Project description:The taxonomy of medically important parasites continues to evolve. This minireview provides an update of additions and updates in the field of human parasitology from June 2020 through June 2022. A list of previously reported nomenclatural changes that have not been broadly adapted by the medical community is also included.
Project description:The readout of genome information is controlled by transcriptional regulatory elements, but a comprehensive view of the combinatorial control by these DNA sequences, which bind regulatory protein and/or the modified histones in regulating gene transcription, is clearly preliminary. We have developed an experimental strategy for comprehensive determination of such functional elements in human DNA. This strategy involves the application of genome-wide location analysis, also known as ChIP-chip, to a panel of well-characterized regulatory proteins and histones with specific modifications, known to generally associate with transcriptional regulatory elements in vivo. Identification of their genomic binding sites will allow us to determine the sequence features in the human genome that carry out transcriptional regulatory function. We have designed and produced DNA microarrays to represent all the non-repetitive sequences in the 30 million basepair ENCODE regions of the human genome to map various types of transcriptional regulatory elements in three model cell types. We have identified promoters by mapping the genomic sequences associated with RNA polymerase II and the general transcription factor TFIID in cells, enhancer elements by mapping the genomic sequences associated with transcriptional co-activators and enhancer-specific chromatin modifications, and insulators by mapping the genomic sequences associated with the insulator binding protein CTCF. The raw microarray results are released periodically prior to publication. Keywords: ChIP-chip ENCODE
Project description:A recent temperature reconstruction of global annual temperature shows Early Holocene warmth followed by a cooling trend through the Middle to Late Holocene [Marcott SA, et al., 2013, Science 339(6124):1198-1201]. This global cooling is puzzling because it is opposite from the expected and simulated global warming trend due to the retreating ice sheets and rising atmospheric greenhouse gases. Our critical reexamination of this contradiction between the reconstructed cooling and the simulated warming points to potentially significant biases in both the seasonality of the proxy reconstruction and the climate sensitivity of current climate models.
Project description:How fast the Northern Hemisphere (NH) forest biome tracks strongly warming climates is largely unknown. Regional studies reveal lags between decades and millennia. Here we report a conundrum: Deglacial forest expansion in the NH extra-tropics occurs approximately 4000 years earlier in a transient MPI-ESM1.2 simulation than shown by pollen-based biome reconstructions. Shortcomings in the model and the reconstructions could both contribute to this mismatch, leaving the underlying causes unresolved. The simulated vegetation responds within decades to simulated climate changes, which agree with pollen-independent reconstructions. Thus, we can exclude climate biases as main driver for differences. Instead, the mismatch points at a multi-millennial disequilibrium of the NH forest biome to the climate signal. Therefore, the evaluation of time-slice simulations in strongly changing climates with pollen records should be critically reassessed. Our results imply that NH forests may be responding much slower to ongoing climate changes than Earth System Models predict.
Project description:BackgroundIn medical research and practice, the p-value is arguably the most often used statistic and yet it is widely misconstrued as the probability of the type I error, which comes with serious consequences. This misunderstanding can greatly affect the reproducibility in research, treatment selection in medical practice, and model specification in empirical analyses. By using plain language and concrete examples, this paper is intended to elucidate the p-value confusion from its root, to explicate the difference between significance and hypothesis testing, to illuminate the consequences of the confusion, and to present a viable alternative to the conventional p-value.Main textThe confusion with p-values has plagued the research community and medical practitioners for decades. However, efforts to clarify it have been largely futile, in part, because intuitive yet mathematically rigorous educational materials are scarce. Additionally, the lack of a practical alternative to the p-value for guarding against randomness also plays a role. The p-value confusion is rooted in the misconception of significance and hypothesis testing. Most, including many statisticians, are unaware that p-values and significance testing formed by Fisher are incomparable to the hypothesis testing paradigm created by Neyman and Pearson. And most otherwise great statistics textbooks tend to cobble the two paradigms together and make no effort to elucidate the subtle but fundamental differences between them. The p-value is a practical tool gauging the "strength of evidence" against the null hypothesis. It informs investigators that a p-value of 0.001, for example, is stronger than 0.05. However, p-values produced in significance testing are not the probabilities of type I errors as commonly misconceived. For a p-value of 0.05, the chance a treatment does not work is not 5%; rather, it is at least 28.9%.ConclusionsA long-overdue effort to understand p-values correctly is much needed. However, in medical research and practice, just banning significance testing and accepting uncertainty are not enough. Researchers, clinicians, and patients alike need to know the probability a treatment will or will not work. Thus, the calibrated p-values (the probability that a treatment does not work) should be reported in research papers.
Project description:Pregnancy is an immunological challenge to the mother. The fetal tissues including the placenta must be protected from activation of the maternal immune system. On the other hand, the placental tissue sheds into the maternal circulation and must be adequately identified and phagocytized by the maternal immune system. During a healthy pregnancy, numerous immunosuppressive processes take place that allow the allograft fetus to thrive under exposure to humoral and cellular components of the maternal immune system. Breakdown of immune tolerance may result in sterile inflammation and cause adverse pregnancy outcomes such as preeclampsia, a vascular disease of the pregnancy with unpredictable course and symptoms from several organs. Immunological incompatibility between mother and fetus is strongly indicated in preeclampsia. Recently, genetic factors linking immunological pathways to predisposition to preeclampsia have been identified. In this mini-review genetic variation in immunological factors are discussed in the context of preeclampsia. Specifically, we explore immunogenetic and immunomodulary mechanisms contributing to loss of tolerance, inflammation, and autoimmunity in preeclampsia.
Project description:Fat necrosis of the breast is a benign non-suppurative inflammation of the adipose tissue and often mimics breast cancers, posing a diagnostic challenge for the clinician and radiologist. It has a myriad of appearances on different imaging techniques, ranging from the pathognomic oil cyst and benign dystrophic calcifications to indeterminate focal asymmetries, architectural distortions, and masses. A combination of different modalities can assist a radiologist in reaching a logical conclusion to avoid unnecessary interventions. The aim of this review article was to provide a comprehensive literature on the various imaging appearances of fat necrosis in the breast. Although a purely benign entity, the imaging appearances on mammography, contrast-enhanced mammography, ultrasound, and magnetic resonance imaging can be quite misleading, especially in post-therapy breasts. The purpose is to provide a comprehensive and all-inclusive review on fat necrosis with a proposed algorithm allowing a systematic approach to diagnosis.
Project description:Chronic obstructive pulmonary disease (COPD) remains a leading cause of morbidity and mortality worldwide. Despite this, there has been little progress so far in terms of disease-modifying therapies over the last few decades and this is in part due to poor understanding of the definition and mechanisms surrounding early disease before it becomes established and increasingly complex. In this review, the nuances and difficulty in defining early disease in COPD are discussed. There are clear benefits in identifying patients early; however, usually diagnosis is made in the presence of significant lung damage. We consider what can be learned of early disease from COPD studies and highlight the lack of inclusion of young smokers (who may be at risk of COPD) or those with mild disease. We discuss promising clinical measures that are being used in an effort to detect early disease. These include symptom assessment, lung physiology measures and computed tomography (CT) imaging modalities. There is emerging evidence for the role of neutrophils and their proteinases in early COPD. This may form an important biomarker to investigate the pathophysiological processes of early COPD. Given the importance of the early disease, it is recommended that future COPD studies focus on capturing the earliest manifestations of disease, to understand the initiating mechanisms and to identify novel treatment targets.
Project description:Alternative gene splicing, occurring ubiquitously in multicellular organisms can produce several protein isoforms with putatively different functions. The enormously extended genomic structure of mucin genes characterized by the presence of multiple exons encoding various domains may result in functionally diverse repertoire of mucin proteins due to alternative splicing. Splice variants (Svs) and mutations in mucin genes have been observed in various cancers and shown to participate in cancer progression and metastasis. Although several mucin Svs have been identified, their potential functions remain largely unexplored with the exception of the Svs of MUC1 and MUC4. A few studies have examined the expression of MUC1 and MUC4 Svs in cancer and indicated their potential involvement in promoting cancer cell proliferation, invasion, migration, angiogenesis and inflammation. Herein we review the current understanding of mucin Svs in cancer and inflammation and discuss the potential impact of splicing in generating a functionally diverse repertoire of mucin gene products. We also performed mutational analysis of mucin genes across five major cancer types in International Cancer Genome Consortium database and found unequal mutational rates across the panel of cancer-associated mucins. Although the functional role of mucins in the pathobiology of various malignancies and their utility as diagnostic and therapeutic targets remain undisputed, these attributes need to be reevaluated in light of the potentially unique functions of disease-specific genetic variants of mucins. Thus, the expressional and functional characterization of the genetic variants of mucins may provide avenues to fully exploit their potential as novel biomarkers and therapeutic targets.