bluuebunny/crossref_metadata_2025_split huggingface dataset:
Computational Pathways Analysis and Personalized Medicine in
HER2-Positive Breast Cancer
Authors: Bitto Alessandra , Lui Maria , Giosa Domenico , Romeo Orazio 
Published: April 2022

Background:
The heterogeneity of some diseases, such as cancer, makes the decisions on
therapeutic strategy very challenging. In this context, pathway analysis can support the identification
of the best treatment and indeed prevent the issues arising from the trial and error process, in terms of
best overall efficacy and lowest toxicity, ultimately saving time and resources. In a pathway, each gene
is represented by a node and the pathway analysis can be performed using algorithms that interpolate
data from different sources (i.e. sequencing, microarray, drug efficacy and interactions).

Objective:
The purpose of this study was to evaluate the effects of erbb2 amplification on HER2- positive
breast cancer and to predict, with a pathway based computational approach, the efficacy of a therapy
with Trastuzumab and Palbociclib, alone or in combination.

Methods:
One of the available and most integrated algorithms is PHENSIM that was used in this
study to evaluate the gene dysregulations caused by the erbb2 amplification on its related pathways
and the effects of Trastuzumab and Palbociclib on these deregulations. The effects have been estimated
considering the drugs alone or in a combination therapy.

Results:
A reduction of the number of pro-proliferative signals has been observed for both drugs alone
or in combination. Regarding genes involved in MAPK signaling pathway, a total of 69 nodes were
activated by the erbb2 mutation. A simulated treatment with Palbociclib reduced the number of activated
genes down to 60, while with Trastuzumab the activated nodes were only 53. The combined
therapy revealed an intriguing result providing a significant and remarkable reduction of the activated
genes from 69 to 33.

Conclusion:
These results let us hypothesize that there could be an increased efficacy giving the combination
therapy to subjects with HER2 positive breast cancer. Finally, pathway analysis could be specifically
used to design clinical trials predicting the efficacy of combination therapies or untested
drugs on a specific disease.
Kinetic and Mechanistic Study of Oxidative Degradation and Detoxification
of Fast Yellow Azo Dye Using Surfactant Assisted Ir-Ni Bimetallic
Nanocatalyst
Authors: Shikha  , Goel Anjali 
Published: April 2022

Aim:
Catalytic degradation of azo dye.

Background:
Azo dyes are toxic agents and pollutants and the degradation of these dyes has an important application in the treatment of textile industry wastes. Catalytic decolorization of fast yellow dye by hexacyanoferrate (III), abbreviated as HCF(III) using polyvinylpyrrolidone abbreviated as PVP stabilized Ir-Ni bimetallic nanocrystals has been evaluated by kinetic spectrophotometric method at 440nm wavelength of the reaction mixture.

Methods:
The impact of various operational factors such as fast yellow dye abbreviated as [FY], oxidant [HCF(III)] ions, promoter iridium-nickel bimetallic nanoparticles abbreviated as [(Ir-Ni)] BMNPs, and solution pH on the rate of the reaction have been examined.

Results:
The results represent that the reaction follows first -order kinetics model with respect to [oxidant] at optimum pH 8 and fix temperature 40±0.1◦C. Thermodynamic parameters such as activation energy (Ea), enthalpy (ΔH#), entropy (ΔS#), frequency factor (A), and free energy of activation (ΔF#) have been evaluated by examining the reaction rate at four temperatures i.e. 40⁰C, 45⁰C, 50⁰C, and 55⁰C. On the basis of experimental outcomes, an appropriate mechanism involving complex formation has been proposed.

Conclusion:
Analytical techniques such as UV-Vis spectroscopy, FTIR, and LCMS of degraded products represent the formation of easier and less harmful compounds.
Efecto de la altitud, pendiente y exposición geográfica en la distribución de helechos arborescentes
Authors: Antúnez Pablo , López-Serrano Pablito Marcelo , González-Adame Gabriel , Rubio Camacho Ernesto Alonso , Mendoza-Díaz María Magdalena 
Published: April 2022

Antecedentes y Objetivos: El conocimiento de los rasgos topográficos de un sitio es importante para comprender la diversidad local y monitorear la respuesta de las plantas de alto interés de conservación al cambio climático o al cambio de uso de suelo. El objetivo de este trabajo fue examinar el patrón de distribución de cuatro especies de helechos arborescentes en función de la altitud, la exposición y la pendiente a lo largo de un continuo altitudinal.Métodos: Se estudió el efecto de la altitud, pendiente y exposición geográfica en la distribución de Alsophila firma, Cyathea bicrenata, Cyathea myosuroides y Sphaeropteris horrida, en La Chinantla, al norte de Oaxaca, México. La hipótesis de homogeneidad de proporciones a los factores topográficos se verificó con la prueba de Chi cuadrada y la magnitud de incidencia mediante funciones polinómicas.Resultados clave: Se observaron diferencias significativas entre las proporciones de cada especie en función de cada variable topográfica. En promedio, la pendiente mostró un índice de importancia 43.48 veces más que la orientación geográfica y 2.50 veces más que la altitud. Se observaron similitudes entre el nicho parcial de Cyathea bicrenata y de Alsophila firma, pero disimilitudes entre Alsophila firma y Cyathea myosuroides. Conclusiones: La distribución de proporciones de los helechos arborescentes a nivel local es discontinua y no uniforme, atribuible a la acción de los factores locales predominantes, principalmente a la topografía. Una topografía heterogénea propicia patrones de distribución más aleatorios.
Endothelial Dysfunction Diagnostic “Platform” in patients with diabetes mellitus
Authors: Khripun I. A. , Khripun A. V. 
Published: April 2022

Objective: to determine the diagnostic signifi cance of endothelial dysfunction (ED) laboratory markers.Material and methods: we examined 276 men with type 2 diabetes mellitus (age 54.0[49;60] years). Patients underwent general clinical studies, analysis of carbohydrate and lipid metabolism parameters, adipohormones: leptin, resistin, adiponectin. Endothelial function was assessed by ultrasound examination of endothelium-dependent vasodilation (EDVD) of the brachial artery during a test with reactive hyperemia and determination of biochemical parameters of endothelial function — nitric oxide (NO), endothelial synthase NO type3, endothelin, ICAM-1, VCAM-1, p- and e-selectins, cadherin, PAI-1, VEGF-1, homocysteine B, C-reactive protein (CRP), osteoprotegerin. To assess the diagnostic signifi cance of the methods and to determine the cut-off , ROC analysis was used.Results: independent signifi cance in the diagnosis of ED was demonstrated by NO, ICAM-1, resistin (p<0.001), CRP (p=0.006). Th e odds ratio of ED for resistin was 6.97, which is 1.9 times higher than NO and ICAM-1 and 3.7 times higher than CRP. Th e cut-off for diagnostic of ED are: NO — 97.3 μmol/L, ICAM-1 — 309.4 ng/ml, resistin — 6.32 ng/ml, CRP — 6.25 mg/L.Conclusion: the diagnostic platform for determining ED, along with the ultrasound assessment of EDVD, should include the analysis of its biochemical markers: NO, ICAM-1, resistin, CRP. Resistin is an independent, high-precision marker of ED, which is the pathogenetic link between endothelial dysfunction and adipose tissue dysmetabolism.
Serum TSH level in hospitalized patients with moderate-to-severe COVID-19
Authors: Mikhailova A. A. , Lagutina D. I. , Golovatuk K. A. , Karonova T. L. , Andreeva A. T. , Vasilieva E. Yu , Grineva E. N. 
Published: April 2022

Objective: to measure the serum TSH level in hospitalized patients with moderate-to-severe COVID-19.Material and methods: this was a retrospective study at Almazov National Medical Research Centre enrolled 133 hospitalized COVID-19 patients without known thyroid disorders. Clinical data, biochemical parameters (TSH, 25(OH)D, C-reactive protein, Lactate dehydrogenase and Ferritin), fi ndings of chest computed tomography (CT) imaging as well as obtained corticosteroids therapy were analyzed.Results: the median TSH level at the 1st-2nd day of hospitalization and at the 9-10th day was 1,15 mIU/L [0, 76; 1, 8] and 1,04 mIU/L [0,7; 1,78] respectively. Th e initial level of TSH <0,4 mIU/L was found in four patients, while by the 9-10th day of hospitalization their number doubled and reached 9 (11,7%). Furthermore, by the 9-10th day of hospitalization the TSH level more than 4,5 mIU/L was detected in four patients (4,2%). Th us, 13 out of 77 patients had the serum TSH level outside the reference range by the 9-10th day of hospitalization.Conclusions: in case of alteration in the serum TSH level it is necessary to take into account the personal history of thyroid disorders. Th e level of thyroid hormones and autoimmune markers as well as thyroid ultrasound results may be useful in clinical interpretation of thyroidal insults during and aft er COVID-19. Th e hypothalamic-pituitary-thyroid axis may also be aff ected by drugs used to treat COVID-19.
New coronavirus disease 2019 (COVID-19): Is there an impact on male reproductive health
Authors: Ibishev Kh. S. , Prokop J. O. 
Published: April 2022

The male reproductive health depends on several factors that can be divided into two main groups: the first group, genetic or hereditary (in particular, Klinefelter syndrome, etc.), the second acquired factors that depend on the person's lifestyle (bad habits, diet), stress, infectious diseases of the genitourinary system, etc. The presence of infectious and inflammatory diseases of the male reproductive system leads to impaired reproductive and endocrine function, significantly reducing the reproductive potential. In the last three years of our time around the world, including Russia, the number of people who have become ill with a new viral infection (COVID-19) caused by the new coronavirus (SARS-CoV-2), which causes dysfunction and has a negative effect on many organs and organs, body systems.The overview of recent publications is devoted to the study of the effect of SARS-CoV-2 on the reproductive health of men. The search was performed using the Medline, PubMed, and EMBASE databases.
Assessing the influence of cardiovascular risk factors on the severity of erectile dysfunction: a multivariate statistical analysis
Authors: Kamalov A. A. , Matskeplishvili S. T. , Chaliy M. E. , Strigunov A. A. , Okhobotov D. A. , Sorokin N. I. , Nesterova O. Yu. , Kadrev A. V. , Dyachuk L. I. , Bogachev R. K. 
Published: April 2022

Introduction. The American Heart Association identifies 7 major factors that affect the condition of the vascular wall: smoking, blood pressure, total cholesterol, glucose, body mass index, physical activity, and diet. The vascular wall lesions most often manifest clinically as vasculogenic erectile dysfunction (ED). Consequently, evaluating patients for the presence of the above risk factors can not only help in the treatment of ED, but can also significantly increase the chances of early detection of cardiac pathology.Purpose of the study. To assess cardiovascular disorder markers’ role in prognosing of the presence or absence of ED and its severity.Materials and methods. The study included 40 patients aged 33 – 60 years. Erectile function was assessed using the device «Androscan – MIT» ("Minimally invasive technologies" LLC, Moscow, Russian Federation) and the IIEF-15 questionnaire. Statistical data processing was carried out using Statistica 12 («StatSoft Inc.», Tusla, CA, USA) и IBMÒ SPSS Statistics 26 («SPSS: An IBM Company», IBM SPSS Corp., Armonk, NY, USA).Results. For patients with more severe ED, a greater deviation of the parameters studied from normal is typical. The most significant impact on the detection of different ED degrees using the device «Androscan – MIT» had TC, HDL, LDL, RP, BMI, triglycerides и HbA1c levels. Based on the androscanning data, a classification tree with two branches (branching conditions — the level of TC and LDL) and four terminal vertices (depending on the degree of ED) was obtained. There were no classification errors predicting ED degrees, which in this case indicates the good significance of the mathematical prediction. Only IIEF-15 scores had the greatest impact on ED detection using IIEF-15. The only condition for branching when constructing classification trees was the number of IIEF-15 points (two branches with three terminal vertices were obtained).Conclusion. Cardiovascular risk factors are predictors of vascular ED, detected by androscanning, while the widespread IIEF-15 questionnaire remains completely dependent on subjective feelings of patients without relying on laboratory and instrumental research methods.
Alternative trans-parenchymal access for percutaneous contact nephrolithotripsy
Authors: Malinin Yu. Yu. 
Published: April 2022

Introduction. An actual issue of modern endoscopic surgery for urolithiasis is the development of techniques for optimal access to the stone. Percutaneous access during contact nephrolithotripsy (PCNL) is believed to reach the pyelocalyceal system (PCS) along the shortest trajectory and pass through the small calyces. It assumes multi-accessibility, as well as interventional cascading. Anatomically, the kidney is divided into five relatively independent segments in terms of blood supply. The thickness of the posterior one is only a quarter of the thickness of the kidney, which allows us to assume a significantly smaller number of vessels in this segment even outside the Zondek (Brödel) bloodless line.Purpose of the study.To prove the possibility of using an optimized transparenchymal approach in PCNL based on the renal vascular structure.Material and methods. A prospective analysis of the treatment of 41 patients with urolithiasis who hadPCNL. Before surgery, patients were randomized by gender, age, average stone size, and urolithiasis forms. Subjects were divided into two groups. Group 1 (study) —20 (48.8%) patients underwent PCNL through trans-parenchymal access to the inferior-lateral parts of the pelvis or the large lower renal calyx due to the ventral orientation of the lower small calyces. Group 2 (control) — 21 (51.2%) patients underwent standard PCNL. The creation of access to PCS was provided simultaneously with Doppler ultrasound of the renal vessels to prevent damage to the segmental and interlobular vessels of the kidney.Results. In 73.2% of patients, the blood supply in the region of standard access to the PCS goes through the posterior segmental artery, which does not supply blood to the lower half of the kidney (type 1 blood supply). In 26.8% of patients, branches of the posterior segmental artery cross the projection of the inferior calyces (type 2 blood supply). In cases where it is impossible to perform a standard puncture of the PCL (patients of the first group), type 1 blood supply allows you to safely make an alternative trans-parenchymal access directly to the lower calyx or pelvis through the inferior-lateral dorsal wall. The optimization of the access decreasesthe average operation time by 1.4 times and the average number of accesses by 1.3 times.Conclusion. Doppler ultrasound scanning allows to visualize of arterial vessels, which helps to provide safe trans-cutaneous puncture access to PCS. In 73.2% of patients, the region of the posterior surface of the pelvis and the lower calyx was identified with the possibility of an anatomically justified low-traumatic trans-parenchymal access. It significantly expands the area of the parts of the PCS accessible for direct intervention. The creation of a trans-parenchymal access to the lower lateral parts of the renal pelvis allows reducing the total number of accesses to the PCS, which reduces the operation time and the number of complications.
Optimization of HIFU monotherapy for prostate cancer
Authors: Pozdnyakov K. V. , Bazaev V. V. , Dutov V. V. 
Published: April 2022

Introduction. One of the most researched alternative treatments for localized prostate cancer (PCa) is ultrasound ablation (HIFU ¾ High-intensity Focused Ultrasound). Although the world history of the application of this method of PCa treatment is more than 15 years old, the scope of the application of the method has not finally been determined.Purpose of the study. To study the results of the application of ultrasound ablation in the treatment of patients with localized and locally advanced PCa.Materials and methods. The study included 147 patients with PCa who underwent HIFU treatment using the AblathermÒ device («EDAP TMS», Vaulx-en-Velin, Lyon, France). Group 1 included patients with localized and locally advanced PCa treated at the stage of gaining experience and evaluating the results of treatment (n = 82). Group 2 consisted of patients with localized PCa of low and moderate oncological risk (n = 65). The number of sessions in group 1 varied from 1 (65) to 2 (17). The need to perform a second session was associated with the ineffectiveness of the first. HIFU was also performed after the failure of external beam radiation (2), and photodynamic (1) therapy. In group 2, 61 patients received one treatment session, 4 patients received 2 sessions each. The mean follow-up time for the patients in group 1 was 17.4 ± 5.2 (3 – 29) months, for group 2 was 18.2 ± 7.3 (3 – 29) months.Results. In group 1 of patients with a low degree of oncological risk, a decrease in blood prostate-specific antigen (PSA) below the threshold value and the absence of its significant increase during the observation period was noted in 87.5% of cases (28 patients), with an average degree of oncological risk in 65.6% of cases (21 patients), with a high degree in 27.7% of cases (5 patients). In 34.1% (28 patients), the treatment was ineffective, 21 of them underwent repeated ultrasound ablation of the prostate, and 7 patients received subsequent external beam radiation therapy. These results led us to abandon the use of HIFU in patients with baseline blood PSA levels greater than 20 ng/ml and locally advanced disease. In group 2, biochemical recurrence was noted in 9 patients. A control biopsy in 6 patients confirmed local recurrence, which became the basis for a second HIFU session (4). Five patients received adjuvant hormonal therapy. The total effectiveness of the treatment in group 2 was 86.2%.Conclusion. The results support the notion that HIFU is a treatment option for localized PCa only. The evaluation of the initial results led us to abandon treatment with this method in patients with locally advanced and high-risk localized PCa.
The non-biological simulator with the ability to regulate the position of the kidney and bone landmarks: use for training puncture access in percutaneous nephrolithotripsy
Authors: Guliev B. G. , Talyshinskiy A. E. , Stetsik E. O. , Agagyulov M. U. 
Published: April 2022

Introduction. The non-biological simulators presented in the literature are far from the real human anatomy and are primarily aimed at developing the skill of the pyelocalyceal system (PCS) puncture without the possibility of imitating various intraoperative scenarios.Purpose of the study. To describe the manufacturing and initial testing of the ultrasound-guided PCS puncture simulator with arbitrary placement of bone landmarks and a kidney model, along with the use of a retrograde view during PCS puncture.Materials and methods. This study included training for 5 resident and 2 urologists. Each participant performed the puncture 5 times using an 18-gauge ultrasound-guided needle. A comparison was made between the number of attempts to form access, the duration of the puncture and its correctness (puncture into the small calyx through the papilla), as well as the correctness of determining the target calyx. The trajectory of the needle was retrogradely assessed using a semi-rigid ureteroscope, and the anatomical identification of the selected calyx was assessed using our mobile application.Results. The total number of attempts was 49 and 14 among residents and urologists, respectively. The average duration of the puncture step was 25.2 and 12.0 seconds. In 9/25 cases, residents were able to correctly analyze visual ultrasound information to determine the target calyx. When a contrast agent was injected into the PCS after 63 punctures, no contrast leakage was found.Conclusion. The proposed PCS puncture simulator allows to develop to develop all the necessary skills for cost-effective training of young urologists in the technique of percutaneous access.
YV-plasty in the treatment of patients with recurrent bladder neck stenosis
Authors: Popov S. V. , Orlov I. N. , Tsoy A. V. , Topuzov T. M. , Chernysheva D. Yu. 
Published: April 2022

Introduction. Bladder neck stenosis (BNS) is a late complication of surgical treatment for benign prostatic hyperplasia. Available methods of endoscopic correction in primary BNS have limited effectiveness, while in recurrent cases their use does not lead to satisfactory results at all. YV-plasty of the bladder neck (BN) is one of the available methods of treatment for recurrent BNS.Purpose of the study. To evaluate the treatment results of patients with recurrent BNS using endovideoscopic YV-plasty of the BN.Materials and methods. We retrospectively analyzed the treatment results of 8 patients with recurrent BNS who underwent endovideoscopic YV-plasty of the BN in the Urology Division No.1 of the St. Luke St. Petersburg Clinical Hospital from 2019 to 2021.Results. Endovideoscopic YV-plasty of the bladder neck was successfully performed in all 8 patients. The mean preoperative Qmax was 3.7 ml/s (1.8 – 5.7). At 6 months after surgery, the mean Qmax was 21.4 mL/s (16.7 – 24.1). The mean preoperative I-PSS score was 20.5 (17 – 24). The mean I-PSS score 6 months after surgery was 7.1 (5.0 – 9.0). No cases of de-novo stress urinary incontinence were registered.Conclusions. Endovideoscopic YV-plasty of the BN may be an effective and safe method of treatment of patients with recurrent BNS. However, further studies are needed to obtain long-term results.