MicroRNAs: Genomics, Biogenesis, Mechanism, and Function

http://bartellab.wi.mit.edu/publication_reprints/Bartel_Cell09.pdf

MicroRNAs: Target Recognition and Regulatory Functions

All cancers are caused by somatic mutations; however, understanding of the biological processes generating these mutations is limited. The catalogue of somatic mutations from a cancer genome bears the signatures of the mutational processes that have been operative. Here we analysed 4,938,362 mutations from 7,042 cancers and extracted more than 20 distinct mutational signatures. Some are present in many cancer types, notably a signature attributed to the APOBEC family of cytidine deaminases, whereas others are confined to a single cancer class. Certain signatures are associated with age of the patient at cancer diagnosis, known mutagenic exposures or defects in DNA maintenance, but many are of cryptic origin. In addition to these genome-wide mutational signatures, hypermutation localized to small genomic regions, 'kataegis', is found in many cancer types. The results reveal the diversity of mutational processes underlying the development of cancer, with potential implications for understanding of cancer aetiology, prevention and therapy.

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Signatures of mutational processes in human cancer

I have developed "tennis elbow" from lugging this book around the past four weeks, but it is worth the pain, the effort, and the aspirin. It is also worth the (relatively speaking) bargain price. Including appendixes, this book contains 894 pages of text. The entire panorama of the neural sciences is surveyed and examined, and it is comprehensive in its scope, from genomes to social behaviors. The editors explicitly state that the book is designed as "an introductory text for students of biology, behavior, and medicine," but it is hard to imagine any audience, interested in any fragment of neuroscience at any level of sophistication, that would not enjoy this book. The editors have done a masterful job of weaving together the biologic, the behavioral, and the clinical sciences into a single tapestry in which everyone from the molecular biologist to the practicing psychiatrist can find and appreciate his or

Principles of Neural Science

MicroRNAs are a family of small, non-coding RNAs that regulate gene expression in a sequence-specific manner. The two founding members of the microRNA family were originally identified in Caenorhabditis elegans as genes that were required for the timed regulation of developmental events. Since then, hundreds of microRNAs have been identified in almost all metazoan genomes, including worms, flies, plants and mammals. MicroRNAs have diverse expression patterns and might regulate various developmental and physiological processes. Their discovery adds a new dimension to our understanding of complex gene regulatory networks.

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MicroRNAs: small RNAs with a big role in gene regulation

A fundamental question in neurodevelopmental biology is how flexibly the nervous system changes during development. To address this, we reconstructed the complete connectome of dauer, an alternative developmental stage of nematodes with distinct behavioral characteristics, by volumetric reconstruction and automated synapse detection using deep learning. With the basic architecture of the nervous system preserved, structural changes in neurons, large or small, were closely associated with connectivity changes, which in turn evoked dauer-specific behaviors such as nictation. Graph theoretical analyses revealed significant dauer-specific rewiring of sensory neuron connectivity and increased clustering within motor neurons in the dauer connectome. We suggest that the nervous system in the nematode, probably animals in general, has evolved to respond to harsh environments by reversibly developing a quantitatively and qualitatively differentiated connectome.

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Mind of a dauer: Comparative connectomics reveals developmental plasticity

Channel state feedback plays a pivotal role to realize the full potential of multi-input multi-output (MIMO) evolution. Inspired by impressive success of deep learning (DL) in diverse fields, DL empowered channel state feedback has also drawn extensive attention to address the curse of dimensionality by learning compressible structure of high-dimensional MIMO channels. However, most of work mainly focus on extracting continuous features to reduce the dimension of feedback and much less attention is paid on their discrete form imposed by finite-rate constraints of resource-starved feedback links. Therefore, we propose channel state feedback designs by interpreting it as a discrete autoencoder. A practical approach to quantizing continuous features is developed using the concept of vector quantization. To be specific, given the feedback constraints the output vector (latent vector) of the encoder is accordingly partitioned and then all segments are quantized over a commonly designed codebook constituted by a finite collection of codewords. In order to jointly optimize parameters of neural networks and the codebook, the discrete representation learning is adopted where the loss function is defined as the sum of reconstruction and codebook alignment losses. To encourage desirable property, the regularization is further introduced in the loss function, which sheds light on the intricate interplay between the codebook structure and the neural networks during training. The simulation results show the tangible advantages of the discrete representation learning with the segmented vector quantization in designing limited feedback systems.

Channel State Feedback with Neural Networks: A Discrete Representation Learning Approach

Complex dorsal dislocations of the metacarpophalangeal joint are usually a complication of hyperextension injury and are irreducible to closed maneuvers. The volar plate displaced between the dorsum of the metacarpal head and the volar base of the proximal phalanx is the obstacle that prevents reduction. While the pathophysiology of complexity is relatively clear, such injuries are uncommon and reduction requires experience. We describe a case of complex fracture dislocation of the index metacarpophalangeal joint with a review of the literature on relative anatomy and treatment armamentarium.

Complex Dorsal Dislocation of the Metacarpophalangeal Joint: A Case Report and Comprehensive Review

A disruption of the ossicular chain of the middle ear causes conductive hearing loss. Ossicular reconstruction is performed to restore hearings in those patients with congenital ossicular chain anomaly or ossicular chain disruption caused by chronic otitis media or cholesteatoma. A study from Japan with 52 auditory ossicular malformation revealed that 44% of the patients had a fixation of the stapes, 40% had incudostapedial joint defects followed by fixation of the malleus and/or incus and defects in the incudostapedial joint with a fixation of the stapes. One of the most common ossicular chain anomalies in Korea was a stapes footplate fixation (54.5%) followed by a mobile stapes footplate with other anomalies (19.7%) including a stapes without suprastructure and an incus long process, stapes without anterior crus and an incus long process. One of the most common ossicular chain anomalies is the absence of an incus with or without an intact stapes suprastructure. In incudostapedial deformed ears, ossiculoplasty is mandatory to restore the hearing process. Ossiculoplasty is also needed in cases with incus long process erosion with inflammation. As the most vulnerable ossicles, one report said that incus erosion is found in 80% of the chronic otitis media. Austin-Kartush classified ossicular chain disruptions into four categories after 1,151 operation on chronic otitis media. Group A ears with an intact malleus handle and a stapes suprastructure was found in 59.2% followed by group B ears with an intact malleus handle but an eroded stapes suprastructure Audiologic Results of Ossiculoplasty Using Malleus Footplate Assembly: The Comparison between Autologous Incus and Hydroxyapatite

Audiologic Results of Ossiculoplasty Using Malleus Footplate Assembly: The Comparison between Autologous Incus and Hydroxyapatite

Background Axillary osmidrosis is a disease characterized by axillary malodor. The conventional treatment method of subdermal excision uses Metzenbaum scissors. Recently, subdermal excision using the Versajet system was introduced. However, it is an expensive surgical tool, and a recent study demonstrated a higher frequency of axillary skin necrosis with the Versajet. We propose a novel, cost-effective, and safe subdermal excision method that utilizes an electrosurgical tip cleaner (ETC).Methods Our retrospective cohort study included 27 patients who underwent subdermal excision from June 2012 to November 2021. The patients were classified into three groups according to the surgical method: Metzenbaum scissors, Versajet, and ETC. The operation time, hospitalization cost, and postoperative complications were investigated.Results The number of patients in the Metzenbaum scissors, Versajet, and ETC groups was seven, eleven, and nine, respectively. The mean operation time and hospitalization cost were significantly different among the three groups (P<0.05). The longest mean operation time was observed in the Metzenbaum scissors group (112.9±23.6 minutes), followed by the ETC and Versajet groups (76.4±27.1 and 64.2±24.8 minutes, respectively). The most expensive method was the Versajet ($2,346.1±517.7), followed by the ETC and Metzenbaum scissors ($1,391.8±317.7 and $1,279.6±287.5, respectively). No postoperative complications were observed.Conclusions The ETC is a novel method of subdermal excision, comparable to Metzenbaum scissors or Versajet. Therefore, it is recommended for situations where it is necessary to consider both the time and cost of surgery.

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Junho Lee

Papers

Mind of a dauer: Comparative connectomics reveals developmental plasticity

Channel State Feedback with Neural Networks: A Discrete Representation Learning Approach

Complex Dorsal Dislocation of the Metacarpophalangeal Joint: A Case Report and Comprehensive Review

Audiologic Results of Ossiculoplasty Using Malleus Footplate Assembly: The Comparison between Autologous Incus and Hydroxyapatite

Novel surgical use of electrosurgical tip cleaners in subdermal excision for axillary osmidrosis