Language vs individuals in cross-linguistic corpus typology

Published as a special publication of Language Documentation & Conservation (No. 25).Peer reviewe

Genomic analysis of atypical fibroxanthoma

Atypical fibroxanthoma (AFX), is a rare type of skin cancer affecting older individuals with sun damaged skin. Since there is limited genomic information about AFX, our study seeks to improve the understanding of AFX through whole-exome and RNA sequencing of 8 matched tumor-normal samples. AFX is a highly mutated malignancy with recurrent mutations in a number of genes, including COL11A1, ERBB4, CSMD3, and FAT1. The majority of mutations identified were UV signature (C>T in dipyrimidines). We observed deletion of chromosomal segments on chr9p and chr13q, including tumor suppressor genes such as KANK1 and CDKN2A, but no gene fusions were found. Gene expression profiling revealed several biological pathways that are upregulated in AFX, including tumor associated macrophage response, GPCR signaling, and epithelial to mesenchymal transition (EMT). To further investigate the presence of EMT in AFX, we conducted a gene expression meta-analysis that incorporated RNA-seq data from dermal fibroblasts and keratinocytes. Ours is the first study to employ high throughput sequencing for molecular profiling of AFX. These data provide valuable insights to inform models of carcinogenesis and additional research towards tumor-directed therapy

Effect of TNF-α genetic variants and CCR5Δ32 on the vulnerability to HIV-1 infection and disease progression in Caucasian Spaniards

<p>Abstract</p> <p>Background</p> <p>Tumor necrosis factor alpha (TNF-α) is thought to be involved in the various immunogenetic events that influence HIV-1 infection.</p> <p>Methods</p> <p>We aimed to determine whether carriage of the <it>TNF-α-238G>A, -308G>A </it>and <it>-863 C>A </it>gene promoter single nucleotide polymorphisms (SNP) and the <it>CCR5Δ32 </it>variant allele influence the risk of HIV-1 infection and disease progression in Caucasian Spaniards. The study group consisted of 423 individuals. Of these, 239 were uninfected (36 heavily exposed but uninfected [EU] and 203 healthy controls [HC]) and 184 were HIV-1-infected (109 typical progressors [TP] and 75 long-term nonprogressors [LTNP] of over 16 years' duration). <it>TNF-α </it>SNP and the <it>CCR5Δ32 </it>allele were assessed using PCR-RFLP and automatic sequencing analysis methods on white blood cell DNA. Genotype and allele frequencies were compared using the χ 2 test and the Fisher exact test. Haplotypes were compared by logistic regression analysis.</p> <p>Results</p> <p>The distribution of <it>TNF-α-238G>A, -308G>A </it>and <it>-863 C>A </it>genetic variants was non-significantly different in HIV-1-infected patients compared with uninfected individuals: <it>-238G>A</it>, p = 0.7 and p = 0.3; <it>-308G>A</it>, p = 0.05 and p = 0.07; <it>-863 C>A</it>, p = 0.7 and p = 0.4, for genotype and allele comparisons, respectively. Haplotype analyses, however, indicated that carriers of the haplotype H3 were significantly more common among uninfected subjects (p = 0.04). Among the infected patients, the distribution of the three <it>TNF-α </it>genetic variants assessed was non-significantly different between TP and LTNP: <it>-238G>A</it>, p = 0.35 and p = 0.7; <it>-308G>A</it>, p = 0.7 and p = 0.6: <it>-863 C>A</it>, p = 0.2 and p = 0.2, for genotype and allele comparisons, respectively. Haplotype analyses also indicated non-significant associations. Subanalyses in the LTNP subset indicated that the <it>TNF-α-238A </it>variant allele was significantly overrepresented in patients who spontaneously controlled plasma viremia compared with those who had a detectable plasma viral load (genotype comparisons, p = 0.02; allele comparisons, p = 0.03). The <it>CCR5Δ32 </it>distribution was non-significantly different in HIV-1-infected patients with respect to the uninfected population (p = 0.15 and p = 0.2 for genotype and allele comparisons, respectively) and in LTNP vs TP (p = 0.4 and p = 0.5 for genotype and allele comparisons, respectively).</p> <p>Conclusions</p> <p>In our cohort of Caucasian Spaniards, <it>TNF-α </it>genetic variants could be involved in the vulnerability to HIV-1 infection. <it>TNF-α </it>genetic variants were unrelated to disease progression in infected subjects. The <it>-238G>A </it>SNP may modulate the control of viremia in LTNP. Carriage of the <it>CCR5Δ32 </it>variant allele had no effect on the risk of infection and disease progression.</p

Early infant HIV-1 diagnosis programs in resource-limited settings: opportunities for improved outcomes and more cost-effective interventions

Early infant diagnosis (EID) of HIV-1 infection confers substantial benefits to HIV-infected and HIV-uninfected infants, to their families, and to programs providing prevention of mother-to-child transmission (PMTCT) services, but has been challenging to implement in resource-limited settings. In order to correctly inform parents/caregivers of infant infection status and link HIV-infected infants to care and treatment, a 'cascade' of events must successfully occur. A frequently cited barrier to expansion of EID programs is the cost of the required laboratory assays. However, substantial implementation barriers, as well as personnel and infrastructure requirements, exist at each step in the cascade. In this update, we review challenges to uptake at each step in the EID cascade, highlighting that even with the highest reported levels of uptake, nearly half of HIV-infected infants may not complete the cascade successfully. We next synthesize the available literature about the costs and cost effectiveness of EID programs; identify areas for future research; and place these findings within the context of the benefits and challenges to EID implementation in resource-limited settings

Pathogenic and targetable genetic alterations in 70 urachal adenocarcinomas

Urachal cancer (UrC) is a rare but aggressive malignancy often diagnosed in advanced stages requiring systemic treatment. Although cytotoxic chemotherapy is of limited effectiveness, prospective clinical studies can hardly be conducted. Targeted therapeutic treatment approaches and potentially immunotherapy based on a biological rationale may provide an alternative strategy. We therefore subjected 70 urachal adenocarcinomas to targeted next-generation sequencing, conducted in situ and immunohistochemical analyses (including PD-L1 and DNA mismatch repair proteins (MMR)) and evaluated the microsatellite instability (MSI) status. The analytical findings were correlated with clinicopathological and outcome data and Kaplan-Meier and univariable/multivariable Cox regression analyses were performed. The patients had a mean age of 50 years, 66% were male and a 5-year overall survival (OS) of 58% and recurrence-free survival (RFS) of 45% was detected. Sequence variations were observed in TP53 (66%), KRAS (21%), BRAF (4%), PIK3CA (4%), FGFR1 (1%), MET (1%), NRAS (1%), and PDGFRA (1%). Gene amplifications were found in EGFR (5%), ERBB2 (2%), and MET (2%). We detected no evidence of MMR-deficiency (MMR-d)/MSI-high (MSI-h), whereas 10 of 63 cases (16%) expressed PD-L1. Therefore, anti-PD-1/PD-L1 immunotherapy approaches might be tested in UrC. Importantly, we found aberrations in intracellular signal transduction pathways (RAS/RAF/PI3K) in 31% of UrCs with potential implications for anti-EGFR therapy. Less frequent potentially actionable genetic alterations were additionally detected in ERBB2 (HER2), MET, FGFR1, and PDGFRA. The molecular profile strengthens the notion that UrC is a distinct entity on the genomic level with closer resemblance to colorectal than to bladder cancer. This article is protected by copyright. All rights reserved

Disparities in emergency department access, resource allocation, and outcomes between migrants and the local population

AIMS: To characterize a group of migrant emergency department (ED) patients regarding demographics, access to the ED, mode of referral, use of resources, and short-term outcomes, and to compare them to a group of local ED patients. METHODS: Prospective cohort study with consecutive enrollment of adult patients presenting to the ED of a Swiss tertiary care hospital from October 21st to November 11th, 2013 and February 1st to February 23rd, 2015. In accordance with the International Organization for Migration, we defined migrants as persons who have changed their country of usual residence, irrespective of their legal status. The primary outcome was defined as the number of resources allocated to migrants, as compared to local patients, using uni- and multivariable quasi-Poisson regressions. Acute morbidity, hospitalization, intensive care unit (ICU) admission, and 30-day mortality were assessed as secondary outcomes. RESULTS: Migrant patients were younger, more often male and self-presenters, and of lower acuity. After adjustment for age, gender and acuity, we observed a non-significant difference of 3.6% in the mean number of resources allocated to migrant patients as compared to local patients (adjusted RR 0.964, CI 0.923-1.006). No difference in 30-day mortality (adjusted OR 0.777, CI 0.346-1.559) was observed between the two patient groups, but migrant patients had lower odds of acute morbidity (adjusted OR 0.652, CI 0.560-0.759), hospitalization (adjusted OR 0.666, CI 0.555-0.799), and ICU admission (adjusted OR 0.649, CI 0.456-0.910). CONCLUSIONS: ED access approximation, resource allocation, and mortality were comparable between migrant patients and local patients. Lower admission rates to wards and the ICU may raise concerns but can be explained by lower acute morbidity in migrant patients