Hyb:A bioinformatics pipeline for the analysis of CLASH (crosslinking, ligation and sequencing of hybrids) data

Peer reviewedPublisher PD

The role of the dorsal hippocampus in two versions of the touchscreen automated paired associates learning (PAL) task for mice.

RATIONALE: The CANTAB object-location paired-associate learning (PAL) test can detect cognitive deficits in schizophrenia and Alzheimer's disease. A rodent version of touch screen PAL (dPAL) has been developed, but the underlying neural mechanisms are not fully understood. Although there is evidence that inactivation of the hippocampus following training leads to impairments in rats, this has not been tested in mice. Furthermore, it is not known whether acquisition, as opposed to performance, of the rodent version depends on the hippocampus. This is critical as many mouse models may have hippocampal dysfunction prior to the onset of task training. OBJECTIVES: The objectives of this study are to examine the effects of dorsal hippocampal (dHp) dysfunction on both performance and acquisition of mouse dPAL and to determine if hippocampal task sensitivity could be increased using a newly developed context-disambiguated PAL (cdPAL) paradigm. METHODS: In experiment 1, C57Bl/6 mice received post-acquisition dHp infusions of the GABA agonist muscimol. In experiment 2, C57Bl/6 mice received excitotoxic dHp lesions prior to dPAL/cdPAL acquisition. RESULTS: Post-acquisition muscimol dose-dependently impaired dPAL and cdPAL performance. Pre-acquisition dHp lesions had only mild effects on both PAL tasks. Behavioural challenges including addition of objects and degradation of the visual stimuli with noise did not reveal any further impairments. CONCLUSIONS: dPAL and cdPAL performance is hippocampus-dependent in the mouse, but both tasks can be learned in the absence of a functional dHp.CHK received funding from the Korean Health Technology R&D Project, Ministry of Health & Welfare, Republic of Korea (HI11C1183). CJH, LMS and TJB were funded by Medical Research Council/Wellcome Trust grant 089703/Z/09/Z. BAK was funded by a Gates-Cambridge Fellowship. LMS and TJB also received funding from the Innovative Medicine Initiative Joint Undertaking under grant agreement no 115008 of which resources are composed of EFPIA inkind contribution and financial contribution from the European Union’s Seventh Framework Programme (FP7/2007-2013).This is the final published version. It first appeared from Springer at http://dx.doi.org/10.1007/s00213-015-3949-

History and Status of ALSEP and the Apollo Lunar Data Project

A suite of automated scientific instruments (the Apollo Lunar Surface Experiment Package, or ALSEP) was installed at each of the landing sites of Apollo 12, 14, 15, 16, and 17 from 1969 to 1972. They operated from deployment until decommissioning on 30 September 1977. These data were continuously transmitted to Earth and saved on the Range Tapes, which were recorded at the Manned Space Flight Network stations. These data were also broken out by experiment and sent to the experiment Principal Investigators on what were called the P.I. Tapes. Starting in April 1973 the Range Tape data were stored in digital format on 7-track magnetic tapes, the ARCSAV Tapes. In February 1976, the handling of the Range Tapes was transferred to UT Galveston. They produced 9-track tapes referred to as the Work Tapes. Following the Apollo program the Range and ARCSAV tapes, which were never archived, were lost. The Work Tapes were archived at the National Space Science Data Center (NSSDC). Some investigators archived their individual experiment data with NSSDC as well, but much of the data had minimal documentation, were not in digital form, or were stored in difficult to translate formats. Data from many experiments were never delivered to the NSSDC. The Lunar Data Project was started to address the problem of both missing and not readily usable data. Our effort has resulted in recovery of some of the ARCSAV tapes, recovery and digitization of a large volume of Apollo scientific and technical documentation, and restoration of many ALSEP and other Apollo data collections. Restoration involves deciphering formats, assembling necessary ancillary data (metadata), and packaging data in digital format to be archived with the Planetary Data System (PDS). Recovery of the data from the ARCSAV tapes involved having the tapes read on special equipment and extracting the individual experiment data out of the integrated data stream. We will report on the history and status of the various recovery efforts

Effect of bleaching using sodium hydroxide on pulp derived from Sesbania grandiflora

World demand for paper is increasing. Short rotation pulpwood is needed. Sesbania grandiflora also known as Turi, is a fast growing and straight log species. The scholarly information of Turi as pulpwood are still limited. This paper aims to provide information of sodium hydroxide effect on the paper made from pulp derived from Turi. Sodium hydroxide is a common chemical using as part of full stage chemical bleaching in pulp industrial. Kraft pulp that produced using Turi, was bleached with sodium hydroxide at 3%, 6% and 9% based on pulp weight, respectively. Unbleached pulp was served as blank test. The optical and mechanical properties of handsheet paper made from bleached kraft pulp were evaluated according to TAPPI standard. The brightness and opacity of handsheet made from bleached pulp were improved with increasing the concentration of sodium hydroxide. The mechanical properties of handsheet were improved with using 3% sodium hydroxide and gradually decreased after 3% sodium hydroxide. In conclusion, sodium hydroxide is potential to improve optical properties of Turi pulp and improve the mechanical properties of paper made from Turi pulp at certain level. Excessive usage of sodium hydroxide brings adverse effect to mechanical properties of paper made from Turi pulp

Effect of bleaching using sodium hydroxide on pulp derived from Sesbania grandiflora

World demand for paper is increasing. Short rotation pulpwood is needed. Sesbania grandiflora also known as Turi, is a fast growing and straight log species. The scholarly information of Turi as pulpwood are still limited. This paper aims to provide information of sodium hydroxide effect on the paper made from pulp derived from Turi. Sodium hydroxide is a common chemical using as part of full stage chemical bleaching in pulp industrial. Kraft pulp that produced using Turi, was bleached with sodium hydroxide at 3%, 6% and 9% based on pulp weight, respectively. Unbleached pulp was served as blank test. The optical and mechanical properties of handsheet paper made from bleached kraft pulp were evaluated according to TAPPI standard. The brightness and opacity of handsheet made from bleached pulp were improved with increasing the concentration of sodium hydroxide. The mechanical properties of handsheet were improved with using 3% sodium hydroxide and gradually decreased after 3% sodium hydroxide. In conclusion, sodium hydroxide is potential to improve optical properties of Turi pulp and improve the mechanical properties of paper made from Turi pulp at certain level. Excessive usage of sodium hydroxide brings adverse effect to mechanical properties of paper made from Turi pulp

Longitudinal evaluation of Tau‐P301L transgenic mice reveals no cognitive impairments at 17 months of age

Tau is a microtubule-associated binding protein implicated in neurodegenerative tauopathies, including frontotemporal dementia (FTD) and Alzheimer’s disease (AD). These diseases result in the intracellular accumulation of hyperphosphorylated tau in the form of neurofibrillary tangles, the presence of which is associated with cognitive deficits. We conducted a longitudinal behavioral study to provide a profile of the TgTau(P301L)23027 transgenic mouse in multiple cognitive domains across multiple ages. P301L is the tau mutation most frequently observed in patients with frontotemporal dementia with parkinsonism linked to chromosome 17 (FTDP-17) and this mouse model recapitulates the progressive development of glial and neurofibrillary tangles, and associated cerebral atrophy observed in patients. We examined frontal cortex-dependent executive function and attention with the touchscreen 5-choice serial reaction time test (5-CSRTT) and assessed the function of temporal cortical structures using novel object recognition (OR). Despite using sensitive tasks, there were no apparent changes in executive function, attention, or recognition memory in the transgenic mice from 5 – 17 months of age. This study represents the first comprehensive longitudinal analysis of cognition in the TgTauP301L mouse model, and suggests that this model is not ideal for studying early attention and recognition memory impairments associated with tauopathy. However, spatial and object recognition memory impairments were observed during follow-up assessments when the mice were 18 and 21 months, respectively. These impairments are consistent with previous publications, and with a dementia-like phenotype in these mice when aged

Genetic association study of adiposity and melanocortin-4 receptor (MC4R) common variants: Replication and functional characterization of non-coding regions

Common genetic variants 3′ of MC4R within two large linkage disequilibrium (LD) blocks spanning 288 kb have been associated with common and rare forms of obesity. This large association region has not been refined and the relevant DNA segments within the association region have not been identified. In this study, we investigated whether common variants in the MC4R gene region were associated with adiposity-related traits in a biracial population-based study. Single nucleotide polymorphisms (SNPs) in the MC4R region were genotyped with a custom array and a genome-wide array and associations between SNPs and five adiposity-related traits were determined using race-stratified linear regression. Previously reported associations between lower BMI and the minor alleles of rs2229616/Val103Ile and rs52820871/Ile251Leu were replicated in white female participants. Among white participants, rs11152221 in a proximal 3′ LD block (closer to MC4R) was significantly associated with multiple adiposity traits, but SNPs in a distal 309 LD block (farther from MC4R ) were not. In a case-control study of severe obesity, rs11152221 was significantly associated. The association results directed our follow-up studies to the proximal LD block downstream of MC4R. By considering nucleotide conservation, the significance of association, and proximity to the MC4R gene, we identified a candidate MC4R regulatory region. This candidate region was sequenced in 20 individuals from a study of severe obesity in an attempt to identify additional variants, and the candidate region was tested for enhancer activity using in vivo enhancer assays in zebrafish and mice. Novel variants were not identified by sequencing and the candidate region did not drive reporter gene expression in zebrafish or mice. The identification of a putative insulator in this region could help to explain the challenges faced in this study and others to link SNPs associated with adiposity to altered MC4R expression. © 2014 Evans et al

Surgical site infection after gastrointestinal surgery in high-income, middle-income, and low-income countries: a prospective, international, multicentre cohort study

Background: Surgical site infection (SSI) is one of the most common infections associated with health care, but its importance as a global health priority is not fully understood. We quantified the burden of SSI after gastrointestinal surgery in countries in all parts of the world. Methods: This international, prospective, multicentre cohort study included consecutive patients undergoing elective or emergency gastrointestinal resection within 2-week time periods at any health-care facility in any country. Countries with participating centres were stratified into high-income, middle-income, and low-income groups according to the UN's Human Development Index (HDI). Data variables from the GlobalSurg 1 study and other studies that have been found to affect the likelihood of SSI were entered into risk adjustment models. The primary outcome measure was the 30-day SSI incidence (defined by US Centers for Disease Control and Prevention criteria for superficial and deep incisional SSI). Relationships with explanatory variables were examined using Bayesian multilevel logistic regression models. This trial is registered with ClinicalTrials.gov, number NCT02662231. Findings: Between Jan 4, 2016, and July 31, 2016, 13 265 records were submitted for analysis. 12 539 patients from 343 hospitals in 66 countries were included. 7339 (58·5%) patient were from high-HDI countries (193 hospitals in 30 countries), 3918 (31·2%) patients were from middle-HDI countries (82 hospitals in 18 countries), and 1282 (10·2%) patients were from low-HDI countries (68 hospitals in 18 countries). In total, 1538 (12·3%) patients had SSI within 30 days of surgery. The incidence of SSI varied between countries with high (691 [9·4%] of 7339 patients), middle (549 [14·0%] of 3918 patients), and low (298 [23·2%] of 1282) HDI (p < 0·001). The highest SSI incidence in each HDI group was after dirty surgery (102 [17·8%] of 574 patients in high-HDI countries; 74 [31·4%] of 236 patients in middle-HDI countries; 72 [39·8%] of 181 patients in low-HDI countries). Following risk factor adjustment, patients in low-HDI countries were at greatest risk of SSI (adjusted odds ratio 1·60, 95% credible interval 1·05–2·37; p=0·030). 132 (21·6%) of 610 patients with an SSI and a microbiology culture result had an infection that was resistant to the prophylactic antibiotic used. Resistant infections were detected in 49 (16·6%) of 295 patients in high-HDI countries, in 37 (19·8%) of 187 patients in middle-HDI countries, and in 46 (35·9%) of 128 patients in low-HDI countries (p < 0·001). Interpretation: Countries with a low HDI carry a disproportionately greater burden of SSI than countries with a middle or high HDI and might have higher rates of antibiotic resistance. In view of WHO recommendations on SSI prevention that highlight the absence of high-quality interventional research, urgent, pragmatic, randomised trials based in LMICs are needed to assess measures aiming to reduce this preventable complication