. Outside of clinical trials, high-dose therapy with stem cell transplantation is recommended in fit patients up to 75 years without significant comorbidities. Ongoing studies address the question about the least toxic and the most effective treatment. Therefore, inclusion of patients in therapeutic trials and use of novel agent combinations is highly recommended, e.g. with 3(rd) generation-IMIDs (pomalidomide), new proteasome inhibitors, such as carfilzomib, ixazomib or oprozomib, antibodies, such as elotuzumab, daratumumab or SAR650984, siltuximab, tabalumab, denosumab, romosozumab, BTK-, HSP-inhibitors and other innovative phase I/II agents. CONCLUSION Based on new insights in the pathogenesis of the disease, treatment options for MM have changed significantly in recent years. There is a significantly larger treatment diversity, i.e. more MM-active agents and combinations are available today. Even with relapsed MM, patients with the disease often live longer and have fewer complications.
The cyclin-dependent kinase 8 module sterically blocks Mediator interactions with RNA polymerase II

CDK8 (cyclin-dependent kinase 8), along with CycC, Med12, and Med13, form a repressive module (the Cdk8 module) that prevents RNA polymerase II (pol II) interactions with Mediator. Here, we report that the ability of the Cdk8 module to prevent pol II interactions is independent of the Cdk8-dependent kinase activity. We use electron microscopy and single-particle reconstruction to demonstrate that the Cdk8 module forms a distinct structural entity that binds to the head and middle region of Mediator, thereby sterically blocking interactions with pol II.
Angioscotomata and morphological features of related vessels in automated perimetry.

AIMS--To determine principles which regulate the occurrence of angioscotomata in automated static perimetry, variations in light sensitivity were correlated with the location and diameter of neighbouring retinal vessels. METHODS--Ten normal eyes were tested with the Octopus 2000R, using a 0.431 degree light stimulus. Sensitivity was quantified in points located around the blind spot, according to a regular, 0.5 degree constant, grid pattern. From 336 to 443 locations were tested in each eye. The resulting printouts were superimposed on corresponding fundus photographs. At each tested point, the following five additional variables were evaluated: the diameters of the closest and the second closest vessel (in 0.1 degree units); the distances of the apparent location of the tested point to the closest and the second closest vessel (in 0.25 degree units); and the distance between the two closest vessels (in 0.25 degree units). Altogether, 3869 locations were tested and 23,214 values were quantified. RESULTS--The following two conditions were found to be related to a reduction in sensitivity: (1) proximity (< 0.25 degree) to a large vessel (> or = 0.5 degree in diameter); (2) proximity (< 0.25 degree) to one of two adjacent (< 0.5 degree distant), moderately large vessels (0.3 degree to 0.4 degree in diameter). In condition 1, sensitivity was 51.3% and specificity was 92.2%; in condition 2, sensitivity was 16.2% and specificity was 98.3%; and with a combination of conditions 1 and 2, sensitivity was 67.6% and specificity was 90.5%. Increase by 0.1 degree of an adjacent vessel which was 0.4 degree in diameter markedly affected light sensitivity. CONCLUSION--Modifications in vessel diameter are observed in a number of circumstances, including adaptive vascular response to changes in ambient conditions and obstructive disorders of retinal vessels. These findings indicate that changes in vessel diameter over time can result in fluctuation of sensitivity. It is concluded that, in contrast with what is commonly stated, when ocular media are unaltered and the subject's collaboration is adequate, temporal variations in measured thresholds do not necessarily reflect functional changes in nervous tissues in the visual pathways.
A Systematic Comparison of the Impact of Inflammatory Signaling on Absorption, Distribution, Metabolism, and Excretion Gene Expression and Activity in Primary Human Hepatocytes and HepaRG Cells

Inflammatory processes are associated with compromised metabolism and elimination of drugs in the liver, largely mediated by proinflammatory cytokines, such as interleukin-6. The Hepa-RG cell line is an established surrogate for primary human hepatocytes (PHH) in drug metabolism and toxicity studies. However, the impact of inflammatory signaling on HepaRG cells has not been well characterized. In this study, the response of primary human hepatocytes and HepaRG cells to interleukin (IL)-6 was comparatively analyzed. For this purpose, broad-spectrum gene expression profiling, including acute-phase response genes and a large panel of drug-metabolizing enzyme and transporter (DMET) genes as well as their modifiers and regulators, was conducted in combination with cytochrome P450 (P450) activity measurements. Exposure of PHH and HepaRG cells to IL-6 resulted in highly similar coordinated reduction of DMET mRNA, including major ATP-binding cassette transporters (ABCs), P450s, glutathione S-transferases (GSTs), uridine diphosphate glucuronosyltransferases (UGTs), and solute carriers (SLCs). Enzyme activities of CYP1A2, CYP2B6, CYP2C8, CYP2C9, CYP2C19, and CYP3A4 were reduced upon 48–72 hours exposure to IL-6 in PHH and HepaRG. However, although these effects were not significant in PHH due to large interindividual donor variability, the impact on HepaRG was more pronounced and highly significant, thus emphasizing the advantage of HepaRG as a more reproducible model system. Exposure of HepaRG cells to interleukin-1β and tumor necrosis factor α resulted in similar effects on gene expression and enzyme activities. The present study emphasizes the role of proinflammatory cytokines in the regulation of drug metabolism and supports the use of HepaRG in lieu of PHH to minimize subject variability.
Recent developments in diisocyanate asthma

Despite recent advances in our understanding of diisocyanate-induced asthma, this disease remains a perplexing phenomenon. Studies reported in the past year have focused on: (i) diisocyanate antigens; (ii) the role of airway and skin epithelium; (iii) human immune responses to exposure; (iv) neurogenic pathways; and (v) genetic factors that may confer susceptibility. These studies support the hypothesis that diisocyanate asthma results from the host immune response to these chemicals, and may represent a mixed T helper type 1/2 response. A better understanding of the pathogenesis of diisocyanate asthma should facilitate the development of better diagnostic tests and strategies for disease surveillance and intervention.
Regulation of ASIC activity by ASIC4 – new insights into ASIC channel function revealed by a yeast two‐hybrid assay

ASIC4 is a member of the acid‐sensing ion channel family that is broadly expressed in the mammalian nervous system, but has no known function. We demonstrate here that transfected ASIC4 is targeted to the plasma membrane in CHO‐K1 cells, where it associates with ASIC1a and downregulates exogenous ASIC1a expression. This effect could also be observed on endogenous H+‐gated currents in TSA‐201 cells and ASIC3 currents in CHO‐K1 cells, suggesting a physiological role for ASIC4 in regulating ASIC currents involved in pain mechanisms. Using a yeast two‐hybrid assay we found that ASICs interact with proteins involved in diverse functions, including cytoskeletal proteins, enzymes, regulators of endocytosis and G‐protein‐coupled pathways. ASIC4 is the sole member of this ion channel class to interact strongly with polyubiquitin. The distinct functionally related sets of interacting proteins that bind individual ASICs identified in the yeast two‐hybrid screen suggest potential roles for ASICs in a variety of cellular functions.