Validation and standardization of DNA extraction and library construction methods for metagenomics-based human fecal microbiome measurements.

BACKGROUND: Validation and standardization of methodologies for microbial community measurements by high-throughput sequencing are needed to support human microbiome research and its industrialization. This study set out to establish standards-based solutions to improve the accuracy and reproducibility of metagenomics-based microbiome profiling of human fecal samples. RESULTS: In the first phase, we performed a head-to-head comparison of a wide range of protocols for DNA extraction and sequencing library construction using defined mock communities, to identify performant protocols and pinpoint sources of inaccuracy in quantification. In the second phase, we validated performant protocols with respect to their variability of measurement results within a single laboratory (that is, intermediate precision) as well as interlaboratory transferability and reproducibility through an industry-based collaborative study. We further ascertained the performance of our recommended protocols in the context of a community-wide interlaboratory study (that is, the MOSAIC Standards Challenge). Finally, we defined performance metrics to provide best practice guidance for improving measurement consistency across methods and laboratories. CONCLUSIONS: The validated protocols and methodological guidance for DNA extraction and library construction provided in this study expand current best practices for metagenomic analyses of human fecal microbiota. Uptake of our protocols and guidelines will improve the accuracy and comparability of metagenomics-based studies of the human microbiome, thereby facilitating development and commercialization of human microbiome-based products. Video Abstract.

Strengthening retina eye care services in Nepal: retina eye care of Nepal project.

BACKGROUND: Retinal diseases are very difficult to treat. So, early diagnoses and preventions are very important. But, few eye doctors can treat patients with retinal diseases in Nepal. Retina Eye Care of Nepal (RECON) project was designed to strengthen retina eye care services in Nepal. METHODS: RECON was implemented from May 2016 to February 2019 in Nepal. Four Master Eye Doctors (MED) received Training of Trainers (TOT) from Tokushima University, Japan. MEDs developed training materials for different cadres of ophthalmic human resources, enhanced retina eye care facilities, and conducted retina-screening camp in Nepal. RESULTS: Twenty ophthalmologists, 16 optometrists, 48 ophthalmic assistants and 17 ophthalmic nurses, 76 physicians and 28 health workers were trained in retina care. Eight outreach retina camps were conducted. CONCLUSIONS: The project was a novel approach to strengthen retina services in Nepal. The aim of the project was accomplished with the ultimate benefits to the needy retina patients who otherwise were going to miss the retina services.

A Unique Experience of Retinal Diseases Screening in Nepal.

BACKGROUND: Recently, the number of retinal patients is increasing in Nepal. The retinal problems are the second common cause of blindness in Nepal. Retinal diseases are challenging to manage due to the lack of simple and cost-effective screening methods, limited human resources, poverty, and lack of awareness in Nepal. Hospital for Children, Eye, ENT & Rehabilitation Services (CHEERS), Nepal conducted retina screening camps and education in communities through Retina Eye Care of Nepal project (RECON) in the years 2017 and 2018. MATERIALS AND METHODS: We screened retinal patients with an indirect ophthalmoscope coupled with plus 20 Dioptre lens and portable fundus camera. We referred the patients needing interventions to the base hospital (CHEERS) using a screening algorithm, where they received retinal laser and surgery. Besides, we also provided on-site educational programs for retinal disease awareness to the community. RESULTS: Retinal problems found from two static outreach clinics (SORC) and a day screening and treatment service (DSTS) were 18.3%, 20%, and 20%, respectively, while from a remote rural health camp (RRHC) was 2.61%. Likewise, patients referred to CHEERS for retinal laser or other retinal interventions were 15%, 16.6%, 16%, and 1.96% from 2 SORCs, 1 DSTS, and 1 RRHC, respectively. CONCLUSION: Retina camp is a cost-effective approach to early detection and referral for retinal-related vision impairment patients. It is also one opportunity to educate the community. The purpose of the project was to provide retina care to the community who otherwise could not afford it. We recommend a similar screening model on a large scale in a low-resource setting for the maximum benefits to the rural community.

Neoadjuvant chemotherapy plus surgery for high-risk advanced gastric cancer: long-term results of KDOG1001 trial.

PURPOSE: The purpose of this study is to evaluate the long-term survival outcomes of KDOG1001 trial after a minimum follow-up of 3 years. METHODS: Patients with bulky N2 lymph nodes, linitis plastica (type 4), or large ulcero-invasive-type tumors (type 3) received up to four 28-day cycles of DCS neoadjuvant chemotherapy (docetaxel at 40 mg/m2, cisplatin at 60 mg/m2 on day 1, and S-1 at 40 mg/m2 twice daily for 2 weeks) followed by gastrectomy with D2 lymphadenectomy plus adjuvant S-1 therapy for 1 year. The final preplanned analysis of long-term outcomes including overall survival and relapse-free survival was conducted after minimum follow-up of 3 years. This trial is registered with the University Hospital Medical Information Network Clinical Trials Registry, number UMIN 000003642, and has been completed. RESULTS: From May 2010 through January 2017, 40 patients were enrolled. All included patients underwent neoadjuvant chemotherapy with DCS followed by gastrectomy with D2 lymphadenectomy, and 32 (80%) completed adjuvant S-1 therapy for 1 year. After a median follow-up for surviving patients of 68 months at the last follow-up in January 2020, 3-year overall survival rate was 77.5% (95% confidence interval 62.1-87.9%), while 3-year relapse-free survival rate was 62.5% (95% confidence interval 46.8-76.0%). CONCLUSION: Neoadjuvant chemotherapy with 4 cycles of DCS followed by D2 gastrectomy plus adjuvant S-1 was associated with relatively good long-term oncologic outcomes for patients with the high-risk gastric cancer.

An Integrated Genomic and Transcriptomic Analysis Reveals Candidates of Susceptibility Genes for Crohn's Disease in Japanese Populations.

Expression quantitative trait locus (eQTL) analyses have enabled us to predict the function of disease susceptibility SNPs. However, eQTL for the effector memory T cells (TEM) located in the lamina propria mononuclear cells (LPMCs), which play an important role in Crohn's disease (CD), are not yet available. Thus, we conducted RNA sequencing and eQTL analyses of TEM cells located in the LPMCs from IBD patients (n = 20). Genome-wide association study (GWAS) was performed using genotyping data of 713 Japanese CD patients and 2,063 controls. We compared the results of GWAS and eQTL of TEM, and also performed a transcriptome-wide association study using eQTL from Genotype Tissue Expression project. By eQTL analyses of TEM, correlations of possible candidates were confirmed in 22,632 pairs and 2,463 genes. Among these candidates, 19 SNPs which showed significant correlation with tenascin-XA (TNXA) expression were significantly associated with CD in GWAS. By TWAS, TNFSF15 (FDR = 1.35e-13) in whole blood, ERV3-1 (FDR = 2.18e-2) in lymphocytes, and ZNF713 (FDR = 3.04e-2) in the sigmoid colon was significantly associated with CD. By conducting integration analyses using GWAS and eQTL data, we confirmed multiple gene transcripts are involved in the development of CD.

[Conversion Surgery for Locally Advanced Unresectable Pancreatic Cancer Treated with FOLFIRINOX Therapy and Proton Beam Therapy Combined with S-1 Chemotherapy-A Case Report].

We report a case of locally advanced unresectable(UR-LA)pancreatic cancer in a patient who underwent conversion surgery after FOLFIRINOX and proton beam therapy(PBT)combined with S-1. A 68-year-old woman was referred to our hospital for a pancreatic tumor. The abdominal CT scan revealed a 40mm pancreatic body tumor with an abutment(>180°) of the celiac artery and the superior mesenteric artery. Moreover, the tumor was classified as UR-LA with a contact to the abdominal aorta. The tumor was histologically diagnosed as adenocarcinoma via an endoscopic ultrasound-guided fine-nee- dle aspiration. After 2 courses of FOLFIRINOX, PBT(50 GyE/25 Fr)combined with S-1 were administered. The tumor shrunk to 30mm at the CT scan. After 5 courses of FOLFIRINOX, the tumor reduced to 20 mm. No distant metastasis or malignant cells in abdominal washing cytology was detected using staging laparoscopy. Then, distal pancreatectomy with celiac axis resection(DP-CAR)was performed. According to the General Rules for the Study of Pancreatic Cancer(7th edition)from Japan Pancreas Society, the histological findings were suggestive of ypT3, ypN0, R0, and Grade 3 histological effect. The patient had a Grade A delayed gastric emptying post-operation. He was discharged 35 days after the surgery and has been alive without recurrence on imaging for 11 months post-operation.

Observation of Ciliary Body Changes during Accommodation Using Anterior OCT.

AIM: To evaluate the anatomical changes in the ciliary body (CB) during naturally stimulated accommodation in children using anterior segment optical coherence tomography (OCT). METHODS: This study was a prospective, observational, noncomparative case series included 18 eyes of 9 children (8 males and 1 female) aged from 4 to 10 years. Ciliary body thickness (CBT) was measured temporally by Anterior OCT at 1, 2 and 3 mm posterior to the scleral spur. Measurements were performed in the accommodated state and the unaccommodated state (with cycloplegia). RESULTS: The mean CBT significantly increased by accommodation at 1 mm posterior to the scleral spur from 751 42 to 818 40 µm (P 0.001) and significantly decreased at 2 and 3 mm from 506 66 to 445 59 µm and from 290 54 to 240 50 µm respectively (P 0.001). CONCLUSION: During accommodation, the anterior portion of the ciliary body thickens, while the posterior portion decreases in thickness. These findings imply that the circular ciliary muscles are mainly involved in accommodation and not the longitudinal muscles. J. Med. Invest. 65:60-63, February, 2018.

Air Bubble Technique for Fundus Visualization during Vitrectomy in Aphakia.

PURPOSE: To evaluate the efficacy and safety of air bubble technique for vitrectomy in aphakia. STUDY DESIGN: Prospective interventional uncontrolled case series. METHODS: This study included 53 eyes of 53 patients who are phakic and indicated for phacovitrectomy (7 eyes, group 1), aphakic and indicated for vitrectomy (22 eyes, group 2), or underwent unplanned vitrectomy for immediate management of a phacoemulsification surgery complicated by rupture posterior capsule with dropped nucleus, fragments, or IOL (24 eyes, group 3). Cases with complicated vitreoretinal pathology were not included in this study. All vitrectomy surgeries were conducted by the air bubble technique in the anterior chamber. Main outcomes included anatomical success, visual acuity, and intraoperative and postoperative complications. RESULTS: The surgical success was achieved in 50 eyes (94.3%). Conversion to BIOM viewing system was needed in the retinal detachment cases of groups 1 and 2. The mean overall LogMAR visual acuity was significantly improved from 1.29 ± 0.58 preoperatively to 0.56 ± 0.19 at the final visit, 6 months postoperatively (P < 0.001). CONCLUSION: The air bubble technique as visualization method for vitrectomy in aphakia is an effective and cheap technique for immediate management of complications of phacoemulsification surgery. This trial is registered with Pan African Clinical Trial Registry PACTR201709002466296.

Corneal topographic changes and surgically induced astigmatism following combined phacoemulsification and 25-gauge vitrectomy.

AIM: To evaluate corneal topographic changes and surgically induced astigmatism (SIA) after combined phacoemulsification and 25-gauge transconjunctival sutureless vitrectomy (25-G TSV). METHODS: A retrospective study on 96 eyes of 87 patients who underwent combined phacoemulsification and 25-G TSV. The different topographic parameters and SIA were analyzed pre- and postoperatively. RESULTS: There was no significant changes in corneal topographic parameters at different follow up periods. Only surface regularity index changed significantly in the 2nd postoperative week and then returned to baseline values thereafter. Mean SIA gradually decreased to reach 0.12 D by the 6th postoperative month. CONCLUSION: Corneal surface and astigmatic changes are insignificant in either early or late postoperative periods following combined phacoemulsification and 25-G TSV. The SIA was the minimum among previous reports on sutureless vitrectomy alone or combined with phacoemulsification. Improvement of SIA did not stop at the 3rd postoperative month but it continued till the 6th month postoperatively.

Secondary neuroendocrine tumor after allogeneic bone marrow transplantation.

Here we report a case of aggressive neuroendocrine tumor (NET), which is an extremely rare secondary solid tumor that occurs after allogeneic hematopoietic cell transplantation (allo-HSCT). A patient with chronic active Epstein-Barr virus infection received allo-HSCT from an HLA-DR two allele-mismatched unrelated donor. Four years later, he developed NET with multiple metastases. He received thoraco-abdominal irradiation as a conditioning regimen, and developed repeated episodes of intestinal graft-versus-host disease, for which he received long-term immunosuppressive therapy. Although these factors may be potential contributing factors to the development of secondary NET, the exact pathogenesis remains unclear.

Optical Coherence Tomography Reveals New Insights into the Accommodation Mechanism.

Purpose. To evaluate the movement of the anterior and posterior lens poles during naturally stimulated accommodation in children using anterior segment optical coherence tomography (OCT). Methods. This is a prospective, observational, noncomparative case series including 18 eyes of nine children. Analysis of the anterior segment in the accommodated and unaccommodated state (with cycloplegia) was done using anterior segment OCT. The main outcome measures were the position of the anterior and posterior lens poles (in relation to the cornea) and lens thickness (LT). Results. A Statistically significant forward movement of the anterior lens pole and backward movement of the posterior lens pole with an increase in LT were found during accommodation (P < 0.001). There was no significant difference between the degree of movement of the anterior lens pole and the posterior lens pole during accommodation (P = 0.944). Conclusions. Anterior segment OCT provides a rapid noncontact method for studying accommodation in children. The backward movement of the posterior lens pole during accommodation nearly equals the forward movement of its anterior pole. These data minimize the theoretical hydraulic effect of the vitreous during accommodation, adding more support to the capsular theory of Helmholtz.

Case of adult-onset Coats' disease with epiretinal membrane treated with 25-gauge pars plana vitrectomy.

We describe a case of untreated adult-onset Coats' disease with a proliferative epiretinal membrane (ERM) treated successfully with 25-gauge pars plana vitrectomy (25GPPV). A 26-year-old man presented with a 3-week history of decreased vision in his left eye. At the initial examination, the decimal best-corrected visual acuity (BCVA) was 0.7 in the left eye. Ophthalmoscopy revealed the typical appearance of Stage 2A Coats' disease but with a proliferative ERM in the posterior pole. The patient received 2 monthly intravitreal injections of 2.5 mg bevacizumab, 5 laser photocoagulations to the area of telangiectasia, and 1 session of cryoretinopexy. Nine months after the initial visit, a traction by the ERM on the parafoveal area developed causing macular edema which reduced the BCVA to 0.3. He underwent 25GPPV with the removal of the ERM. In addition, the peripheral telangiectasia was treated intraoperatively with both laser photocoagulation and cryoretinopexy. Postoperatively, the traction to the parafoveal area was released and the BCVA improved to 0.6 which remained stable during the follow-up period of 13 months. We conclude that 25GPPV combined with ERM peeling, laser photocoagulation, and cryoretinopexy can be effective for adult-onset Coats' disease associated with an ERM.

Expression of intraocular peroxisome proliferator-activated receptor gamma in patients with proliferative diabetic retinopathy.

AIMS: To determine whether peroxisome proliferator-activated receptor gamma (PPARγ), which is recognized as a component of the exosomes circulating in plasma, is expressed intraocularly in patients with proliferative diabetic retinopathy (PDR). METHODS: The concentrations of PPARγ and vascular endothelial growth factor (VEGF) in the aqueous humor and vitreous of 50 eyes with PDR and 38 control eyes were determined by ELISA. The levels of the mRNA and protein of PPARγ were determined in proliferative membranes from 12 PDR and 5 control eyes by quantitative RT-PCR and immunohistochemical analyses. RESULTS: PPARγ was detected in the culture media of human umbilical vein endothelial cells indicating that PPARγ can be released into the extracellular fluid. The PPARγ concentrations in the aqueous humor and vitreous fluid were significantly higher in PDR patients than in controls (P<0.0005). There was a significant positive correlation between the PPARγ and VEGF concentrations (P<0.0005). The level of PPARγ increased as the clinical stage advanced. The expressions of the mRNA and protein of PPARγ were higher in the membranes of PDR than those of controls. Anti-VEGF therapy significantly reduced the VEGF concentration (P<0.0001) but not the PPARγ concentration. CONCLUSIONS: PPARγ may play an important role in the pathogenesis of PDR.

Achromobacter buckle infection diagnosed by a 16S rDNA clone library analysis: a case report.

BACKGROUND: In clinical settings, bacterial infections are usually diagnosed by isolation of colonies after laboratory cultivation followed by species identification with biochemical tests. However, biochemical tests result in misidentification due to similar phenotypes of closely related species. In such cases, 16S rDNA sequence analysis is useful. Herein, we report the first case of an Achromobacter-associated buckle infection that was diagnosed by 16S rDNA sequence analysis. This report highlights the significance of Achromobacter spp. in device-related ophthalmic infections. CASE PRESENTATION: A 56-year-old woman, who had received buckling surgery using a silicone solid tire for retinal detachment eighteen years prior to this study, presented purulent eye discharge and conjunctival hyperemia in her right eye. Buckle infection was suspected and the buckle material was removed. Isolates from cultures of preoperative discharge and from deposits on the operatively removed buckle material were initially identified as Alcaligenes and Corynebacterium species. However, sequence analysis of a 16S rDNA clone library using the DNA extracted from the deposits on the buckle material demonstrated that all of the 16S rDNA sequences most closely matched those of Achromobacter spp. We concluded that the initial misdiagnosis of this case as an Alcaligenes buckle infection was due to the unreliability of the biochemical test in discriminating Achromobacter and Alcaligenes species due to their close taxonomic positions and similar phenotypes. Corynebacterium species were found to be contaminants from the ocular surface. CONCLUSIONS: Achromobacter spp. should be recognized as causative agents for device-related ophthalmic infections. Molecular species identification by 16S rDNA sequence analysis should be combined with conventional cultivation techniques to investigate the significance of Achromobacter spp. in ophthalmic infections.

Prepapillary vascular loops complicated by suspected macroaneurysm rupture.

We present a case of prepapillary vascular loops complicated by a suspected macroaneurysm rupture which was treated with intravitreal bevacizumab (IVB). A 62-year-old woman presented with decreased vision and myodesopsia in her left eye. Her best-corrected visual acuity (BCVA) was 0.6 in the left eye. Fundus examination disclosed an elevated, round, and reddish lesion, retinal hemorrhage at the superior aspect of the optic disc, retinal opacification along the superior branch retinal artery, and a small vitreous hemorrhage. Optical coherence tomography showed a serous retinal detachment, and indocyanine green angiography demonstrated prepapillary vascular loops and a hypofluorescent area with hyperfluorescent margins. These findings suggested the presence of a macroaneurysm. No filling of the dye in the aneurysm-like dilatation suggested a blockage of the lumen with a thrombus which might be associated with a branch retinal artery occlusion (BRAO). A diagnosis of prepapillary vascular loops complicated by a suspected macroaneurysm rupture and BRAO was made. Because of a persistent serous retinal detachment, IVB was performed. One month later, the BCVA improved to 1.0. Fundus examination disclosed an organized yellowish-white macroaneurysm and resolution of the serous retinal detachment. We recommend careful monitoring of patients with prepapillary vascular loops because of complications such as macroaneurysm rupture and BRAO.

Changes of fundus autofluorescence and spectral-domain optical coherence tomographic findings after treatment of primary intraocular lymphoma.

BACKGROUND: We report the fundus autofluorescence (FAF), spectral-domain optical coherence tomographic (SD-OCT), microperimetric, and multifocal electroretinographic (mfERG) findings before, during, and after successful treatment of a primary intraocular lymphoma (PIOL). FINDINGS: A 57-year-old man had biopsy-proven PIOL in his left eye, and he was treated with intravitreal methotrexate injections for 8 months. Before treatment, fundus examination disclosed many small, yellow lesions with distinct boundaries in the posterior fundus which became atrophic 9 months after the initial treatment. FAF showed a pattern of granular hypoautofluorescence and hyperautofluorescence before the treatments and patchy hypoautofluorescence corresponding to retinal pigment epithelial (RPE) atrophy after the treatments. SD-OCT showed increased nodularity at the level of and above the RPE, a separation of Bruch membrane from the RPE, partial damage of the RPE, disruption of the photoreceptor inner segment/outer segment (IS/OS) junction, multiple hyperreflective signals in the inner retina, foveal thinning, and parafoveal thickening. After treatment, the hyperreflective infiltrations in the inner retina were markedly decreased, and the RPE and IS/OS junction were restored. The foveal thinning and parafoveal thickening resolved, and the central choroidal thickness decreased. During the follow-up, the mfERGs remained decreased. In contrast, microperimetry showed a partial improvement of the retinal sensitivity. CONCLUSION: FAF and SD-OCT are useful noninvasive methods to evaluate the retinal and choroidal changes before and after treatment of PIOL. Our results suggest that visual recovery after successful treatment may be limited once macula is infiltrated.

Spectral-domain optical coherence tomographic and fundus autofluorescence findings in eyes with primary intraocular lymphoma.

BACKGROUND: The purpose of this study was to evaluate the findings on spectral-domain optical coherence tomography (SD-OCT) and fundus autofluorescence (FAF) in three eyes with primary intraocular lymphoma (PIOL). METHODS: The medical records of three eyes from three patients with biopsy-proven PIOL and retinal infiltrations were reviewed. The SD-OCT and fluorescein angiographic findings were evaluated in the three eyes and FAF images in two eyes. RESULTS: The PIOL in the three patients was monocular. Vitreous opacities and retinal infiltrations were observed in the three eyes, and iritis was present in two eyes. The cytologic diagnosis was class V in two eyes and class III in one eye. The interleukin-10/interleukin-6 ratio was >1.0 in the vitreous and aqueous humor of the three eyes. The FAF images for two eyes showed abnormal granular hyperautofluorescence and hypoautofluorescence which were the reverse of the pattern in the fluorescein angiographic images. In all three eyes, SD-OCT showed hyper-reflective infiltrations at the level of the retinal pigment epithelium (RPE), a separation of the Bruch membrane from the RPE, damage to the RPE, disruption of the photoreceptor inner segment/outer segment junction, and multiple hyper-reflective signals in the inner retina. CONCLUSION: Because of the characteristic FAF and SD-OCT findings in these eyes with PIOL, we suggest that these noninvasive methods may be used for a rapid diagnosis of PIOL and also for understanding the pathology of PIOL.

[A case of advanced gallbladder cancer with mediastinum lymph node metastasis successfully treated with multimodality therapy].

A 69 -year-old female with advanced gallbladder cancer underwent cholecystectomy, S4a/S5 segmentectomy of the liver, and resection of the extra-hepatic bile duct in October 2005. Adjuvant chemotherapy consisted of gemcitabine (GEM) and tegafururacil (UFT) administered consecutively. Four years after surgery, computed tomography revealed a single enlarged lymph node in the mediastinum, along with ¹8F-fluorodeoxyglucose accumulation and increased carcinoembryonic antigen (CEA) levels. Therefore, the mediastinal lymph node was considered to be a metastasis and GEM was readministered. Although the patient was treated with GEM for 1 year, the accumulation of 18F-fluorodeoxyglucose in the lymph node remained elevated. No other distant metastases were detected. Abronchoscopic biopsy histologically confirmed mucinous adenocarcinoma in the lymph node. Thus, the mediastinal lymph node was resected. Post-surgery, there was no evidence of recurrence during the 30-month follow up period without chemotherapy. Herein, we report a successful case of surgical treatment for solitary mediastinal lymph node metastasis of gallbladder cancer and review the relevant literature.

[A case report of complete pathological response of a locally advanced rectal cancer after long term chemotherapy].

A-39-year-old man presented to a nearby clinic owing to long-term diarrhea and painful defecation. He was diagnosed with a well-differentiated tubular adenocarcinoma of the rectosigmoid and underwent a laparotomy at another hospital. At surgery, the tumor was seen to deeply invade into the urinary bladder with the presence of intra-abdominal abscess. Loop sigmoid colostomy was performed due to possible invasion into the pelvic wall and peritoneal dissemination. The patient was referred to the our hospital for systemic chemotherapy. After 32 courses of FOLFIRI, 10 courses of CapeOX + Bmab, and 34 courses of LV5FU2 + Bmab, radiographic examination revealed complete response (CR) of the rectal tumor, and low anterior resection of the rectum was carried out. Since pathological examination showed no viable cancer cells in any specimen, the patient was considered to have achieved a CR from a pathological standpoint.