The practical and educational value of scleral buckling with chandelier illumination.

PURPOSE: To compare the surgical results in cases of primary rhegmatogenous retinal detachments between standard scleral buckling (SSB) and scleral buckling with chandelier illumination (SBC) and to analyse the differences in SBC surgical results between an experienced ophthalmologist and inexperienced ophthalmologists. METHODS: Consecutive surgical case series of 155 eyes that underwent scleral buckling were retrospectively reviewed and divided into four groups: SSB performed by an experienced ophthalmologist (n = 54), SBC performed by an experienced ophthalmologist (n = 52), SBC performed by inexperienced ophthalmologists (n = 40) and SSB performed by inexperienced ophthalmologists (n = 9). Then, these four groups were compared. RESULTS: No significant differences were observed between SSB and SBC procedures both performed by the experienced ophthalmologist with regard to demographics, preoperative findings, contents of the surgery, intraoperative complications, retinal reattachment, postoperative findings and postoperative complications. Between SBC performed by the experienced ophthalmologist and SBC performed by the inexperienced ophthalmologists, no significant differences were found regarding intraoperative complications, retinal reattachment, postoperative findings and postoperative complications. Between SSB and SBC procedures both performed by the inexperienced ophthalmologist, a significant difference was found regarding intraoperative complications. CONCLUSION: There were no significant differences in surgical results between SSB and SBC when both were performed by the experienced ophthalmologist. In addition, the surgical results were equal between the experienced ophthalmologist and the inexperienced ophthalmologist as far as SBC was concerned. Learning scleral buckling skills by using SBC is a reasonable course of action for inexperienced ophthalmologists.

Blowout fracture-associated orbital cellulitis progressing to panophthalmitis: a case report.

BACKGROUND: Parvimonas micra is known as a causative agent of chronic periodontal disease. This Gram-positive obligate anaerobic coccus was cultured from the ocular surface of blowout fracture-related orbital cellulitis progressing to panophthalmitis. CASE PRESENTATION: The patient was a woman in her fifties who had panic disorder and subsequently was a victim of domestic violence. These factors led to delayed consultation. At the initial visit to an ophthalmologist, the ocular surface of the right eye was covered with pus. Swelling of the upper and lower eyelids prevented the eyelid from closing and exophthalmos, severe corneal ulcer, panophthalmitis, and no light perception were observed. Head computed tomography revealed an old blowout fracture and chronic sinusitis with orbital cellulitis. P. micra were isolated from culture of pus samples from the sinus and from the ocular surface. CONCLUSIONS: There is a possibility that P. micra invaded the orbit via the fragile bony site and caused orbital cellulitis, severe corneal ulcer, and panophthalmitis that required enucleation. In cases of coexisting old blowout fracture and chronic sinusitis, the chronic sinusitis should be treated as quickly as possible.

Panacea: Visual exploration system for analyzing trends in annual recruitment using time-varying graphs.

Annual recruitment data of new graduates are manually analyzed by human resources (HR) specialists in industries, which signifies the need to evaluate the recruitment strategy of HR specialists. Different job seekers send applications to companies every year. The relationships between applicants' attributes (e.g., English skill or academic credentials) can be used to analyze the changes in recruitment trends across multiple years. However, most attributes are unnormalized and thus require thorough preprocessing. Such unnormalized data hinder effective comparison of the relationship between applicants in the early stage of data analysis. Thus, a visual exploration system is highly needed to gain insight from the overview of the relationship among applicant qualifications across multiple years. In this study, we propose the Polarizing Attributes for Network Analysis of Correlation on Entities Association (Panacea) visualization system. The proposed system integrates a time-varying graph model and dynamic graph visualization for heterogeneous tabular data. Using this system, HR specialists can interactively inspect the relationships between two attributes of prospective employees across multiple years. Further, we demonstrate the usability of Panacea with representative examples for finding hidden trends in real-world datasets, and we discuss feedback from HR specialists obtained throughout Panacea's development. The proposed Panacea system enables HR specialists to visually explore the annual recruitment of new graduates.

Long-read sequencing for non-small-cell lung cancer genomes.

Here, we report the application of a long-read sequencer, PromethION, for analyzing human cancer genomes. We first conducted whole-genome sequencing on lung cancer cell lines. We found that it is possible to genotype known cancerous mutations, such as point mutations. We also found that long-read sequencing is particularly useful for precisely identifying and characterizing structural aberrations, such as large deletions, gene fusions, and other chromosomal rearrangements. In addition, we identified several medium-sized structural aberrations consisting of complex combinations of local duplications, inversions, and microdeletions. These complex mutations occurred even in key cancer-related genes, such as STK11, NF1, SMARCA4, and PTEN The biological relevance of those mutations was further revealed by epigenome, transcriptome, and protein analyses of the affected signaling pathways. Such structural aberrations were also found in clinical lung adenocarcinoma specimens. Those structural aberrations were unlikely to be reliably detected by conventional short-read sequencing. Therefore, long-read sequencing may contribute to understanding the molecular etiology of patients for whom causative cancerous mutations remain unknown and therapeutic strategies are elusive.

Visualization tools for human structural variations identified by whole-genome sequencing.

Visualizing structural variations (SVs) is a critical step for finding associations between SVs and human traits or diseases. Given that there are many sequencing platforms used for SV identification and given that how best to visualize SVs together with other data, such as read alignments and annotations, depends on research goals, there are dozens of SV visualization tools designed for different research goals and sequencing platforms. Here, we provide a comprehensive survey of over 30 SV visualization tools to help users choose which tools to use. This review targets users who wish to visualize a set of SVs identified from the massively parallel sequencing reads of an individual human genome. We first categorize the ways in which SV visualization tools display SVs into ten major categories, which we denote as view modules. View modules allow readers to understand the features of each SV visualization tool quickly. Next, we introduce the features of individual SV visualization tools from several aspects, including whether SV views are integrated with annotations, whether long-read alignment is displayed, whether underlying data structures are graph-based, the type of SVs shown, whether auditing is possible, whether bird's eye view is available, sequencing platforms, and the number of samples. We hope that this review will serve as a guide for readers on the currently available SV visualization tools and lead to the development of new SV visualization tools in the near future.

MoMI-G: modular multi-scale integrated genome graph browser.

BACKGROUND: Genome graph is an emerging approach for representing structural variants on genomes with branches. For example, representing structural variants of cancer genomes as a genome graph is more natural than representing such genomes as differences from the linear reference genome. While more and more structural variants are being identified by long-read sequencing, many of them are difficult to visualize using existing structural variants visualization tools. To this end, visualization method for large genome graphs such as human cancer genome graphs is demanded. RESULTS: We developed MOdular Multi-scale Integrated Genome graph browser, MoMI-G, a web-based genome graph browser that can visualize genome graphs with structural variants and supporting evidences such as read alignments, read depth, and annotations. This browser allows more intuitive recognition of large, nested, and potentially more complex structural variations. MoMI-G has view modules for different scales, which allow users to view the whole genome down to nucleotide-level alignments of long reads. Alignments spanning reference alleles and those spanning alternative alleles are shown in the same view. Users can customize the view, if they are not satisfied with the preset views. In addition, MoMI-G has Interval Card Deck, a feature for rapid manual inspection of hundreds of structural variants. Herein, we describe the utility of MoMI-G by using representative examples of large and nested structural variations found in two cell lines, LC-2/ad and CHM1. CONCLUSIONS: Users can inspect complex and large structural variations found by long-read analysis in large genomes such as human genomes more smoothly and more intuitively. In addition, users can easily filter out false positives by manually inspecting hundreds of identified structural variants with supporting long-read alignments and annotations in a short time. SOFTWARE AVAILABILITY: MoMI-G is freely available at https://github.com/MoMI-G/MoMI-G under the MIT license.

A strategy for building and using a human reference pangenome.

In March 2019, 45 scientists and software engineers from around the world converged at the University of California, Santa Cruz for the first pangenomics codeathon. The purpose of the meeting was to propose technical specifications and standards for a usable human pangenome as well as to build relevant tools for genome graph infrastructures. During the meeting, the group held several intense and productive discussions covering a diverse set of topics, including advantages of graph genomes over a linear reference representation, design of new methods that can leverage graph-based data structures, and novel visualization and annotation approaches for pangenomes. Additionally, the participants self-organized themselves into teams that worked intensely over a three-day period to build a set of pipelines and tools for specific pangenomic applications. A summary of the questions raised and the tools developed are reported in this manuscript.

Scleral buckling procedure with chandelier illumination for pediatric rhegmatogenous retinal detachment.

PURPOSE: To assess the treatment of pediatric patients with rhegmatogenous retinal detachment (RRD) by scleral buckling with chandelier illumination. METHODS: Three eyes were treated in three patients, healthy boys aged 7 years, 12 years, and 11 years, with RRD, macular involvement, and small retinal holes, of which two were preoperatively undetectable. Conventional scleral buckling with cryoretinopexy was performed under the contact lens for vitreous surgery or noncontact wide-angle viewing system using 27-gauge twin chandelier illumination. RESULTS: The only known predisposing factor for retinal detachment was myopia stronger than 3 D with lattice retinal degeneration in two of the three patients. Retinal reattachment was achieved in all cases without intra- or postoperative complications. However, visual recovery was limited in one of the three patients. CONCLUSION: Scleral buckling with chandelier illumination is effective for pediatric RRD, especially if the retinal hole is difficult to detect preoperatively. However, visual recovery was sometimes limited because of macular involvement due to late diagnosis, which is one of the characteristic features of pediatric RRD.

Familial cases of Norrie disease detected by copy number analysis.

PURPOSE: Norrie disease (ND, MIM#310600) is an X-linked disorder characterized by severe vitreoretinal dysplasia at birth. We report the results of causative NDP gene analysis in three male siblings with Norrie disease and describe the associated phenotypes. METHODS: Three brothers with suspected Norrie disease and their mother presented for clinical examination. After obtaining informed consent, DNA was extracted from the peripheral blood of the proband, one of his brothers and his unaffected mother. Exons 1-3 of the NDP gene were amplified by polymerase chain reaction (PCR), and direct sequencing was performed. Multiplex ligation-dependent probe amplification (MLPA) was also performed to search for copy number variants in the NDP gene. RESULTS: The clinical findings of the three brothers included no light perception, corneal opacity, shallow anterior chamber, leukocoria, total retinal detachment and mental retardation. Exon 2 of the NDP gene was not amplified in the proband and one brother, even when the PCR primers for exon 2 were changed, whereas the other two exons showed no mutations by direct sequencing. MLPA analysis showed deletion of exon 2 of the NDP gene in the proband and one brother, while there was only one copy of exon 2 in the mother. CONCLUSION: Norrie disease was diagnosed in three patients from a Japanese family by clinical examination and was confirmed by genetic analysis. To localize the defect, confirmation of copy number variation by the MLPA method was useful in the present study.

Histopathologic analysis of the internal limiting membrane surgically peeled from eyes with diffuse diabetic macular edema.

PURPOSE: To investigate the pathogenesis of diffuse diabetic maculae edema (DME). METHODS: Internal limiting membrane (ILM) specimens were surgically peeled from 16 eyes of 15 patients with diffuse DME (diabetic retinopathy (DR) group) and from 12 eyes of 12 patients without diabetes (non-DR group). The specimens were then examined by light microscopy (LM), transmission electron microscopy (TEM), and immunohistochemistry. RESULTS: Examination by LM revealed numerous cells on the inner surface of the ILM specimens in the DR-group, among which five different cell types (glial cell, fibroblast-like cell, macrophages, neutrophils, and lymphocytes) were confirmed. Examination by TEM revealed that the thickness of the peeled ILMs in the DR group was significantly greater, and four types of cellular element (glial, fibroblast-like, macrophages, and lymphocytes) were confirmed on the surface of the vitreous side of the specimens. The existence of glial cells and macrophages was confirmed by immunohistochemistry. CONCLUSIONS: In diffuse DME, the ILM is thickened and a variety of cellular elements, especially numerous kinds of inflammatory cell, adhere to the inner surface of the ILM. To attenuate diffuse DME, vitrectomy combined with ILM peeling to remove the inflammatory cells and the physical barrier might be effective.

Typing of Clostridium difficile isolates endemic in Japan by sequencing of slpA and its application to direct typing.

A typing system for Clostridium difficile using sequencing of the surface-layer protein A encoding gene (slpA) was evaluated and used to analyse clinical isolates in Japan. A total of 160 stool specimens from symptomatic patients in Japan was examined and 87 C. difficile isolates were recovered. slpA sequence typing was found to have reliable typability and discriminatory power in comparison with PCR ribotyping, and the typing results were highly reproducible and comparable. slpA sequence typing was used to type C. difficile in DNA extracted directly from stool specimens. Among the 90 stool specimens in which direct typing results were obtained, 77 specimens were positive for C. difficile culture, and typing results from isolated strains agreed with those from direct typing in all 77 specimens. The slpA sequence type smz was dominant at all four hospitals examined, and this endemic type was detected by culture and/or direct typing in 61 (62 %) of 99 stool specimens positive for toxic culture and/or direct slpA sequence typing. Comparison of epidemic strains reported throughout the world revealed one isolate identified as slpA sequence type gc8, which was found to correspond to PCR ribotype 027 (BI/NAP1/027), whereas no isolates were found with the slpA gene identical to that of PCR ribotype 078 strain. slpA sequence typing is valuable for comparison of C. difficile strains epidemic in diverse areas because the typing results are reproducible and can easily be shared. In addition, slpA sequence typing could be applied to direct typing without culture.

A distance meter using a terahertz intermode beat in an optical frequency comb.

We propose a distance meter that utilizes an intermode beat of terahertz frequency in an optical frequency comb to perform high resolution and high dynamic range absolute distance measurements. The proposed system is based on a novel method, called multiheterodyne cross-correlation detection, in which intermode beat frequencies are scaled down to radio frequencies by optical mixing of two detuned optical frequency combs with a nonlinear optical crystal. Using this method, we obtained a 1.056 THz intermode beat and achieved a distance resolution of 0.820 microm from its phase measurement. Absolute distance measurement using 1.056 THz and 8.187 GHz intermode beats was also demonstrated in the range of 10 mm, resulting in a precision of 0.688 microm.

A case of oculodentodigital dysplasia syndrome with novel GJA1 gene mutation.

PURPOSE: To report a case of oculodentodigital dysplasia syndrome (ODDD) with a heterozygous mutation in GJA1 (connexin 43) gene. METHODS: A 9-year-old girl visited our hospital complaining of visual disturbances. The patient had microphthalmia, a small nose with hypoplastic alae nasi, and syndactyly. Visual acuity with prescribed glasses improved to 0.5 (1.2) OU 2 months after the first visit. She was satisfied with the new glasses and the improvement in visual acuity. Genomic DNA was extracted from leukocytes of the patient's peripheral blood in accordance with standard procedures, after obtaining parental informed consent. We amplified GJA1 exon 2 from her genomic DNA by the PCR method, and sequenced the product using the dye terminator method. RESULTS: S5C (c. 13A > T), a novel mutation in exon 2 of GJA1, was found in the patient. The parents had no mutation of GJAI, nor was there any sign of abnormality in other family members. No similar mutation could be found in the 50 genotyped normal subjects in the control group. CONCLUSIONS: A novel GJA1 mutation was detected in a Japanese ODDD patient. Glaucoma complications associated with ODDD have already been reported. Careful long-term monitoring and treatment are also necessary.

Bilateral anterior granulomatous keratouveitis with sunset glow fundus in a patient with autoimmune polyglandular syndrome.

AIM: To report the case of a patient with bilateral anterior granulomatous keratouveitis and sunset glow fundus. METHOD: Review of case record. RESULTS: A 15-year-old patient had bilateral anterior granulomatous keratouveitis and sunset glow fundus similar to findings in Vogt-Koyanagi-Harada disease (VKH). However, the patient also suffered additional autoimmune disease against endocrine glands. In addition to anti-thyroid antibody and anti-glutamic acid decarboxylase antibody, anti-melanocyte autoantibody was detected in serum from this patient. The authors finally diagnosed autoimmune polyglandular syndrome. CONCLUSION: If resistance against treatment exists for VKH, particularly in pediatric cases, this disease should be considered and other endocrine disorders examined.

[A clinical study of intraocular malignant lymphoma].

PURPOSE: We investigated whether vitreous cytology and the measurement of intravitreous cytokine were useful for the diagnosis of intraocular malignant lymphoma. SUBJECTS AND METHODS: 8 eyes of 5 patients with suspected intraocular malignant lymphoma during the past 15 months. 3 vitreous samples were collected from 3 patients at the time of pars plana vitrectomy. Polymerase chain reaction(PCR) amplification and flowcytometric analysis(FACS) of the vitreous samples were performed. Interleukin (IL)-10 and IL-6 concentrations were measured. RESULTS: Vitreous cytology showed increased atypical B lymphocytes. The vitreous IL-10/IL-6 ratio was higher than 1 in all cases. Monoclonal rearrangement of the immunoglobulin heavy chain gene and the light chain restriction of immunoglobulin were detected. CONCLUSION: The detection of the monoclonality of infiltrated cells into the vitreous by PCR amplification and FACS, and the measurements of IL-10 and IL-6 concentrations in the vitreous fluid may be useful in the diagnosis of intraocular malignant lymphoma.

Central retinal vein occlusion caused by human herpesvirus 6.

We describe a 1-year-old girl with central retinal vein occlusion caused by human herpesvirus 6. She received systemic corticosteroid therapy. Although there was retinal recovery after the therapy, the visual acuity in her left eye still could not be measured.

Rapid and simple method for detecting the toxin B gene of Clostridium difficile in stool specimens by loop-mediated isothermal amplification.

We applied the loop-mediated isothermal amplification (LAMP) assay to the detection of the toxin B gene (tcdB) of Clostridium difficile for identification of toxin B (TcdB)-positive C. difficile strains and detection of tcdB in stool specimens. tcdB was detected in all toxin A (TcdA)-positive, TcdB-positive (A(+)B(+)) and TcdA-negative, TcdB-positive (A(-)B(+)) C. difficile strains but not from TcdA-negative, TcdB-negative strains. Of the 74 stool specimens examined, A(+)B(+) or A(-)B(+) C. difficile was recovered from 39 specimens, of which 38 specimens were LAMP positive and one was negative. Amplification was obtained in 10 specimens that were culture negative, indicating that LAMP is highly sensitive. The LAMP assay was applied to detection of tcdB in DNA extracted by a simple boiling method from 47 of those 74 specimens, which were cultured overnight in cooked-meat medium (CMM). Twenty-two of 24 culture-positive specimens were positive for LAMP on DNA from the culture in CMM. Four specimens were culture negative but positive by LAMP on DNA from CMM cultures. The LAMP assay is a reliable tool for identification of TcdB-positive C. difficile as well as for direct detection of tcdB in stool specimens with high sensitivity. Detection of tcdB by LAMP from overnight cultures in CMM could be an alternative method of diagnostic testing at clinical laboratories without special apparatus.

Macular hole secondary to epiretinal membrane in a juvenile patient.

PURPOSE: To report a macular hole secondary to an idiopathic epiretinal membrane in a 14-year-old girl. DESIGN: Interventional case report. METHODS: A 3-year-old girl who failed a public visual-screening test was examined. Since then, she had been followed-up for her epiretinal membrane, which began to peel spontaneously in the left eye for 11 years until a macular hole was observed. She was treated by vitrectomy and membranectomy, and the membrane was histologically examined. RESULT: The macular hole was successfully closed, and her visual acuity improved. The membrane appeared to have a homogenous structure and contained no cells. CONCLUSIONS: The juvenile idiopathic epiretinal membrane sometimes peels spontaneously. However, long-term follow-up is needed because vitreous traction of the membrane by intraocular aging change may result in a macular hole.

Typing by sequencing the slpA gene of Clostridium difficile strains causing multiple outbreaks in Japan.

Previous reports have documented that a surface layer protein (SlpA) varies among Clostridium difficile isolates. The typing system by sequencing the variable region of the slpA gene was applied to typing C. difficile strains belonging to one PCR ribotype, type smz, which has been identified as frequently causing outbreaks in Japan. The PCR ribotype smz strains recovered from patients at different hospitals in Japan were examined. Among 10 type smz strains tested, three subtypes, smz-1, -2 and -3, were identified that differed from each other by one nucleotide. slpA sequence typing was also applied to direct typing on DNA extracted from stool specimens. Of 22 stool specimens examined, 17 were PCR positive for slpA; eight were typed as slpA sequence type smz-1 and nine as type smz-2. C. difficile was cultured from 12 of these 17 stool specimens, and the sequence results of the recovered isolates were compared with those from the DNA extracted from the stool specimens. In all 12 of these stool specimens, the sequence results of DNA from recovered C. difficile isolates completely agreed with those of DNA extracted directly from stool specimens. The remaining five stool specimens were culture-negative for C. difficile. Sequence typing has the advantage of enabling easy comparison of typing results among multiple laboratories via the Internet without exchanging reference strains as is required in typing systems which depend on banding-pattern analyses. slpA sequence typing appears to be a reproducible and reliable typing system for C. difficile as well as being useful for the typing of C. difficile when stool specimens contain only small numbers of C. difficile or are inappropriate for culturing.