Exome sequencing reveals the likely involvement of SOX10 in uveal melanoma

PURPOSE

To identify the spectrum of somatic mutations in an Asian Indian patient with uveal melanoma (UM) without metastasis using exome sequencing.

CASE REPORT

A 49-year-old man from India was diagnosed as having cilio-choroidal (uveal) melanoma (UM), without metastasis, in his right eye with the help of magnetic resonance imaging. This was later confirmed by histopathological evaluation. Two individuals from India with non-neoplastic blind eyes were recruited as controls. The affected eyes from the UM patient and the two control individuals were enucleated, and uveal tissues were collected. DNA was extracted from uveal tissue, and the matched blood sample from each of the three individuals was followed by exome sequencing. Statistical and bioinformatic analyses were done to identify somatic mutations and their putative associations with UM. Thirty-one somatic mutations (25 amino acid altering) in protein-coding (exonic) regions were detected in the UM patient. Of the amino acid-altering somatic mutations, 16 mutations were predicted to be candidate mutations relevant to UM. Somatic mutations, putatively causal for UM, were identified in GNAQ, SF3B1, and SOX10.

CONCLUSIONS

Somatic mutations in GNAQ and SF3B1 genes were probable drivers of UM in the Indian patient; these were also reported earlier in some White patients. In addition, a frameshift deletion of 20 base pairs has been identified in SOX10 in the UM patient. Somatic mutations in SOX10, a transcription factor, which acts upstream of microphthalmia-associated transcription factor and synergizes with microphthalmia-associated transcription factor, was identified in some melanoma cell lines. The transcription factor SOX10 was found to have an essential role in melanocyte development and pigmentation. Our finding of the frameshift deletion (p.H387fs) in exon 4 of SOX10 in UM provides an important insight and complements earlier findings of mutations in GNAQ and SF3B1 on the genomic basis of UM.

Precision measurement of the top quark mass in lepton + jets final States

We measure the mass of the top quark in lepton+jets final states using the full sample of pp collision data collected by the D0 experiment in Run II of the Fermilab Tevatron Collider at sqrt[s] = 1.96 TeV, corresponding to 9.7 fb(-1) of integrated luminosity. We use a matrix element technique that calculates the probabilities for each event to result from tt production or background. The overall jet energy scale is constrained in situ by the mass of the W boson. We measure m(t) = 174.98 ± 0.76 GeV. This constitutes the most precise single measurement of the top-quark mass.

Prevalence and causes of blindness and visual impairment and their associated risk factors, in three tribal areas of Andhra Pradesh, India

Objective

To assess the prevalence of blindness and visual impairment (VI), their associated causes and underlying risk factors in three tribal areas of Andhra Pradesh, India and compare this data in conjunction with data from other countries with low and middle income settings.

Methods

Using a validated Rapid Assessment of Avoidable Blindness methodology, a two stage sampling survey was performed in these areas involving probability proportionate to size sampling and compact segment sampling methods. Blindness, VI and severe visual impairment (SVI) were defined as per the WHO guidelines and Indian definitions.

Results

Based on a prior enumeration, 7281 (97.1%) subjects were enrolled (mean age  = 61.0+/−7.9 years). Based on the presenting visual acuity (PVA), the prevalences of VI, SVI and blindness were 16.9% (95% CI: 15.7–18.1), 2.9% (95% CI: 2.5–3.4), and 2.3% (95% CI: 1.9–2.7), respectively. When based on the Pinhole corrected visual acuity (PCVA), the prevalences were lower in VI (6.2%, 95% CI: 5.4–6.9), SVI (1.5%, 95% CI: 1.2–1.9) and blindness (2.1%, 95% CI: 1.7–2.5). Refractive error was the major cause of VI (71.4%), whereas, cataract was the major cause of SVI and blindness (70.3%). Based on the PVA, the odds ratio (OR) of blindness increased in the age groups of 60–69 years (OR = 3.8, 95% CI: 2.8, 5.1), 70–79 years (OR = 10.6, 95% CI: 7.2, 15.5) and 80 years and above (OR = 30.7, 95% CI: 19.2, 49). The ORs were relatively higher in females (OR = 1.3, 95% CI: 1.0, 1.6) and illiterate subjects (OR = 4.3, 95% CI: 2.2, 8.5), but lower in those wearing glasses (OR = 0.2, 95% CI: 0.1, 0.4).

Conclusions

This is perhaps the first study to assess the prevalence of blindness and VI in these tribal regions and the majority of the causes of blindness and SVI were avoidable (88.5%). These findings may be useful for planning eye care services in these underserved regions.

Relationship between first treatment contact and supernatural beliefs in caregivers of patients with schizophrenia

OBJECTIVE. To explore the relationship between attribution of symptoms to supernatural beliefs and first treatment contact in caregivers of patients with schizophrenia attending a tertiary care hospital located in North India. METHODS. A total of 122 caregivers (aged ≥ 18 years, staying with patient ≥ 1 year and involved in patients' care) of consecutive patients with diagnosis of schizophrenia (according to the ICD-10) were evaluated for their supernatural beliefs and first treatment contact. RESULTS. The first treatment contact was a government or private psychiatrist in slightly more than half (53.3%) of the patients, while it was faith healers in 23.8% of the patients. Around three quarters (74.6%) of the caregivers attributed patients' symptoms to ≥ 1 supernatural belief (like sorcery / witchcraft, ghosts, spirit intrusion, divine wrath, planetary influences, evil spirits, and bad deeds in previous life) and more than half (57.4%) of the caregivers attributed patients' symptoms to > 1 supernatural belief. It was observed that those who contacted faith healers for their patients' treatment had significantly higher attribution of the symptoms to supernatural causes. CONCLUSIONS. Supernatural beliefs were common in caregivers of patients with schizophrenia and the majority attributed their patients' symptoms to these beliefs. It signifies an urgent need for mental health literacy in India.

Oxidative stress and amyloid beta toxicity in Alzheimer's disease: intervention in a complex relationship by antioxidants

The elucidation of the intriguing relationship between oxidative stress and Alzheimer's disease is crucial to understand the pathogenesis of the disease as also to design a suitable drug trial with antioxidants against this condition. We begin by reviewing the basic facts about Alzheimer's disease and the chemistry and biology of oxygen free radicals with particular reference to the cellular adaptive response through redox-signalling pathways. The post-mortem evidence of oxidative damage in the brain of Alzheimer's disease patients is overwhelming which is also supported by the similar changes in transgenic mice models of this disease. However, the causal relationship of oxidative stress with amyloid beta pathology or the genesis of Alzheimer's disease is not clear. Considering the available evidence the review suggests that the oxidative stress could be an early event in the disease process and may trigger various adaptive responses such as the alterations of amyloid beta metabolism and the activation of stress responsive kinases which can subsequently lead to neuronal degeneration and AD pathology. Further, we have presented a large body of evidence from various studies to highlight the beneficial effects of antioxidants against amyloid beta toxicity or AD pathology in animal or cell based models of AD. The failure of clinical trials with antioxidants against AD has been mentioned and the possible causes of such failures have been analysed.

Observation of s-channel production of single top quarks at the Tevatron

We report the first observation of single-top-quark production in the s channel through the combination of the CDF and D0 measurements of the cross section in proton-antiproton collisions at a center-of-mass energy of 1.96 TeV. The data correspond to total integrated luminosities of up to 9.7 fb(-1) per experiment. The measured cross section is σ(s) = 1.29(-0.24)(+0.26) pb. The probability of observing a statistical fluctuation of the background to a cross section of the observed size or larger is 1.8 × 10(-10), corresponding to a significance of 6.3 standard deviations for the presence of an s-channel contribution to the production of single-top quarks.

Tubercular breast abscess--a diagnostic dilemma

Tuberculosis affects many organs, however isolated tubercular breast lesion is rare. Clinically as well as radiologically it may mimic both pyogenic abscess and malignancy. One such case is being reported where a middle aged woman presented with painful, gradually increasing breast lump and was diagnosed clinically, radiologically, cytologically and even histologically as pyogenic abscess. Poor response to antibiotics raised the suspicion of malignancy for which repeat fine needle aspiration cytology was done. Well formed granulomas, necrosis and finally demonstration of acid fast bacilli established the diagnosis of tubercular abscess. No other organs were involved by tuberculosis in this case. Patient responded well to antitubercular drugs. Thus diagnostic challenge lies in the demonstration of acid fast bacilli in cases of equivocal morphology in routine cytology as well as histology. High clinical suspicion, poor response to antibiotics, suggestive radiological findings, cytology, histology and demonstration of acid fast bacilli -all contributes to the diagnosis of breast tuberculosis.

Measurement of the W boson production charge asymmetry in pp̄→W+X→eν+X events at √s=1.96 TeV

We present a measurement of the W boson production charge asymmetry in pp̄→W+X→eν+X events at a center of mass energy of 1.96 TeV, using 9.7  fb-1 of integrated luminosity collected with the D0 detector at the Fermilab Tevatron Collider. The neutrino longitudinal momentum is determined by using a neutrino weighting method, and the asymmetry is measured as a function of the W boson rapidity. The measurement extends over wider electron pseudorapidity region than previous results and is the most precise to date, allowing for precise determination of proton parton distribution functions in global fits.

Hashimoto's Thyroiditis and Medullary Carcinoma of Thyroid

Hashimoto's thyroiditis (HT) has been found to be associated with lymphoma, papillary carcinoma and Hürthle cell neoplasms of thyroid. In contrast, there are only a few reports of co-existence of HT with medullary carcinoma of thyroid. An overall prevalence of medullary carcinoma of only 0.35% has been reported in HT patients. Such a rare combination is being presented here. A 33 year old female presented with history of goiter for one year. Fine needle aspiration cytology (FNAC) of the swelling revealed cytological features suggestive of medullary carcinoma of thyroid. Histopathological examination of total thyroidectomy specimen revealed Hashimoto's thyroiditis along with medullary carcinoma of thyroid. Although Hashimoto's thyroiditis can uncommonly co-exist with thyroid neoplasm, its association with medullary carcinoma is extremely rare and hence being presented.

TNF-α (g.-308 G > A) and ADIPOQ (g. + 45 T > G) gene polymorphisms in type 2 diabetes and microvascular complications in the region of Punjab (North-West India)

AIMS

The present study aims to examine the association of tumor necrosis factor-α (TNF-α) g.-308 G > A and adiponectin (ADIPOQ) g. + 45 T > G gene polymorphisms in type 2 diabetes (T2D) and its microvascular complications diabetic retinopathy (DR) and diabetic nephropathy (DN).

MATERIALS AND METHODS

A total of 672 individuals were analysed from the North-West population of Punjab. Genotyping was accomplished by a combination of allele specific amplification refractory mutation system and restriction digestion for TNF-α g. - 308 G > A and ADIPOQ g. + 45 T > G polymorphisms, respectively. Further, in silico modeling was done to predict secondary structure of mRNA for g. + 45 T > G polymorphism in the ADIPOQ gene by RNA fold.

RESULTS

The minor allele frequency observed in the controls for the TNF-α G > A and ADIPOQ T > G polymorphisms were 0.07 and 0.10, respectively. The results show no significant association with TNF-α g. - 308 G > A polymorphism in T2D as well as in any of the microvascular complication. However, the ADIPOQ g. + 45 T > G polymorphism shows significant association in T2D (p = 0.048) and DR (p = 0.001) but in DN patients, no association was observed. Interactive analysis revealed that the two polymorphisms jointly conferred a 1.45-fold risk towards the occurrence of T2D [p = 0.031; OR = 1.45 (1.03-2.05)]. In the secondary structure of mRNA, slight free energy change was observed between the wild ( - 1370.28 kcal/mol) and variant allele (-1369.08 kcal/mol).

CONCLUSIONS

Our results indicated a higher risk of T2D and DR in the background of ADIPOQ TT genotype. Further, the ADIPOQ g. + 45 T > G and TNF-α g. - 308 G > A polymorphisms jointly give 1.45-fold risk towards T2D.

Measurement of the direct CP-violating charge asymmetry in Ds ± → ϕ π ± decays

We present a measurement of the direct CP-violating charge asymmetry in Ds+ → ϕ π(±) decays where the ϕ meson decays to K(+)K(-), using the full Run II data set with an integrated luminosity of 10.4  fb-1 of proton-antiproton collisions collected using the D0 detector at the Fermilab Tevatron Collider. The normalized difference A(CP) in the yield of D(s)(+) and D(s)(-) mesons in these decays is measured by fitting the difference between their reconstructed invariant mass distributions. This results in an asymmetry of A(CP) = [-0.38 ± 0.27]%, which is the most precise measurement of this quantity to date. The result is consistent with the standard model prediction of zero CP asymmetry in this decay.

Measurement of associated production of z bosons with charm quark jets in pp collisions at √s=1.96 TeV

We present the first measurements of the ratios of cross sections σ(pp → Z+c jet)/σ(pp → Z+jet) and σ(pp → Z+c jet)/σ(pp → Z+b jet) for the associated production of a Z boson with at least one charm or bottom quark jet. Jets have transverse momentum ​pT(jet)​>20  GeV and pseudorapidity |​η(jet)​|<2.5. These cross section ratios are measured differentially as a function of jet and Z boson transverse momenta, based on 9.7  fb(-1) of pp collisions collected with the D0 detector at the Fermilab Tevatron Collider at √s=1.96  TeV. The measurements show significant deviations from perturbative QCD calculations and predictions from various event generators.

Cataract, visual impairment and long-term mortality in a rural cohort in India: the Andhra Pradesh Eye Disease Study

BACKGROUND

A large-scale prevalence survey of blindness and visual impairment (The Andhra Pradesh Eye Diseases Study [APEDS1]) was conducted between 1996-2000 on 10,293 individuals of all ages in three rural and one urban clusters in Andhra Pradesh, Southern India. More than a decade later (June 2009-March 2010), APEDS1 participants in rural clusters were traced (termed APEDS2) to determine ocular risk factors for mortality in this longitudinal cohort.

METHODS AND FINDINGS

Mortality hazard ratio (HR) analysis was performed for those aged >30 years at APEDS1, using Cox proportional hazard regression models to identify associations between ocular exposures and risk of mortality. Blindness and visual impairment (VI) were defined using Indian definitions. 799/4,188 (19.1%) participants had died and 308 (7.3%) had migrated. Mortality was higher in males than females (p<0.001). In multivariable analysis, after adjusting for age, gender, diabetes, hypertension, body mass index, smoking and education status the mortality HR was 1.9 (95% CI: 1.5-2.5) for blindness; 1.4 (95% CI: 1.2-1.7) for VI; 1.8 (95% CI: 1.4-2.3) for pure nuclear cataract, 1.5 (95% CI: 1.1-2.1) for pure cortical cataract; 1.96 (95% CI: 1.6-2.4) for mixed cataract, 2.0 (95% CI: 1.4-2.9) for history of cataract surgery, and 1.58 (95% CI: 1.3-1.9) for any cataract. When all these factors were included in the model, the HRs were attenuated, being 1.5 (95% CI: 1.1-2.0) for blindness and 1.2 (95% CI: 0.9-1.5) for VI. For lens type, the HRs were as follows: pure nuclear cataract, 1.6 (95% CI: 1.3-2.1); pure cortical cataract, 1.5 (95% CI: 1.1-2.1); mixed cataract, 1.8 (95% CI: 1.4-2.2), and history of previous cataract surgery, 1.8 (95% CI: 1.3-2.6).

CONCLUSIONS

All types of cataract, history of cataract surgery and VI had an increased risk of mortality that further suggests that these could be potential markers of ageing.