Miracle-dz/UniFAR-FTUs huggingface dataset:
Microarray analysis of cutaneous squamous cell carcinomas reveals enhanced expression of epidermal differentiation complex genes

Gene expression profiles were determined for 12 cutaneous squamous cell carcinomas (SCC) removed from sun‐exposed sites on nonimmunosuppressed patients. Gene expression in each SCC was compared to that in sun‐exposed skin from the same patient using the Affymetrix HGU133 2.0 PlusGeneChip. We identified 440 genes with increased expression in SCC and 738 with decreased expression; overall we identified a large number of small changes in gene expression rather than a few marked changes that distinguished SCC from sun‐exposed skin. Analyzing this robust data set according to biofunctional pathways using DAVID, transcriptional control elements using oPOSSUM, and chromosomal location using GSEA suggested genetic and epigenetic mechanisms of gene expression regulation in SCC. Some altered patterns of gene expression in SCC were consistent with regulation of spatially separated genes by a number of developmentally important transcription factors (forkhead, HMG, and homeo factors) that negatively regulated gene expression and to a few factors that positively regulated expression (Creb‐1, NFκB, RelA, and Sp‐1). We also found that coordinately enhanced expression of epidermal differentiation complex genes on chromosome 1q21 was a hallmark of SCC. A novel finding in our study was enhanced expression of keratin 13 in SCC, a result validated by immunohistochemical staining of an SCC tumor tissue array. © 2010 Wiley‐Liss, Inc.
High-resolution DNA methylome analysis of primordial germ cells identifies gender-specific reprogramming in mice

Dynamic epigenetic reprogramming occurs during mammalian germ cell development, although the targets of this process, including DNA demethylation and de novo methylation, remain poorly understood. We performed genome-wide DNA methylation analysis in male and female mouse primordial germ cells at embryonic days 10.5, 13.5, and 16.5 by whole-genome shotgun bisulfite sequencing. Our high-resolution DNA methylome maps demonstrated gender-specific differences in CpG methylation at genome-wide and gene-specific levels during fetal germline progression. There was extensive intra- and intergenic hypomethylation with erasure of methylation marks at imprinted, X-linked, or germline-specific genes during gonadal sex determination and partial methylation at particular retrotransposons. Following global demethylation and sex determination, CpG sites switched to de novo methylation in males, but the X-linked genes appeared resistant to the wave of de novo methylation. Significant differential methylation at a subset of imprinted loci was identified in both genders, and non-CpG methylation occurred only in male gonocytes. Our data establish the basis for future studies on the role of epigenetic modifications in germline development and other biological processes.
Genome-wide bimolecular fluorescence complementation analysis of SUMO interactome in yeast

The definition of protein–protein interactions (PPIs) in the natural cellular context is essential for properly understanding various biological processes. So far, however, most large-scale PPI analyses have not been performed in the natural cellular context. Here, we describe the construction of a Saccharomyces cerevisiae fusion library in which each endogenous gene is C-terminally tagged with the N-terminal fragment of Venus (VN) for a genome-wide bimolecular fluorescence complementation assay, a powerful technique for identifying PPIs in living cells. We illustrate the utility of the VN fusion library by systematically analyzing the interactome of the small ubiquitin-related modifier (SUMO) and provide previously unavailable information on the subcellular localization, types, and protease dependence of SUMO interactions. Our data set is highly complementary to the existing data sets and represents a useful resource for expanding the understanding of the physiological roles of SUMO. In addition, the VN fusion library provides a useful research tool that makes it feasible to systematically analyze PPIs in the natural cellular context.
Interactions between cigarette smoking and selected polymorphisms in xenobiotic metabolizing enzymes in risk for colorectal cancer: A case‐only analysis

The metabolism of xenobiotics is complex and involves multiple steps and multiple enzymes. Genetic variation in the genes encoding these enzymes as well as the level of exposure to the substrates of these enzymes could alter metabolism and clearance of potential carcinogens and thus alter cancer susceptibility. This study examined interaction effect between smoking and two single nucleotide polymorphisms (SNPs)—CYP1A1 c.1384A>G (p.Ile462Val) and EPHX1 c.337T>C (p.Tyr113His)—in modulating colorectal cancer (CRC) risk. The SNPs were selected a priori based on functional significance. In a case‐only analysis, unconditional logistic regression was used to examine the associations between smoking and each SNP and between the two SNPs in 786 patients with nonfamilial CRC. There was significant multiplicative interaction for CRC risk between smoking and EPHX1 c.337T>C (odds ratio [OR] = 1.37, 95% confidence interval [CI] = 1.03–1.81, P = 0.03), particularly among smokers with a history of greater than 20 pack‐years of smoking (OR = 1.52, 95% CI = 1.07–2.16, P = 0.02). In addition, there was gene–gene interaction between EPHX1 c.337T>C and CYP1A1 c.1384A>G (OR = 1.61, 95% CI = 1.02–2.55, P = 0.04). Smokers with any variant allele of EPHX1 were at increased risk for CRC, as were individuals with any variant allele of CYP1A1 together with any variant allele of EPHX1. Thus, the study of gene–environment and gene–gene interactions may help to identify high‐risk subgroups that can be targeted for intensive smoking cessation and CRC screening interventions. © 2010 Wiley‐Liss, Inc.
Maintain Strength‐‐‐Reduce Limitations

MANY STUDIES HAVE SHOWN that increasing muscular strength can decrease the risk of injury and enhance performance. These results affect many of our athletes and clients. However, the relationship between muscular strength and physical function affects all of us. Currently, there is little information available relating muscular strength and endurance to functional limitations among healthy adults under age 65. The purpose of this investigation by Brill et al. (1) was to evaluate the relationship of muscular strength and endurance at baseline with the prevalence of functional limitations at follow-up. Subjects were selected from those who received preventive medical examinations at the Cooper Clinic in Dallas, TX. The study participants were 3,069 men and 589 women age 30–82. Besides signing a consent form, participants completed a muscular strength and endurance evaluation, achieved at least 85% of age-predicted maximal heart rate on a maximal exercise treadmill test, and responded to a mail-back survey. Using a composite score from the bench press, leg press, and sit-up tests, a muscular strength and endurance index composite score was calculated. Clinical assessments included a comprehensive preventive medical evaluation. The questions included in the survey were designed by a panel of experts in the area of physical activity and aging. The results showed that 7% of men and 12% of women reported at least 1 functional limitation after an average follow-up of 5 years. Weaker men and women had a higher body mass index (BMI), lower treadmill times, and a higher percentage of reported functional limitations than their stronger peers. Men and women in the high-strength group were about half as likely to report functional problems as those in the low-strength group. The relationship between muscular strength and endurance and the subsequent prevalence of functional limitations found in this study indicates that this relationship exists among middle-aged as well as older adults. These results encourage all adults to include activities that increase muscular strength in addition to increasing aerobic physical activity. As professionals in the strength and conditioning field, we need to make sure our athletes and clients participate in a well-rounded program incorporating exercises that benefit the musculoskeletal as well as the cardiovascular system. ▲
Cartilage tympanoplasty: literature review

Abstract There has been renewed interest in the use of cartilage for middle-ear reconstructions. The aim of the present review is to examine the indications, techniques and surgical outcomes of cartilage tympanoplasties reported in the literature. There have been concerns regarding weakening of cartilage struts, from histological studies involving explants; as a result, cartilage struts for ossiculoplasty have not gained popularity. On the other hand, cartilage tympanoplasty is now an established procedure for tympanic membrane and attic reconstruction. The commonest techniques involve cartilage palisades and composite cartilage–perichondrial island grafts. There are many variations on the shape, size and thickness of the cartilage grafts. The perceived benefit of cartilage tympanoplasty is to prevent retraction pockets at the grafted site, even though many otologists accept that this technique may not deal with the causal factors involved in the retraction process. Concerns that the stiffness and mass of cartilage grafts may adversely affect hearing have not been substantiated in clinical reports thus far.
Oculo‐visual changes and clinical considerations affecting older patients with dementia

Dementia is associated with various alterations of the eye and visual function. Over 60% of cases are attributable to Alzheimer's disease, a significant proportion of the remainder to vascular dementia or dementia with Lewy bodies, while frontotemporal dementia, and Parkinson's disease dementia are less common. This review describes the oculo‐visual problems of these five dementias and the pathological changes which may explain these symptoms. It further discusses clinical considerations to help the clinician care for older patients affected by dementia.
Pharmacogenomics in sepsis and septic shock

The promise of pharmacogenomics lies in the ability to tailor patient therapies based on a genetic risk profile. This risk profile may be based on known literature single nucleotide polymorphisms or it may be encompassed by genome‐wide scans for risk alleles. In either case, it is the polymorphisms of a patient that will be the focus in the search for better individualized therapies. The risk profile for sepsis has been indicated to be heavily influenced by various alleles of candidate genes. Several likely genes have been investigated, some in depth, while others have received less attention. We review the case for genetic susceptibility to sepsis and summarize the literature to date investigating the use of single nucleotide polymorphisms and haplotypes in the search for risk profiles. We discuss the methods in use for structuring associations between complex diseases and genomics. Finally, we summarize the literature to date dealing with risk polymorphisms in candidate genes including tumor necrosis factor (TNF)‐α, lymphotoxin‐α (LTA), interleukin (IL)‐6 and ‐10, as well as others. Drug Dev Res 64:181–194, 2005. © 2005 Wiley‐Liss, Inc.
Defining cell types and states with single-cell genomics

A revolution in cellular measurement technology is under way: For the first time, we have the ability to monitor global gene regulation in thousands of individual cells in a single experiment. Such experiments will allow us to discover new cell types and states and trace their developmental origins. They overcome fundamental limitations inherent in measurements of bulk cell population that have frustrated efforts to resolve cellular states. Single-cell genomics and proteomics enable not only precise characterization of cell state, but also provide a stunningly high-resolution view of transitions between states. These measurements may finally make explicit the metaphor that C.H. Waddington posed nearly 60 years ago to explain cellular plasticity: Cells are residents of a vast “landscape” of possible states, over which they travel during development and in disease. Single-cell technology helps not only locate cells on this landscape, but illuminates the molecular mechanisms that shape the landscape itself. However, single-cell genomics is a field in its infancy, with many experimental and computational advances needed to fully realize its full potential.
Genomic approaches for understanding the genetics of complex disease

There are thousands of known associations between genetic variants and complex human phenotypes, and the rate of novel discoveries is rapidly increasing. Translating those associations into knowledge of disease mechanisms remains a fundamental challenge because the associated variants are overwhelmingly in noncoding regions of the genome where we have few guiding principles to predict their function. Intersecting the compendium of identified genetic associations with maps of regulatory activity across the human genome has revealed that phenotype-associated variants are highly enriched in candidate regulatory elements. Allele-specific analyses of gene regulation can further prioritize variants that likely have a functional effect on disease mechanisms; and emerging high-throughput assays to quantify the activity of candidate regulatory elements are a promising next step in that direction. Together, these technologies have created the ability to systematically and empirically test hypotheses about the function of noncoding variants and haplotypes at the scale needed for comprehensive and systematic follow-up of genetic association studies. Major coordinated efforts to quantify regulatory mechanisms across genetically diverse populations in increasingly realistic cell models would be highly beneficial to realize that potential.
PI3K regulation of RAC1 is required for KRAS-induced pancreatic tumorigenesis in mice.

BACKGROUND & AIMS New drug targets are urgently needed for the treatment of patients with pancreatic ductal adenocarcinoma (PDA). Nearly all PDAs contain oncogenic mutations in the KRAS gene. Pharmacological inhibition of KRAS has been unsuccessful, leading to a focus on downstream effectors that are more easily targeted with small molecule inhibitors. We investigated the contributions of phosphoinositide 3-kinase (PI3K) to KRAS-initiated tumorigenesis. METHODS Tumorigenesis was measured in the Kras(G12D/+);Ptf1a(Cre/+) mouse model of PDA; these mice were crossed with mice with pancreas-specific disruption of genes encoding PI3K p110α (Pik3ca), p110β (Pik3cb), or RAC1 (Rac1). Pancreatitis was induced with 5 daily intraperitoneal injections of cerulein. Pancreata and primary acinar cells were isolated; acinar cells were incubated with an inhibitor of p110α (PIK75) followed by a broad-spectrum PI3K inhibitor (GDC0941). PDA cell lines (NB490 and MiaPaCa2) were incubated with PIK75 followed by GDC0941. Tissues and cells were analyzed by histology, immunohistochemistry, quantitative reverse-transcription polymerase chain reaction, and immunofluorescence analyses for factors involved in the PI3K signaling pathway. We also examined human pancreas tissue microarrays for levels of p110α and other PI3K pathway components. RESULTS Pancreas-specific disruption of Pik3ca or Rac1, but not Pik3cb, prevented the development of pancreatic tumors in Kras(G12D/+);Ptf1a(Cre/+) mice. Loss of transformation was independent of AKT regulation. Preneoplastic ductal metaplasia developed in mice lacking pancreatic p110α but regressed. Levels of activated and total RAC1 were higher in pancreatic tissues from Kras(G12D/+);Ptf1a(Cre/+) mice compared with controls. Loss of p110α reduced RAC1 activity and expression in these tissues. p110α was required for the up-regulation and activity of RAC guanine exchange factors during tumorigenesis. Levels of p110α and RAC1 were increased in human pancreatic intraepithelial neoplasias and PDAs compared with healthy pancreata. CONCLUSIONS KRAS signaling, via p110α to activate RAC1, is required for transformation in Kras(G12D/+);Ptf1a(Cre/+) mice.
VALIDITY AND RELIABILITY OF THREE METHODS USED IN THE DIAGNOSIS OF RAYNAUD'S PHENOMENON

Three different assessment methods for the classification of Raynaud's phenomenon (RP) were compared. These were (i) a previously validated method using colour charts supplemented with a short questionnaire, (ii) answers to a questionnaire based on criteria derived from the consensus opinion of a group of clinicians, and (iii) individual clinician's assessment using standard descriptions based upon the same consensus view. We report the results of a study involving six clinicians and 30 subjects investigating the level of repeatability between the three methods and also the reliability between the six clinicians. There did not exist any overall systematic bias between the six clinicians. Further, agreement between them, as assessed by the kappa statistic, ranged from moderate to good. However, there did exist systematic bias between the results from all three of the classification approaches with agreement between them ranging from only poor to moderate. We conclude that the previously validated colour chart assessment is too insensitive to detect RP. Further, a structured questionnaire based on perceived clinician's opinion could not reproduce clinicians' classification in practice. By contrast, supplying clinicians with standard descriptions did yield a reliable classification system for RP.
Street-level bureaucrats and the implementation of cleaning and sanitation practices in foodservice: case findings from a study in Danish hospitals and nursing homes

Proper cleaning and sanitation that can to maintain the sanitary and hygienic level in the catering kitchens is an important routine to prevent food-borne diseases and good management of cleaning and sanitation is an important part of any hygiene management system. But large scale industrial kitchens in general seems to be quite slow in initiating change processes required to implementing new routines and only very few large industrial kitchens in Denmark had compulsory self-inspection programs or auto-control operating as required. Against this background a study was carried out in Danish institutional kitchens to study the implementation process of cleaning and sanitation practices at practitioner level. The aim of the study was to study how policies aiming at improving hygiene management in foodservice have been implemented at kitchen level when it comes to cleaning and sanitation. The study was conducted as a multiple case study in nursing home and hospital kitchens. The methodology was based on individual telephone interviews in combination with a quantitative questionnaire. A total of 15 kitchens participated in the study which were based on and open-ended interview guide, focusing on applied cleaning methods, principles for choice of cleaning procedures and methods, cleaning management, including existing documentation for cleaning quality, as well as suggestions for improvements and advancements in cleaning and sanitation. The study shows that street-level bureaucrats responsible for cleaning and sanitation feel themselves faced with number of challenges that they don’t have the right background to be able to handle properly and this is mirrored in their views and attitudes towards cleaning and sanitation. Street-level bureaucrats find: that cleaning and sanitation is boring, monotonous and has low status; that help and guidelines for implementing their self-inspection program is needed; that planning and management tools and techniques are lacking; that tacit knowledge is the guiding principle rather than written procedures; and that educational opportunities are lacking and that there are few opportunities for networking and sharing of knowledge. In general street-level bureaucrats responsible for cleaning and sanitation feel themselves faced with number of challenges that they don’t have the right background to be able to handle properly and this is mirrored in their views and attitudes towards cleaning and sanitation.
Direct estimate of the rate of germline mutation in a bird

The fidelity of DNA replication together with repair mechanisms ensure that the genetic material is properly copied from one generation to another. However, on extremely rare occasions when damages to DNA or replication errors are not repaired, germline mutations can be transmitted to the next generation. Because of the rarity of these events, studying the rate at which new mutations arise across organisms has been a great challenge, especially in multicellular nonmodel organisms with large genomes. We sequenced the genomes of 11 birds from a three-generation pedigree of the collared flycatcher (Ficedula albicollis) and used highly stringent bioinformatic criteria for mutation detection and used several procedures to validate mutations, including following the stable inheritance of new mutations to subsequent generations. We identified 55 de novo mutations with a 10-fold enrichment of mutations at CpG sites and with only a modest male mutation bias. The estimated rate of mutation per site per generation was 4.6 × 10−9, which corresponds to 2.3 × 10−9 mutations per site per year. Compared to mammals, this is similar to mouse but about half of that reported for humans, which may be due to the higher frequency of male mutations in humans. We confirm that mutation rate scales positively with genome size and that there is a strong negative relationship between mutation rate and effective population size, in line with the drift-barrier hypothesis. Our study illustrates that it should be feasible to obtain direct estimates of the rate of mutation in essentially any organism from which family material can be obtained.
Single-cell transcriptome analysis of fish immune cells provides insight into the evolution of vertebrate immune cell types

The immune system of vertebrate species consists of many different cell types that have distinct functional roles and are subject to different evolutionary pressures. Here, we first analyzed conservation of genes specific for all major immune cell types in human and mouse. Our results revealed higher gene turnover and faster evolution of trans-membrane proteins in NK cells compared with other immune cell types, and especially T cells, but similar conservation of nuclear and cytoplasmic protein coding genes. To validate these findings in a distant vertebrate species, we used single-cell RNA sequencing of lck:GFP cells in zebrafish and obtained the first transcriptome of specific immune cell types in a nonmammalian species. Unsupervised clustering and single-cell TCR locus reconstruction identified three cell populations, T cells, a novel type of NK-like cells, and a smaller population of myeloid-like cells. Differential expression analysis uncovered new immune-cell–specific genes, including novel immunoglobulin-like receptors, and neofunctionalization of recently duplicated paralogs. Evolutionary analyses confirmed the higher gene turnover of trans-membrane proteins in NK cells compared with T cells in fish species, suggesting that this is a general property of immune cell types across all vertebrates.