bluuebunny/crossref_metadata_2025_split huggingface dataset:
Long term outcomes of patients who underwent radical hsyterectomy for cervical cancer
Authors: BİLGİ Ahmet , ATEŞ Mete Can , KESER ŞAHİN Havva Hande , AVCI Fazıl , KULHAN Mehmet , GÜLER Abdül Hamid , ÇİNTESUN Ersin , CELİK Cetin 
Published: January 2022

Introduction: We aimed to examine the parameters affecting long-term prognosis and survival in patients diagnosed with early stage cervical cancer and undergoing radical hysterectomy in our Gynecology and Obstetrics Clinic.
Material and Method: The files of 86 cervical cancer patients who underwent radical hysterectomy and pelvic paraaortic lymph node dissection for cervical cancer between 2010 and 2021 were retrospectively reviewed. Tumor size, FIGO stage, vagina, endometrium, ovary, parametrium, pelvic lymph node, paraaortic lymph node and deep stromal involvement were examined by examining the files and pathology reports of the patients. Then, the effects of these parameters on pelvic and paraaortic lymph node involvement, postoperative prognosis and survival of the patients were tried to be revealed.
Results: The 86 patients included in the analysis had a mean age of 55.2 (range: 38-72) and a median tumor size of 35 mm (range: 2-74). Cell type was squamous cell carcinoma in 81.4% and adenocarcinoma in 18.6% of the patient group. During the follow-ups, recurrence was detected in 22 (25.6%) patients. During the follow-up period, it was found that 18 (20.9%) patients died. In univariate analysis, the presence of metastases in any lymph node was found to reduce DFS and OS. The mean follow-up period of the cases examined was 66 (min:12-max:132) months; The mean OS and DFS of the patients were 111.84 (95% CI:103.26-120.43) and 105.72 (95% CI:95.87-115.57) months, respectively.
Conclusion: Pelvic and paraaortic lymph node involvement was found to be the most important prognostic factor regardless of histological type in cervical cancers. Survival was found to be significantly lower in patients with any lymph node involvement.
Metastatic infectious complications in tunneled dialysis catheter-associated infections: a single-center experience
Authors: TÜRKMEN Ercan 
Published: January 2022

Aim: Although the guidelines recommend arteriovenous fistula (AVF) primarily as vascular access in hemodialysis patients, tunneled catheter (TC) use is gradually increasing. TCs are associated with an increased risk of infection. TC infections can cause many metastatic infectious complications such as infective endocarditis (IE), spondylodiscitis (SpD), and paravertebral abscess. This study aimed to determine the frequency, risk factors, and prognosis of metastatic infectious complications in patients admitted to our hospital with TC infections.
Material and Method: Patients with TCs hospitalized to the Nephrology unit of Ondokuz Mayıs University Hospital between January 1, 2015, and January 1, 2020, with catheter infection, were included in the study. Demographic, clinical, and microbiological information was obtained from the patients' medical records retrospectively. Metastatic infectious complications were defined as IE, SpD, paravertebral or epidural abscess, and septic embolisms in any focus. Binary logistic regression analyzes were used to identify risk factors for metastatic infectious complications.
Results: One hundred and forty-eight catheter episodes were included in the study. Eighty-seven (58.8%) of the patients were women. Metastatic infectious complications developed in 22 (14.9%) of the patients. Of these, ten patients had IE, ten patients had SpD, and two patients had both IE and SpD. Coagulase-negative staphylococci was obtained as pathogenic microorganism in most cases (9/22, 49%). Patients with infectious complications had higher length of hospital stay [46.5 (10-171) vs 18 (6-92); p
Pain levels of patients undergoing ultrasound guided biopsies and associated factors: a cross-sectional study
Authors: AKIN Mustafa Emre 
Published: January 2022

Aim: Patients may experience pain in minimally invasive biopsy procedures. It is important to evaluate the degree of pain and to know the factors that determine the level of pain felt by patients for adequate pain management. The aim of this study is to determine the pain levels felt by patients and socio-demographic and clinical factors associated with higher pain levels in breast and liver biopsy procedures.
Material and Method: In this cross-sectional observational study, patients who will undergo ultrasound-guided breast and liver biopsy procedures in the study center were invited to the study. The pain level was measured with the Visual Analogue Scale (VAS). Pain measurements above 45mm were classified as moderate-to-high pain levels. The State-Trait Anxiety Scale was used to measure the anxiety levels of the patients and the radiologist. Sociodemographical (sex, age, education level, job, income) and clinical factors (biopsy site, duration, bosy mass index, anxiety level of the patient and the radiologist) that may be associated with the pain levels of the patients were analyzed.
Results: The sample consisted of 76 patients, 62 were female (81.6%). The procedures consisted of 43 breast biopsies (56.6%), 33 liver biopsies (43.4%). The median pain level measurement determined by the VAS is 20.0mm (IQR: 9.3- 38.5). Most of the sample (59.2%) stated that they felt mild pain. It was found that patients with higher anxiety levels and patients underwent liver biopsy had statistically significantly higher moderate-to-high pain levels than patients with lower anxiety (OR: 3.683 95% CI: 1.159- 11.705, p=0.220), patients who underwent breast biopsies (OR: 3.521, 95% CI: 1.153- 10.752, p=0.023). A positive correlation was found between the level of pain and the level of anxiety (r=0.267, p=0.020).
Conclusion: This study demonstrated that most ultrasound-guided biopsy procedures were performed with mild or no pain although higher patient anxiety levels were associated with higher pain levels during the procedures. Patients undergoing liver biopsy procedures had higher pain levels than breast biopsy procedures.
Komparasi Distribusi Pencahayaan Alami, Rumah Panggung dengan Rumah Tidak Panggung
Authors: Mufidah Mufidah , Purwanto LMF , Satwiko Prasasto 
Published: January 2022

Dewasa ini desain rumah tinggal di Surabaya cenderung mempunyai ukuran relatif kecil, dengan pola tatanan berderet dan berhimpit dengan bangunan tetangga, mempunyai jumlah lantai lebih dari satu. Kondisi ini mengakibatkan semakin sulit mendapatkan kenyamanan visual (pencahayaan alami) di dalam bangunan, terutama untuk ruangan di bawah lantai. Selain itu, dengan semakin banyak memasukkan pencahayaan alami dari atap dan dinding muka bangunan, maka radiasi matahari juga ikut masuk ke dalam bangunan. Oleh karena itu dibutuhkan alternatif desain yang dapat menambah luasan selubung bangunan, namun tidak langsung berhadapan dengan radiasi matahari, salah satunya dengan menggunakan lantai panggung. Tujuan dalam penelitian ini adalah mempelajari kinerja pencahayaan pada desain rumah panggung dibandingkan dengan rumah tidak panggung, yang lantai dasarnya menempel di atas permukaan tanah. Metode penelitian ini menggunakan komparasi, dengan membandingkan pola distribusi perolehan daylight factor pada rumah tinggal tidak panggung (RTP) dibandingkan dengan rumah panggung (RP). Software yang digunakan dalam simulasi adalah Ecotect Analysis 2011, dengan menggunakan data iklim dari stasiun pengukuran iklim Gedangan, Surabaya. Hasil dari simulasi menunjukkan bahwa pada pola distribusi daylight foctor pada rumah panggung lebih merata dibandingkan dengan rumah tidak panggung, baik secara horizontal pada lantai, maupun secara vertikal pada dinding bangunan. Selain itu juga tidak terjadi kontras pada pencahayaan di dalam ruang, sehingga ruangan tetap nyaman.
Histogram Profil Proyeksi sebagai Metode Ekstraksi Fitur pada Pengenalan Karakter Tulisan Tangan
Authors: Anggraeny Fetty Tri , Munir M Syahrul , Purbasari Intan Yuniar 
Published: January 2022

Penelitian tentang pengenalan karakter masih sangat diminati sampai saat ini karena area aplikasinya yang luas. Topik penelitiannya dapat terkait dengan preprocessing, ekstraksi fitur dan metode pengenalan karakter. Dalam bidang pengenalan karakter ada beberapa metode ekstraksi fitur yang dapat digunakan, salah satunya profil proyeksi. Profil proyeksi adalah suatu histogram yang memproyeksikan piksel citra kearah horisontal maupun vertikal. Histogram proyeksi menghitung jumlah piksel non-background pada arah spesifik tertentu, horisontal dan vertikal. Dalam penelitian ini dilakukan analisa terhadap penggunakan proyeksi vertikal, horisontal, dan gabungan terhadap karakter huruf Roman yang diklasifikasi menggunakan k-NN. Hasil dari penelitian ini memberikan performa akurasi terbaik 80,95% dengan waktu yang dibutuhkan 0,66 detik.
SEGMENTASI CITRA JANIN PADA CITRA ULTRASONOGRAFI (USG) JANIN MENGGUNAKAN METODE PREWITT DAN CANNY
Authors: Selviana Selviana , Wulan Tri Deviasari 
Published: January 2022

Abstrak—Ultrasonografi (USG) merupakan alat yang digunakan untuk mendeteksi kondisi kesehatan janin pada ibu hamil. Penggunaan USG yang dilakukan untuk mengetahui anatomi (perkembangan) janin maka perlu dilakukan USG janin. Tipe USG 2D banyak dipilih oleh ibu hamil karena harganya murah dan mudah didapatkan di Rumah Sakit dan Puskesmas. USG janin dua dimensi sendiri memiliki kekurangan seperti banyaknya derau yang terdapat pada citra dan bentuk dari antomi janin yang tidak terlalu terlihat. Penelitian ini bertujuan untuk mendapatkan hasil segmentasi dari citra USG 2D. Tahapan penelitian memiliki tiga langkah yaitu pra-pemrosesan, deteksi tepi dan penilaian akurasi. Preprosessing Citra USG 2D bertujuan untuk mengubah citra asli menjadi citra biner dan filtering citra. Tahapan kedua, segmentasi citra menggunakan deteksi tepi memiliki tujuan untuk mendapatkan garis tepi yang terdapat pada citra. Proses segmentasi menggunakan metode deteksi tepi Prewitt dan Canny. Tahapan terakhir penilaian akurasi dengan membandingkan hasil sistem dan expert judgement. Hasil penelitian menunjukkan hasil akurasi segmentasi citra USG 2D menggunakan metode canny sebesar 65% lebih akurat dibandingkan dengan menggunakan metode Prewitt yang sebesar 62%.
Treatment Strategies in Adult Dysphagia
Authors: Kantanavičiūtė-Petružė Rita , Grigaliūnaitė Saulė 
Published: January 2022

Background. Swallowing disorders are becoming more common in an aging society, so it is important to understand and know the phases of swallowing, including the voluntary and involuntary aspects of the swallowing process, in order to be able to apply strategies to overcome swallowing disorders.
Aim. To reveal the strategies in adult dysphagia treatment.
Methods. Theoretical scientific research. This method enables to reveal and analyse the concept of swallowing disorders in the context of Lithuania and foreign countries, analyzes the variety of rehabilitation strategies applied to overcome swallowing disorders, and emphasizes the importance of complex dysphagia assessment and treatment. Adult dysphagia treatment strategies are compared and summarized.
Results. The analysis of Lithuanian and foreign science research showed that complex strategies are most often applied for adult dysphagia treatment. Rehabilitative dysphagia treatment strategies are used to accelerate the recovery of swallowing function, and compensatory strategies are applied to ensure patient safety during eating.
Conclusion. In each case, speech therapy differs depending on individual personal and external factors that affect swallowing disorder. Adult dysphagia treatment is usually complex in Lithuania: both rehabilitative and compensatory models are applied in dysphagia treatment.
Keywords: swallowing disorders, dysphagia treatment strategies, rehabilitative dysphagia treatment strategies, compensatory dysphagia treatment strategies.
RecruitPlotEasy: An Advanced Read Recruitment Plot Tool for Assessing Metagenomic Population Abundance and Genetic Diversity
Authors: Gerhardt Kenji , Ruiz-Perez Carlos A. , Rodriguez-R Luis M. , Conrad Roth E. , Konstantinidis Konstantinos T. 
Published: January 2022

Mapping of short metagenomic (or metatranscriptomic) read data to reference isolate or single-cell genomes or metagenome-assembled genomes (MAGs) to assess microbial population relative abundance and/or structure represents an essential task of many studies across environmental and clinical settings. The filtering for the quality of the read match and assessment of read mapping results are frequently performed without visual aids or with the assistance of visualizations produced through ad-hoc, in-house approaches. Here, we introduce RecruitPlotEasy, a fully automated, user-friendly pipeline for these purposes that integrates statistical approaches to quantify intra-population sequence and gene-content diversity and identify co-occurring relative populations in the sample. Hence, RecruitPlotEasy should also greatly facilitate population genetics studies.RecruitPlotEasy is implemented in Python and R languages and is freely available open source software under the Artistic License 2.0 from https://github.com/KGerhardt/RecruitPlotEasy.
Interpreting Functional Impact of Genetic Variations by Network QTL for Genotype–Phenotype Association Study
Authors: Yuan Kai , Zeng Tao , Chen Luonan 
Published: January 2022

An enormous challenge in the post-genome era is to annotate and resolve the consequences of genetic variation on diverse phenotypes. The genome-wide association study (GWAS) is a well-known method to identify potential genetic loci for complex traits from huge genetic variations, following which it is crucial to identify expression quantitative trait loci (eQTL). However, the conventional eQTL methods usually disregard the systematical role of single-nucleotide polymorphisms (SNPs) or genes, thereby overlooking many network-associated phenotypic determinates. Such a problem motivates us to recognize the network-based quantitative trait loci (QTL), i.e., network QTL (nQTL), which is to detect the cascade association as genotype → network → phenotype rather than conventional genotype → expression → phenotype in eQTL. Specifically, we develop the nQTL framework on the theory and approach of single-sample networks, which can identify not only network traits (e.g., the gene subnetwork associated with genotype) for analyzing complex biological processes but also network signatures (e.g., the interactive gene biomarker candidates screened from network traits) for characterizing targeted phenotype and corresponding subtypes. Our results show that the nQTL framework can efficiently capture associations between SNPs and network traits (i.e., edge traits) in various simulated data scenarios, compared with traditional eQTL methods. Furthermore, we have carried out nQTL analysis on diverse biological and biomedical datasets. Our analysis is effective in detecting network traits for various biological problems and can discover many network signatures for discriminating phenotypes, which can help interpret the influence of nQTL on disease subtyping, disease prognosis, drug response, and pathogen factor association. Particularly, in contrast to the conventional approaches, the nQTL framework could also identify many network traits from human bulk expression data, validated by matched single-cell RNA-seq data in an independent or unsupervised manner. All these results strongly support that nQTL and its detection framework can simultaneously explore the global genotype–network–phenotype associations and the underlying network traits or network signatures with functional impact and importance.
Homologous Cloning of Potassium Channel Genes From the Superior Apple Rootstock Line 12-2, Which is Tolerant to Apple Replant Disease
Authors: Mao Yunfei , Yin Yijun , Cui Xueli , Wang Haiyan , Su XiaFei , Qin Xin , Liu Yangbo , Hu Yanli , Shen Xiang 
Published: January 2022

Potassium channels are important ion channels that are responsible for the absorption of potassium in the plant nutrient uptake system. In this study, we used homologous molecular cloning to obtain 8 K+ channel genes from the superior apple rootstock line 12-2 (self-named): MsAKT1-1, MsKAT3-2, MsKAT1-3, MsK2P3-4, MsK2P3-5, MsK2P5-6, MsK2P3-7, and MsK2P3-8. Their lengths varied from 942 bp (MsK2P5-6) to 2625 bp (MsAKT1-1), and the number of encoded amino acids varied from 314 (MsK2P5-6) to 874 (MsAKT1-1). Subcellular localization predictions showed that MsAKT1-1, MsKAT3-2, and MsKAT1-3 were localized on the plasma membrane, and MsK2P3-4, MsK2P3-5, MsK2P5-6, MsK2P3-7, and MsK2P3-8 were localized on the vacuole and plasma membrane. The 8 K+ channel proteins contained α helices, extended strands, β turns, and random coils. MsKAT1-3 had four transmembrane structures, MsKAT3-2 had six, and the other six K+ channel genes had five. Protein structure domain analysis showed that MsAKT1-1 contained nine protein domains, followed by MsKAT3-2 with four, MsKAT1-3 with three, and the other five two-pore domain K+ channel proteins with two. Semi-quantitative RT-PCR detection of the K+ channel genes showed that their expression levels were high in roots. qRT-PCR analysis showed that the relative expression levels of the 8 genes changed after exposure to ARD stress. The above results provide a theoretical basis for further research on the functions of potassium channel genes in 12-2 and a scientific basis for the breeding of ARD-resistant rootstock.
Impact of COVID-19 on Gender-Based Violence Prevention and Response Services in Kenya, Uganda, Nigeria, and South Africa: A Cross-Sectional Survey
Authors: Roy Charlotte M. , Bukuluki Paul , Casey Sara E. , Jagun Moriam O. , John Neetu A. , Mabhena Nicoletta , Mwangi Mary , McGovern Terry 
Published: January 2022

BackgroundEpidemics and other complex emergencies historically have had a disproportionate impact on women and girls, increasing their vulnerability to gender-based violence (GBV). The COVID-19 pandemic has been no different, with reports of rising cases of GBV emerging worldwide. Already a significant problem in Kenya, Uganda, Nigeria, and South Africa, GBV in these countries has been exacerbated by government restrictions intended to contain the spread of COVID-19. The purpose of this study was to understand how the COVID-19 pandemic affected the availability of GBV prevention and response services from the perspective of the organizations that provide them.MethodsA cross-sectional online survey of people who work in GBV prevention and response in Kenya, Uganda, Nigeria, and South Africa was administered from July to October 2020. A convenience sample was identified through web search, contacts of in-country consultants, and relevant listservs and technical working groups. Descriptive analyses were completed using SPSS.ResultsA total of 187 respondents completed the survey. Nearly all (98.9%) survey respondents reported that COVID-19 impacted their work. The majority (77.9%) stated that work decreased due to government restrictions or GBV services being deemed non-essential. The types of service most impacted were community-based prevention, shelters, and legal services. Survey respondents overwhelmingly agreed (99.3%) that COVID-19 impacted GBV prevalence and identified adolescents and women with disabilities as particularly vulnerable groups.ConclusionsGBV prevention and response services in Kenya, Uganda, Nigeria, and South Africa were highly impacted by the COVID-19 pandemic, largely due to government restrictions and the failure of governments to deem GBV services as essential. Preparedness for future crises should ensure that GBV is adequately prioritized in the initial response in order to maintain service availability with special attention paid to at-risk populations.
Purine-Induced IFN-γ Promotes Uric Acid Production by Upregulating Xanthine Oxidoreductase Expression
Authors: Wang Huanhuan , Xie Lingzhu , Song Xuhong , Wang Jing , Li Xinyan , Lin Zhike , Su Ting , Liang Bin , Huang Dongyang 
Published: January 2022

ObjectiveLimiting purine intake, inhibiting xanthine oxidoreductase (XOR) and inhibiting urate reabsorption in proximal tubule by uricosuric drugs, to reduce serum uric acid (UA) levels, are recognized treatments for gout. However, the mechanism of increased how XOR expression and activity in hyperuricemia and gout remains unclear. This study aims to explore whether exogenous purines are responsible for increased XOR expression and activity.MethodsHepG2 and Bel-7402 human hepatoma cells were stimulated with exogenous purine, or were exposed to conditioned growth medium of purine-stimulated Jurkat cells, followed by measurement of XOR expression and UA production to determine the effect of lymphocyte-secreted cytokines on XOR expression in hepatocytes. The expression of STAT1, IRF1 and CBP and their binding on theXDHpromoter were detected by western blotting and ChIP-qPCR. The level of DNA methylation was determined by bisulfite sequencing PCR. Blood samples from 117 hyperuricemia patients and 119 healthy individuals were collected to analyze the correlation between purine, UA and IFN-γ concentrations.ResultsExcess of purine was metabolized to UA in hepatocyte metabolism by XOR that was induced by IFN-γ secreted in the conditioned growth medium of Jurkat cells in response to exogenous purine, but it did not directly induce XOR expression. IFN-γ upregulated XOR expression due to the enhanced binding of STAT1 to IRF1 to further recruit CBP to theXDHpromoter. Clinical data showed positive correlation of serum IFN‐γ with both purine and UA, and associated risk of hyperuricemia.ConclusionPurine not only acts as a metabolic substrate of XOR for UA production, but it induces inflammation through IFN-γ secretion that stimulates UA production through elevation of XOR expression.
CD19 CAR-T Cell Therapy Induced Immunotherapy Associated Interstitial Pneumonitis: A Case Report
Authors: Sun Zhuanyi , Xie Caiqin , Liu Hui , Yuan Xianggui 
Published: January 2022

BackgroundChimeric antigen receptor-modified T cells (CAR-T) targeting CD19 has produced a high durable response in refractory or relapsed diffuse large B-cell lymphoma. Besides well-known cytokine release syndrome (CRS) or immune effector cell–associated neurotoxicity syndrome during CAR-T cell therapy, there were several rarely encountered fatal complications.Case ReportA 63-year-old male patient with refractory EBV-positive diffuse large B-cell lymphoma, developed interstitial pneumonitis with prolonged hypoxemia at 16 weeks after CD19 CAR-T cell therapy. There was no evidence of CRS and any infections. The patient recovered after intravenous immunoglobulin without tocilizumab or glucocorticoid administration. Now he is still in remission without interstitial pneumonitis 3 years after CAR-T cell therapy.ConclusionThis is the first report of immunotherapy-associated interstitial pneumonitis after CAR-T cell therapy. Our finding suggested the importance of careful follow-up and proper treatments for immunotherapy-associated pneumonitis in the CAR-T cell therapy schedule.