DNA Pre-alignment Filter using Processing Near Racetrack Memory

Recent DNA pre-alignment filter designs employ DRAM for storing the reference genome and its associated meta-data. However, DRAM incurs increasingly high energy consumption background and refresh energy as devices scale. To overcome this problem, this paper explores a design with racetrack memory (RTM)--an emerging non-volatile memory that promises higher storage density, faster access latency, and lower energy consumption. Multi-bit storage cells in RTM are inherently sequential and thus require data placement strategies to mitigate the performance and energy impacts of shifting during data accesses. We propose a near-memory pre-alignment filter with a novel data mapping and several shift reduction strategies designed explicitly for RTM. On a set of four input genomes from the 1000 Genome Project, our approach improves performance and energy efficiency by 68% and 52%, respectively, compared to the state of the art proposed DRAM-based architecture

Outcome of home mechanical ventilation

OBJECTIVE: To determine the outcome of patients discharged home on portable ventilator. DESIGN: Descriptive study. PLACE AND DURATION OF STUDY: The Aga Khan University Hospital, Karachi from January 2000 to December 2004. PATIENTS AND METHODS: All ventilator-dependent patients discharged home were contacted. Survivors were administered the EQ-5D Quality-of-Life instrument. SPSS version 13 was used to analyze data. RESULTS: Eleven patients were discharged home on invasive ventilation. Mean age was 49 years (range 10-98 years). Cause of ventilatory failure were cervical spine trauma in 36%, primary neurological disease in 27%, critical illness neuropathy and respiratory failure in 18% each. Survival rate was 73%, with three deaths. Mean duration of ventilation was 9.45 months (95% CI 3.24, 15.67). Rate of successful weaning after discharge was 36%, with 4 patients off all forms of ventilatory support and 2 on only nocturnal support. A 2.8 (95% CI 0.5, 16.6) relative risk towards successful weaning was associated with the presence of a family member as the primary care giver. Mean scores on the EQ-5D descriptive tool were; mobility 2 (-/+0.82), self-care 2 (-/+0.82), usual activities 1.86 (-/+0.69), pain/discomfort 1.43(-/+0.79), anxiety/depression 1.29 (-/+0.76). Mean score on the EQ-VAS was 48.2(-/+ 27.3). CONCLUSION: In carefully selected patients, home ventilation is a viable option with the expectation of successful weaning and survival. Patients discharged home on ventilation reported a reasonably good quality of life with proportionately more problems related to independence compared to overall well-being

Effect of GABA Application on the Growth and Yield of Bitter Gourd (Momordica charantia)

An experiment was conducted to investigate the effect of GABA (GA3 1% & SBA Brassicasteroids as STC 0.3%) application on growth, yield and yield contributing traits of bitter gourd. GABA was applied at 0.5, 1.0, 1.5 and 2.0 mg L-1 as foliar spray at 30 days after sowing, while control plants received no GABA. The experiment was laid out in a randomized complete block design (RCBD) with four replications. Result showed that GABA had positive regulatory effect on morphological growth, yield and yield related traits of bitter gourd; nonetheless GABA application at 1.5 mg L-1 was found the most effective in improving length and diameter of main vine, individual branch length, number of branches, total branch length, number of nodes per plant, vine diameter, days to first male and female flowering, numbers of male and female flower, number of fruit, weight of individual fruit, length and diameter of fruit, percentage of fruit set and number of seeds per fruit. Hence GABA application at 1.5 mg L-1 as foliar spray could be the suitable concentration for enhancing growth and yield of bitter gourd

Catching up with Method and Process Practice: An Industry-Informed Baseline for Researchers

Software development methods are usually not applied by the book.companies are under pressure to continuously deploy software products that meet market needs and stakeholders\u27 requests. To implement efficient and effective development processes, companies utilize multiple frameworks, methods and practices, and combine these into hybrid methods. A common combination contains a rich management framework to organize and steer projects complemented with a number of smaller practices providing the development teams with tools to complete their tasks. In this paper, based on 732 data points collected through an international survey, we study the software development process use in practice. Our results show that 76.8% of the companies implement hybrid methods.company size as well as the strategy in devising and evolving hybrid methods affect the suitability of the chosen process to reach company or project goals. Our findings show that companies that combine planned improvement programs with process evolution can increase their process\u27 suitability by up to 5%

No widespread dissemination of Chlamydia trachomatis diagnostic-escape variants and the impact of Neisseria gonorrhoeae positivity on the Aptima Combo 2 assay

OBJECTIVES: A Finnish Chlamydia trachomatis (CT) new variant was detected in 2019 that escaped detection in the Hologic Aptima Combo 2 (AC2) assay due to a C1515T mutation in the CT 23S rRNA target region. Reflex testing of CT-negative/CT-equivocal specimens as well as those positive for Neisseria gonorrhoeae (NG) with the Hologic Aptima CT (ACT) assay was recommended to identify any CT variants. METHODS: From June to October 2019, specimens with discrepant AC2/ACT CT results were submitted to Public Health England and screened for detectable CT DNA using an inhouse real-time (RT)-PCR. When enough DNA was present, partial CT 23S rRNA gene sequencing was performed. Analysis of available relative light units and interpretative data was performed. RESULTS: A total of 317 discordant AC2/ACT specimens were collected from 315 patients. Three hundred were tested on the RT-PCR; 53.3% (n=160) were negative and 46.7% (n=140) were positive. Due to low DNA load in most specimens, sequencing was successful for only 36 specimens. The CT 23S rRNA wild-type sequence was present in 32 specimens, and two variants with C1514T or G1523A mutation were detected in four specimens from three patients. Of the discordant specimens with NG interpretation, 36.6% of NG-negative/CT-negative AC2 specimens had detectable CT DNA on the inhouse RT-PCR vs 53.3% of NG-positive/CT-negative specimens. CONCLUSIONS: No widespread dissemination of AC2 diagnostic-escape CT variants has occurred in England. We however identified the impact of NG positivity on the discordant AC2/ACT specimens; a proportion appeared due to NG positivity and the associated NG signal, rather than any diagnostic-escape variants or low DNA load. Several patients with gonorrhoea may therefore receive false-negative AC2 CT results. Single diagnostic targets and multiplex diagnostic assays have their limitations such as providing selection pressure for escape mutants and potentially reduced sensitivity, respectively. These limitations must be considered when establishing diagnostic pathways

Exploring the evidence base for national and regional policy interventions to combat resistance

The effectiveness of existing policies to control antimicrobial resistance is not yet fully understood. A strengthened evidence base is needed to inform effective policy interventions across countries with different income levels and the human health and animal sectors. We examine three policy domains—responsible use, surveillance, and infection prevention and control—and consider which will be the most effective at national and regional levels. Many complexities exist in the implementation of such policies across sectors and in varying political and regulatory environments. Therefore, we make recommendations for policy action, calling for comprehensive policy assessments, using standardised frameworks, of cost-effectiveness and generalisability. Such assessments are especially important in low-income and middle-income countries, and in the animal and environmental sectors. We also advocate a One Health approach that will enable the development of sensitive policies, accommodating the needs of each sector involved, and addressing concerns of specific countries and regions

Myofibrillogenesis regulator 1 (MR-1) is a novel biomarker and potential therapeutic target for human ovarian cancer

<p>Abstract</p> <p>Background</p> <p>Myofibrillogenesis regulator 1 (MR-1) is overexpressed in human cancer cells and plays an essential role in cancer cell growth. However, the significance of MR-1 in human ovarian cancer has not yet been explored. The aim of this study was to examine whether MR-1 is a predictor of ovarian cancer and its value as a therapeutic target in ovarian cancer patients.</p> <p>Methods</p> <p>Reverse-transcription polymerase chain reaction (PCR) and quantitative real-time PCR were used to detect MR-1 mRNA levels in tissue samples from 26 ovarian cancer patients and 25 controls with benign ovarian disease. Anti-MR-1 polyclonal antibodies were prepared, tested by ELISA and western blotting, and then used for immunohistochemical analysis of the tissue samples. Adhesion and invasion of 292T cells was also examined after transfection of a pMX-MR-1 plasmid. Knockdown of MR-1 expression was achieved after stable transfection of SKOV3 cells with a short hairpin DNA pGPU6/GFP/Neo plasmid against the MR-1 gene. In addition, SKOV3 cells were treated with paclitaxel and carboplatin, and a potential role for MR-1 as a therapeutic target was evaluated.</p> <p>Results</p> <p>MR-1 was overexpressed in ovarian cancer tissues and SKOV3 cells. 293T cells overexpressed MR-1, and cellular spread and invasion were enhanced after transfection of the pMX-MR-1 plasmid, suggesting that MR-1 is critical for ovarian cancer cell growth. Knockdown of MR-1 expression inhibited cell adhesion and invasion, and treatment with anti-cancer drugs decreased its expression in cancer cells. Taken together, these results provide the first evidence of the cellular and molecular mechanisms by which MR-1 might serve as a novel biological marker and potential therapeutic target for ovarian cancer.</p> <p>Conclusions</p> <p>MR-1 may be a biomarker for diagnosis of ovarian cancer. It may also be useful for monitoring of the effects of anti-cancer therapies. Further studies are needed to clarify whether MR-1 is an early diagnostic marker for ovarian cancer and a possible therapeutic target.</p

Takotsubo cardiomyopathy after a dancing session: a case report

<p>Abstract</p> <p>Introduction</p> <p>Stress-induced (Takotsubo) cardiomyopathy is a rare form of cardiomyopathy which presents in a manner similar to that of acute coronary syndrome. This sometimes leads to unnecessary thrombolysis therapy. The pathogenesis of this disease is still poorly understood. We believe that reporting all cases of Takotsubo cardiomyopathy will contribute to a better understanding of this disease. Here, we report a patient who, in the absence of any recent stressful events in her life, developed the disease after a session of dancing.</p> <p>Case presentation</p> <p>A 69-year-old Caucasian woman presented with features suggestive of acute coronary syndrome shortly after a session of dancing. Echocardiography and a coronary angiogram showed typical features of Takotsubo cardiomyopathy and our patient was treated accordingly. Eight weeks later, her condition resolved completely and the results of echocardiography were totally normal.</p> <p>Conclusions</p> <p>Takotsubo cardiomyopathy, though transient, is a rare and serious condition. Although it is commonly precipitated by stressful life events, these are not necessarily present. Our patient was enjoying one of her hobbies (that is, dancing) when she developed the disease. This case has particular interest in medicine, especially for the specialties of cardiology and emergency medicine. We hope that it will add more information to the literature about this rare condition.</p

Multi-band Extension of the Wideband Timing Technique

The wideband timing technique enables the high-precision simultaneous estimation of Times of Arrival (ToAs) and Dispersion Measures (DMs) while effectively modeling frequency-dependent profile evolution. We present two novel independent methods that extend the standard wideband technique to handle simultaneous multi-band pulsar data incorporating profile evolution over a larger frequency span to estimate DMs and ToAs with enhanced precision. We implement the wideband likelihood using the libstempo python interface to perform wideband timing in the tempo2 framework. We present the application of these techniques to the dataset of fourteen millisecond pulsars observed simultaneously in Band 3 (300 - 500 MHz) and Band 5 (1260 - 1460 MHz) of the upgraded Giant Metrewave Radio Telescope (uGMRT) as a part of the Indian Pulsar Timing Array (InPTA) campaign. We achieve increased ToA and DM precision and sub-microsecond root mean square post-fit timing residuals by combining simultaneous multi-band pulsar observations done in non-contiguous bands for the first time using our novel techniques.Comment: Submitted to MNRA