Pathological and immunohistochemical findings of lungs,heart,liver,and kidneys,and unexpected findings of fungi and parasites in lungs of deceased COVID-19 patients:A case series

Objective:To define histopathologic and immunohistochemical features of the lungs,heart,liver,and kidneys in patients who died from coronavirus disease 2019(COVID-19),and to determine the presence of SARS-CoV-2 in all tissues,as well as the presence of fungi and parasites in lung tissues.Methods:This retrospective case study was conducted in the intensive care units of Dokuz Eylül University Hospital,and patients(≥18 years)who died due to COVID-19 between October 2020 and April 2021 were included.The biopsy samples of the patient’s lung,heart,liver,and kidney tissues were studied.Results:In the study,we enrolled 12 patients(mean age:70 years;50%male).Alveolar epithelial cell damage and diffuse alveolar damage were predominant in lung tissues.Lobular lymphocyte infiltration,centrilobular sinusoidal dilatation,and microvesicular steatosis in the liver,together with pigmented cast,non-isometric vacuolar degeneration,and capillary plugging in the kidneys,were commonly found among the patients.SARS-CoV-2 nucleocapsid protein antibodies were detected in three lung and two kidney tissues,and so did angiotensin-converting enzyme 2 receptor positivity in one lung and more than half of the kidney tissues.The RT-PCR tests were positive in three lungs and one kidney tissue.After DNA isolation from lung tissues,Pneumocystis jirovecii was detected in nine patients,Aspergillus fumigatus in two,Microsporidia in three,and Cryptosporidium in two.Conclusions:SARS-CoV-2 is a multisystemic disease.Fungi and parasites should be investigated in critically ill COVID-19 patients prescribed corticosteroids.

Clinical role and importance of fluorescence in situ hybridization method in diagnosis of H pylori infection and determination of clarithromycin resistance in H pylori eradication therapy

H pylori is etiologically associated with gastritis, gas-tric and duodenal ulcers, gastric adenocarcinoma and mucosa-associated lymphoid tissue (MALT) lymphoma. Eradicating H pylori may convert rapidly the outcome of related diseases with the use of more accurate diagnostic molecular tests. Indeed some of the tests cannot give the evidence of current infection; H pylori can be detected by noninvasive and invasive methods, the latter requiring an endoscopy. Eradication failure is a big problem in H pylori infection. Recently, clarithromycin resistance in H pylori strains is increasing and eradicati-on therapy of this bacterium is becoming more difficult. Molecular methods have frequently been applied besides phenotypic methods for susceptibility testing to detect clarithromycin resistance due to mutations in the 2143 and 2144 positions of 23S rRNA gene. Fluorescence in situ hybridization (FISH) method on paraffin embedded tissue is a rapid, accurate and cost-effective method for the detection of H pylori infection and to determine clarithromycin resistance within three hours according to the gold standards as a non-culture method. This method can also be applied to fresh biopsy samples and the isolated colonies from a culture of H pylori, detecting both the culturable bacillary forms and the coccoid forms of H pylori, besides the paraffin embedded tissue secti-ons. This technique is helpful for determining the bac-terial density and the results of treatment where clarith-romycin has been widely used in populations to increase the efficacy of the treatment and to clarify the treatment failure in vitro.

Importance of antimicrobial susceptibility testing for the management of eradication in Helicobacter pylori infection

The management of Helicobacter pylori(H. pylori) infection treatment differs from the common treatment protocol for other infectious diseases. Because culture-or molecular-guided approaches face several practical issues, such as the invasive procedures required to obtain gastric biopsy specimens and the lack of availability of routine laboratory testing in some places, H. pylori treatment includes the administration of two or three empirically selected antibiotics combined with a proton pump inhibitor rather than evidence-based eradication treatment. The efficacy of empirical therapy is decreasing, mostly due to increasing multiple resistance. Multiresistance to levofloxacin, clarithromycin, and metronidazole, which are commonly used in empirical treatments, appears to have increased in many countries. Mutations play a primary role in the antimicrobial resistance of H. pylori, but many different mechanisms can be involved in the development of antibiotic resistance. Determining and understanding these possible mechanisms might allow the development of new methods for the detection of H. pylori and the determination of antimicrobial resistance. A treatment based on the detection of antimicrobial resistance is usually more effective than empirical treatment. Nevertheless, such an approach before treatment is still not recommended in the Maastricht guidelines due to the difficulty associated with the routine application of available cultureor molecular-based susceptibility tests, which are usually administered in cases of treatment failure. The management of first and rescue treatments requires further research due to the steadily increase in antimicrobial resistance.

Geochemistry and Zircon U-Pb Dates of Felsic-Intermediate Members of the Late Cretaceous Yüksekova Arc Basin: Constraints on the Evolution of the Bitlis–Zagros Branch of Neotethys(Elazig, E Turkey)

During the Late Cretaceous in the Eastern Mediterranean, the northern branch of the southern Neotethys was closed by multiple northward subductions. Of these, the most northerly located subduction created the Baskil continental arc at around 82–84 Ma. The more southerly and intra-oceanic subduction, on the other hand, produced an arc-basin system,the Yüksekova Complex, as early as the late Cenomanian–early Turonian. The abundant and relatively well-studied basaltic rocks of this complex were intruded by dykes, sills and small stocks of felsic–intermediate rocks, not previously studied in detail. The intrusives collected from five different localities in the Elazig region of eastern Turkey are all subalkaline, with low Nb/Y values. Most of them have been chemically classified as rhyodacites/dacites, whereas a small number appear to be andesites. In normal mid-ocean-ridge basalt(N-MORB)-normalised plots, the intrusives are characterised by relative enrichments in Th and La over Nb, Zr, Hf, Ti and high field strength elements(HREEs), indicating their derivation from a subduction-modified source. While their relatively high, positive εN d(i) values(+6.4 and +7.2) might suggest a depleted mantle source for their ultimate origin, somewhat radiogenic Pb values indicate a sedimentary contribution to the source of the rocks. The overall geochemical characteristics indicate their generation in an oceanic arc setting. The zircon U-Pb Laser ablation-inductively coupled plasma-mass spectrometry(LA-ICP-MS) data obtained from five felsic-intermediate rock samples yielded intrusion dates of 80–88 Ma. This suggests that the Elazig oceanic arc-related intrusives are slightly younger than those of the Yüksekova arc-basin system, but coeval with the Baskil continental arc. However, the felsic–intermediate intrusives show different geochemical characteristics(oceanic arc-type, with a lack of crustal contamination)to those of the Baskil continental arc. This indicates that these two igneous systems are unrelated and likely developed in different tectonic settings. This, in turn, supports a geodynamic model in which the northern strand of the southern Neotethys was consumed by multiple northward subductions.

Detection of H pylori infection by ELISA and Western blot techniques and evaluation of anti CagA seropositivity in adult Turkish dyspeptic patients

AIM: To detect H pylori infection and to evaluate the anti CagA seropositivity in adult Turkish dyspeptic patients. METHODS: We evaluated anti-H pylori IgA, IgG and anti-CagA antibodies using commercial enzyme-linked immunoassay (ELISA) and Western blot in dyspeptic Turkish patients. H pylori status was determined by histology and rapid urease testing. RESULTS: Fifty-six patients were entered. Forty-eight (85.7%) out of the 56 patients were positive for H pylori. H pylori IgG seropositivity was 82.1%, IgA seropositivity 48.2%. CagA ELISA showed that IgG was positive in 50% and IgA in 30.4% of those with H pylori infections. Western blot showed that IgG seropositivity was 80.4% and IgA seropositivity 33.9%. Western blot detected IgG antibodies with reactivity to CagA in 50%, VacA in 62.5%, UreB in 87.5%, UreA in 80.4%, and OMP in 57.1%. None of the tests had a sensitivity and specifi city above 80%. CONCLUSION: None of these commercial tests seems clinically useful for H pylori detection in adult dyspeptic patients, while Western blot can give seropositivity and determine anti-CagA, VacA virulence factor status of Turkish dyspeptic patients in the Izmir region.

Electron transport in electrically biased inverse parabolic double-barrier structure

A theoretical study of resonant tunneling is carried out for an inverse parabolic double-barrier structure subjected to an external electric field. Tunneling transmission coefficient and density of states are analyzed by using the non-equilibrium Green＇s function approach based on the finite difference method. It is found that the resonant peak of the transmission coefficient, being unity for a symmetrical case, reduces under the applied electric field and depends strongly on the variation of the structure parameters.

The Impact of Marine Aquaculture on the Environment;the Importance of Site Selection and Carrying Capacity

A growing increase in the world’s population and a gradual decline in poverty necessitate a search for new sources of protein in order to guarantee food security. Aquaculture has been identified as a potential sector capable of meeting the requirements for increased protein production without making excessive demands on the ecosystem. Although water makes up 70% of the earth’s surface, aquaculture cannot feasibly be practised everywhere;it requires a unique set of natural, social and economic resources to be managed in an environmentally responsible way. Finding suitable sites for aquaculture is becoming an ever increasing problem in the development of the sector as precautions need to be taken in setting up sites to ensure appropriate environmental characteristics exist and that good water quality can be maintained. Additionally, the effects of aquaculture on coastal and inland resources must be clearly determined to implement policies and regulatory frameworks to control its impact. Marine cage farming is gaining momentum, specifically in the Mediterranean and Black Sea coastal regions. For these sites to be further developed there is a need to minimize the effects on the environment and conflicts with other coastal users. To this aim the concept of allocated zones for aquaculture (AZA) is being adopted to provide specific areas for marine aquaculture to avoid environmental degradation. When choosing an (AZA) suitable site, it is vital to calculate ‘carrying capacity’ to reduce the risks and to protect the marine ecosystems. In this study the MERAMOD model was used to investigate the carrying capacity of marine fish farms. Modelling offers the possibility to simulate and predict the environmental impact of fish farms.

Magnetic and Thermal Behaviour of One-Dimensional Antiferromagnetic Spin-1 Ising Chain at Low Temperatures

We investigate magnetic and thermal behaviours of one-dimensional antiferromagnetic spin-i Ising chain with single-ion anisotropy at very low temperatures using the classical transfer matrix technique. Magnetic plateaus, phase diagram, specific heat, susceptibility of the spin chain have been evaluated numerically from the free energy. The results are in good agreement with the experimental data for the spin-1 compounds [Ni2 （Medpt）2 （μ- ox）（H2O）2]（ClO4）22H2O, [Ni2（Medpt）2（μ-ox）（μ-N3）]（ClO4）0.5H2O, Ni（C2H8N2）Ni（CN）4 and Ni（C10H8N2）2 Ni（CN）4·H2O.

Hydrodynamic Conditions in Front of a Vertical Wall with an Overhanging Horizontal Cantilever Slab

Transforming wave heights from offshore to the shoreline is the first step of any coastal engineering work. Wave breaking is analyzed to understand hydrodynamic conditions. For vertical breakwaters and sea walls, wave reflection is an important process that affects the determination of the wave height. Many of the design formulas presented in the literature depend on empirical studies based on the structures tested. In this study, the hydrodynamic conditions in front of a vertical wall with an overhanging horizontal cantilever slab with a foreshore slope of 1/20 are determined experimentally under regular wave conditions to assess the applicability of the formulas of Goda(2000) for predicting the nearshore wave height and breaker index equation(Goda, 2010). The selection of wave measurements used to determine the design wave height, the reflection coefficients, and wave breaking is also analyzed, and the reflection equations are derived from the dataset covering different breaker types. Small-scale tests show that the incident wave height is a good representative of the design wave height and that the values predicted by Goda are in good agreement with actual measurements. However, the predicted Hmax values are overestimated. In addition, the inception of the wave breaking point is postponed because of the reflection and/or turbulence left over from preceding waves, which is an effect of the vertical wall. At higher water levels, the effect of the vertical wall on the inception point becomes more significant.

A novel mutation in the sodium channel α1 subunit gene in a child with Dravet syndrome in Turkey

Dravet syndrome is a rare epileptic encephalopathy characterized by frequent seizures beginning in the first year of life and behavioral disorders. Mutations in the sodium channel α1 subunit gene are the main cause of this disease. We report two patients with refractory seizures and psychomotor retardation in whom the final diagnosis was Dravet syndrome with confirmed mutations in the sodium channel α1 subunit gene. The mutation identified in the second patient was a novel frame shift mutation, which resulted from the deletion of five nucleotides in exon 24.

Alternative Approach to Time Evaluation of Schrodinger Wave Functions

Time evaluation of wave functions for any quantum mechanical system/particle is essential nevertheless quantum mechanical counterpart of the time dependant classical wave equation does simply not appear. Epistemologically and ontologically considered time dependant momentum operator is initially defined and an Alternative Time Dependant Schrodinger Wave Equation (ATDSWE) is plainly derived. Consequent equation is primarily solved for the free particles, in a closed system, signifying a good agreement with the outcomes of the ordinary TDSWE. Free particle solution interestingly goes further possibly tracing some signs of new pathways to resolve the mysterious quantum world.

Seasonal variations and distributions of dissolved free and total carbohydrates at the ?zmir Bay, Aegean Sea

Seasonal variations and distributions of dissolved carbohydrate concentrations at the ？zmir Bay were investigated with salinity, chlorophyll a（Chl a）, and dissolved organic carbon（DOC） levels to understand their relationships.Samples were collected from surface, subsurface and bottom depths at seven stations. DOC concentrations ranged from 32.2 to 244.2 μmol/L, and in general, DOC levels increased from winter to summer, then slightly decreased in autumn. Monosaccharide（MCHO）, polysaccharide（PCHO） and total dissolved carbohydrate（TDCHO） levels were found between 0.7–8.3, 0.7–19.5, and 2.6–24.6 μmol/L. DOC, MCHO, PCHO and TDCHO levels were found higher in middle-inner bays, under the influence of anthropogenic inputs, compared to outer bay. Seasonal changes of MCHO/DOC, PCHO/DOC and TDCHO/DOC ratios were statistically significant（p〈0.05）and the ratios showed decrease trends from winter to summer-autumn seasons. Distributions of TDCHO/DOC ratios at wide ranges（2.5%–42.3%） indicated the presence of newly forming and degrading fractions of DOM.According to results of factor analysis, Chl a, MCHO and TDCHO were explained in the same factor groups. In conclusion, the results showed that dissolved carbohydrate levels in the ？zmir Bay might be influenced by biological processes and terrestrial/anthropogenic inputs.

Comparison of invasive methods and two different stool antigen tests for diagnosis of H pylori infection in patients with gastric bleeding

瞄准：为了比较二不同 H pylori 凳子抗原，作为非侵略的诊断方法测试。方法：学习人口由为病人放血的 22 上面的胃肠的系统组成了。脲呼吸测试(UBT ) ，快速的 urease (车辙) 和组织病理学说的检查被用于所有病人。从这些病人的凳子标本被快速的长带检验 ! 为 H pylori 抗原的察觉的 HpSA 和 HpSA 步骤 simple H pylori 抗原盒子测试。结果：为这 22 个病人，(68.2%) 15 作为积极被诊断，(31.8%) 七是为由标准答案方法的 H pylori 感染的诊断 negative。而(45.5%) 10 是积极的，(54.5%) 12 被诊断由快速的长带否定 ! HpSA 测试。敏感，特性，积极、否定的预兆的价值分别地是 60% ， 86% ， 90% 和 50% 。什么时候与标准答案方法相比，这些差别不是重要的。然而，六个病人(27.3%) 是积极的，并且(72.7%) 16 由简单 H pylori 凳子抗原盒子测试是否定的。敏感，特性，积极、否定的预兆的价值分别地是 33% ， 86% ， 83% 和 38% 。比作标准答案方法，简单 H pylori 凳子抗原盒子测试结果是显著地不同的(P = 0.012 ) 。结论：快速的长带 ! HpSA 测试能在微生物学实验室作为一个平淡的诊断工具被使用在上面的胃肠的系统流血估计 H pylori 的临床的意义和根除控制病人。

Effect of Hydrostatic Pressure on Interband Transitions in Coupled Quantum Wires

我们计算在 arectangular 的光吸收联合了的激子绑定精力和 interband 在在 effective-massapproximation 的静水力学的压力下面的量电线，用变化途径。这被发现 interband 光 absorptionstrongly 取决于静水力学的压力和联合参数，并且为在联合的量电线中的 HH1-E1 转变的大小 ofthe 吸收系数比 thatof 大单个量电线。

Clinical effectiveness of adding probiotics to a low FODMAP diet:Randomized double-blind placebo-controlled study

BACKGROUND There are various studies showing the relationship between irritable bowel syndrome(IBS)and diet,and some dietary adjustments are recommended to reduce symptoms.In recent years,there is a growing number of studies that show a 4-8 wk low fermentable oligo,di-and mono-saccharides and polyols(FODMAP)diet has a 50%-80%significant effect on symptoms in IBS patients.There is strong evidence suggesting that changes in fecal microbiota have an impact on IBS pathogenesis.Based on this argument,probiotics have been used in IBS treatment for a long time.As is seen,the FODMAP diet and probiotics are used separately in IBS treatment.AIM To evaluate the effectiveness of adding probiotics to a low FODMAP diet to control the symptoms in patients with IBS.METHODS The patients who were admitted to the Gastroenterology Clinic of Dokuz Eylul University Hospital and diagnosed with IBS according to Rome IV criteria were enrolled into the study.They were randomized into 2 groups each of which consisted of 50 patients.All patients were referred to a dietitian to receive dietary recommendations for the low FODMAP diet with a daily intake of 9 g.The patients were asked to keep a diary of foods and beverages they consumed.The patients in Group 1 were given supplementary food containing probiotics(2 g)once a day in addition to their low FODMAP diet,while the patients in Group 2 were given a placebo once a day in addition to their low FODMAP diet.Visual analogue scale(VAS),the Bristol Stool Scale and IBS Symptom Severity Scale(IBSSSS)scores were evaluated before and after the 21 d treatment.RESULTS The rate of adherence of 85 patients,who completed the study,to the FODMAP restricted diet was 92%,being 90%in Group 1 and 94%in Group 2.The mean scores of VAS and IBS-SSS of the patients in Group 1 before treatment were 4.6±2.7 and 310.0±78.4,respectively,and these scores decreased to 2.0±1.9 and 172.0±93.0 after treatment(both P<0.001).The mean VAS and IBS-SSS scores of the patients in Group 2 before treatment were 4.7±2.7 and 317.0±87.5,respectively,and these scores decreased to 1.8±2.0 and 175.0±97.7 after treatment(both P<0.001).The IBS-SSS score of 37 patients(86.04%)in Group 1 and 36 patients(85.71%)in Group 2 decreased by more than 50 points.Group 1 and Group 2 were similar in terms of differences in VAS and IBS-SSS scores before and after treatment.When changes in stool shape after treatment were compared using the Bristol Stool Scale,both groups showed significant change.CONCLUSION This study is the randomized controlled study to examine the efficiency of probiotic supplementation to a low FODMAP diet in all subtypes of IBS.The low FODMAP diet has highly positive effects on symptoms of all subtypes of IBS.It was seen that adding probiotics to a low FODMAP diet does not make an additional contribution to symptom response and adherence to the diet.

Effects of stem cells applications on oxidative stress and apoptosis during implantation

Objective:To investigate the effects of bone marrow derived mesenchymal stem cell (BMSC) application into the rat endometrium on oxidative stress, cell proliferation and apoptosis.Methods: The female rats selected in estrous cycle were divided into three groups (saline, media and BMSC group). The intrauterine and intraperitoneal injections were performed using the saline (200 μL), culture media (200 μL) and 1×106 BMSCs/200 μL culture media, and then they were mated with male rats. On the 7th day of the pregnancy, uterine samples were harvested and dyed with heamatoxylin-eosin histochemically, anti-endothelial nitric oxide synthase and anti-inducible nitric oxide synthase, and anti-proliferating cell nuclear antigen immunohistochemically, with terminal deoxynucleotidyl transferas dUTP nick end labeling for apoptosis. The stainings were evaluated by H-score and the results were analyzed using one-way ANOVA test statistically.Results: It was found that BMSCs increased the endometrial thickness, endometrial epithelium thickness and number of endometrial glands compared to control and sham groups. The intrauterine BMSC application decreased both anti-endothelial nitric oxide synthase and anti-inducible nitric oxide synthase immunoreactivities and the number of apoptotic cells compared to the intraperitoneal applications whereas the immunoreactivity of proliferating cell nuclear antigen was increased.Conclusions: In current study, we define that stem cells do not cause any structural damages. Also they change the distribution of oxidative stress and cell proliferation marker. These findings support the reliability of stem cells in clinical use in the case of infertility.

Effects of an Intense Laser Field and Hydrostatic Pressure on the Intersubband Transitions and Binding Energy of Shallow Donor Impurities in a Quantum Well

We have calculated the intersubband transitions and the ground-state binding energies of a hydrogenic donor impurity in a quantum well in the presence of a high-frequency laser field and hydrostatic pressure.The calculations are performed within the effective mass approximation,using a variational method.We conclude that the laser field amplitude and the hydrostatic pressure provide an important effect on the electronic and optical properties of the quantum wells.According to the results obtained from the present work,it is deduced that(i)the binding energies of donor impurity decrease as the laser field increase,(ii)the binding energies of donor impurity increase as the hydrostatic pressure increase,(iii)the intersubband absorption coefficients shift toward lower energies as the hydrostatic pressure increases,(iv)the magnitude of absorption coefficients decrease and also shift toward higher energies as the laser field increase.It is hopeful that the obtained results will provide important improvements in device applications.

Introduction to the Special Issue on Numerical Methods for Differential and Integral Equations

Differential and integral equations have a major role in many applied areas of science and engineering,For example,physics,chemistry,astronomy,biology,mechanics,electronic,economics,potential theory,electrostatics.So,the obtaining of solutions of these equations is important.Since the mentioned equations are usually difficult to solve analytically,numerical methods are required.Therefore,this Special Issue contributes to new numerical methods for solving the above-mentioned equations and thus,many problems in science and engineering can be solved using new numerical methods analyzed in this special issue.

Future of Architecture: Buildings as Power Plants

After the energy crisis in 1970s,buildings began to be used as a platform for the elements which produce energy from renewable energies to return them into energy producing power plants.This is a safe,clean and economic way to produce energy since the energy is produced where it is needed and they use renewable energy resources.So,it promises hope for the future energy production.Therefore,the aim of this study is to examine buildings which produce electricity by using renewable energy resources and to show that this is one of the safest,cleanest and most economic ways to be used to produce energy in the future.This is done by describing power plants and how buildings are used as power producing stations by the use of renewable energy resources or other energy producing materials,then by examining case studies which are constructed and already being used,case studies which are just a design that have not yet been constructed,and by making projections to the future energy producing techniques that are just a proposal in 2021.In the conclusion,buildings are proposed as the future power plants,either here on earth or on another planet like Mars.

Shape effects on the ground-state energy of a three-electron quantum dot

In this work we will theoretically study the ground-state electronic structure of three-electron polygonal quantum dots by means of the configuration interaction method. Transition from a weakly correlated regime to a strongly correlated regime is investigated for quantum dots with hexagonal, square, and triangular geometries. Our numerical results reveal that the ground-state spin and the charge density distribution of the system are sensitive to the shape of the quantum dot.