Swiss Army Knife Research Articles

A Technology Swiss Army Knife

A Technology Swiss Army Knife

SRNAminer, a swiss army knife in small RNA research.

sRNAminer, a swiss army knife in small RNA research.

The genetic engineering Swiss army knife.

The genetic engineering Swiss army knife.

The commander complex is the Swiss Army knife of endosomal trafficking.

The commander complex is the Swiss Army knife of endosomal trafficking.

Analogy as the Swiss Army Knife of Human-like Learning

There is ample psychological evidence that analogy is ubiquitous in human learning, suggesting that computational models of analogy can play important roles in AI systems that learn in human-like ways. This talk will provide evidence for this, focusing mostly on recent advances in hierarchical analogical learning and working-memory analogical generalizations.

Rapid eye movement sleep, the Swiss army knife in neurodegenerative disease?

Rapid eye movement sleep, the Swiss army knife in neurodegenerative disease?

SeqKit2: A Swiss army knife for sequence and alignment processing.

In the era of ubiquitous high-throughput sequencing studies, there is a growing need for analysis tools that are not just performant but also comprehensive and user-friendly enough to cater to both novice and advanced users. This article introduces SeqKit2, the next iteration of the widely used sequence analysis tool SeqKit, featuring expanded functionality, performance optimizations, and support for additional compression methods. Retaining a pragmatic subcommand architecture, SeqKit2 represents substantial enhancement through the inclusion of 19 additional subcommands, expanding its overall repertoire to a total of 38 in eight categories. The new subcommands add functionality such as amplicon processing and robust, error-tolerant parsing of sequence records. In addition, three subcommands designed for real-time analysis are added for periodic monitoring of properties of FASTQ and Binary Alignment/Map alignment records and real-time streaming from multiple sequence files. The performance of SeqKit2 is benchmarked against the old version of SeqKit, Bioawk, Seqtk, and SeqFu tools. SeqKit2 consistently outperforms its predecessor, albeit with marginally higher memory usage, while maintaining competitive runtimes against other tools. With its broad functionality, proven usability, and ongoing development driven by user feedback, we hope that bioinformaticians will find SeqKit2 useful as a "Swiss army knife" of sequence and alignment processing-equally adept at facilitating ad hoc analyses and seamlessly integrating into larger pipelines.

The ‘Swiss Army knife’ of antibacterials

The ‘Swiss Army knife’ of antibacterials

Endoscopic Ultrasonography In Diagnostic Endohepatology: The Hepatologist's Swiss Army Knife.

In recent years, significant advances have been made in endoscopic ultrasonography (EUS) processors, transducers, and the instruments used. In parallel with these developments, the importance of EUS in the diagnosis, treatment, and management of chronic liver diseases has increased considerably. One of the most important advantages of EUS is that the ultrasound probe can examine the liver area under examination from a very close distance. Additionally, EUS provides the ability to provide excellent spatial files and realtime images; Doppler, elastography, and contrast methods are also widely used to increase diagnostic accuracy in EUS evaluations. Endoscopic ultrasound-guided procedures are an alternative method used when percutaneous approaches are not feasible. Endoscopic ultrasound-based advanced applications such as EUSguided liver biopsy (LB), EUS-guided ascites assessment, the use of EUS in the evaluation of focal lesions of the liver, and EUS portal pressure gradient (EUS-PPG) measurements are becoming increasingly common and important. As a result of the developments in EUS devices and instruments, it is possible to perform all diagnostic procedures in hepatology with EUS. In other words, EUS can provide all the imaging and interventional procedures that a hepatologist would require for diagnosis in a single session, without the need for any other expertise other than the gastroenterologist (such as a radiologist, interventional radiologist, or surgeon). This is called the single-procedure diagnostic approach, or "all in one" in hepatology. From a hepatologist's perspective, EUS can be thought of as the "hepatologist's Swiss army knife."

Retention of the RNA ends provides the molecular memory for maintaining the activation of the Csm complex.

The type III CRISPR-Cas effector complex Csm functions as a molecular Swiss army knife that provides multilevel defense against foreign nucleic acids. The coordinated action of three catalytic activities of the Csm complex enables simultaneous degradation of the invader's RNA transcripts, destruction of the template DNA and synthesis of signaling molecules (cyclic oligoadenylates cAn) that activate auxiliary proteins to reinforce CRISPR-Cas defense. Here, we employed single-molecule techniques to connect the kinetics of RNA binding, dissociation, and DNA hydrolysis by the Csm complex from Streptococcus thermophilus. Although single-stranded RNA is cleaved rapidly (within seconds), dual-color FCS experiments and single-molecule TIRF microscopy revealed that Csm remains bound to terminal RNA cleavage products with a half-life of over 1 hour while releasing the internal RNA fragments quickly. Using a continuous fluorescent DNA degradation assay, we observed that RNA-regulated single-stranded DNase activity decreases on a similar timescale. These findings suggest that after fast target RNA cleavage the terminal RNA cleavage products stay bound within the Csm complex, keeping the Cas10 subunit activated for DNA destruction. Additionally, we demonstrate that during Cas10 activation, the complex remains capable of RNA turnover, i.e. of ongoing degradation of target RNA.

Hysteroscopic Metroplasty Using Holmium: YAG Laser for Treatment of Septate Uterus

To demonstrate the safety, efficacy, and ease of hysteroscopic metroplasty using holmium:YAG (Ho:YAG) laser for treatment of septate uterus. Stepwise demonstration of surgical technique with narrated video footage. Septate uterus is the most common type of uterine anomaly. The incidence of uterine septum in women presenting with infertility and recurrent abortions is 15.4% [1,2]. Hysteroscopic septal incision is associated with improvement in live-birth rate in these women [3]. Hysteroscopic metroplasty for septate uterus can be done with the use of scissors and energy sources such as monopolar and bipolar electrosurgery and lasers. Ho:YAG laser is commonly used by urologists for various surgeries because of its "Swiss Army Knife" action of cutting, coagulation, and vaporization [4]. Ho:YAG laser is known for its precision. It causes lesser depth of tissue injury and necrosis and minimal collateral thermal damage compared with the electrosurgical devices and other lasers used for hysteroscopic surgery [5-8]. This is advantageous in hysteroscopic metroplasty given that it reduces the risk of uterine perforation during surgery and hence uterine rupture in the subsequent pregnancy. Reduced collateral damage to the surrounding endometrium helps promote early endometrial healing and prevent postoperative intrauterine adhesions. A 28-year-old patient with history of 2 spontaneous abortions came to our hospital for investigations. 3D transvaginal sonography of the patient showed presence of partial septate uterus with a fundal indentation of 1.5 cm (Supplemental video 1). Diagnostic hysteroscopy followed by septal incision using Ho: YAG laser was planned. We used a 2.9 mm BETTOCCHI Hysteroscope (Karl Storz SE & Co.) with a 5 mm operative sheath. Normal saline was used as the distending medium and the intrauterine pressure was maintained at 80 to 100 mm Hg. The procedure was done under total intravenous anesthesia using propofol injection. Vaginoscopic entry into the uterus (without any cervical dilatation) showed evidence of a partial uterine septum with tubal ostia on either side of the septum. A 400 micron quartz fiber was passed through a laser guide into the 5-Fr working channel of the operative hysteroscope. Ho:YAG laser (Auriga XL 50-Watt, Boston Scientific) with power settings of 15 watts (1500 mJ energy at 10 Hz) was used. Incision of the septum was started at the apex of the septum in the midline and continued in a horizontal manner from side to side toward the base (Supplemental video 2). Incision of the septum is continued till the tip of the hysteroscope can move freely from one ostium to the other (Supplemental video 3). The operative time was 12 minutes. There were no intra- or postoperative complications. Postoperative estrogen therapy was given for 2 months in the form of estradiol valerate 2 mg (tablet, Progynova, Zydus Cadila) 12 hourly orally for 25 days and medroxyprogesterone acetate 10 mg (tablet, Meprate, Serum Institute of India, Ltd) 12 hourly orally added in the last 5 days [9]. 3D transvaginal ultrasound was done on day 8 of menses. It showed a triangular uterine cavity with a very small fundal indentation of 0.37 cm. A second look hysteroscopy that was done on day 9 of menses showed an uterine cavity of good shape and size [10]. Few fundal adhesions were seen and they were incised using Ho:YAG laser. The patient conceived 5 months after the primary surgery and delivered by cesarean section at 38 weeks, giving birth to a healthy baby of 2860 grams. There were no complications during her pregnancy and delivery. A comparative study is essential to prove its advantages over other energy sources for this surgery. Hysteroscopic metroplasty using Ho:YAG laser for treatment of septate uterus is a simple, precise, safe, and effective procedure. VIDEO ABSTRACT.

An RNA polymerase that became a Swiss army knife

RNA polymerases (RNAPs) control the first step of gene expression in all forms of life by transferring genetic information from DNA to RNA, a process known as transcription. In this issue of Cell, Webster etal. and Wu etal. report three-dimensional structures of RNAP complexes from chloroplasts.

Soluble B-cell maturation antigen in multiple myeloma.

B-cell maturation antigen (BCMA) has emerged as a promising immunotherapeutic target in multiple myeloma (MM) management, with the successive approval of antibody-drug conjugates, bispecific antibodies, and chimeric antigen receptor T-cell therapies directed to this membrane receptor. Soluble BCMA (sBCMA), a truncated version produced through gamma-secretase cleavage, can be quantified in serum/plasma samples from patients with MM via electrochemiluminescence, fluorescence, or enzyme-linked immunosorbent assays, as well as through mass spectrometry-based proteomics. Besides its short serum half-life and independence from kidney function, sBCMA represents a reliable and convenient tool for MM monitoring in patients with nonsecretory or oligosecretory disease. Numerous studies have suggested a potential utility of this bioanalyte in the risk stratification of premalignant plasma cell disorders, diagnosis and prognostication of MM, and response evaluation following anti-myeloma therapies. In short, sBCMA might be the "Swiss army knife" of MM laboratory testing, but is it ready for prime time?

Super-appification: Conglomeration in the global digital economy

‘Super apps’ are on the rise. This study explores the characteristics, origins, and manifestations of these apps worldwide, presenting the concept of ‘super-appification’ to describe processes of conglomeration in the global digital economy. Super apps aim to become deeply integrated into people’s everyday lives, capturing and monetising essential activities. By analysing 41 super apps, we identify four distinct types of ‘super-app constellations’, showcasing different patterns and dynamics of conglomeration: ‘Swiss-Army Knife’ apps that consolidate services in one app, ‘Family’ apps that expand through subsidiaries, and ‘Host’ and ‘Hub’-style apps that leverage external developers. This typology offers a comprehensive understanding of the conglomeration patterns underpinning the rise of super apps, involving corporate, development and international expansion strategies. Ultimately, super-appification represents an intensified form of ‘appification’, as these apps increasingly pervade and commodify various aspects of everyday life, such as payment, insurance, grocery delivery, mobility and travel, with significant sociopolitical implications.

The History of Agrobacterium Rhizogenes: From Pathogen to a Multitasking Platform for Biotechnology.

Agrobacterium's journey has been a roller coaster, from being a pathogen to becoming a powerful biotechnological tool. While A. tumefaciens has provided the scientific community with a versatile tool for plant transformation, Agrobacterium rhizogenes has given researchers a Swiss army knife for developing many applications. These applications range from a methodology to regenerate plants, often recalcitrant, to establish bioremediation protocols to a valuable system to produce secondary metabolites. This chapter reviews its discovery, biology, controversies over its nomenclature, and some of the multiple applications developed using A. rhizogenes as a platform.

The NeuGRID Workflow: a “Swiss Army knife” for MRI processing

AbstractBackgroundThe advent of big data and artificial intelligence has energized the neuroimaging community with powerful processing tools and the need for large‐scale computational resources for data analysis has increased. Not all neuroscientists have access to extensive resources or have sufficient expertise to configure these libraries, making them difficult to use.MethodA collection of popular MRI scan processing software, (i.e.: Fsl, FreeSurfer, Ants, SPM, Adaboost, Neuromorphometrics, LPA, Tracula) was selected as a proof of concept to be included in the NeuGRID Workflow to produce an advanced tool for group analysis and biomarkers assessment.ResultThe NeuGRID Workflow was designed to allow the user to build a custom MRI processing pipeline by means of a layered structure (Fig.1) available for users at the URL https://neugrid2.eu/index.php/workflowgroup. In the first layer, the user must upload a compressed file containing T13D, FLAIR, and DWI scans of subjects. In the second layer, the user selects which kind of MRI sequence to process. If DICOMs were uploaded, the third layer provides tools to convert DICOMs into NIFTI, the default format for all subsequent workflow processes. All DICOMs are anonymized upon upload. The fourth layer allows the user to choose how images are preprocessed, and the preprocessing pipelines can be customized for different modalities. In the final layer, the user can choose how to analyze the images to calculate volume, thickness, area and curvature of brain regions, quantify white‐matter lesions and reconstruct major white‐matter pathways. The triggered job is efficiently parallelized using a Sun Grid Engine scheduler to reduce computation time. After the scans are processed in the NeuGRID cluster (450 CPUs, 2.5TB memory, 400TB storage), the user is notified by email that the job is finished and the results can be downloaded.ConclusionThe NeuGRID Workflow is a practical tool that allows researchers without computational resources and/or expertise to design a custom pipeline to process large amounts of data from anywhere using a traditional laptop or personal computer. The collection of heterogeneous tools provides a high degree of freedom in pipeline design, making NeuGRID Workflow a Swiss Army knife for MRI processing

Modular cytosine base editing promotes epigenomic and genomic modifications.

Prokaryotic and eukaryotic adaptive immunity differ considerably. Yet, their fundamental mechanisms of gene editing via Cas9 and activation-induced deaminase (AID), respectively, can be conveniently complimentary. Cas9 is an RNA targeted dual nuclease expressed in several bacterial species. AID is a cytosine deaminase expressed in germinal centre B cells to mediate genomic antibody diversification. AID can also mediate epigenomic reprogramming via active DNA demethylation. It is known that sequence motifs, nucleic acid structures, and associated co-factors affect AID activity. But despite repeated attempts, deciphering AID's intrinsic catalytic activities and harnessing its targeted recruitment to DNA is still intractable. Even recent cytosine base editors are unable to fully recapitulate AID's genomic and epigenomic editing properties. Here, we describe the first instance of a modular AID-based editor that recapitulates the full spectrum of genomic and epigenomic editing activity. Our 'Swiss army knife' toolbox will help better understand AID biology per se as well as improve targeted genomic and epigenomic editing.

Legal Scalpel or Regulatory Swiss Army Knife? The New Article 102, What Market Investigations Can Tell Us about the Difference between Law and Regulation, and What That Means for Article 102’s Ultimate Purpose

Legal Scalpel or Regulatory Swiss Army Knife? The New Article 102, What Market Investigations Can Tell Us about the Difference between Law and Regulation, and What That Means for Article 102’s Ultimate Purpose

III–V semiconductor devices grown by metalorganic chemical vapor deposition—The development of the Swiss Army Knife for semiconductor epitaxial growth

Metalorganic chemical vapor deposition (MOCVD) epitaxial materials technology for the growth of compound semiconductors has been developed over the past 60-plus years to become the dominant process for both research and production of light-emitting devices as well as many other electronic and optoelectronic devices. Today, MOCVD has become the “Swiss Army Knife” of semiconductor epitaxial growth, covering a wide variety of compound semiconductors and device applications. Because of the flexibility and control offered by this process and the material quality produced by MOCVD, many important III–V semiconductor devices have become commercially viable. This paper attempts to provide a personal view of the early development of MOCVD and some brief historical discussion of this important and highly versatile materials technology for the growth of high-quality devices employing ultrathin layers and heterojunctions of III–V compound semiconductors, e.g., quantum-well lasers, light-emitting diodes, heterojunction solar cells, transistors, and photonic integrated circuits.

Using Cooperative Learning to Teach the Sustainable Development Goals

This article advocates for the use of cooperative learning by students and others toward the achievement of the United Nations’ Sustainable Development Goals (SDGs). First, the Goals are explained. Second, background is provided on cooperative learning, including explanation of eight cooperative learning principles and exemplification of how one cooperative learning technique might mobilize the eight principles. Third, how cooperative learning fits with student centered learning is explored. Fourth, two cooperative learning techniques are explained for their particular relevance to efforts to achieve the SDGs. These techniques are Group Investigation and Cooperative Debate. Fifth, two cooperative learning principles, positive interdependence and cooperation as a value, and their links to SDGs receive further exploration. Finally, we consider cooperative learning as a Swiss Army Knife and discuss its versatility with SDG examples.