SARS-COV-2 MRNA vaccine-associated cutaneous vasculitis

During the coronavirus disease 2019 pandemic, global approach was to isolate populations with quarantine procedures to reduce the spread of this deadly virus until effective treatments are found or vaccines are developed. mRNA-based vaccines became available in the United States in March 2020. The Food and Drug Administration even issued an Emergency Use Authorization for individuals 16 years and older in December 2020. However, these rapid developments have brought along other problems such as possible side effects. As we develop and test a new treatment, it became clear how important side-effect management is. Here, we present a case of cutaneous vasculitis that developed on the fourth day of SARS-CoV-2 mRNA vaccination. The patient was successfully treated with medium-dose methylprednisolone

Tracheobronchopathia osteochondroplastica and cervical spine involvement in rheumatoid arthritis

A 62-year-old man presented to our outpatient clinic with a neck pain that began 4-month ago. The pain was increasing in severity without any neurological symptom or radiating to arms. The patient had a history of cerebrovascular accident without sequelae (1 year ago), 40 pack-year smoking, and diagnosis of rheumatoid arthritis (RA) 10 years ago. He had received an irregular treatment with prednisolone, methotrexate, and rituximab (discontinued 2 years ago)

Türk Üniversite Öğrencilerinin Yaşam Doyumları ve Akademik Ertelemelerini Belirlemede Akademik Motivasyonun Rolü

The present study aims to determine the motivational profiles of university students through a person-centered approach and to examine the relationship between motivational profiles, academic procrastination, and life satisfaction. The study participants comprised 1,770 undergraduates (1019 female, 749 male, and 2 not specified), who were categorized into three main profiles: (a) students with high levels of both intrinsic and extrinsic motivation but with a low level of amotivation (33.8%), those with a "high-level academic motivation profile"; (b) students with moderate levels of both intrinsic and extrinsic motivation but with low levels of amotivation (44.9%), those with a "medium-level academic motivation profile"; and (c) students with low levels of both intrinsic and extrinsic motivation with high levels of amotivation (21.3%), those with a "low-level academic motivation profile. The results of this study revealed that students with a high-level academic motivation profile have a high level of life satisfaction and a low level of academic procrastination. The results also show that students with medium-level academic motivation profiles have higher levels of life satisfaction than students with low-level academic motivation profiles. However, the academic procrastination level of students with medium-level academic motivation was found to be lower than that of students with a low-level academic motivation profile.Bu araştırmanın amacı birey merkezli yöntem ile üniversite öğrencilerinin motivasyon profillerini belirlemek ve bu profiler ile akademik erteleme ve yaşam doyumları arasındaki ilişkiyi incelemektir. Bu çalışmanın katılımcıları olan 1770 üniversite öğrencisi (1019 kadın, 749 erkek and 2 belirtmemiş), şu üç profile ayrılmıştır: (a) hem içsel hem de dışsal motivasyon düzeyleri yüksek fakat motivasyonsuzluk düzeyleri düşük öğrencilerden oluşan (%38) “yüksek düzeyde motivasyonlu profil” (b) hem içsel hem de dışsal motivasyon düzeyleri orta düzeyde olan fakat motivasyonsuzluk düzeyleri düşük olan öğrencilerde oluşan (%44.9) “orta düzeyde motivasyonlu profil”, (c) hem içsel hem de dışsal motivasyon düzeyleri düşük fakat motivasyonsuzluk düzeyleri yüksek öğrencilerden oluşan (%21.3) “düşük düzeyde motivasyonlu profil”. Bu çalışmanın sonuçları, yüksek düzeyde motivasyonlu profildeki öğrencilerin yüksek düzeyde yaşam doyumu ve düşük düzeyde akademik erteleme gösterdiğini ortaya koymuştur. Sonuçlar ayrıca orta düzeyde akademik motivasyonlu profildeki öğrencilerin, düşük düzeyde motivasyonlu profildeki öğrencilere göre daha yüksek düzeyde yaşam doyumuna sahip olduğunu göstermiştir. Ayrıca orta düzeyde motivasyonlu profildeki öğrencilerin akademik erteleme düzeylerinin düşük düzeyde motivasyonlu profilde yer alan öğrencilere göre daha düşük düzeyde olduğu bulunmuştur

Sınıf Rehber Öğretmenlerinin Psikolojik Danışma ve Rehberlik Anlayışları ile Psikolojik Danışma ve Rehberliğe Yönelik Tutumları

In this study, it was aimed to study the relationships between counseling and guidance understanding of guidance teachers, who are in charge of giving counseling and guidance service to a class, and their attitudes towards counseling and guidance, and how their understanding of counseling and guidance and their attitudes towards counseling and guidance differentiate in terms of various variables. Within the framework of relational screening model, the Counseling and Guidance Inventory (Kepçeoğlu, 1975) and the Guidance Counselor Attitude Scale (Demir, 2010) were used in the study, which was conducted with 595 guidance teachers working in primary and secondary education institutions in Eskişehir. As a result of the study, it was determined that there was a moderate level relationship (r= .44) between guidance teachers’ understanding level of counseling and guidance and their attitude levels towards counseling and guidance. The female guidance teachers were found to have higher understanding of counseling and guidance and attitudes towards counseling and guidance than those of the male teachers. It was also determined that the guidance teachers’ understanding of counseling and guidance and their attitudes towards counseling and guidance did not differentiate in terms of branch. On the other hand, the guidance teachers who attended the in-service training about counseling and guidance were found to have more positive attitudes only towards counseling and guidance than the ones who didn’t attend the in-service training, whereas the guidance teachers working in primary education were found to have higher levels of both counseling and guidance understanding and attitudes towards counseling and guidance than the ones working in secondary education in terms of the stage of education the teachers work in. Similarly, the counselors who had 1-9 and 10-19 years of seniority had higher counseling and guidance understandings than the ones who had 20 and more years of seniority. The findings obtained as a result of the study were discussed in the light of relevant literature.Bu çalışmada bir sınıfın rehberlik hizmetlerini yürütmekle görevli olan sınıf rehber öğretmenlerinin psikolojik danışma ve rehberlik anlayışları ve psikolojik danışma ve rehberliğe yönelik tutumları arasındaki ilişkilerle, psikolojik danışma ve rehberlik anlayışları ve psikolojik danışma ve rehberliğe yönelik tutumların çeşitli değişkenler açısından nasıl farklılaştığı araştırılmıştır. İlişkisel tarama modeli çerçevesinde Eskişehir ilinde ilköğretim ve ortaöğretim kurumlarında görevli 595 sınıf rehber öğretmeni ile gerçekleştirilen bu araştırmada, Rehberlik Anlayış Envanteri (Kepçeoğlu, 1975) ve Sınıf Rehber Öğretmen Tutum Ölçeği (Demir, 2010) kullanılmıştır. Araştırma sonucunda, sınıf rehber öğretmenlerinin psikolojik danışma ve rehberlik anlayış düzeyleri ile psikolojik danışma ve rehberliğe yönelik tutum düzeyleri arasında orta düzeyde pozitif (r= .44) bir ilişki olduğu saptanmıştır. Ayrıca kadın sınıf rehber öğretmenin hem psikolojik danışma ve rehberlik anlayışlarının hem de psikolojik danışma ve rehberliğe yönelik tutumlarının erkeklere göre daha yüksek olduğu, branşa göre sınıf rehber öğretmenlerin psikolojik danışma ve rehberlik anlayışlarının ve psikolojik danışma ve rehberliğe yönelik tutumlarının farklılaşmadığı belirlenmiştir. Rehberlikle ilgili hizmet içi eğitime katılmış sınıf rehber öğretmenlerinin, katılmayanlara kıyasla sadece psikolojik danışma ve rehberliğe yönelik tutumlarının daha olumlu olduğu, çalışılan eğitim kademesine göre ise ilköğretimde çalışan sınıf rehber öğretmenlerinin hem psikolojik danışma ve rehberlik anlayış düzeylerinin hem de psikolojik danışma ve rehberliğe yönelik tutum düzeylerinin ortaöğretimde çalışanlardan daha yüksek olduğu saptanmıştır. Kıdemleri 1-9 yıl ve 10-19 yıl arasında olan sınıf rehber öğretmenlerinin psikolojik danışma ve rehberlik anlayışlarının, 20 ve daha fazla kıdem yılına sahip olanlara göre daha yüksek olduğu belirlenmiştir. Araştırma sonucunda elde edilen bulgular, ilgili literatür ışığında tartışılmıştır

FastRemap: A Tool for Quickly Remapping Reads between Genome Assemblies

A genome read data set can be quickly and efficiently remapped from one reference to another similar reference (e.g., between two reference versions or two similar species) using a variety of tools, e.g., the commonly-used CrossMap tool. With the explosion of available genomic data sets and references, high-performance remapping tools will be even more important for keeping up with the computational demands of genome assembly and analysis. We provide FastRemap, a fast and efficient tool for remapping reads between genome assemblies. FastRemap provides up to a 7.82$\times$ speedup (6.47$\times$, on average) and uses as low as 61.7% (80.7%, on average) of the peak memory consumption compared to the state-of-the-art remapping tool, CrossMap. FastRemap is written in C++. The source code and user manual are freely available at: github.com/CMU-SAFARI/FastRemap. Docker image available at: https://hub.docker.com/r/alkanlab/fast. Also available in Bioconda at: https://anaconda.org/bioconda/fastremap-bio.Comment: FastRemap is open source and all scripts needed to replicate the results in this paper can be found at https://github.com/CMU-SAFARI/FastRema

A case of quadriparesis due to renal tubular acidosis accompanied by vitamin D deficiency in Sjögren’s syndrome

Renal tubular acidosis (RTA) is metabolic acidosis disorder with a normal anion gap that occurs resulting from bicarbonate reabsorption or disorder in the hydrogen excretion from the kidney. A variety of tests are required to be administered in a stepwise fashion for the diagnosis and characterization of RTA. Correct diagnosis involves careful evaluation, including exclusion of other entities causing acidosis. The patients were treated with potassium and bicarbonate supplementation. A fifty-one years old female patient presented to the emergency department with quadriparesis dependent on hypokalemia and vitamin D deficiency, was diagnosed with distal renal tubular acidosis (dRTA) combined with Sjögren's Syndrome (SS). We submitted this case in order to draw attention to the presentation of the RTA with SS

Utilization of recreational opportunities spectrum’s method in planning touristic recreationTuristik rekreasyon planlamasında rekreasyonel fırsat dağılımı yönteminin kullanımı

A variety of traditional methods are used in planning recreational activities for touristic purposes. Dimensions such as accessibility, health, social structure (local people) and quality perceptions are taken into consideration in these methods known as traditional. But in recent years for this purpose, Recreational Opportunities Spectrum (ROS) method has been used for micro and macro scale spatial plan. ROS method is a behavioral approach which has been developed for area administrators in order to assist them in planning and to ensure the diversity of recreational opportunities. Besides, this method is also used as a tool for the control of conflicts in the planning area. Beyond making generalizations for carrying out recreational activities, ROS approach is also important as a method that helps to determine people’s desires for activities. This method is applied in two stages: a) area mapping, b) determining the level of user satisfaction. In this study, recommendations are made for planning touristic recreation areas by assessing the examples of the use of this method in the World and Turkey. Özet Turistik amaçlı rekreasyon aktivitelerin planlanmasında çeşitli geleneksel yöntemler kullanılmaktadır. Geleneksel olarak bilinen bu yöntemlerde; erişebilirlik, sağlık, sosyal yapı (yerel halk) ve kalite algısı gibi boyutlar dikkate alınmaktadır. Ancak son yıllarda bu amaçla, makro ve mikro ölçekli mekânsal planlarda Rekreasyonel Fırsat Dağılımı (RFD) yöntemi kullanılmaya başlanmıştır. RFD yöntemi, halka açık alanlarda rekreasyonel fırsatların çeşitliliğini sağlamak ve planlamada yardımcı olmak amacıyla alan yöneticileri için geliştirilmiş davranışsal bir yaklaşımdır. Ayrıca, bu yöntem alan planlamasında çatışmaların kontrolünü sağlayan bir araç olarak da kullanılmaktadır. RFD yaklaşımı, rekreasyonel aktivitelerin yapılması için gerçekleştirilen genellemelerin daha ötesinde, insanların arzuladığı aktivitelerin kesin olarak tespit edilmesini sağlayan bir yöntem olarak önemlidir. Bu yöntem iki aşamalı olarak uygulanmaktadır: Alanı haritalandırma ve kullanıcı memnuniyet düzeylerinin belirlenmesi. Çalışmada yöntemin Dünyada ve Türkiye’deki kullanım örnekleri üzerinden bir değerlendirme yapılarak, turistik rekreasyon alanlarının planlaması için öneriler geliştirilmiştir

TargetCall: Eliminating the Wasted Computation in Basecalling via Pre-Basecalling Filtering

Basecalling is an essential step in nanopore sequencing analysis where the raw signals of nanopore sequencers are converted into nucleotide sequences, i.e., reads. State-of-the-art basecallers employ complex deep learning models to achieve high basecalling accuracy. This makes basecalling computationally-inefficient and memory-hungry; bottlenecking the entire genome analysis pipeline. However, for many applications, the majority of reads do no match the reference genome of interest (i.e., target reference) and thus are discarded in later steps in the genomics pipeline, wasting the basecalling computation. To overcome this issue, we propose TargetCall, the first fast and widely-applicable pre-basecalling filter to eliminate the wasted computation in basecalling. TargetCall's key idea is to discard reads that will not match the target reference (i.e., off-target reads) prior to basecalling. TargetCall consists of two main components: (1) LightCall, a lightweight neural network basecaller that produces noisy reads; and (2) Similarity Check, which labels each of these noisy reads as on-target or off-target by matching them to the target reference. TargetCall filters out all off-target reads before basecalling; and the highly-accurate but slow basecalling is performed only on the raw signals whose noisy reads are labeled as on-target. Our thorough experimental evaluations using both real and simulated data show that TargetCall 1) improves the end-to-end basecalling performance of the state-of-the-art basecaller by 3.31x while maintaining high (98.88%) sensitivity in keeping on-target reads, 2) maintains high accuracy in downstream analysis, 3) precisely filters out up to 94.71% of off-target reads, and 4) achieves better performance, sensitivity, and generality compared to prior works. We freely open-source TargetCall at https://github.com/CMU-SAFARI/TargetCall

RawHash: Enabling Fast and Accurate Real-Time Analysis of Raw Nanopore Signals for Large Genomes

Nanopore sequencers generate electrical raw signals in real-time while sequencing long genomic strands. These raw signals can be analyzed as they are generated, providing an opportunity for real-time genome analysis. An important feature of nanopore sequencing, Read Until, can eject strands from sequencers without fully sequencing them, which provides opportunities to computationally reduce the sequencing time and cost. However, existing works utilizing Read Until either 1) require powerful computational resources that may not be available for portable sequencers or 2) lack scalability for large genomes, rendering them inaccurate or ineffective. We propose RawHash, the first mechanism that can accurately and efficiently perform real-time analysis of nanopore raw signals for large genomes using a hash-based similarity search. To enable this, RawHash ensures the signals corresponding to the same DNA content lead to the same hash value, regardless of the slight variations in these signals. RawHash achieves an accurate hash-based similarity search via an effective quantization of the raw signals such that signals corresponding to the same DNA content have the same quantized value and, subsequently, the same hash value. We evaluate RawHash on three applications: 1) read mapping, 2) relative abundance estimation, and 3) contamination analysis. Our evaluations show that RawHash is the only tool that can provide high accuracy and high throughput for analyzing large genomes in real-time. When compared to the state-of-the-art techniques, UNCALLED and Sigmap, RawHash provides 1) 25.8x and 3.4x better average throughput and 2) an average speedup of 32.1x and 2.1x in the mapping time, respectively. Source code is available at https://github.com/CMU-SAFARI/RawHash