Prediction of the composition of urinary stones using deep learning

PURPOSE

This study aimed to predict the composition of urolithiasis using deep learning from urinary stone images.

MATERIALS AND METHODS

We classified 1,332 stones into 31 classes according to the stone composition. The top 4 classes with a frequency of 110 or more (class 1: calcium oxalate monohydrate [COM] 100%, class 2: COM 80%+struvite 20%, class 3: COM 60%+calcium oxalate dihydrate [COD] 40%, class 4: uric acid 100%) were selected. With the 965 stone images of the top 4 classes, we used the seven convolutional neural networks (CNN) to classify urinary stones and compared their classification performances.

RESULTS

Among the seven models, Xception_Ir0.001 showed the highest accuracy, precision, and recall and was selected as the CNN model to predict the stone composition. The sensitivity and specificity for the 4 classes by Xception_Ir0.001 were as follows: class 1 (94.24%, 91.73%), class 2 (85.42%, 96.14%), class 3 (86.86%, 99.59%), and class 4 (94.96%, 98.82%). The sensitivity and specificity of the individual components of the stones were as follows. COM (98.82%, 94.96%), COD (86.86%, 99.64%), struvite (85.42%, 95.59%), and uric acid (94.96%, 98.82%). The area under the curves for class 1, 2, 3, and 4 were 0.98, 0.97, 1.00, and 1.00, respectively.

CONCLUSIONS

This study showed the feasibility of deep learning for the diagnostic ability to assess urinary stone composition from images. It can be an alternative tool for conventional stone analysis and provide decision support to urologists, improving the effectiveness of diagnosis and treatment.

Recent Trends in Transurethral Surgeries and Urological Outpatient Procedures: a Nationwide Population-based Cohort Study

BACKGROUND

Demographic change and advances in technology affect transurethral surgery and outpatient procedures in the urologic field. There are few population-based studies that accurately assess the trend of transurethral surgery and outpatient procedures including diagnostic tests. We investigated the recent epidemiologic trends in transurethral surgeries and urological outpatient procedures from 2009 to 2016 in Korea using the entire population-based cohort.

METHODS

We analyzed medical service claim data of transurethral surgery, urological outpatient procedures submitted by medical service providers from the Health Insurance Review and Assessment Service from 2009 to 2016.

RESULTS

Transurethral ureter surgery increased by 134.9% from 14,635 in 2009 to 34,382 in 2016 (B = 2,698; R² = 0.98; P < 0.001). The transurethral bladder surgery increased by 65.5% from 12,482 in 2009 to 20,658 in 2016 (B = 1,149; R² = 0.97; P < 0.001). Over the 8-years period, there were not significant changes in transurethral prostate (B = 43; R² = 0.04; P = 0.617) and urethral surgery (B =-12; R² = 0.18; P = 0.289). The significantly increasing trends in cystoscopy (B = 5,260; R² = 0.95; P < 0.001) and uroflowmetry (B = 53,942; R² = 0.99; P < 0.001) were observed during the 8-year period. There was no difference in bladder catheterization during the 8-year period. Urodynamic study (UDS: B =-2,156; R² = 0.77; P = 0.003) and electrical stimulation treatment (EST: B =-1,034; R² = 0.87; P < 0.001) significantly decreased.

CONCLUSION

In Korea, transurethral ureter surgery and transurethral bladder surgery have been continuously increasing. Transurethral prostate surgery and transurethral urethral surgery remained constant with no increase or decrease. Cystoscopy and uroflowmetry continue to increase, while UDS and EST continue to decrease.

The Suppressive Effect of Leucine-Rich Glioma Inactivated 3 (LGI3) Peptide on Impaired Skin Barrier Function in a Murine Model Atopic Dermatitis

This study aimed to restore the skin barrier function from atopic dermatitis (AD) via treatment with leucine-rich glioma inactivated 3 (LGI3) peptide. Male NC/Nga mice (7 weeks, 20 g) were randomly allocated into three groups (control, AD, and LGI3 group). After induction of AD skin lesions with Dermatophagoides farinae ointment, mice were treated with LGI3. The clinical score of AD was the highest and the dorsal skin thickness was the thickest in the AD group. In contrast, LGI3 treatment improved the clinical score and the dorsal skin thickness compared to the AD model. LGI3 treatment suppressed histopathological thickness of the epithelial cell layer of the dorsal skin. LGI3 treatment could indirectly reduce mast cell infiltration through restoring the barrier function of the skin. Additionally, the filaggrin expression was increased in immunohistochemical evaluation. In conclusion, the ameliorating effect and maintaining skin barrier homeostasis in the AD murine model treated with LGI3 could be attributed to complete re-epithelialization of keratinocytes. Hence, LGI3 might be considered as a new potential therapeutic target for restoring skin barrier function in AD.

P2Y(11), a purinergic receptor acting via cAMP, mediates secretion by pancreatic duct epithelial cells

Pancreatic duct epithelial cells (PDEC) mediate the exocrine secretion of fluid and electrolytes. We previously reported that ATP and UTP interact with P2Y(2) receptors on nontransformed canine PDEC to increase intracellular free Ca2+ concentration ([Ca2+](i)) and stimulate Ca2+-activated Cl- and K+ channels. We now report that ATP interacts with additional purinergic receptors to increase cAMP and activate Cl- channels. ATP, 2-methylthio-ATP, and ATP-gamma-S stimulated a 4- to 10-fold cAMP increase with EC(50) of 10-100 microM. Neither UTP nor adenosine stimulated a cAMP increase, excluding a role for P2Y(2) or P1 receptors. Although UTP stimulated an (125)I(-) efflux that was fully inhibited by 1,2-bis(2-aminophenoxy)ethane-N,N,N',N'-tetraacetic acid tetra(acetoxymethyl) ester (BAPTA-AM), ATP stimulated a partially resistant efflux, suggesting activation of additional Cl- conductances through P2Y(2)-independent and Ca2+-independent pathways. In Ussing chambers, increased cAMP stimulated a much larger short-circuit current (I(sc)) increase from basolaterally permeabilized PDEC monolayers than increased [Ca2+](i). Luminal ATP and UTP and serosal UTP stimulated a small Ca2+-type I(sc) increase, whereas serosal ATP stimulated a large cAMP-type I(sc) response. Serosal ATP effect was inhibited by P2 receptor blockers and unaffected by BAPTA-AM, supporting ATP activation of Cl- conductances through P2 receptors and a Ca2+-independent pathway. RT-PCR confirmed the presence of P2Y(11) receptor mRNA, the only P2Y receptor acting via cAMP.

Activation of a heterologously expressed octopamine receptor coupled only to adenylyl cyclase produces all the features of presynaptic facilitation in aplysia sensory neurons

Short-term behavioral sensitization of the gill-withdrawal reflex after tail stimuli in Aplysia leads to an enhancement of the connections between sensory and motor neurons of this reflex. Both behavioral sensitization and enhancement of the connection between sensory and motor neurons are importantly mediated by serotonin. Serotonin activates two types of receptors in the sensory neurons, one of which is coupled to the cAMP/protein kinase A (PKA) pathway and the other to the inositol triphosphate/protein kinase C (PKC) pathway. Here we describe a genetic approach to assessing the isolated contribution of the PKA pathway to short-term facilitation. We have cloned from Aplysia an octopamine receptor gene, Ap oa(1), that couples selectively to the cAMP/PKA pathway. We have ectopically expressed this receptor in Aplysia sensory neurons of the pleural ganglia, where it is not normally expressed. Activation of this receptor by octopamine stimulates all four presynaptic events involved in short-term synaptic facilitation that are normally produced by serotonin: (i) membrane depolarization; (ii) increased membrane excitability; (iii) increased spike duration; and (iv) presynaptic facilitation. These results indicate that the cAMP/PKA pathway alone is sufficient to produce all the features of presynaptic facilitation.

Cloning and functional characterization of a Caenorhabditis elegans muscarinic acetylcholine receptor

A cDNA clone encoding a muscarinic acetylcholine receptor (mAChR) has been isolated from the nematode Caenorhabditis elegans. The nematode mAChR, consisted of 585 amino acids, displays a high degree of amino acid sequence homology to other invertebrate and vertebrate mAChRs. Excluding a highly variable middle portion of the third intracellular loop, the C. elegans mAChR shares about 51% amino acid sequence identity with a Drosophila mAChR and 42-44% identity with human m1-m5 mAChR subtypes. Comparison of the cDNA sequence with the corresponding genomic sequence reveals that the C. elegans mAChR gene contains ten introns, eight of them in the coding region. Pharmacological profiles of the C. elegans mAChR expressed in Chinese hamster ovary (CHO) cells were shown to be similar to those of mammalian counterparts, indicating that ligand binding domains of the receptor have been conserved during evolution. When this cloned receptor was expressed in Xenopus oocytes, acetylcholine evoked a transient Cl- current. Furthermore, activation of the receptor with oxotremorine, acetylcholine or carbachol resulted in the stimulation of phosphatidylinositol metabolism in CHO cells, suggesting that the receptor is coupled to phospholipase C activation.

Spectrum of opportunistic infections and malignancies in patients with human immunodeficiency virus infection in South Korea

To determine the frequency and types of major opportunistic diseases in patients with HIV infection in South Korea, we reviewed the medical records of 173 HIV-infected patients. The patients were seen from 1985 to 1998 at a referral hospital for AIDS in South Korea. Most patients (85%) were male, and 107 (62%) were infected by heterosexual contacts. CD4+ lymphocyte counts at presentation were <200/microL in 27% of the patients. Tuberculosis was the most frequent opportunistic infection (25% of patients), followed by candidiasis (21%), herpes zoster (20%), Pneumocystis carinii pneumonia (10%), cytomegalovirus disease (9.8%). There were no cases of toxoplasmosis. Kaposi's sarcoma developed in 3 patients (1.7%), and non-Hodgkin's lymphoma, in 2 (1.2%). Eleven patients (6.4%) developed peripheral neuropathy, and 8 (4.6%) had HIV encephalopathy. Tuberculosis was the single most important HIV-related infection in South Korean patients.

Interactions of Escherichia coli primary replicative helicase DnaB protein with nucleotide cofactors

Interactions between the Escherichia coli primary replicative helicase DnaB protein and nucleotide cofactors have been studied using several fluorescent nucleotide analogs and unmodified nucleotides. The thermodynamically rigorous fluorescent titration technique has been used to obtain true binding isotherms, independently of the assumptions of any relationships between the observed quenching of protein fluorescence and the degree of nucleotide binding. Fluorescence titrations using several MANT derivatives of nucleoside diphosphates (MANT-ADP, 3',2'-O-(N-methylantraniloyl)adenosine-5'-diphosphate; MANT-GDP, 3',2'-O(N-methylantraniloyl)guanosine-5'-diphosphate; MANT-CDP, 3',2'-O-(N-methylantraniloyl)cytidine-5'-diphosphate; MANT-UDP, 3',2'-O-(N-methylantraniloyl)uridine-5'-diphosphate) have shown that the DnaB helicase has a preference for purine nucleotides. Binding of all modified nucleotides is characterized by similar negative cooperativity, indicating that negative cooperative interactions are base-independent. Thermodynamic parameters for the interactions of the unmodified nucleotides (ADP, GDP, CDP, and UDP) and inorganic phosphate (P(i)) have been obtained by using the competition titration approach. To analyze multiple ligand binding to a finite circular lattice, for a general case in which each lattice binding site can exist in different multiple states, we developed a matrix method approach to derive analytical expressions for the partition function and the average degree of binding for such cases. Application of the theory to competition titrations has allowed us to extract the intrinsic binding constants and cooperativity parameters for all unmodified ligands. This is the first quantitative estimate of affinities and the mechanisms of binding of different unmodified nucleotides and inorganic phosphate for a hexameric helicase. The intrinsic affinities of all of the studied ATP analogs are lower than the intrinsic affinities of the corresponding ADP analogs. The implications of these results for the mechanism of helicase action are discussed.

Binding of Escherichia coli primary replicative helicase DnaB protein to single-stranded DNA. Long-range allosteric conformational changes within the protein hexamer

Quantitative analyses of the interactions of the Escherichia coli primary replicative helicase DnaB protein with single-stranded DNA have been performed using the thermodynamically rigorous fluorescence titration technique. This approach allowed us to obtain absolute stoichiometries of the formed complexes and interaction parameters, without any assumptions about the relationship between the observed signal change and the degree of binding. The analysis of the DnaB helicase interactions with nonfluorescent, unmodified nucleic acids has been performed, using a novel spectroscopic Macromolecular Competition Titration (MCT) method developed in the accompanying paper [Jezewska, M. J., & Bujalowski, W. (1996) Biochemistry 35, 2117-2128]. In the presence of the ATP nonhydrolyzable analog AMP-PNP, the DnaB helicase binds polymer DNA with a site-size of 20 +/- 3 nucleotides per protein hexamer. This site-size is independent of the type of nucleic acid base as well as the salt concentration and type of salt. Direct thermodynamic studies of the polynucleotide and oligomer binding to the DnaB hexamer, as well as the competition studies, show that independently of the type of nucleic acid base, as well as salt concentration and type of salt in solution, the helicase has only a single, strong binding site for DNA. Only this site is used when the protein interacts with polymer DNA. Moreover, UV photo-cross-linking experiments with oligonucleotides of different lengths, dT(pT)19, dT(pT)55, and dT(pT)69, suggest that primarily a single subunit of the DnaB helicase hexamer is in contact with the DNA. In interactions with polymer nucleic acids, the DnaB protein shows preferential intrinsic affinity for poly(dA), characterized in our standard conditions (pH 8.1, 10 degrees C, 100 mM NaCl, 5 mM MgCl2) by the intrinsic binding constant K = 6 +/- 2 x 10(6) M-1. These affinities are comparable to the affinities of the single-strand binding proteins in the corresponding solution conditions and strongly suggest that the helicase is capable of binding DNA without additional facilitating factors. Both the intrinsic affinity and the cooperativity are salt dependent. The formation of the DnaB-DNA complex is accompanied by the net release of approximately 2 ions, while another net release of approximately 2 ions accompanies the cooperative interactions. The data indicate an anion effect on the studied interactions and suggests that the released ions most probably originate from both the protein and the nucleic acid. The presence of a single, strong binding site on the hexamer, built of six chemically identical subunits, the very low site-size of the large helicase-DNA complex, and the involvement of a single subunit in contact with the nucleic acid indicate the presence of long-range allosteric interactions in the DnaB helicase which encompass the entire DnaB hexamer. Our sedimentation velocity measurements of the DnaB protein-(AMP-PNP)-5'-fluorescein-(dT)20 ternary complex show that the sedimentation coefficient of the complex is S20,W = 12.3 +/- 0.3, compared with S20,W = 10.5 +/- 0.3 of the free enzyme, indicating large changes in the hydrodynamic properties of the enzyme in the complex. These results provide direct evidence that the DnaB hexamer undergoes dramatic conformational changes which include all six subunits of the enzyme in the ternary complex. Moreover, sedimentation velocity studies of the ternary complex provide direct evidence that the hexamer is the species which binds ss nucleic acid. The significance of these results for a mechanistic model of the functioning of the DnaB helicase in DNA replication is discussed.

Effect of ethidium binding and superhelix density on the apparent supercoiling free energy and torsion constant of pBR322 DNA

The value of the twist energy parameter (ET) of pBR322 is determined near zero superhelix density from topoisomer distributions created under various conditions. The resulting value, ET = 1155 +/- 65, at 37 degrees C is essentially unaffected by adding 10 mM Mg2+, or by changing the kind of Topo I from chicken-red-cell to calf-thymus. This value significantly exceeds that (ET = 950 +/- 80) measured for p30 delta DNA under identical conditions by the same method in the preceding paper. Decreasing the temperature from 37 to 21 degrees C yields a slightly larger value, ET = 1340 +/- 130, but the statistical significance of the increase is marginal. Attempts to determine reliable ET values for pBR322 at higher superhelix densities by ethidium binding were frustrated by the fact that good fits of the equilibrium dialysis results could not be achieved using a single value of ET. Moreover, the curves of apparent ET versus binding ratio r vary considerably from one preparation to another, and for a given preparation vary with time after cell lysis up to about seven weeks, after which they settle in to nearly reproducible behavior. The apparent ET values obtained from competitive dialysis experiments are typically rather low (ET approximately 700) for small r and nearly native superhelix density, and rise up to 1300 to 1500 with increasing binding ratio (up to r = 0.055) and decreasing negative superhelix density.(ABSTRACT TRUNCATED AT 250 WORDS)

Dynamics and structures of DNA: long-range effects of a 16 base-pair (CG)8 sequence on secondary structure

The effects of inserting 16 base pair (bp) of alternating CG [(CG)8] near the middle of a much longer restriction fragment (1097 bp) are investigated by measuring various properties that are sensitive to secondary and tertiary structure. Results for this fragment are compared with those for a control fragment (1089 bp) with the identical sequence except at the insert. Another fragment (1382 bp), which contains a 296-bp extension at the 5'-end of the 1089-bp control fragment, is also used as a secondary control in some experiments. When the 1097-bp (CG)8 insert fragment is compared with the control fragments in 0.1 M NaCl buffer, the (CG)8 insert is found to induce disproportionately large relative changes in the molar ellipticity at 273 nm ([theta]273), the torsion constant (alpha) measured by fluorescence polarization anisotropy, the optical melting profile, and the susceptibility to S1 nuclease. Estimates of the minimum distance over which the (CG)8 insert alters the secondary structure range from 330 to 550 bp. With increasing NaCl concentration, the 1097-bp insert fragment undergoes a structural transition between 2.0 and 2.5 M that is manifested in the apparent diffusion coefficient (Dplat) from dynamic light scattering at large scattering vector. This transition, which is not exhibited by the control DNAs, is presumed to involve formation of Z-helix at the insert. However, the observed decrease in (Dplat) is attributed to an increase in bending rigidity, which perforce must be globally distributed far beyond the (CG)8 insert per se. In 4.25 M NaCl (but not in 0.1 M NaCl), the addition of 1 ethidium dye per 300 bp induces an extensive structural transition in the 1097 bp (CG)8 insert fragment. This transition, which also is not exhibited by the control DNAs, significantly decreases the bending rigidity, doubles [theta]273, and takes place on a time scale of a few days. Removal of ethidium and salt by dialysis vs 0.1 M NaCl buffer restores the original properties of the 1097-bp (CG)8 insert fragment. The present results are consistent with a (fluctuating, long-range) description of the secondary structure in which a given short sequence transiently fluctuates among two or more distinct secondary structures that extend over much larger domains of variable position and size, and whose relative stabilities depend on distant as well as close-lying base pairs.

Renal angiomyolipoma associated with neurofibromatosis and primary carcinoid of mesentery

A patient with von Recklinghausen's disease manifested by dermal neurofibromatosis and cafe-au-lait spots presented with complaints of malaise, weight loss, lower extremity weakness, and a palpable left lower abdominal quadrant mass. Evaluation revealed a lumbar neurofibroma, a localized primary carcinoid tumor of the mesentery, and a left renal angiomyolipoma. Although an association between neurofibromatosis and carcinoid has been previously reported, we believe this is the first report documenting the association of all three entities.

Dynamic light scattering from weakly bending rods: estimation of the dynamic bending rigidity of the M13 virus

A theory is presented for the dynamic structure factor [S(K,t]) of weakly bending rods. This treatment is based on a discrete bead model for the Brownian dynamics in which all bead motions associated with bending are constrained to occur in a plane perpendicular to the end-to-end vector, thus prohibiting extension or contraction along that axis. Preset hydrodynamic interactions are incorporated in a numerically exact manner. The predicted normalized dynamic structure factor S(K,t)/S(K,0) should be valid for short times t such that the rms rotation of the end-to-end vector around any transverse axis is much less than 1.0 radian. With geometrical parameters appropriate for the M13 virus, the intensity autocorrelation function G(2) (K,t) = 1 + magnitude of S(K,t)/S(K,0)2 is calculated over a range of times and scattering vectors K for selected values of the persistence length P. The calculated G(2) (K,t) are fitted to a single exponential with unit baseline over the same range of times as the experimental photon correlation functions, and the apparent diffusion coefficients Dapp (K) are obtained from the best-fit relaxation times. For the sake of completeness, an exact expression is derived for the apparent diffusion coefficient obtained from the initial slope of the dynamic structure factor. However, this does not reduce to the known correct result in the rigid rod limit. To obtain the correct result, the limit of infinite bending rigidity must be taken before the limit of zero time. For this and other reasons, the initial slope value of Dapp (K) is not useful for weakly bending rods. Photon correlation functions are measured for the M13 virus, which is virtually identical to the often-studied fd virus. The experimental photon correlation functions are fitted over 8 relaxation times to a single-exponential plus baseline, and the Dapp (K) are calculated from the best-fit relaxation times. Theoretical curves of Dapp (K) vs K2 for selected values of P are compared with the experimental data, which are satisfactorily reproduced when P = 22000 +/- 2000 A. This dynamic value is close to the static value, P = 20000 +/- 2000 A, reported for the very similar fd virus. The most recent theories of Maeda and Fujime and their dynamic light scattering studies of fd virus are compared with the present results in some detail. Their optimum value of P is in surprisingly good agreement with the present value.

Benign symmetrical lipomatosis

Benign symmetrical lipomatosis is an unusual disorder of fat metabolism that results in a characteristic accumulation of adipose tissue around the head and neck. Surgical extirpation is the only known effective therapy. Physical examination does not provide a comprehensive delineation of tumor extent. We present the first reported use of CT scanning to investigate the anatomic limits of BSL and to plan the operative approach.

Postoperative intussusception after vaginal vault suspension

Postoperative intussusception in the adult is a rarely reported and poorly understood condition. Presented is the case of a patient developing incomplete small bowel obstruction after an uneventful vaginal vault suspension. Jejunojejunal intussusception, requiring resection, was found at celiotomy. Intussusception must be considered in treating patients developing postoperative intestinal obstruction.

Peripheral lymphocytes in carcinoma of the colon and rectum

Changes in peripheral lymphocyte counts have been reported in many different malignant conditions. We have studied 202 patients with carcinoma of the colon and rectum and have evaluated the relationship between peripheral lymphocytes and stage of disease as well as sex, location of tumor and carcinoembryonic antigen levels. We found a correlation between advancing stage of disease and lower levels of peripheral lymphocytes. An inverse relationship for carcinoembryonic antigen levels and lymphocyte values was also noted for the entire group as well as for individual Stages B anc C. It was suggested that the combination of both lymphocyte levels and carcinoembryonic antigen determinations might be useful as a prognostic indicator.

Prognostic significance of peripheral lymphocyte counts and carcinoembryonic antigens in colorectal carcinoma

An association between pretreatment lymphocyte counts and 5-year prognosis was noted in colorectal cancer. Among 188 patients with 5-year follow-up significant difference in survival rates in relation to lymphocyte counts was noted: 61% for patients with counts greater than 2,000/cm, 30% for those with counts less than 1,000/cmm, and 58% for the intermediate group. Similar differences were also noted within groups with Dukes' B and C lesions and in elderly patients. Highly significant differences were noted in women. Those with Dukes' B and C lesions with counts greater than 2,000/cmm had an 81% survival rate, compared to 50% for those with lower counts X2 = 6.81 P LESS THAN 0.01. Women had significantly higher lymphocyte counts and higher survival rates than men. An inverse correlation was noted between pretreatment lymphocytes and simultaneously determined carcinoembryonic antigens. These observations indicate that lymphocyte counts may be of prognostic value in colorectal cancer when used in association with carcinoembryonic antigens.

Physical Adsorption of the Quantum Gas

The significant structure theory of quantum liquids such as hydrogen, deuterium, and helium has been applied to the physical adsorption occurring in the submonolayer region. The partition function for the two-dimensional adsorbed fluid has been derived. The properties of isothermal and isosteric heat show good agreement with the available data from the literature.