scholarly journals Analysis of Sequence-Tagged-Connector Strategies for DNA Sequencing

1999 ◽  
Vol 9 (3) ◽  
pp. 297-307 ◽  
Author(s):  
Andrew F. Siegel ◽  
Barbara Trask ◽  
Jared C. Roach ◽  
Gregory G. Mahairas ◽  
Leroy Hood ◽  
...  
Keyword(s):  
Decision Rule ◽  
Sequence Similarity ◽  
Sequencing Technology ◽  
Total Cost ◽  
Sequencing Project ◽  
Highly Sensitive ◽  
Sequencing Cost ◽  
Bac End Sequencing ◽  
The Cost ◽  
Minimum Tiling Path

The BAC-end sequencing, or sequence-tagged-connector (STC), approach to genome sequencing involves sequencing the ends of BAC inserts to scatter sequence tags (STCs) randomly across the genome. Once any BAC or other large segment of DNA is sequenced to completion by conventional shotgun approaches, these STC tags can be used to identify a minimum tiling path of BAC clones overlapping the nucleation sequence for sequence extension. Here, we explore the properties of STC-sequencing strategies within a mathematical model of a random target with homologous repeats and imperfect sequencing technology to understand the consequences of varying various parameters on the incidence of problem clones and the cost of the sequencing project. Problem clones are defined as clones for which either (A) there is no identifiable overlapping STC to extend the sequence in a particular direction or (B) the identified STC with minimum overlap comes from a nonoverlapping clone, either owing to random false matches or repeat-family homology. Based on the minimum overlap, we estimate the number of clones to be entirely sequenced and, then, using cost estimates, identify the decision rule (the degree of sequence similarity required before a match is declared between an STC and a clone) to minimize overall sequencing cost. A method to optimize the overlap decision rule is highly desirable, because both the total cost and the number of problem clones are shown to be highly sensitive to this choice. For a target of 3 Gb containing ∼800 Mb of repeats with 85%–90% identity, we expect <10 problem clones with 15 times coverage by 150-kb clones. We derive the optimal redundancy and insert sizes of clone libraries for sequencing genomes of various sizes, from microbial to human. We estimate that establishing the resource of STCs as a means of identifying minimally overlapping clones represents only 1%–3% of the total cost of sequencing the human genome, and, up to a point of diminishing returns, a larger STC resource is associated with a smaller total sequencing cost.

scholarly journals The Development of Patient Scheduling Groups for an Effective Appointment System

2016 ◽  
Vol 07 (01) ◽  
pp. 43-58 ◽  
Author(s):  
Yu Li Huang
Keyword(s):  
Access To Care ◽  
Treatment Time ◽  
Optimization Technique ◽  
Urgent Care ◽  
Patient Scheduling ◽  
Total Cost ◽  
Patient Type ◽  
Clinic Efficiency ◽  
The Cost ◽  
The Impact

SummaryPatient access to care and long wait times has been identified as major problems in outpatient delivery systems. These aspects impact medical staff productivity, service quality, clinic efficiency, and health-care cost.This study proposed to redesign existing patient types into scheduling groups so that the total cost of clinic flow and scheduling flexibility was minimized. The optimal scheduling group aimed to improve clinic efficiency and accessibility.The proposed approach used the simulation optimization technique and was demonstrated in a Primary Care physician clinic. Patient type included, emergency/urgent care (ER/UC), follow-up (FU), new patient (NP), office visit (OV), physical exam (PE), and well child care (WCC). One scheduling group was designed for this physician. The approach steps were to collect physician treatment time data for each patient type, form the possible scheduling groups, simulate daily clinic flow and patient appointment requests, calculate costs of clinic flow as well as appointment flexibility, and find the scheduling group that minimized the total cost.The cost of clinic flow was minimized at the scheduling group of four, an 8.3% reduction from the group of one. The four groups were: 1. WCC, 2. OV, 3. FU and ER/UC, and 4. PE and NP. The cost of flexibility was always minimized at the group of one. The total cost was minimized at the group of two. WCC was considered separate and the others were grouped together. The total cost reduction was 1.3% from the group of one.This study provided an alternative method of redesigning patient scheduling groups to address the impact on both clinic flow and appointment accessibility. Balance between them ensured the feasibility to the recognized issues of patient service and access to care. The robustness of the proposed method on the changes of clinic conditions was also discussed.

scholarly journals A MEAN FIELD GAME ANALYSIS OF SIR DYNAMICS WITH VACCINATION

2020 ◽  
pp. 1-18
Author(s):  
Josu Doncel ◽  
Nicolas Gast ◽  
Bruno Gaujal
Keyword(s):  
Mean Field ◽  
Vaccination Strategy ◽  
Game Analysis ◽  
Total Cost ◽  
Mean Field Game ◽  
Vaccination Behavior ◽  
Switching Curve ◽  
The One ◽  
The Cost ◽  
Vaccination Period

We analyze a mean field game model of SIR dynamics (Susceptible, Infected, and Recovered) where players choose when to vaccinate. We show that this game admits a unique mean field equilibrium (MFE) that consists in vaccinating at a maximal rate until a given time and then not vaccinating. The vaccination strategy that minimizes the total cost has the same structure as the MFE. We prove that the vaccination period of the MFE is always smaller than the one minimizing the total cost. This implies that, to encourage optimal vaccination behavior, vaccination should always be subsidized. Finally, we provide numerical experiments to study the convergence of the equilibrium when the system is composed by a finite number of agents ( $N$ ) to the MFE. These experiments show that the convergence rate of the cost is $1/N$ and the convergence of the switching curve is monotone.

scholarly journals HapSolo: an optimization approach for removing secondary haplotigs during diploid genome assembly and scaffolding

2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Edwin A. Solares ◽  
Yuan Tao ◽  
Anthony D. Long ◽  
Brandon S. Gaut
Keyword(s):  
Cost Function ◽  
Anopheles Funestus ◽  
Hill Climbing ◽  
Optimization Approach ◽  
Sequencing Technology ◽  
Genome Data ◽  
A Genome ◽  
Long Read ◽  
Downstream Analysis ◽  
The Cost

Abstract Background Despite marked recent improvements in long-read sequencing technology, the assembly of diploid genomes remains a difficult task. A major obstacle is distinguishing between alternative contigs that represent highly heterozygous regions. If primary and secondary contigs are not properly identified, the primary assembly will overrepresent both the size and complexity of the genome, which complicates downstream analysis such as scaffolding. Results Here we illustrate a new method, which we call HapSolo, that identifies secondary contigs and defines a primary assembly based on multiple pairwise contig alignment metrics. HapSolo evaluates candidate primary assemblies using BUSCO scores and then distinguishes among candidate assemblies using a cost function. The cost function can be defined by the user but by default considers the number of missing, duplicated and single BUSCO genes within the assembly. HapSolo performs hill climbing to minimize cost over thousands of candidate assemblies. We illustrate the performance of HapSolo on genome data from three species: the Chardonnay grape (Vitis vinifera), with a genome of 490 Mb, a mosquito (Anopheles funestus; 200 Mb) and the Thorny Skate (Amblyraja radiata; 2650 Mb). Conclusions HapSolo rapidly identified candidate assemblies that yield improvements in assembly metrics, including decreased genome size and improved N50 scores. Contig N50 scores improved by 35%, 9% and 9% for Chardonnay, mosquito and the thorny skate, respectively, relative to unreduced primary assemblies. The benefits of HapSolo were amplified by down-stream analyses, which we illustrated by scaffolding with Hi-C data. We found, for example, that prior to the application of HapSolo, only 52% of the Chardonnay genome was captured in the largest 19 scaffolds, corresponding to the number of chromosomes. After the application of HapSolo, this value increased to ~ 84%. The improvements for the mosquito’s largest three scaffolds, representing the number of chromosomes, were from 61 to 86%, and the improvement was even more pronounced for thorny skate. We compared the scaffolding results to assemblies that were based on PurgeDups for identifying secondary contigs, with generally superior results for HapSolo.

Penetapan Tarif Ambulans Untuk Evakuasi Medis Berbasis Unit Cost

2021 ◽  
Vol 7 (1) ◽  
pp. 167-173
Author(s):  
Kelvin Riupassa ◽  
Narizma Nova ◽  
Endah Lestari ◽  
Sri Juniarti Azis ◽  
Wahyu Sulistiadi
Keyword(s):  
Recovery Rate ◽  
Unit Cost ◽  
Cost Recovery ◽  
Maintenance Costs ◽  
Total Cost ◽  
Medical Evacuation ◽  
Operational Costs ◽  
Emergency Ambulance ◽  
The Cost ◽  
Cost Components

Background: An ambulance is a vehicle designed to be able to handle emergency patients, provide first aid and carry out intensive care while on the way to a referral hospital. Ambulance operations require a large amount of funds obtained from APBD funds through tariffs that were passed through the DKI Jakarta Governor Regulation five years ago. For this reason, a new tariff is required to adjust to current conditions. Objectives: The purpose of this study is to calculate the unit cost of ambulance services in DKI Jakarta to be a consideration in the tariff setting policy in DKI Jakarta province. Research Metodes: This study uses a quantitative descriptive approach to obtain information about the unit cost of the Jakarta ambulance production unit. The method used is the calculation of real cost using the basis of the causes of costs. This research was conducted at the DKI Jakarta Emergency Ambulance using secondary data on investment costs, operational costs and maintenance costs in 2018. Results: The total cost of emergency ambulance in 2018 is known that the proportion of three cost components, namely operational costs, is 76%, followed by investment costs of 20% and maintenance costs of 3%. The calculation of the total cost of medical evacuation using the double distribution method is Rp. 98,915,016,805.00 divided by the number of medical evacuations in 2018 of 37,564 activities, the unit cost of medical evacuation for the AGD of DKI Jakarta Health Office is Rp. 2,633,215.00 without subsidies. APBD costs, while if the subsidy component is included in the calculation, the unit cost for one trip to the AGD of the Health Office is Rp. 604,071.00. This is still far above the current tariff of Rp. 450.00, so the cost recovery rate (CRR) is still below. 100%. Conclusion: From the three cost components consisting of investment, operational and maintenance costs,the largest proportion was operational costs at 76%. The Cost Recovery Rate has not reached 100% so that the existing rates have not covered the costs incurred.   Keywords: ambulance; price fixing; unit cost

D. Perhitungan HPP Telur Asin Dengan Pendekatan Variabel Costing Pada UD Mulya Jaya

2019 ◽  
Vol 4 (1) ◽  
pp. 30
Author(s):  
Neno Pratiwi ◽  
Andre Setiawan ◽  
Ilmi Cayono ◽  
Johan Trinanto
Keyword(s):  
Decision Making ◽  
Production Process ◽  
Raw Materials ◽  
Selling Price ◽  
Assistance Program ◽  
Total Cost ◽  
Cost Of Production ◽  
The Cost ◽  
A Company ◽  
Important Objective

ABSTRAK Pada umumnya harga pokok produksi dalam akuntansi diartikan dengan jumlah biaya dari seluruh pemakaian yang telah dilakukan selama proses produksi atau kegiatan yang mana mengubah bahan baku menjadi produk jadi (produk siap pakai/siap saji). Tujuan penting dalam tugas ini yaitu memperhitungkan harga pokok produksi dari UD Mulya Jaya dengan menggunakan pendekatan variabel costing untuk mengetahui besarnya harga pokok pada setiap produk yang diproduksi. Pentingnya penentuan harga pokok produksi dapat dilakukan sebelum para usaha menentukan harga jual. Pendampingan ini bertujuan untuk membantu mencari dan menentukan harga pokok produksi yang dapat digunakan untuk menetapkan harga jual. Pendampingan ini dilakukan untuk membantu wirausaha dalam program kerja, yaitu bimbingan akuntansi dengan fokus perhitungan harga pokok produksi. Dalam menentukan harga pokok produksi pada UD Mulya Jaya dapat menggunakan pendekatan variable costing yang biasanya metode ini digunakan untuk semacam pengambilan keputusan dalam perusahaan. Melalui program pendampingan kewirausahaan didapatkan hasil perhitungan harga pokok produksi yang menggunakan pendekatan variabel costing. Hasil tersebut dapat menjadi suatu keputusan bagi UD Mulya Jaya untuk dapat menetapkan harga pokok produksi pada setiap produk telur asin. Kata Kunci : Kewirausahaan, HPP, Harga.   ABSTRACT In general, the cost of production in accounting is defined as the total cost of all uses that have been made during the production process or activities which convert raw materials into finished products (ready-to-use / ready-to-serve products). An important objective in this task is to calculate the cost of goods manufactured from UD Mulya Jaya by using a variable costing approach to find out the cost of goods on each product produced. The importance of determining the cost of production can be done before businesses determine the selling price. This assistance aims to help find and determine the cost of production that can be used to set the selling price. This assistance is carried out to help entrepreneurs in work programs, namely accounting guidance with a focus on calculating the cost of production. In determining the cost of production at UD Mulya Jaya, it can use the variable costing approach, which is usually used for a kind of decision making in a company. Through the entrepreneurship assistance program, the results of the calculation of the cost of production are obtained using the variable costing approach. These results can be a decision for UD Mulya Jaya to be able to set the cost of production for each salted egg product. Keywords: Entrepreneurship, COGS, Price

scholarly journals Cost analysis of breast cancer diagnostic assessment programs

2017 ◽  
Vol 24 (5) ◽  
pp. 354 ◽  
Author(s):  
G.N. Honein-AbouHaidar ◽  
J.S. Hoch ◽  
M.J. Dobrow ◽  
T. Stuart-McEwan ◽  
D.R. McCready ◽  
...  
Keyword(s):  
Breast Cancer ◽  
Cost Effectiveness ◽  
Medical Records ◽  
Diagnostic Tests ◽  
Estimation Method ◽  
Financial Data ◽  
Diagnostic Assessment ◽  
Future Cost ◽  
Total Cost ◽  
The Cost

Objectives Diagnostic assessment programs (daps) appear to improve the diagnosis of cancer, but evidence of their cost-effectiveness is lacking. Given that no earlier study used secondary financial data to estimate the cost of diagnostic tests in the province of Ontario, we explored how to use secondary financial data to retrieve the cost of key diagnostic test services in daps, and we tested the reliability of that cost-retrieving method with hospital-reported costs in preparation for future cost-effectiveness studies.Methods We powered our sample at an alpha of 0.05, a power of 80%, and a margin of error of ±5%, and randomly selected a sample of eligible patients referred to a dap for suspected breast cancer during 1 January–31 December 2012. Confirmatory diagnostic tests received by each patient were identified in medical records. Canadian Classification of Health Intervention procedure codes were used to search the secondary financial data Web portal at the Ontario Case Costing Initiative for an estimate of the direct, indirect, and total costs of each test. The hospital-reported cost of each test received was obtained from the host-hospital’s finance department. Descriptive statistics were used to calculate the cost of individual or group confirmatory diagnostic tests, and the Wilcoxon signed-rank test or the paired t-test was used to compare the Ontario Case Costing Initiative and hospital-reported costs.Results For the 191 identified patients with suspected breast cancer, the estimated total cost of $72,195.50 was not significantly different from the hospital-reported total cost of $72,035.52 (p = 0.24). Costs differed significantly when multiple tests to confirm the diagnosis were completed during one patient visit and when confirmatory tests reported in hospital data and in medical records were discrepant. The additional estimated cost for non-salaried physicians delivering diagnostic services was $28,387.50.Conclusions It was feasible to use secondary financial data to retrieve the cost of key diagnostic tests in a breast cancer dap and to compare the reliability of the costs obtained by that estimation method with hospital-reported costs. We identified the strengths and challenges of each approach. Lessons learned from this study have to be taken into consideration in future cost-effectiveness studies.

scholarly journals Cymbidium Ringspot Virus Harnesses RNA Silencing To Control the Accumulation of Virus Parasite Satellite RNA

2008 ◽  
Vol 82 (23) ◽  
pp. 11851-11858 ◽  
Author(s):  
Vitantonio Pantaleo ◽  
József Burgyán
Keyword(s):  
Rna Silencing ◽  
Sequence Similarity ◽  
Helper Virus ◽  
Ringspot Virus ◽  
Silencing Suppressor ◽  
Short Interfering Rna ◽  
Satellite Rna ◽  
The Cost ◽  
Interfering Rna ◽  
Rna Replicon

ABSTRACT Cymbidium ringspot virus (CymRSV) satellite RNA (satRNA) is a parasitic subviral RNA replicon that replicates and accumulates at the cost of its helper virus. This 621-nucleotide (nt) satRNA species has no sequence similarity to the helper virus, except for a 51-nt-long region termed the helper-satellite homology (HSH) region, which is essential for satRNA replication. We show that the accumulation of satRNA strongly depends on temperature and on the presence of the helper virus p19 silencing suppressor protein, suggesting that RNA silencing plays a crucial role in satRNA accumulation. We also demonstrate that another member of the Tombusvirus genus, Carnation Italian ringspot virus (CIRV), supports satRNA accumulation at a higher level than CymRSV. Our results suggest that short interfering RNA (siRNA) derived from CymRSV targets satRNA more efficiently than siRNA from CIRV, possibly because of the higher sequence similarity between the HSH regions of the helper and CIRV satRNAs. RNA silencing sensor RNA carrying the putative satRNA target site in the HSH region was efficiently cleaved when transiently expressed in CymRSV-infected plants but not in CIRV-infected plants. Strikingly, replacing the CymRSV HSH box2 sequence with that of CIRV restores satRNA accumulation both at 24°C and in the absence of the p19 suppressor protein. These findings demonstrate the extraordinary adaptation of this virus to its host in terms of harnessing the antiviral silencing response of the plant to control the virus parasite satRNA.

Cost-Consequence Analysis of Single-Dose Dalbavancin Versus Standard of Care for the Treatment of Acute Bacterial Skin and Skin Structure Infections in a Multisite Healthcare System

2020 ◽  
Author(s):  
Julia Gonzalez ◽  
Diana Carolina Andrade ◽  
JianLi Niu
Keyword(s):  
Healthcare System ◽  
Treatment Success ◽  
Standard Of Care ◽  
Cost Of Care ◽  
Secondary Outcome ◽  
Total Cost ◽  
Skin Structure ◽  
Cost Consequence ◽  
The Difference ◽  
The Cost

Abstract Background Acute bacterial skin and skin structure infections (ABSSSIs) are common infectious diseases that cause a significant economic burden on the healthcare system. This study aimed to compare the cost-effectiveness of dalbavancin vs standard of care (SoC) in the treatment of ABSSSI in a community-based healthcare system. Methods This was a retrospective study of adult patients with ABSSSI treated with dalbavancin or SoC during a 27-month period. Patients were matched based on age and body mass index. The primary outcome was average net cost of care to the healthcare system per patient, calculated as the difference between reimbursement payments and the total cost to provide care to the patient. The secondary outcome was proportion of cases successfully treated, defined as no ABSSSI-related readmission within 30 days after the initiation of treatment. Results Of the 418 matched patients, 209 received SoC and 209 received dalbavancin. The average total cost of care per patient was greater with dalbavancin vs SoC ($4770 vs $2709, P &lt; .0001). The average reimbursement per patient was $3084 with dalbavancin vs $2633 SoC (P = .527). The net cost, calculated as revenue minus total cost, was $1685 with dalbavancin vs $75 with SoC (P = .013). The overall treatment success rate was 74% with dalbavancin vs 85% with SoC (P = .004). Conclusions Dalbavancin was more costly than SoC for the treatment of ABSSSI, with a higher 30-day readmission rate. Dalbavancin does not offer an economic or efficacy advantage.

scholarly journals Potato Late Blight in the Columbia Basin: An Economic Analysis of the 1995 Epidemic

Plant Disease ◽  
1997 ◽  
Vol 81 (1) ◽  
pp. 103-106 ◽  
Author(s):  
D. A. Johnson ◽  
T. F. Cummings ◽  
P. B. Hamm ◽  
R. C. Rowe ◽  
J. S. Miller ◽  
...  
Keyword(s):  
Late Blight ◽  
Management Practice ◽  
Columbia Basin ◽  
Copper Hydroxide ◽  
Total Cost ◽  
Late Season ◽  
The Mean ◽  
The Cost ◽  
Mean Cost ◽  
First Time

The cost of managing late blight in potatoes during a severe epidemic caused by new, aggressive strains of Phytophthora infestans in the Columbia Basin of Washington and Oregon in 1995 was documented. The mean number of fungicide applications per field varied from 5.1 to 6.3 for early- and midseason potatoes, and from 8.2 to 12.3 for late-season potatoes in the northern and southern Columbia Basin, respectively. In 1994, a year when late blight was not severe, the mean number of fungicide applications per field made to early- and midseason potatoes was 2.0; whereas late-season potatoes received a mean of 2.5 applications. The mean per acre cost of individual fungicides applied varied from $4.90 for copper hydroxide to $36.00 for propamocarb + chlorothalonil. Total per acre expenses (application costs plus fungicide material) for protecting the crop from late blight during 1995 ranged from $106.77 to $110.08 for early and midseason potatoes in different regions of the Columbia Basin and from $149.30 to $226.75 for lateseason potatoes in the northern and southern Columbia Basin, respectively. Approximately 28% of the crop was chemically desiccated before harvest as a disease management practice for the first time in 1995, resulting in an additional mean cost of $34.48/acre or $1.3 million for the region. Harvested yields were 4 to 6% less than in 1994. The total cost of managing late blight in the Columbia Basin in 1995 is estimated to have approached $30 million.

Positive behavioural support for children and adolescents with learning disabilities and behaviour that challenges: an initial exploration of service use and costs

2016 ◽  
Vol 21 (4) ◽  
pp. 169-180 ◽  
Author(s):  
Valentina Iemmi ◽  
Martin Knapp ◽  
Caroline Reid ◽  
Catherine Sholl ◽  
Monique Ferdinand ◽  
...  
Keyword(s):  
Learning Disabilities ◽  
Children And Adolescents ◽  
Service Use ◽  
Potential Cost ◽  
Content Type ◽  
Total Cost ◽  
Behavioural Support ◽  
Delphi Exercise ◽  
The Cost

Purpose Positive behavioural support has been considered as a valuable alternative to residential care for children and adolescents with learning disabilities and behaviour that challenges. While recent evidence suggests it has a positive impact on behaviour and carer ability to cope, there is little evidence of its economic costs or benefits. The paper aims to discuss this issue. Design/methodology/approach An exploratory cross-sectional study was conducted to evaluate the cost of providing positive behavioural support to ten children and adolescents with learning disabilities and behaviour that challenges living in the community in Ealing, West London. Comparison was also made with the cost estimate of possible alternative support packages for children and adolescents with learning disabilities and behaviour that challenges in the UK, as obtained through a Delphi exercise. Findings Total cost of services per child was £1,454 per week for young people supported short-term, and £1,402 supported long-term. Children and adolescents were making use of a range of social care, education and health services. Over the full sample, half of the total cost was accounted for by education services. The Delphi exercise estimated the weekly cost of residential-based care as more expensive than the cost of community-based care for children and adolescents with learning disabilities and behaviour that challenges. At the end of the ITSBS, all ten children and adolescents initially at risk of imminent residential placement were living in the community with less service-intensive and less expensive support. This suggests that avoiding residential-based care could reduce costs in the long term. Originality/value Positive behavioural support has potential to support people with learning disabilities and behaviour that challenges in the community, leading to potential cost advantages. However, this is a small study and more robust research is needed.

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