Automatic segmentation of inconstant fractured fragments for tibia/fibula from CT images using deep learning

Orthopaedic surgeons need to correctly identify bone fragments using 2D/3D CT images before trauma surgery. Advances in deep learning technology provide good insights into trauma surgery over manual diagnosis. This study demonstrates the application of the DeepLab v3+ -based deep learning model for the automatic segmentation of fragments of the fractured tibia and fibula from CT images and the results of the evaluation of the performance of the automatic segmentation. The deep learning model, which was trained using over 11 million images, showed good performance with a global accuracy of 98.92%, a weighted intersection over the union of 0.9841, and a mean boundary F1 score of 0.8921. Moreover, deep learning performed 5-8 times faster than the experts' recognition performed manually, which is comparatively inefficient, with almost the same significance. This study will play an important role in preoperative surgical planning for trauma surgery with convenience and speed.

Viral stimulation modulates endotype-related ACE2 expression in eosinophilic chronic rhinosinusitis

BACKGROUND

Angiotensin-converting enzyme 2 (ACE2), a receptor targeted by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), is highly expressed in the nasal mucosa. Chronic rhinosinusitis (CRS) shows diverse endotypes and is aggravated by viral infection. Whether viral stimulation and CRS endotype influence ACE2 expression remains unclear. We investigated the expression of ACE2 and the transmembrane protease, serine 2 (TMPRSS2), which mediate the entry of SARS-CoV-2 into cells, and assessed polyinosinic:polycytidylic acid (poly[I:C])-induced changes based on CRS endotype.

METHODOLOGY

ACE2 and TMPRSS2 expression was evaluated based on CRS phenotype, endotype, and tissue type. Correlations between ACE2/TMPRSS2 expression and inflammatory mediators in nasal polyps (NP) were examined. Air-liquid interface culture experiments were performed to assess the effects of major cytokines or poly(I:C) stimulation on ACE2/TMPRSS2 expression in primary epithelial cells from healthy nasal mucosa, eosinophilic NP (ENP), and non-eosinophilic NP (NENP).

RESULTS

In primary nasal epithelial cells, interleukin (IL)-13 decreased ACE2 expression but increased TMPRSS2. Eosinophilic CRS showed lower ACE2 expression than non-eosinophilic CRS, regardless of CRS phenotype. CRS endotype was an independent factor associated with ACE2/TMPRSS2 expression in NP. Serum and tissue eosinophilic marker levels were inversely correlated with ACE2 expression, whereas tissue neutrophilic marker levels and ACE2 expression were positively correlated in NP. ACE2 expression was suppressed in ENP tissues; however, a combination of poly(I:C) and IL-13 induced ACE2/TMPRSS2 upregulation in ENP.

CONCLUSIONS

ENP tissues have lower ACE2 expression than NENP; however, viral stimulation promotes ACE2/TMPRSS2 upregulation in ENP.

Phylogenetic placement of Cibicidoides wuellerstorfi (Schwager, 1866) from methane seeps and non-seep habitats on the Pacific margin

Benthic foraminifera are among the most abundant groups found in deep-sea habitats, including methane seep environments. Unlike many groups, no endemic foraminiferal species have been reported from methane seeps, and to our knowledge, genetic data are currently sparse for Pacific deep-sea foraminifera. In an effort to understand the relationships between seep and non-seep populations of the deep-sea foraminifera Cibicidoides wuellerstorfi, a common paleo-indicator species, specimens from methane seeps in the Pacific were analyzed and compared to one another for genetic similarities of small subunit rDNA (SSU rDNA) sequences. Pacific Ocean C. wuellerstorfi were also compared to those collected from other localities around the world (based on 18S gene available on Genbank, e.g., Schweizer et al., 2009). Results from this study revealed that C. wuellerstorfi living in seeps near Costa Rica and Hydrate Ridge are genetically similar to one another at the species level. Individuals collected from the same location that display opposite coiling directions (dextral and sinstral) had no species level genetic differences. Comparisons of specimens with genetic information available from Genbank (SSU rDNA) showed that Pacific individuals, collected for this study, are genetically similar to those previously analyzed from the North Atlantic and Antarctic. These observations provide strong evidence for the true cosmopolitan nature of C. wuellerstorfi and highlight the importance of understanding how these microscopic organisms are able to maintain sufficient genetic exchange to remain within the same species between seep and non-seep habitats and over global distances.

Prospective phase II trial of a combination of gemcitabine, cisplatin and UFT as first-line treatment in patients with advanced, unresectable, non-small cell lung carcinoma

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Background: Most patients with advanced non-small cell lung cancer (NSCLC) receive either single agents or doublet chemotherapy. For non-elderly patients in good performance status, platinum-based double combinations represent the standard treatment. And oral UFT had the survival advantage in adjuvant setting. Therefore we performed a phase II study using the combination of gemcitabine, cisplatin and UFT as a first line therapy in patients with advanced NSCLC. Methods: Eligible patients had histologically or cytologically confirmed stage IIIB or IV NSCLC with good performance status and were chemotherapy-naive. This study was two-stage design and planned number of patients was forty-seven. Gemcitabine (1,250 mg/m2, 10 mg/kg/min on days 1 and 8) and cisplatin (75 mg/m2 on day 1) were injected intravenously and UFT (400 mg/day) was administered orally on day 1–14. Treatment repeated every 3 weeks. Primary end point was overall response rate and secondary end points were overall survival, time to progression and toxicity. Results: Thirty seven patients with advanced NSCLC were enrolled. The median age of the patients was 60 years (range: 44 to 72). The performance status (WHO) was 0 in 4, 1 in 30 and 2 in 3 patients. Twenty three patients completed six cycles. Complete response was achieved in 1 (3%) patient, partial response in 22 (59%) patients, stable disease in 9 (24%) patients. Overall response rate was 62% on intent to treat basis. Among patients who response evaluation was possible (33 patients), response rate was 70%. The median survival time was 14.5 months (95% CI 6.9, 22.3) and the 1 year survival was 35% and then median time to progression was 3.4 months(95% CI 3, 3.9). Toxicities were moderate and mostly hematological adverse events. Grade 3/4 neutropenia occurred in 37%, 5 patients with febrile neutropenia. Grade 3/4 anemia and thrombocypenia was occurred in 37% and 5%. Nonhematologic toxicities were mild. Conclusion: The combination therapy consisted of gemcitabine, cisplatin and UFT is active and well tolerable first line regimen for NSCLC patients.

No significant financial relationships to disclose.

Identification of a C-terminal region that regulates mitogen-activated protein kinase kinase-1 cytoplasmic localization and ERK activation

The C-terminal region of mitogen-activated protein kinase kinase-1 and 2 (MKK1 and MKK2) may function in regulating interactions with upstream kinases or the magnitude and duration of ERK mitogen-activated protein kinase activity. The MKK C-terminal region contains a proline-rich region that reportedly functions in regulating interactions with the Raf-1 kinase and ERK activity. In addition, phosphorylation sites in the C terminus of MKK1 have been suggested to either sustain or attenuate MKK1 activity. To further understand how phosphorylation at the C terminus of MKK1 and protein interactions regulate MKK1 function, we have generated several MKK1 C-terminal deletion mutants and examined their function in regulating MKK1 localization, ERK protein activation, and cell growth. A deletion of C-terminal amino acids encompassing two putative alpha-helices between residues 330 and 379 caused a re-distribution of mutant MKK1 proteins to membrane compartments. Immunofluorescence analysis of MKK1 mutants revealed a loss of homogenous cytosolic distribution that is typically observed with MKK1 wild type, suggesting this region regulates MKK1 cellular localization. In contrast, MKK1 C-terminal deletion mutants localized to various sized punctate regions that overlapped with lysosome compartments. ERK activation in response to constitutively active Raf-1 or growth factor stimulus was attenuated in cells expressing MKK1 C-terminal deletion mutants. This could be partly explained by the inability of Raf-1 to phosphorylate MKK1 C-terminal deletion mutants even though the phosphorylation sites were intact in these mutants. Finally, we show that cells expressing MKK1 C-terminal deletion mutants displayed characteristic patterns of apoptotic cell death and reduced cell proliferation. These findings identify a novel C-terminal region between amino acid residues 330 and 379 on MKK1 that is necessary for regulating the cytoplasmic distribution and subsequent ERK protein activation necessary for cell survival and viability.

Rice non-specific lipid transfer protein: the 1.6 A crystal structure in the unliganded state reveals a small hydrophobic cavity

This study describes the high-resolution X-ray structure of the non-specific lipid transfer protein (ns-LTP) from rice seeds in the unliganded state. The model has been refined to a crystallographic R-factor of 0.186 for 8.0 to 1.6 A data (with Fo > 2 sigma F). It accounts for all 91 amino acid residues, 68 water molecules, one sulfate ion, and two molecules of 3-[cyclohexylamino]-1-propanesulfonic acid. The root-mean-square deviations from ideal bond lengths and angles are 0.017 A and 1.76 degrees, respectively. The overall fold of rice ns-LTP is very similar to that of maize ns-LTP. A superposition of 91 common C alpha atoms in rice and maize ns-LTPs, both in the unliganded state, gives a root-mean-square deviation of 1.2 A. Large structural differences from the crystal structure of maize ns-LTP are observed in two regions: the loop between two alpha-helices H1 and H2, where one residue deletion (Gln21 of maize sequence) occurs, and the C-terminal region around Tyr79. The C-terminal region of rice protein is somewhat collapsed into the hydrophobic cavity. As a consequence, its hydrophobic cavity is considerably smaller than that of maize protein (144 A3 versus 408 A3 for van der Waals cavity volumes), despite a high level of sequence identity (79%) between them. In the rice ns-LTP structure, the side-chain of Arg44 partially blocks the mouth of the cavity, while the side-chain of Ile81 effectively closes the other end by protruding into the cavity. And the side-chain of Tyr79 divides the cavity into two parts, with the larger part being shielded from the solvent. The present study illuminates the structure-function relationship of rice ns-LTP and allows a detailed structural comparison with other plant ns-LTPs.

Determination of the three-dimensional structure of hordothionin-alpha by nuclear magnetic resonance

The high-resolution three-dimensional solution structure of the plant toxin hordothionin-alpha obtained from korean barley was determined by using two-dimensional NMR techniques combined with distance geometry and restrained molecular dynamics. Experimentally derived restraints including 292 interproton distances from nuclear Overhauser effect measurements, 16 hydrogen bond restraints together with four disulphide bridge restraints were used as input to calculations of distance geometry and restrained molecular dynamics. Also included in the calculations were 36 phi and 17 chi 1 torsion angles obtained from 33JHN alpha and 3J alpha beta coupling constants in double quantum filtered COSY and primitive exclusive COSY experiments, respectively. The overall protein fold is similar to crambin and purothionin-alpha 1. Two alpha-helices running in opposite directions are found on the basis of 3JHN alpha and 3J alpha beta and deuterium exchange rates for backbone NH protons, and encompass residues 7-18 and 22-28. These two helices are connected by a turn and form a 'helix-turn-helix' motif. A short stretch of an anti-parallel beta-sheet exists between residues 1-4 and 31-34. the two protein termini of hordothionin-alpha are 'well-anchored'; the N-terminus of the protein is immobilized by this short beta-sheet whereas the C-terminus is 'pasted' to the carbonyl group of Cys-4 by a very stable hydrogen bond. The average root-mean-square differences for the backbone and heavy atoms after the restrained molecular dynamics calculations are 0.62 and 1.16 A respectively. These numbers represent a significant improvement over the corresponding values for the previous NMR structures of other thionins. The distance violation from the experimental interproton distances for the final structures is 0.14 for all atoms.