mbs: modifying Hudson's ms software to generate samples of DNA sequences with a biallelic site under selection

<p>Abstract</p> <p>Background</p> <p>The pattern of single nucleotide polymorphisms, or SNPs, contains a tremendous amount of information with respect to the mechanisms of the micro-evolutionary process of a species. The inference of the roles of these mechanisms, including natural selection, relies heavily on computer simulations. A coalescent simulation is extremely powerful in generating a large number of samples of DNA sequences from a population (species) when all mutations are neutral, and Hudson's <b>ms </b>software is frequently used for this purpose.</p> <p>However, it has been difficult to incorporate natural selection into the coalescent framework.</p> <p>Results</p> <p>We herein present a software application to generate samples of DNA sequences when there is a biallelic site targeted by selection. This software application, referred to as <b>mbs</b>, is developed by modifying Hudson's <b>ms</b>. The <b>mbs </b>software is so flexible that it can incorporate any arbitrary histories of population size changes and any mode of selection as long as selection is operating on a biallelic site.</p> <p>Conclusion</p> <p><b>mbs </b>provides opportunities to investigate the effect of any mode of selection on the pattern of SNPs under various demography.</p

Utility of CD64 on Neutrophils in Orthopedic Infection

【Background】 Musculoskeletal infections are often seen in the daily practice of orthopedics. Several markers [white blood cell (WBC), C-reactive protein (CRP), erythrocyte sedimentation rate (ESR), procalcitonin (PCT)] have been used for diagnosing these infections. However, these markers may be elevated due to surgery or trauma, and may not be infection-related. These markers also show drug-dependent dynamics during infection that differ from its usual dynamics. Such situations make diagnosis of infections difficult, and Cluster of Differentiation 64 (CD64) has been brought to attention. This study aimed to clarify the utility of CD64 on neutrophils by comparing it with conventional infection markers (CRP, PCT) in musculoskeletal infection. 【Methods】 Forty-four patients who were suspected of having musculoskeletal infection between May 2010 and November 2013 in our hospital were enrolled in this study. Patients were divided into subgroups according to their culture results, antibiotics administration, measurement timing, and if they were immunocompromised. The measurements of the infection markers were compared between each group. In addition, the positive rates of each infection marker were compared between groups. 【Results】 There was no difference in the infection marker measurements between several groups. There was no statistically significant difference between groups for the positive rates of CD64, CRP, and PCT. 【Conclusion】 We evaluated the utility of CD64 on neutrophils in musculoskeletal infection. CD64 showed the utility that was equivalent to conventional infection markers in diagnoses of various musculoskeletal infections

Enhanced electrosorption capacity of activated carbon electrodes for deionized water production through capacitive deionization

This research article published by Elsevier B.V., 2020The deionized water (DI) of high purity standards is used in several industrial processes to manufacture products and technologies for high end applications. Currently, DI water is produced by either reverse osmosis or continuous electrodeionization systems, however; both of them are facing several limitations. Therefore there is an urgent need for the alternative technologies for DI water production. This study investigated suitability of producing DI water by using capacitive deionization (CDI) with nitric acid treated activated carbon electrodes (NTAC). Activated carbon (AC) was etched in nitric acid solution to introduce various oxygen functional groups on its surface. The Fourier transform infrared spectroscopy and X-ray photoelectron spectroscopy were used to confirm the increased surface oxygen containing groups on AC after nitric acid treatment that enhanced its salt adsorption capacity. CDI experiments were conducted using water solution of 12.0 μS/cm as a result DI water with the conductivity of 1.6 μS/cm (DI water grade III, according to International Organization of Standards) was produced. Also, electrochemical tests revealed good capacitive behavior due to improved conductivity with NTAC having highest specific capacitance of 381.7 F/g compared to 106.6 F/g of AC electrode. This study provides an insight of the electrosorption performance of materials in desalination of solutions of low ionic strength

Histological Evaluation of Lumbar Spine Changes in Rats with Collagen-induced Arthritis

【Background】 To histologically evaluate lumbar involvement in rheumatoid arthritis (RA) by investigating rats with collagen-induced arthritis (CIA) and to assess the potential effects of RA on the discovertebral joints and facet joints. 【Methods】 Seven-month-old female Sprague-Dawley rats were divided into groups with CIA and without CIA (control). All rats were sacrificed at 8 weeks after initial sensitization and the lumbar spine (L5/6) was harvested. Then the lumbar spine block specimens were stained with Villaneuva bone stain and sectioned in the midsagittal plane. The left facet joints were also sectioned in the midaxial plane. Specimens were studied under a microscope and infiltration of inflammatory cells was investigated. 【Results】 In the CIA group, lumbar lesions were observed in 13/18 rats (76%). Lymphocytes infiltrated into the anterior rim of the vertebral bodies only in 2 rats, while lymphocytes infiltrated the facet joints only in 4 rats. Both sites were involved in 7 rats. In addition, osteoclasts invaded the anterior rim of the vertebral bodies and formed cavities that also contained lymphocytes. Formation of pannus was seen in the facet joints in 11/18 rats. 【Conclusion】 In CIA rats, infiltration of inflammatory cells into the anterior rim of the vertebral bodies alone or into the facet joints alone was demonstrated in 2 rats and 4 rats, respectively, while both sites were involved in 7 rats. Therefore, lesions at the anterior rim of the vertebral body did not arise secondary to facet joint involvement, but were caused by CIA along with synovial lesions of the facet joints

Adsorption-capacitive deionization hybrid system with activated carbon of modified potential of zero charge

This research article was published by Elsevier, 2023In this study water solutions are desalinated with carbon electrodes of modified surface charges. The idea is to endow the electrodes with the ability to physically adsorb salt ions without applying potential so as to save energy. The modification enhanced to decrease the energy consumption of a newly invented adsorption-CDI hybrid system by 19%, since modified activated carbon cell consumed 0.620 (relative error 3.00%) kWh/m3 compared to pristine activated carbon cell which consumed 0.746 (relative error 1.20%) kWh/m3. Further analysis revealed high adsorption capacity of the modified activated carbon electrode cell which exhibited 9.0 (relative error 2.22%) compared to activated carbon cell with 5.3 (relative error 5.66%) mg g−1. These results show the potential of surface modification in adding value to low cost activated carbons for application in CDI

Neurogenic Dumbbell Tumor Resected by Combined Posterior and Thoracoscopic Approaches

The patient was a 51-year-old female with a chief complaint of numbness of the right thigh. A dumbbell tumor compressing the 11th thoracic spinal cord was present in the posterior mediastinum on chest computed tomography and myelography. In surgery, the tumor in the spinal canal was resected by a posterior approach, and the residual tumor was completely excised by thoracoscopic surgery. The tumor measured 78 48 mm, and histopathologically diagnosed as schwannoma. The surgical procedure for neurogenic dumbbell tumors should be decided based on Eden’s classification. For types II and III, such as this patient, excision of the tumor in the spinal canal should be performed to avoid spinal cord damage, followed by thoracoscopic complete resection. Thoracoscopic surgery was applicable even though the tumor was large

Duplication and Gene Conversion in the Drosophila melanogaster Genome

Using the genomic sequences of Drosophila melanogaster subgroup, the pattern of gene duplications was investigated with special attention to interlocus gene conversion. Our fine-scale analysis with careful visual inspections enabled accurate identification of a number of duplicated blocks (genomic regions). The orthologous parts of those duplicated blocks were also identified in the D. simulans and D. sechellia genomes, by which we were able to clearly classify the duplicated blocks into post- and pre-speciation blocks. We found 31 post-speciation duplicated genes, from which the rate of gene duplication (from one copy to two copies) is estimated to be 1.0×10−9 per single-copy gene per year. The role of interlocus gene conversion was observed in several respects in our data: (1) synonymous divergence between a duplicated pair is overall very low. Consequently, the gene duplication rate would be seriously overestimated by counting duplicated genes with low divergence; (2) the sizes of young duplicated blocks are generally large. We postulate that the degeneration of gene conversion around the edges could explain the shrinkage of “identifiable” duplicated regions; and (3) elevated paralogous divergence is observed around the edges in many duplicated blocks, supporting our gene conversion–degeneration model. Our analysis demonstrated that gene conversion between duplicated regions is a common and genome-wide phenomenon in the Drosophila genomes, and that its role should be especially significant in the early stages of duplicated genes. Based on a population genetic prediction, we applied a new genome-scan method to test for signatures of selection for neofunctionalization and found a strong signature in a pair of transporter genes

Graft-versus-host disease in recipients of male unrelated donor compared with parous female sibling donor transplants

Optimal donor selection is critical for successful allogeneic hematopoietic cell transplantation (HCT). Donor sex and parity are well-established risk factors for graft-versus-host disease (GVHD), with male donors typically associated with lower rates of GVHD. Well-matched unrelated donors (URDs) have also been associated with increased risks of GVHD as compared with matched sibling donors. These observations raise the question of whether male URDs would lead to more (or less) favorable transplant outcomes as compared with parous female sibling donors. We used the Center for International Blood and Marrow Transplant Research registry to complete a retrospective cohort study in adults with acute myeloid leukemia, acute lymphoblastic leukemia, or myelodysplastic syndrome, who underwent T-cell replete HCT from these 2 donor types (parous female sibling or male URD) between 2000 and 2012. Primary outcomes included grade 2 to 4 acute GVHD (aGVHD), chronic GVHD (cGVHD), and overall survival. Secondary outcomes included disease-free survival, transplant-related mortality, and relapse. In 2813 recipients, patients receiving male URD transplants (n = 1921) had 1.6 times higher risk of grade 2 to 4 aGVHD (P \u3c .0001). For cGVHD, recipient sex was a significant factor, so donor/recipient pairs were evaluated. Female recipients of male URD grafts had a higher risk of cGVHD than those receiving parous female sibling grafts (relative risk [RR] = 1.43, P \u3c .0001), whereas male recipients had similar rates of cGVHD regardless of donor type (RR = 1.09, P = .23). Donor type did not significantly affect any other end point. We conclude that when available, parous female siblings are preferred over male URDs

Event-free survival at 36 months is a suitable endpoint for diffuse large B-cell lymphoma patients treated with immunochemotherapy: real-world evidence from the North Japan Hematology Study Group

Information regarding follow-up duration after treatment for newly diagnosed diffuse large B-cell lymphoma (DLBCL) is important. However, a clear endpoint has yet to be established. We totally enrolled 2182 patients newly diagnosed with DLBCL between 2008 and 2018. The median age of the patients was 71 years. All patients were treated with rituximab- and anthracycline-based chemotherapies. Each overall survival (OS) was compared with the age- and sex-matched Japanese general population (GP) data. At a median follow-up of 3.4 years, 985 patients experienced an event and 657 patients died. Patients who achieved an event-free survival (EFS) at 36 months (EFS36) had an OS equivalent to that of the matched GP (standard mortality ratio [SMR], 1.17; P=0.1324), whereas those who achieved an EFS24 did not have an OS comparable to that of the matched GP (SMR, 1.26; P=0.0095). Subgroup analysis revealed that relatively old patients (>60 years), male patients, those with limited-stage disease, those with a good performance status, and those with low levels of soluble interleukin 2 receptor already had a comparable life expectancy to the matched GP at an EFS24. In contrast, relatively young patients had a shorter life expectancy than matched GP, even with an EFS36. In conclusion, an EFS36 was shown to be a more suitable endpoint for newly diagnosed DLBCL patients than an EFS24. Of note, younger patients require a longer EFS period than older patients in order to obtain an equivalent life expectancy to the matched GP