SAFARI: shape analysis for AI-segmented images.

BACKGROUND: Recent developments to segment and characterize the regions of interest (ROI) within medical images have led to promising shape analysis studies. However, the procedures to analyze the ROI are arbitrary and vary by study. A tool to translate the ROI to analyzable shape representations and features is greatly needed. RESULTS: We developed SAFARI (shape analysis for AI-segmented images), an open-source R package with a user-friendly online tool kit for ROI labelling and shape feature extraction of segmented maps, provided by AI-algorithms or manual segmentation. We demonstrated that half of the shape features extracted by SAFARI were significantly associated with survival outcomes in a case study on 143 consecutive patients with stage I-IV lung cancer and another case study on 61 glioblastoma patients. CONCLUSIONS: SAFARI is an efficient and easy-to-use toolkit for segmenting and analyzing ROI in medical images. It can be downloaded from the comprehensive R archive network (CRAN) and accessed at https://lce.biohpc.swmed.edu/safari/ .

Empirical likelihood inference for area under the receiver operating characteristic curve using ranked set samples.

The area under a receiver operating characteristic curve (AUC) is a useful tool to assess the performance of continuous-scale diagnostic tests on binary classification. In this article, we propose an empirical likelihood (EL) method to construct confidence intervals for the AUC from data collected by ranked set sampling (RSS). The proposed EL-based method enables inferences without assumptions required in existing nonparametric methods and takes advantage of the sampling efficiency of RSS. We show that for both balanced and unbalanced RSS, the EL-based point estimate is the Mann-Whitney statistic, and confidence intervals can be obtained from a scaled chi-square distribution. Simulation studies and two case studies on diabetes and chronic kidney disease data suggest that using the proposed method and RSS enables more efficient inference on the AUC.

Using Hybrid Organic-Inorganic Surface Technology to Mitigate Analyte Interactions with Metal Surfaces in UHPLC.

Interactions of analytes with metal surfaces in high-performance liquid chromatography (HPLC) instruments and columns have been reported to cause deleterious effects ranging from peak tailing to a complete loss of the analyte signal. These effects are due to the adsorption of certain analytes on the metal oxide layer on the surface of the metal components. We have developed a novel surface modification technology and applied it to the metal components in ultra-HPLC (UHPLC) instruments and columns to mitigate these interactions. A hybrid organic-inorganic surface, based on an ethylene-bridged siloxane chemistry, was developed for use with reversed-phase and hydrophilic interaction chromatography. We have characterized the performance of UHPLC instruments and columns that incorporate this surface technology and compared the results with those obtained using their conventional counterparts. We demonstrate improved performance when using the hybrid surface technology for separations of nucleotides, a phosphopeptide, and an oligonucleotide. The hybrid surface technology was found to result in higher and more consistent analyte peak areas and improved peak shape, particularly when using low analyte mass loads and acidic mobile phases. Reduced abundances of iron adducts in the mass spectrum of a peptide were also observed when using UHPLC systems and columns that incorporate hybrid surface technology. These results suggest that this technology will be particularly beneficial in UHPLC/mass spectrometry investigations of metal-sensitive analytes.

Highly Efficient Photo- and Electroluminescence from Two-Coordinate Cu(I) Complexes Featuring Nonconventional N-Heterocyclic Carbenes.

A series of six luminescent two-coordinate Cu(I) complexes were investigated bearing nonconventional N-heterocyclic carbene ligands, monoamido-aminocarbene (MAC*) and diamidocarbene (DAC*), along with carbazolyl (Cz) as well as mono- and dicyano-substituted Cz derivatives. The emission color can be systematically varied over 270 nm, from violet to red, through proper choice of the acceptor (carbene) and donor (carbazolyl) groups. The compounds exhibit photoluminescent quantum efficiencies up to 100% in fluid solution and polystyrene films with short decay lifetimes (τ ≈ 1 µs). The radiative rate constants for the Cu(I) complexes ( kr = 105-106 s-1) are comparable to state of the art phosphorescent emitters with noble metals such as Ir and Pt. All complexes show strong solvatochromism due to the large dipole moment of the ground states and the transition dipole moment that is in the opposite direction. Temperature-dependent studies of (MAC*)Cu(Cz) reveal a small energy separation between the lowest singlet and triplet states (Δ ES1-T1 = 500 cm-1) and an exceptionally large zero-field splitting (ZFS = 85 cm-1). Organic light-emitting diodes (OLEDs) fabricated with (MAC*)Cu(Cz) as a green emissive dopant have high external quantum efficiencies (EQE = 19.4%) and brightness of 54 000 cd/m2 with modest roll-off at high currents. The complex can also serve as a neat emissive layer to make highly efficient OLEDs (EQE = 16.3%).

"Quick-Silver" from a Systematic Study of Highly Luminescent, Two-Coordinate, d10 Coinage Metal Complexes.

A systematic study is presented on the physical and photophysical properties of isoelectronic and isostructural Cu, Ag, and Au complexes with a common amide (N-carbazolyl) and two different carbene ligands (i.e., CAAC = (5 R,6 S)-2-(2,6-diisopropylphenyl)-6-isopropyl-3,3,9-trimethyl-2-azaspiro[4.5]decan-2-ylidene, MAC = 1,3-bis(2,6-diisopropylphenyl)-5,5-dimethyl-4-keto-tetrahydropyridylidene). The crystal structures of the (carbene)M(I)(N-carbazolyl) (MCAAC) and (MAC)M(I)(N-carbazolyl) (MMAC) complexes show coplanar carbene and carbzole ligands and C-M-N bond angles of ∼180°. The electrochemical properties and energies for charge transfer (CT) absorption and emission compounds are not significantly affected by the choice of metal ion. All six of the (carbene)M(Cz) complexes examined here display high photoluminescence quantum yields of 0.8-1.0. The compounds have short emission lifetimes (τ = 0.33-2.8 µs) that fall in the order Ag < Au < Cu, with the lifetimes of (carbene)Ag(Cz) roughly a factor of 10 shorter than for (carbene)Cu(Cz) complexes. Detailed temperature-dependent photophysical measurements (5-325 K) were carried out to determine the singlet and triplet emission lifetimes (τfl and τph, respectively) and the energy difference between the singlet and triplet excited state, Δ ES1-T1. The τfl values range between 20 and 85 ns, and the τph values are in the 50-200 µs regime. The emission at room temperature is due exclusively to E-type delayed fluorescence or TADF (i.e., T1→ΔS1→S0+hν ). The emission rate at room temperature is fully governed by Δ ES1-T1, with the silver complexes giving Δ ES1-T1 values of 150-180 cm-1 (18-23 meV), whereas the gold and copper complexes give values of 570-590 cm-1 (70-73 meV).

PTK7 regulates radioresistance through nuclear factor-kappa B in esophageal squamous cell carcinoma.

Tumor radioresistance is a major reason for decreased efficiency of cancer radiation therapy. Although a number of factors involved in radioresistance have been identified, the molecular mechanisms underlying radioresistance of esophageal squamous cell carcinoma (ESCC) have not been elucidated. In this study, we investigated the role of oncogenic protein tyrosine kinase 7 (PTK7) in the resistance of ESCC to radiation therapy. ESCC cell lines with high PTK7 expression were more refractive to radiation than those with low PTK7 levels. In radioresistant ESCC cells, PTK7 knockdown by specific siRNAs decreased the survival of irradiated cells and increased radiation-induced apoptosis, while in radiosensitive ESCC cells, PTK7 overexpression promoted cell survival and inhibited radiation-induced apoptosis. We hypothesized that PTK7 could regulate the activation of transcription factor NF-kB known for its role in cancer radioresistance. Our results indicated that the inhibition of PTK7 suppressed nuclear translocation of NF-kB subunit p65 induced by radiation, suggesting relevance of PTK7 expression with NF-kB activation in radioresistant ESCC. Furthermore, the levels of inhibitor of apoptosis proteins (IAPs), XIAP, and survivin, encoded by NF-kB-regulated genes, were induced in irradiated radioresistant cells but not in radiosensitive cells, while PTK7 knockdown downregulated IAP expression. Our findings revealed a novel mechanism underlying radioresistance in ESCC, which is associated with PTK7 and NF-kB-dependent apoptosis. These results suggest that the manipulation of PTK7 expression can be instrumental in enhancing ESCC response to radiotherapy. This study demonstrates that PTK7 plays a significant role in ESCC radioresistance via the NF-kB pathway.

Epigenetic regulation of the novel tumor suppressor cysteine dioxygenase 1 in esophageal squamous cell carcinoma.

Esophageal squamous cell carcinoma (ESCC), the most common subtype of esophageal cancer in East Asian countries, is still associated with a poor prognosis because of the high frequency of lymph node metastasis and invasion. In our previous study, we identified a novel methylation gene, cysteine dioxygenase 1 (CDO1) that is involved in the conversion of cysteine to cysteine sulfinate, and plays a key role in taurine biosynthesis. Decreased expression of CDO1 was observed in ESCC cell lines and tumors derived from patient tissues, and CDO1 silencing could be reversed by treatment with 5-aza-2'-deoxycytidine in six ESCC cell lines. Forced expression of CDO1 in three different ESCC cell lines, TE-4, TE-6, and TE-14, significantly decreased tumor cell growth, cell migration, invasion, and the ability of colony formation. Although CDO1 expression was not found to significantly correlate with survival in ESCC patients, our results suggest that methylation-regulated CDO1 may represent a functional tumor suppressor and a potentially valuable diagnostic biomarker for ESCC.

Modulation of Spinal GABAergic Inhibition and Mechanical Hypersensitivity following Chronic Compression of Dorsal Root Ganglion in the Rat.

Chronic compression of dorsal root ganglion (CCD) results in neuropathic pain. We investigated the role of spinal GABA in CCD-induced pain using rats with unilateral CCD. A stereological analysis revealed that the proportion of GABA-immunoreactive neurons to total neurons at L4/5 laminae I-III on the injured side decreased in the early phase of CCD (post-CCD week 1) and then returned to the sham-control level in the late phase (post-CCD week 18). In the early phase, the rats showed an increase in both mechanical sensitivity of the hind paw and spinal WDR neuronal excitability on the injured side, and such increase was suppressed by spinally applied muscimol (GABA-A agonist, 5 nmol) and baclofen (GABA-B agonist, 25 nmol), indicating the reduced spinal GABAergic inhibition involved. In the late phase, the CCD-induced increase in mechanical sensitivity and neuronal excitability returned to pre-CCD levels, and such recovered responses were enhanced by spinally applied bicuculline (GABA-A antagonist, 15 nmol) and CGP52432 (GABA-B antagonist, 15 nmol), indicating the regained spinal GABAergic inhibition involved. In conclusion, the alteration of spinal GABAergic inhibition following CCD and leading to a gradual reduction over time of CCD-induced mechanical hypersensitivity is most likely due to changes in GABA content in spinal GABA neurons.

Clinical characteristics of acute kidney injury in patients with scrub typhus--RIFLE criteria validation.

There are limited data available on the validity of the RIFLE classification for AKI in patients with scrub typhus. We investigated the incidence and clinical characteristics of scrub typhus associated AKI using the RIFLE criteria. From 2010 to 2012, 238 patients were diagnosed with scrub typhus. Of these, we included 223 patients who were followed up until renal recovery or for at least three months. We evaluated the incidence, clinical characteristics, and severity of AKI based on the RIFLE classification. Of the 223 patients, 47 (21%) had scrub typhus-associated AKI. The incidence of AKI was 21.1%; of which, 10.7%, 9.4% and 1% were classified as Risk, Injury and Failure, respectively. In comparison with patients in the non-AKI group, the patients in the AKI group were older (70 ± 9 vs 61 ± 14 year, P = 0.01) and had one or more comorbidities such as hypertension, diabetes, and chronic kidney disease (77% vs 22%, p = 0.01). In the AKI group, forty-four patients had AKI prior to admission, and three patients experienced AKI during their hospitalization. By multivariate logistic regression analysis, age and comorbidity were significant predictors of AKI. All patients recovered baseline renal function without renal replacement therapy following antibiotics therapy and supportive care. The incidence of AKI in patient with scrub typhus is 21%. Age and co-morbidity are significant predictors of AKI in scrub typhus. In cases of scrub typhus-associated AKI, anti-rickettsia agent and supportive care are very important.

Bayesian Landmark-based Shape Analysis of Tumor Pathology Images.

Medical imaging is a form of technology that has revolutionized the medical field over the past decades. Digital pathology imaging, which captures histological details at the cellular level, is rapidly becoming a routine clinical procedure for cancer diagnosis support and treatment planning. Recent developments in deep-learning methods have facilitated tumor region segmentation from pathology images. The traditional shape descriptors that characterize tumor boundary roughness at the anatomical level are no longer suitable. New statistical approaches to model tumor shapes are in urgent need. In this paper, we consider the problem of modeling a tumor boundary as a closed polygonal chain. A Bayesian landmark-based shape analysis model is proposed. The model partitions the polygonal chain into mutually exclusive segments, accounting for boundary roughness. Our Bayesian inference framework provides uncertainty estimations on both the number and locations of landmarks, while outputting metrics that can be used to quantify boundary roughness. The performance of our model is comparable with that of a recently developed landmark detection model for planar elastic curves. In a case study of 143 consecutive patients with stage I to IV lung cancer, we demonstrated the heterogeneity of tumor boundary roughness derived from our model effectively predicted patient prognosis (p-value < 0.001).

Oncogenic role of protein tyrosine kinase 7 in esophageal squamous cell carcinoma.

Esophageal squamous cell carcinoma (ESCC) is a common subtype of esophageal cancer that is particularly prevalent in East Asian countries. Our previous expression profile analysis showed that the gene encoding protein tyrosine kinase 7 (PTK7) is upregulated in ESCC tissues. Here, we aimed to validate PTK7 as a prognostic factor and a candidate target for molecular treatment of ESCC. Both RT-PCR and Western blot analysis of tissues from ESCC patients revealed that PTK7 was significantly upregulated in tumor tissue samples of ESCC. Immunohistochemical staining of PTK7 showed that increased expression of PTK7 was inversely correlated with overall survival (P = 0.021). In vitro knockdown of PTK7 inhibited proliferation, survival, wound healing, and invasion of ESCC cells. In addition, PTK7 knockdown decreased phosphorylation of Akt, Erk, and focal adhesion kinase (FAK), important determinants of cell proliferation, survival, and migration. Therefore, our findings suggest that PTK7 has potential as a prognostic marker for ESCC and might also be a candidate for targeted therapy in the treatment of ESCC.

Surgical Considerations of One-Stage Reconstruction of Large Extremity Defects Using a Thin Deep Inferior Epigastric Perforator Flap.

Background One-stage reconstruction with "thin perforator flaps" has been attempted to salvage limbs and restore function. The deep inferior epigastric perforator (DIEP) flap is a commonly utilized flap in breast reconstruction (BR). The purpose of this study is to present the versatility of DIEP flaps for the reconstruction of large defects of the extremities. Methods Patients with large tissue defects on extremities who were treated with thin DIEP flaps from January 2016 to January 2018 were included. They were minimally followed up for 36 months. We analyzed the etiology and location of the soft tissue defect, flap design, anastomosis type, outcome, and complications. We also considered the technical differences in the DIEP flap between breast and extremity reconstruction. Results Overall, six free DIEP flaps were included in the study. The flap size ranged from 15 × 12 to 30 × 16 cm 2 . All flaps were transversely designed similar to a traditional BR design. Three flaps were elevated with two perforators. Primary closure of the donor site was possible in all cases. Five flaps survived with no complications. However, partial necrosis occurred in one flap. Conclusion A DIEP flap is not the first choice for soft tissue defects, but it should be considered for one-stage reconstruction of large defects when the circulation zone of the DIEP flap is considered. In addition, this flap has many advantages over other flaps such as provision of the largest skin paddle, low donor site morbidity with a concealed scar, versatile supercharging technique, and a long pedicle.

Pepsin immobilized on high-strength hybrid particles for continuous flow online digestion at 10,000 psi.

Pepsin was immobilized on ethyl-bridged hybrid (BEH) particles, and digestion performance was evaluated in a completely online format, with the specific intent of using the particles for hydrogen-deuterium exchange mass spectrometry (HDX MS) experiments. Because the BEH particles are mechanically strong, they could withstand prolonged, continuous high-pressure at 10,000 psi. Online digestion was performed under isobaric conditions with continuous solvent flow, in contrast to other approaches where the pressure or flow is cycled. As expected, digestion efficiency at 10,000 psi was increased and reproducibly produced more peptic peptides versus digestion at 1000 psi. Prototype columns made with the BEH pepsin particles exhibited robust performance, and deuterium back-exchange was similar to that of other immobilized pepsin particles. These particles can be easily incorporated in existing HDX MS workflows to provide more peptide coverage in experiments where fast, efficient, and reproducible online pepsin digestion is desired.

Aquaporins in Cancer Biology.

Aquaporins (AQPs) are a family of transmembrane water channel proteins, which were initially characterized as a novel protein family that plays a vital role in transcellular and transepithelial water movement. AQP1, AQP2, AQP4, AQP5, and AQP8 are primarily water selective, whereas AQP3, AQP7, AQP9, and AQP10 (called "aqua-glyceroporins") also transport glycerol and other small solutes. Recently, multiple reports have suggested that AQPs have important roles in cancer cell growth, migration, invasion, and angiogenesis, each of which is important in human carcinogenesis. Here, we review recent data concerning the involvement of AQPs in tumor growth, angiogenesis, and metastasis and explore the expression profiles from various resected cancer samples to further dissect the underlying molecular mechanisms. Moreover, we discuss the potential role of AQPs during the development of genomic instability and performed modeling to describe the integration of binding between AQPs with various SH3 domain binning adaptor molecules. Throughout review and discussion of numerous reports, we have tried to provide key evidence that AQPs play key roles in tumor biology, which may provide a unique opportunity in designing a novel class of anti-tumor agents.

A dual-plane approach for surgical treatment of pseudoaneurysm with arteriovenous fistula in hemodialysis patients.

BACKGROUND: We report the efficacy of a dual-plane approach using a Dufourmentel skin flap with a purse-string suture of the de-epithelized dermis to manage pseudoaneurysm at the vascular access site for hemodialysis. METHODS: A retrospective analysis was conducted of 61 patients from 2013 to 2018 with pseudoaneurysms at the arteriovenous fistula or graft who were treated with rhomboid excision, vessel repair with a purse-string suture, and a full-thickness Dufourmentel skin flap. The success rate was defined as the probability of complete wound closure and intact vascular access patency without infection or other complications. RESULTS: The success rate was 93.4% at 6 months postoperatively. Complications included newly occurring pseudoaneurysms (n=2), wound dehiscence (n=1) and bleeding (n=1). There were no complications such as stenosis or thrombosis from the procedure. CONCLUSIONS: A dual-plane approach using a Dufourmentel skin flap with a purse-string suture for vessel repair was shown to be a favorable option for managing stable, small (diameter <2 cm) pseudoaneurysms without infection, rapid expansion, or patency issues of the vascular access.

Molecular Alignment of Homoleptic Iridium Phosphors in Organic Light-Emitting Diodes.

The orientation of facial (fac) tris-cyclometalated iridium complexes in doped films prepared by vacuum deposition is investigated by altering the physical shape and electronic asymmetry in the molecular structure. Angle-dependent photoluminescence spectroscopy and Fourier-plane imaging microscopy show that the orientation of roughly spherical fac-tris(2-phenylpyridyl)iridium (Ir(ppy)3 ) is isotropic, whereas complexes that are oblate spheroids, fac-tris(mesityl-2-phenyl-1H-imidazole)iridium (Ir(mi)3 ) and fac-tris((3,5-dimethyl-[1,1'-biphenyl]-4-yl)-2-phenyl-1H-imidazole)iridium (Ir(mip)3 ), have a net horizontal alignment of their transition dipole moments. Optical anisotropy factors of 0.26 and 0.15, respectively, are obtained from the latter complexes when doped into tris(4-(9H-carbazol-9-yl)phenyl)amine host thin films. The horizontal alignment is attributed to the favorable van der Waals interaction between the oblate Ir complexes and host material. Trifluoromethyl groups substituted on one polar face of the Ir(ppy)3 and Ir(mi)3 complexes introduce chemical asymmetries in the molecules at the expense of their oblate shapes. The anisotropy factors of films doped with these substituted derivatives are lower relative to the parent complexes, indicating that the fluorinated patches reinforce horizontal alignment during deposition. High efficiencies obtained from organic light emitting diodes prepared using the Ir dopants is attributed, in part, to improved outcoupling of electroluminescence brought about by molecular alignment.