Hallucinating symmetric protein assemblies.

Deep learning generative approaches provide an opportunity to broadly explore protein structure space beyond the sequences and structures of natural proteins. Here, we use deep network hallucination to generate a wide range of symmetric protein homo-oligomers given only a specification of the number of protomers and the protomer length. Crystal structures of seven designs are very similar to the computational models (median root mean square deviation: 0.6 angstroms), as are three cryo-electron microscopy structures of giant 10-nanometer rings with up to 1550 residues and C33 symmetry; all differ considerably from previously solved structures. Our results highlight the rich diversity of new protein structures that can be generated using deep learning and pave the way for the design of increasingly complex components for nanomachines and biomaterials.

Cosmetic outcome of implantation of cross-linked human acellular dermal matrix after parotidectomy.

Although skin depression after parotidectomy affects the patient's satisfaction with cosmesis we know of little research about it, so we attempted to alleviate it by inserting human acellular dermal matrix (hADM) after the operation. We made a retrospective analysis of the casenotes of 63 patients who were diagnosed with parotid tumours and were operated on between January 2015 and December 2016. Factors that affect satisfaction with cosmesis, including the use of hADM, sex, age, incision, size of tumour, sample size, complications, and the name of the surgeon were recorded and evaluated on a scale from 1 (most unsatisfactory) to 10 (very satisfactory), and the satisfaction according to each factor was compared. The mean (SD) follow-up period was 13 (6) months, and 19 of the 63 patients developed complications. Satisfaction was significantly better when hADM had been inserted (p=0.0008), when the patient was female (p=0.033), or there were no complications p=0.0161). On linear regression analysis, all three factors showed a significant causal relation with satisfactory cosmesis. Insertion of hADM after operations on the parotid gland seems to be effective in improving this by preventing skin depression.

Procedural and obstetric outcomes after embryo reduction vs fetal reduction in multifetal pregnancy.

OBJECTIVE: To compare the obstetric outcome and incidence of procedure-related adverse events after embryo reduction (ER) vs fetal reduction (FR), in multifetal pregnancies undergoing reduction to twins or singletons. METHODS: We analyzed retrospectively data from multifetal pregnancies that underwent transvaginal ER (n = 181) at a mean gestational age of 7.6 weeks or transabdominal FR (n = 115) at a mean gestational age of 12.9 weeks between December 2006 and January 2017. FR was performed after a detailed fetal anomaly scan. The two groups were compared with respect to obstetric outcomes, such as incidence of miscarriage, early or late preterm delivery, maternal complications and fetal loss, and procedure-related adverse events, including incidence of subchorionic hematoma and procedure-related fetal loss. RESULTS: Compared with pregnancies that underwent ER, the incidence of procedure-related fetal loss was lower in the FR group (7.2% vs 0.9%; P = 0.039; odds ratio (OR), 0.12; 95% CI, 0.02-0.89). Mean gestational age at delivery for twins was 34.2 weeks in the ER group and 35.7 weeks in the FR group (P = 0.014). Compared with the ER group, the FR group had lower miscarriage (8.8% vs 2.6%; P = 0.045; OR, 0.28; 95% CI, 0.08-0.97) and overall fetal loss (13.3% vs 5.2%; P = 0.031; OR, 0.36; 95% CI, 0.14-0.91) rates. CONCLUSIONS: The FR procedure is, overall, a better and safer approach to reducing morbidity and mortality in multifetal pregnancies. Spontaneous demise of one fetus may occur after ER, and FR has the advantage that chorionic villus sampling and ultrasound screening for increased nuchal translucency and anatomical defects can be conducted before the procedure. The ER approach is still reasonable when a patient's religious or other ethical concerns are of primary importance. Copyright © 2018 ISUOG. Published by John Wiley & Sons Ltd.

Role of HSPA1L as a cellular prion protein stabilizer in tumor progression via HIF-1α/GP78 axis.

The cellular prion protein (PrPC) is associated with metastasis, tumor progression and recurrence; however, the precise mechanisms underlying its action is not well understood. Our study found that PrPC degradation decreased tumor progression in colorectal cancer (CRC). In a CRC cell line and human CRC tissue exposed to hypoxia, induced heat-shock 70-kDa protein-1-like (HSPA1L) expression stabilized hypoxia-inducible factor-1α (HIF-1α) protein and promoted PrPC accumulation and tumorigenicity in vivo. PrPC was degraded via the proteasome pathway mediated by the ubiquitin-protein E3 ligase glycoprotein 78 (GP78), which interacts directly with PrPC. However, hypoxia-induced HSPA1L interacted with GP78 and inhibited its functions. HSPA1L knockdown facilitated the interaction of GP78 and PrPC, thereby increasing PrPC ubiquitination. Thus, GP78 was identified as the ubiquitinase for PrPC, thereby revealing an essential mechanism that controls PrPC levels in CRC. Our results suggest that the HSPA1L/HIF-1α/GP78 axis has a crucial role in PrPC accumulation during tumor progression.

A validated web-based tool to display individualised Crohn's disease predicted outcomes based on clinical, serologic and genetic variables.

BACKGROUND: Early treatment for Crohn's disease (CD) with immunomodulators and/or anti-TNF agents improves outcomes in comparison to a slower 'step up' algorithm. However, there remains a limited ability to identify those who would benefit most from early intensive therapy. AIM: To develop a validated, individualised, web-based tool for patients and clinicians to visualise individualised risks for developing Crohn's disease complications. METHODS: A well-characterised cohort of adult patients with CD was analysed. Available data included: demographics; clinical characteristics; serologic immune responses; NOD2 status; time from diagnosis to complication; and medication exposure. Cox proportional analyses were performed to model the probability of developing a CD complication over time. The Cox model was validated externally in two independent CD cohorts. Using system dynamics analysis (SDA), these results were transformed into a simple graphical web-based display to show patients their individualised probability of developing a complication over a 3-year period. RESULTS: Two hundered and forty three CD patients were included in the final model of which 142 experienced a complication. Significant variables in the multivariate Cox model included small bowel disease (HR 2.12, CI 1.05-4.29), left colonic disease (HR 0.73, CI 0.49-1.09), perianal disease (HR 4.12, CI 1.01-16.88), ASCA (HR 1.35, CI 1.16-1.58), Cbir (HR 1.29, CI 1.07-1.55), ANCA (HR 0.77, CI 0.62-0.95), and the NOD2 frameshift mutation/SNP13 (HR 2.13, CI 1.33-3.40). The Harrell's C (concordance index for predictive accuracy of the model) = 0.73. When applied to the two external validation cohorts (adult n = 109, pediatric n = 392), the concordance index was 0.73 and 0.75, respectively, for adult and pediatric patients. CONCLUSIONS: A validated, web-based tool has been developed to display an individualised predicted outcome for adult patients with Crohn's disease based on clinical, serologic and genetic variables. This tool can be used to help providers and patients make personalised decisions about treatment options.

Reliability of tumour grade 1 and endometrioid cell type on preoperative endometrial biopsy.

The aim of this study was to evaluate the reliability of using tumour grade and cell type on preoperative endometrial biopsy for the selection of patients for conservative hormone treatment. We retrospectively reviewed results of 643 patients with endometrial carcinoma for tumour grade and 817 for tumour cell type who underwent endometrial biopsy followed by surgery. Of the 357 patients with a grade 1 tumour on preoperative endometrial biopsy, 58 (16.2%) were upgraded based on a final pathology report from hysterectomy specimens. For grade 1, the preoperative endometrial biopsy showed a sensitivity of 80.4%, a specificity of 78.6%, a positive predictive value (PPV) of 83.8% and a negative predictive value (NPV) of 74.5%. Of the 672 patients with the endometrioid cell type on preoperative biopsy, 46 (5.6%) showed a different cell type on final pathology. For the endometrioid cell type, preoperative endometrial biopsy had a sensitivity of 91.3%, a specificity of 64.9%, a PPV of 93.2% and an NPV of 58.6%. This weak predictive value should be considered when selecting patients for conservative hormone treatment.

Nitric oxide induces apoptosis in human gingival fibroblast through mitochondria-dependent pathway and JNK activation.

AIM: To investigate the molecular mechanisms of nitric oxide (NO)-induced cytotoxic effect in human gingival fibroblast (HGF) cells. METHODOLOGY: After sodium nitroprusside (SNP), as NO donor, was treated to HGF, viability was measured by MTT assay and apoptosis was determined by TUNEL and DNA fragmentation assay. Mitochondrial membrane potential was detected using confocal microscopy, and caspase activity assay was measured by spectrophotometer. Mitogen-activated protein kinases (MAPK) activation, Bax/Bcl-2 ratio and cytochrome c release were analysed by Western blot analyses. Cells were exposed to MAPK inhibitors (U0126, SB203580 and SP600125) before SNP treatment to investigate the effects of MAPK kinases on the NO-induced apoptosis in HGF. Statistical analysis was performed using one-way analysis of variance with the Student-Newman-Keuls post hoc test for multiple group comparison. RESULTS: Apoptosis was significantly increased (P = 0.011 and 0.0004, respectively) in the presence of SNP (1 and 3 mmol L(-1) ) after 12 h in HGF. However, 1H-[1,2,4] oxadiatolo [4, 3-a] cluinoxaline-1-one (ODQ), a soluble guanylate cyclase inhibitor, did not block the decrement of cell viability by NO. SNP treatment induced the loss of mitochondrial membrane potential, release of cytochrome c, increased Bax/Bcl-2 ratio and activation of caspases in HGF. Also, SNP treatment increased phosphorylation of MAPKinases and c-Jun N-terminal kinase (JNK) inhibitor (5 and 10 µmol L(-1) ) rescued cell viability decreased by SNP in HGF (P = 0.024 and 0.0149, respectively). CONCLUSION: Nitric oxide induced apoptosis in human gingival fibroblast through the mitochondria-mediated pathway by regulation of Bcl-2 family and JNK activation.

Rearrangement of a large novel Pseudomonas aeruginosa gene island in strains isolated from a patient developing ventilator-associated pneumonia.

Bacterial gene islands add to the genetic repertoire of opportunistic pathogens. Here, we perform comparative analyses of three Pseudomonas aeruginosa strains isolated sequentially over a 3-week period from a patient with ventilator-associated pneumonia (VAP) who received clindamycin and piperacillin-tazobactam as part of their treatment regime. While all three strains appeared to be clonal by standard pulsed-field gel electrophoresis, whole-genome sequencing revealed subtle alterations in the chromosomal organization of the last two strains; specifically, an inversion event within a novel 124-kb gene island (PAGI 12) composed of 137 open reading frames [ORFs]. Predicted ORFs in the island included metabolism and virulence genes. Overexpression of a gene island-borne putative ß-lactamase gene was observed following piperacillin-tazobactam exposure and only in those strains that had undergone the inversion event, indicating altered gene regulation following genomic remodeling. Examination of a separate cohort of 76 patients with VAP for integration at this tRNA(lys) recombination site demonstrated that patients exhibiting evidence of integration at this site had significantly higher 28-day mortality. These findings provide evidence that P. aeruginosa can integrate, rapidly remodel, and express exogenous genes, which likely contributes to its fitness in a clinical setting.

Two cases of nasopharyngeal branchial cleft cyst treated by powered instrument assisted marsupialisation.

OBJECTIVE: We report two extremely rare cases of symptomatic nasopharyngeal branchial cleft cyst treated by powered instrument assisted marsupialisation. METHODS: Case report and literature review concerning nasopharyngeal branchial cleft cyst and surgical treatment methods. RESULTS: The first case was a two-year-old boy with a 1 × 2 cm, cystic, oropharyngeal mass, who also had severe snoring and sleep apnoea. The second case was a 56-year-old man with right nasal obstruction and a sensation of fullness in the right ear. In both cases, we performed endoscopic marsupialisation using a powered instrument. There was no recurrence in either case over two years of follow up. CONCLUSION: Powered instrument marsupialisation is a simple, effective and less invasive technique for the treatment of nasopharyngeal branchial cleft cyst.

Massive epistaxis due to pseudoaneurysm of the sphenopalatine artery: a rare post-operative complication of orthognathic surgery.

OBJECTIVE: To introduce pseudoaneurysm of the sphenopalatine artery as the possible aetiology of acute massive epistaxis in patients with a history of orthognathic surgery accompanied by Le Fort I osteotomy. METHODS: Case report and literature review. RESULTS: This paper reports a case of acute life-threatening epistaxis following Le Fort I osteotomy. Computed tomography and angiography showed a pseudoaneurysm of the sphenopalatine artery, which was successfully treated by endovascular embolisation. CONCLUSION: Although a pseudoaneurysm of the sphenopalatine artery following Le Fort I osteotomy is extremely rare, it should be considered as the possible aetiology of acute massive epistaxis in patients with a history of orthognathic surgery accompanied by Le Fort I osteotomy.

Development of genetic markers in abalone through construction of a SNP database.

In the absence of a reference genome, single-nucleotide polymorphisms (SNP) discovery in a group of abalone species was undertaken by random sequence assembly. A web-based interface was constructed, and 11 932 DNA sequences from the genus Haliotis were assembled, with 1321 contigs built. Of these, 118 contigs that consisted of at least ten annotation groups were selected. The 1577 putative SNPs were identified from the 118 contigs, with SNPs in several HSP70 gene contigs confirmed by PCR amplification of an 809-bp DNA fragment. SNPs in the HSP70 gene were compared across eight abalone species. A total of 129 polymorphic sites, including heterozygote sites within and among species, were observed. Phylogenetic analysis of the partial HSP70 gene region showed separation of the tested abalone into two groups, one reflecting the southern hemisphere species and the other the northern hemisphere species. Interestingly, Haliotis iris from New Zealand showed a closer relationship to species distributed in the northern Pacific region. Although HSP genes are known to be highly conserved among taxa, the validation of polymorphic SNPs from HSP70 in this mollusc demonstrates the applicability of cross-species SNP markers in abalone and the first step towards universal nuclear markers in Haliotis.

Alternative salvage technique during postcardiotomy electrical storm.

Cardiac electrical storm is generally treated with antiarrhythmic drugs, electrical cardioversion, or catheter ablation. However, these conservative treatment modalities are considered neither curative nor preventive with regard to recurrent arrhythmias in postoperative electrical storm after open heart surgery. We present a case of surgical ventricular assist device placement for postcardiotomy electrical storm in a 38-year-old patient.

Secretion of Pseudomonas aeruginosa type III cytotoxins is dependent on pseudomonas quinolone signal concentration.

Pseudomonas aeruginosa is an opportunistic pathogen that can, like other bacterial species, exist in antimicrobial resistant sessile biofilms and as free-swimming, planktonic cells. Specific virulence factors are typically associated with each lifestyle and several two component response regulators have been shown to reciprocally regulate transition between biofilm-associated chronic, and free-swimming acute infections. Quorum sensing (QS) signal molecules belonging to the las and rhl systems are known to regulate virulence gene expression by P. aeruginosa. However the impact of a recently described family of novel quorum sensing signals produced by the Pseudomonas Quinolone Signal (PQS) biosynthetic pathway, on the transition between these modes of infection is less clear. Using clonal isolates from a patient developing ventilator-associated pneumonia, we demonstrated that clinical observations were mirrored by an in vitro temporal shift in isolate phenotype from a non-secreting, to a Type III cytotoxin secreting (TTSS) phenotype and further, that this phenotypic change was PQS-dependent. While intracellular type III cytotoxin levels were unaffected by PQS concentration, cytotoxin secretion was dependent on this signal molecule. Elevated PQS concentrations were associated with inhibition of cytotoxin secretion coincident with expression of virulence factors such as elastase and pyoverdin. In contrast, low concentrations or the inability to biosynthesize PQS resulted in a reversal of this phenotype. These data suggest that expression of specific P. aeruginosa virulence factors appears to be reciprocally regulated and that an additional level of PQS-dependent post-translational control, specifically governing type III cytotoxin secretion, exists in this species.

Spontaneous basal cell carcinoma in a 7-week-old Sprague-Dawley rat.

Spontaneous basal cell carcinoma (BCC) is very rare in rats, with an incidence rate of only 0.14% reported in aged animals. A spontaneous BCC occurred in a 7-week-old Sprague-Dawley rat housed in a specific-pathogen-free animal facility. The tumor was a single, well-delineated reddish-brown subcutaneous mass measuring 2 x 2 cm and located in the left inguinal region. Microscopically, the tumor consisted of basaloid cells in lobular and cribriform growth patterns and with a high mitotic rate. Immunohistochemically, cytokeratin 14 (an indicator for basal keratinocytes of the epidermis) showed strong reactions throughout the whole tumor, and cytokeratin 18 showed weak but positive reaction in the majority of nested tumor cells. To the authors' knowledge, this is the first report of spontaneous BCC occurrence in young Sprague-Dawley rats.

Clinical features and management of facial nerve paralysis in children: analysis of 24 cases.

OBJECTIVES: To evaluate the causes, treatment modalities and recovery rate of paediatric facial nerve paralysis. MATERIALS AND METHODS: We analysed 24 cases of paediatric facial nerve paralysis diagnosed in the otolaryngology department of Gachon University Gil Medical Center between January 2001 and June 2006. RESULTS: The most common cause was idiopathic palsy (16 cases, 66.7 per cent). The most common degree of facial nerve paralysis on first presentation was House-Brackmann grade IV (15 of 24 cases). All cases were treated with steroids. One of the 24 cases was also treated surgically with facial nerve decompression. Twenty-two cases (91.6 per cent) recovered to House-Brackmann grade I or II over the six-month follow-up period. CONCLUSION: Facial nerve paralysis in children can generally be successfully treated with conservative measures. However, in cases associated with trauma, radiological investigation is required for further evaluation and treatment.

Pressure dressing after excision of preauricular sinus: suture transfixion of silicone sheets.

OBJECTIVE: After excision of a preauricular sinus, a head bandage compressive dressing is usually used to reduce dead space and to decrease the risk of recurrence. However, such use of a head bandage may cause various problems. We assessed a new method of compressive dressing, using suture transfixion of silicone sheets to the former sinus tract, following preauricular sinus excision. METHODS: This retrospective study reviewed the medical records of patients undergoing preauricular sinus excision in a tertiary referral centre over a five-year period. After excision of the preauricular sinus, patients underwent suture transfixion of silicone sheets. Post-operative outcomes were analysed. RESULTS: The new dressing method was performed on 50 ears of 37 patients. The post-operative incidence of recurrence and haematoma formation was 4 and 2 per cent, respectively. Other problems possibly caused by head bandaging, such as headache, facial flushing, and nausea and/or vomiting, were not observed. CONCLUSION: Compressive dressing by suture transfixion of silicone sheets is safe and effective following preauricular sinus excision.

Gastric lesions and immune responses caused by long-term infection with Helicobacter heilmannii in C57BL/6 mice.

Helicobacter heilmannii is a gastric micro-organism that can induce gastritis and B-cell MALT (mucosa-associated lymphoid tissue) lymphoma in mice, in a host-dependent manner. The present study was designed to examine gastric lesions and immune responses caused by intragastric H. heilmannii infection of an inbred mouse strain, C57BL/6. Long-term infection led to the formation of gastric nodules and increased mucosal thickness of the stomach, due to gastric epithelial proliferation. Infection also induced the formation of lymphoid follicles in the corpus mucosa and submucosa. The follicular cells were mainly CD45R+ cells that did not produce immunoglobulin. However, scattered in the lamina propria and corpus submucosa, numerous IgA+ cells were found in infected mice, but not in control mice. RT-PCR results showed that H. heilmannii infection led to increased mRNA expression for IFN-gamma (a Th1 cytokine) and IL-10 (a Th2 cytokine) in the mouse stomach, suggesting that both Th1 and Th2 responses are associated with H. heilmannii infection. The mRNA of other cytokines and chemokines (IL-1beta, IL-12p40, TNF-alpha, MCP-1, KC and MIP-2) was also increased by infection.

Detection of SNPs in porcine haptoglobin and apolipoprotein genes.

To find differentially expressed protein spots using two-dimensional electrophoresis proteomic analysis, we took blood serum samples from 40 purebred Yorkshire pigs at 12, 18, 24, and 30 weeks. Each growth stage contained 10 male pigs having half-sib pedigrees. With the pooled serum samples, two interesting spots, differentially expressed in the growth stages, were identified using MALDI-TOF-TOF MS/MS analysis as haptoglobin alpha 1S (Hp) and apolipoprotein A-IV (APOA4) gene products. The Hp was down-regulated from 12 to 30 weeks, and APOA4 was not expressed much before 18 weeks but was highly expressed in the late growth stages. There may be an inverse relationship between the Hp and APOA4 genes. Four segments for the Hp and APOA4 genes were successfully amplified with sizes around 500 bp. The porcine Hp and APOA4 genes were screened in the 40 purebred Yorkshire pigs and a random cross population (90 pigs), resulting in the location of 6 single nucleotide polymorphisms (SNPs) in the coding regions. The mutations resulted in amino acid changes in segments of Hp627, Hp742, and APOA41203. Further investigation of the function of the Hp and APOA4 genes with SNPs will be necessary to understand fully the different expression profiles and association studies.

Age-and region-dependent changes in three-dimensional microstructural properties of proximal femoral trabeculae.

UNLABELLED: This study investigated regional variations in the 3D microstructure of trabecular bone in human proximal femur, with respect to aging. The results demonstrate that age-related changes in trabecular microstructure significantly varied from different sub-regions of the proximal femur. INTRODUCTION: We hypothesize that the age-related changes in trabecular bone microstructure appear to be varied from specific anatomic sub-regions of the proximal femur followed by non-uniform bone loss. The purpose of this study was therefore to explore regional variations in the 3D microstructure of trabecular bone in human proximal femur, with respect to aging. METHODS: A total of 162 trabecular bone cores from six regions of 27 femora of male cadaver donors were scanned using micro-computed tomography (micro-CT). The following microstructural parameters were calculated: bone volume fraction (BV/TV), trabecular number (Tb.N), thickness (Tb.Th) and separation (Tb.Sp), structure model index (SMI), and degree of anisotropy (DOA). RESULTS: Age-related changes in trabecular microstructure varied from different regions of the proximal femur. There was a significant decrease in bone volume fraction and an almost identical decrease in trabecular thickness associated with aging at any region. Regional analysis demonstrated a significant difference in BV/TV, Tb.Th, Tb.Sp, Tb.N and DOA between superior and inferior neck, as well as a significant difference in BV/TV, Tb.Sp, Tb.N, SMI and DOA between superior and inferior trochanter. CONCLUSIONS: Age-related changes in bone loss and trabecular microstructure within the male proximal femur are not uniform in this cadaveric population.