Detection of Adverse Event Signals with Severity Grade Classification from Cancer Patient Narrative

Adverse event (AE) management is crucial to improve anti-cancer treatment outcomes, but it is reported that some AE signals can be missed in clinical visits. Thus, monitoring AE signals seamlessly, including events outside hospitals, would be helpful for early intervention. Here we investigated how to detect AE signals from texts written by cancer patients themselves by developing deep-learning (DL) models to classify posts mentioning AEs according to severity grade, in order to focus on those that might need immediate treatment interventions. Using patient blogs written in Japanese by cancer patients as a data source, we built DL models based on three approaches, BERT, ELECTRA, and T5. Among these models, T5 showed the best F1 scores for both Grade ≥ 1 and ≥ 2 article classification tasks (0.85 and 0.53, respectively). This model might benefit patients by enabling earlier AE signal detection, thereby improving quality of life.

Bacteriophage T5 dUTPase: Combination of Common Enzymatic and Novel Functions

The main function of dUTPases is to regulate the cellular levels of dUTP and dTTP, thereby playing a crucial role in DNA repair mechanisms. Despite the fact that mutant organisms with obliterated dUTPase enzymatic activity remain viable, it is not possible to completely knock out the dut gene due to the lethal consequences of such a mutation for the organism. As a result, it is considered that this class of enzymes performs an additional function that is essential for the organism's survival. In this study, we provide evidence that the dUTPase of bacteriophage T5 fulfills a supplemental function, in addition to its canonical role. We determined the crystal structure of bacteriophage T5 dUTPase with a resolution of 2.0 Å, and we discovered a distinct short loop consisting of six amino acid residues, representing a unique structural feature specific to the T5-like phages dUTPases. The removal of this element did not affect the overall structure of the homotrimer, but it had significant effects on the development of the phage. Furthermore, it was shown that the enzymatic function and the novel function of the bacteriophage T5 dUTPase are unrelated and independent from each other.

A question-answer generation system for an asynchronous distance learning platform

Distance learning frees the learning process from spatial constraints. Each mode of distance learning, including synchronous and asynchronous learning, has disadvantages. In synchronous learning, students have network bandwidth and noise concerns, but in asynchronous learning, they have fewer opportunities for engagement, such as asking questions. The difficulties associated with asynchronous learning make it difficult for teachers to determine whether students comprehend the course material. Motivated students will consistently participate in a course and prepare for classroom activities if teachers ask questions and communicate with them during class. As an aid to distance education, we want to automatically generate a sequence of questions based on asynchronous learning content. In this study, we will also generate multiple-choice questions for students to answer and teachers to easily correct. The asynchronous distance teaching-question generation (ADT-QG) model, which includes Sentences-BERT (SBERT) in the model architecture to generate questions from sentences with a higher degree of similarity, is proposed in this work. With the Wiki corpus generation option, it is anticipated that the Transfer Text-to-Text Transformer (T5) model will generate more fluent questions and be more aligned with the instructional topic. The results indicate that the questions created by the ADT-QG model suggested in this work have good fluency and clarity indicators, showing that the questions generated by the ADT-QG model are of a certain quality and relevant to the curriculum.

[Editing of Phage Genomes - Recombineering-Assisted SpCas9 Modification of Model Coliphages T7, T5, and T3]

Bacteriophages-viruses that infect bacterial cells - are the most abundant biological entities on Earth. The use of phages in fundamental research and industry requires tools for precise manipulation of their genomes. Yet, compared to bacterial genome engineering, modification of phage genomes is challenging because of the lack of selective markers and thus requires laborious screenings of recombinant/mutated phage variants. The development of the CRISPR-Cas technologies allowed to solve this issue by the implementation of negative selection that eliminates the parental phage genomes. In this manuscript, we summarize current methods of phage genome engineering and their coupling with CRISPR-Cas technologies. We also provide examples of our successful application of these methods for introduction of specific insertions, deletions, and point mutations in the genomes of model Escherichia coli lytic phages T7, T5, and T3.

The Risk Factors and Clinical Features of Acanthamoeba Keratitis: First Time Detection of Acanthamoeba T5 Genotype from Keratitis Patients in Turkey

PURPOSE

The primary aim of this study is to investigate Acanthamoeba in clinical samples of keratitis cases (n = 60), in contact lens (CL) and lens care solutions of asymptomatic CL users (n = 41), and to identify the genotypes in positive samples. The secondary aim is to assess the risk factors and clinical features of Acanthamoeba keratitis (AK) patients.

METHODS

All samples from patients and asymptomatic CL users were examined by microscopy and inoculated in non-nutrient agar plates. PCR was performed using the DNA isolated from corneal scrapings, CL and lens care solution samples. Positive DNA samples were sequenced to determine the genotype of Acanthamoeba.

RESULTS

In none of the samples, Acanthamoeba was identified by microscopy, while Acanthamoeba was detected in a patient with keratitis by culture method. However, Acanthamoeba was detected in 11.66% (7/60) of the keratitis patients by PCR. The genotypes of these isolates detected by sequencing were T4 (4), and T5 (3). Acanthamoeba was detected in none of the samples of asymptomatic CL users by any of the three methods.

CONCLUSION

To best of our knowledge, this is the first study to detect T5 genotype in AK patients from Turkey. In addition, the CL use was found to be an important risk factor for AK.

Elementary Motion Detection in Drosophila: Algorithms and Mechanisms

Motion in the visual world provides critical information to guide the behavior of sighted animals. Furthermore, as visual motion estimation requires comparisons of signals across inputs and over time, it represents a paradigmatic and generalizable neural computation. Focusing on the Drosophila visual system, where an explosion of technological advances has recently accelerated experimental progress, we review our understanding of how, algorithmically and mechanistically, motion signals are first computed.

Symptomatic first-degree atrioventricular block in a young woman after taking a fat burner supplement

A 22-year-old woman collapsed at home and was brought to the accident and emergency department. History revealed that she was fit and taken T5 capsule the night before the collapse. There was no history of similar collapses or seizure. Examination revealed blood pressure (BP) of 104/69 mmHg and a heart rate (HR) of 70 bpm. Chest, cardiovascular, and neurology examination were unremarkable. However, on standing, her HR increased to 120 bpm, and her BP dropped to 62/40 mmHg. Blood Na, K, Ca, Mg, phosphate, creatinine, complete blood count, T4 cortisol, and thyroid-stimulating hormone (TSH) were normal. The electrocardiogram (ECG) on the ambulance revealed sinus rhythm with normal morphology but a significant first-degree atrioventricular block with a PR interval of 280-300 ms. The patient was treated for orthostatic hypotension with intravenous fluids. Her symptoms gradually improved. The repeat ECG taken 24 h after admission showed reduced PR interval to 230ms. The patient was followed up in the clinic after 1 week with normal ECG with a PR interval of 200 ms and a normal echocardiogram. The findings are discussed.

Identification of the ssDNA-binding protein of bacteriophage T5: Implications for T5 replication

In a recent study, we identified and characterized the long-elusive replicative single-stranded DNA-binding protein of bacteriophage T5, which we showed is related to the eukaryotic transcription coactivator PC4. Here, we provide an extended discussion of these data, report several additional observations and consider implications for the recombination-dependent replication mechanism of the T5 genus, which is still poorly understood.